!Series_title	"Short Read Sequencing Data of the Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture (HiSeq 2000, miRNA, batch 1)"
!Series_geo_accession	"GSE58459"
!Series_status	"Public on Dec 23 2016"
!Series_submission_date	"Jun 13 2014"
!Series_last_update_date	"May 15 2019"
!Series_pubmed_id	"28008941"
!Series_summary	"We report the application of Illumina Hiseq2000 sequencing technology for high-throughput miRNA profiling of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA),  with acupuncture and placebo treatments."
!Series_overall_design	"The experiment is designed as 2 arms: epidermal needle manipulation (AP/MEC) and placebo (PLA, used as control) on CIA induced rheumatoid arthritis (RA) rats. Muscle tissue samples sampling was carried out before any therapy in RA rats (RA_T0), and after at 1 hour and 34 days of therapeutic treatments for both AP and PLA. From all the 10 blood collected samples (2 replicates for each group, for each timepoint), total RNA were extracted. Finally, purified RNA were analyzed using illumina hiseq 2000)."
!Series_type	"Non-coding RNA profiling by high throughput sequencing"
!Series_contributor	"Valentina,,Devescovi"
!Series_contributor	"Yuanhua,,Liu"
!Series_contributor	"Christine,,Nardini"
!Series_sample_id	"GSM1412027 GSM1412028 GSM1412029 GSM1412030 GSM1412031 GSM1412032 GSM1412033 GSM1412034 GSM1412035 GSM1412036 "
!Series_contact_name	"Christine,,Nardini"
!Series_contact_email	"christine.nardini.rsrc@gmail.com"
!Series_contact_institute	"PICB"
!Series_contact_address	"Via dei Taurini 9"
!Series_contact_city	"Rome"
!Series_contact_zip/postal_code	"00186"
!Series_contact_country	"Italy"
!Series_supplementary_file	"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58459/suppl/GSE58459_RAW.tar"
!Series_supplementary_file	"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58459/suppl/GSE58459_miRNA_count_rpkm_matrix.txt.gz"
!Series_platform_id	"GPL14844"
!Series_platform_taxid	"10116"
!Series_sample_taxid	"10116"
!Series_relation	"SubSeries of: GSE58460"
!Series_relation	"BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA252673"
!Series_relation	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP043193"

!Sample_title	"RAT_RA_T0_1"	"RAT_RA_T0_2"	"RAT_AP_1h_1"	"RAT_AP_1h_2"	"RAT_PLA_1h_1"	"RAT_PLA_1h_2"	"RAT_AP_34d_1"	"RAT_AP_34d_2"	"RAT_PLA_34d_1"	"RAT_PLA_34d_2"
!Sample_geo_accession	"GSM1412027"	"GSM1412028"	"GSM1412029"	"GSM1412030"	"GSM1412031"	"GSM1412032"	"GSM1412033"	"GSM1412034"	"GSM1412035"	"GSM1412036"
!Sample_status	"Public on Dec 23 2016"	"Public on Dec 23 2016"	"Public on Dec 23 2016"	"Public on Dec 23 2016"	"Public on Dec 23 2016"	"Public on Dec 23 2016"	"Public on Dec 23 2016"	"Public on Dec 23 2016"	"Public on Dec 23 2016"	"Public on Dec 23 2016"
!Sample_submission_date	"Jun 13 2014"	"Jun 13 2014"	"Jun 13 2014"	"Jun 13 2014"	"Jun 13 2014"	"Jun 13 2014"	"Jun 13 2014"	"Jun 13 2014"	"Jun 13 2014"	"Jun 13 2014"
!Sample_last_update_date	"May 15 2019"	"May 15 2019"	"May 15 2019"	"May 15 2019"	"May 15 2019"	"May 15 2019"	"May 15 2019"	"May 15 2019"	"May 15 2019"	"May 15 2019"
!Sample_type	"SRA"	"SRA"	"SRA"	"SRA"	"SRA"	"SRA"	"SRA"	"SRA"	"SRA"	"SRA"
!Sample_channel_count	"1"	"1"	"1"	"1"	"1"	"1"	"1"	"1"	"1"	"1"
!Sample_source_name_ch1	"Muscle tissue from RA before therapy, replicate 1"	"Muscle tissue from RA before therapy, replicate 2"	"Muscle tissue from AP after 1 hour therapy, replicate 1"	"Muscle tissue from AP after 1 hour therapy, replicate 2"	"Muscle tissue from PLA  after 1 hour therapy, replicate 1"	"Muscle tissue from PLA after 1 hour therapy, replicate 2"	"Muscle tissue from AP after 34 days therapy, replicate 1"	"Muscle tissue from AP after 34 days therapy, replicate 2"	"Muscle tissue from PLA after 34 days therapy, replicate 1"	"Muscle tissue from PLA after 34 days therapy, replicate 2"
!Sample_organism_ch1	"Rattus norvegicus"	"Rattus norvegicus"	"Rattus norvegicus"	"Rattus norvegicus"	"Rattus norvegicus"	"Rattus norvegicus"	"Rattus norvegicus"	"Rattus norvegicus"	"Rattus norvegicus"	"Rattus norvegicus"
!Sample_characteristics_ch1	"strain: Wistar"	"strain: Wistar"	"strain: Wistar"	"strain: Wistar"	"strain: Wistar"	"strain: Wistar"	"strain: Wistar"	"strain: Wistar"	"strain: Wistar"	"strain: Wistar"
!Sample_characteristics_ch1	"gender: Female"	"gender: Female"	"gender: Female"	"gender: Female"	"gender: Female"	"gender: Female"	"gender: Female"	"gender: Female"	"gender: Female"	"gender: Female"
!Sample_characteristics_ch1	"tissue: RAT Sub-epidermidis muscle tissue"	"tissue: RAT Sub-epidermidis muscle tissue"	"tissue: RAT Sub-epidermidis muscle tissue"	"tissue: RAT Sub-epidermidis muscle tissue"	"tissue: RAT Sub-epidermidis muscle tissue"	"tissue: RAT Sub-epidermidis muscle tissue"	"tissue: RAT Sub-epidermidis muscle tissue"	"tissue: RAT Sub-epidermidis muscle tissue"	"tissue: RAT Sub-epidermidis muscle tissue"	"tissue: RAT Sub-epidermidis muscle tissue"
!Sample_treatment_protocol_ch1	"Dry frozen collected samples were maintained at -80ºC until the end of the study and then processed in a whole batch for the following extraction."	"Dry frozen collected samples were maintained at -80ºC until the end of the study and then processed in a whole batch for the following extraction."	"Dry frozen collected samples were maintained at -80ºC until the end of the study and then processed in a whole batch for the following extraction."	"Dry frozen collected samples were maintained at -80ºC until the end of the study and then processed in a whole batch for the following extraction."	"Dry frozen collected samples were maintained at -80ºC until the end of the study and then processed in a whole batch for the following extraction."	"Dry frozen collected samples were maintained at -80ºC until the end of the study and then processed in a whole batch for the following extraction."	"Dry frozen collected samples were maintained at -80ºC until the end of the study and then processed in a whole batch for the following extraction."	"Dry frozen collected samples were maintained at -80ºC until the end of the study and then processed in a whole batch for the following extraction."	"Dry frozen collected samples were maintained at -80ºC until the end of the study and then processed in a whole batch for the following extraction."	"Dry frozen collected samples were maintained at -80ºC until the end of the study and then processed in a whole batch for the following extraction."
!Sample_growth_protocol_ch1	"Muscle tissue samples (<500mg) were excided under deep general anesthesia. Samples were immediately dipped in liquid nitrogen for 1 minutes, then moved at -80ºC."	"Muscle tissue samples (<500mg) were excided under deep general anesthesia. Samples were immediately dipped in liquid nitrogen for 1 minutes, then moved at -80ºC."	"Muscle tissue samples (<500mg) were excided under deep general anesthesia. Samples were immediately dipped in liquid nitrogen for 1 minutes, then moved at -80ºC."	"Muscle tissue samples (<500mg) were excided under deep general anesthesia. Samples were immediately dipped in liquid nitrogen for 1 minutes, then moved at -80ºC."	"Muscle tissue samples (<500mg) were excided under deep general anesthesia. Samples were immediately dipped in liquid nitrogen for 1 minutes, then moved at -80ºC."	"Muscle tissue samples (<500mg) were excided under deep general anesthesia. Samples were immediately dipped in liquid nitrogen for 1 minutes, then moved at -80ºC."	"Muscle tissue samples (<500mg) were excided under deep general anesthesia. Samples were immediately dipped in liquid nitrogen for 1 minutes, then moved at -80ºC."	"Muscle tissue samples (<500mg) were excided under deep general anesthesia. Samples were immediately dipped in liquid nitrogen for 1 minutes, then moved at -80ºC."	"Muscle tissue samples (<500mg) were excided under deep general anesthesia. Samples were immediately dipped in liquid nitrogen for 1 minutes, then moved at -80ºC."	"Muscle tissue samples (<500mg) were excided under deep general anesthesia. Samples were immediately dipped in liquid nitrogen for 1 minutes, then moved at -80ºC."
!Sample_molecule_ch1	"total RNA"	"total RNA"	"total RNA"	"total RNA"	"total RNA"	"total RNA"	"total RNA"	"total RNA"	"total RNA"	"total RNA"
!Sample_extract_protocol_ch1	"Total RNA was extracted and purified using Trizol Reagent (Cat#15596-026, Invitrogen) according to the manufacturer's instructions, checked for the RIN number to inspect RNA integrity by the Agilent Bioanalyzer 2100 following the manufacturer's procedures of RNA 600 Nano Kit  (Cat#5067-1511, Agilent Technologies)."	"Total RNA was extracted and purified using Trizol Reagent (Cat#15596-026, Invitrogen) according to the manufacturer's instructions, checked for the RIN number to inspect RNA integrity by the Agilent Bioanalyzer 2100 following the manufacturer's procedures of RNA 600 Nano Kit  (Cat#5067-1511, Agilent Technologies)."	"Total RNA was extracted and purified using Trizol Reagent (Cat#15596-026, Invitrogen) according to the manufacturer's instructions, checked for the RIN number to inspect RNA integrity by the Agilent Bioanalyzer 2100 following the manufacturer's procedures of RNA 600 Nano Kit  (Cat#5067-1511, Agilent Technologies)."	"Total RNA was extracted and purified using Trizol Reagent (Cat#15596-026, Invitrogen) according to the manufacturer's instructions, checked for the RIN number to inspect RNA integrity by the Agilent Bioanalyzer 2100 following the manufacturer's procedures of RNA 600 Nano Kit  (Cat#5067-1511, Agilent Technologies)."	"Total RNA was extracted and purified using Trizol Reagent (Cat#15596-026, Invitrogen) according to the manufacturer's instructions, checked for the RIN number to inspect RNA integrity by the Agilent Bioanalyzer 2100 following the manufacturer's procedures of RNA 600 Nano Kit  (Cat#5067-1511, Agilent Technologies)."	"Total RNA was extracted and purified using Trizol Reagent (Cat#15596-026, Invitrogen) according to the manufacturer's instructions, checked for the RIN number to inspect RNA integrity by the Agilent Bioanalyzer 2100 following the manufacturer's procedures of RNA 600 Nano Kit  (Cat#5067-1511, Agilent Technologies)."	"Total RNA was extracted and purified using Trizol Reagent (Cat#15596-026, Invitrogen) according to the manufacturer's instructions, checked for the RIN number to inspect RNA integrity by the Agilent Bioanalyzer 2100 following the manufacturer's procedures of RNA 600 Nano Kit  (Cat#5067-1511, Agilent Technologies)."	"Total RNA was extracted and purified using Trizol Reagent (Cat#15596-026, Invitrogen) according to the manufacturer's instructions, checked for the RIN number to inspect RNA integrity by the Agilent Bioanalyzer 2100 following the manufacturer's procedures of RNA 600 Nano Kit  (Cat#5067-1511, Agilent Technologies)."	"Total RNA was extracted and purified using Trizol Reagent (Cat#15596-026, Invitrogen) according to the manufacturer's instructions, checked for the RIN number to inspect RNA integrity by the Agilent Bioanalyzer 2100 following the manufacturer's procedures of RNA 600 Nano Kit  (Cat#5067-1511, Agilent Technologies)."	"Total RNA was extracted and purified using Trizol Reagent (Cat#15596-026, Invitrogen) according to the manufacturer's instructions, checked for the RIN number to inspect RNA integrity by the Agilent Bioanalyzer 2100 following the manufacturer's procedures of RNA 600 Nano Kit  (Cat#5067-1511, Agilent Technologies)."
!Sample_extract_protocol_ch1	"Libraries were prepared according to Illumina's instructions accompanying the Illumina® TruSeq™ Small RNA Sample Preparation protocol (Part # 15004197 Rev. C)"	"Libraries were prepared according to Illumina's instructions accompanying the Illumina® TruSeq™ Small RNA Sample Preparation protocol (Part # 15004197 Rev. C)"	"Libraries were prepared according to Illumina's instructions accompanying the Illumina® TruSeq™ Small RNA Sample Preparation protocol (Part # 15004197 Rev. C)"	"Libraries were prepared according to Illumina's instructions accompanying the Illumina® TruSeq™ Small RNA Sample Preparation protocol (Part # 15004197 Rev. C)"	"Libraries were prepared according to Illumina's instructions accompanying the Illumina® TruSeq™ Small RNA Sample Preparation protocol (Part # 15004197 Rev. C)"	"Libraries were prepared according to Illumina's instructions accompanying the Illumina® TruSeq™ Small RNA Sample Preparation protocol (Part # 15004197 Rev. C)"	"Libraries were prepared according to Illumina's instructions accompanying the Illumina® TruSeq™ Small RNA Sample Preparation protocol (Part # 15004197 Rev. C)"	"Libraries were prepared according to Illumina's instructions accompanying the Illumina® TruSeq™ Small RNA Sample Preparation protocol (Part # 15004197 Rev. C)"	"Libraries were prepared according to Illumina's instructions accompanying the Illumina® TruSeq™ Small RNA Sample Preparation protocol (Part # 15004197 Rev. C)"	"Libraries were prepared according to Illumina's instructions accompanying the Illumina® TruSeq™ Small RNA Sample Preparation protocol (Part # 15004197 Rev. C)"
!Sample_taxid_ch1	"10116"	"10116"	"10116"	"10116"	"10116"	"10116"	"10116"	"10116"	"10116"	"10116"
!Sample_description	"small RNA expression data from RA rats before therapy"	"small RNA expression data from RA rats before therapy"	"small RNA expression data from RA rats after 1 hour acupuncture therapy"	"small RNA expression data from RA rats after 1 hour acupuncture therapy"	"small RNA expression data from RA rats after 1 hour placebo therapy"	"small RNA expression data from RA rats after 1 hour placebo therapy"	"small RNA expression data from RA rats after 34 days acupuncture therapy"	"small RNA expression data from RA rats after 34 days acupuncture therapy"	"small RNA expression data from RA rats after 34 days placebo therapy"	"small RNA expression data from RA rats after 34 days placebo therapy"
!Sample_data_processing	"Raw sequences were obtained and were de-multiplexed using the Illumina pipeline CASAVA v1.8. The FastQC1 and FASTX toolkit2 were used for Quality Check [ensured that fastq reads are in entirely normal (green tick: ≥Q28) range in the QC report] and to preprocess the reads prior to mapping respectively."	"Raw sequences were obtained and were de-multiplexed using the Illumina pipeline CASAVA v1.8. The FastQC1 and FASTX toolkit2 were used for Quality Check [ensured that fastq reads are in entirely normal (green tick: ≥Q28) range in the QC report] and to preprocess the reads prior to mapping respectively."	"Raw sequences were obtained and were de-multiplexed using the Illumina pipeline CASAVA v1.8. The FastQC1 and FASTX toolkit2 were used for Quality Check [ensured that fastq reads are in entirely normal (green tick: ≥Q28) range in the QC report] and to preprocess the reads prior to mapping respectively."	"Raw sequences were obtained and were de-multiplexed using the Illumina pipeline CASAVA v1.8. The FastQC1 and FASTX toolkit2 were used for Quality Check [ensured that fastq reads are in entirely normal (green tick: ≥Q28) range in the QC report] and to preprocess the reads prior to mapping respectively."	"Raw sequences were obtained and were de-multiplexed using the Illumina pipeline CASAVA v1.8. The FastQC1 and FASTX toolkit2 were used for Quality Check [ensured that fastq reads are in entirely normal (green tick: ≥Q28) range in the QC report] and to preprocess the reads prior to mapping respectively."	"Raw sequences were obtained and were de-multiplexed using the Illumina pipeline CASAVA v1.8. The FastQC1 and FASTX toolkit2 were used for Quality Check [ensured that fastq reads are in entirely normal (green tick: ≥Q28) range in the QC report] and to preprocess the reads prior to mapping respectively."	"Raw sequences were obtained and were de-multiplexed using the Illumina pipeline CASAVA v1.8. The FastQC1 and FASTX toolkit2 were used for Quality Check [ensured that fastq reads are in entirely normal (green tick: ≥Q28) range in the QC report] and to preprocess the reads prior to mapping respectively."	"Raw sequences were obtained and were de-multiplexed using the Illumina pipeline CASAVA v1.8. The FastQC1 and FASTX toolkit2 were used for Quality Check [ensured that fastq reads are in entirely normal (green tick: ≥Q28) range in the QC report] and to preprocess the reads prior to mapping respectively."	"Raw sequences were obtained and were de-multiplexed using the Illumina pipeline CASAVA v1.8. The FastQC1 and FASTX toolkit2 were used for Quality Check [ensured that fastq reads are in entirely normal (green tick: ≥Q28) range in the QC report] and to preprocess the reads prior to mapping respectively."	"Raw sequences were obtained and were de-multiplexed using the Illumina pipeline CASAVA v1.8. The FastQC1 and FASTX toolkit2 were used for Quality Check [ensured that fastq reads are in entirely normal (green tick: ≥Q28) range in the QC report] and to preprocess the reads prior to mapping respectively."
!Sample_data_processing	"The mapper.pl in miRDeep2 tool was employed to remove the Illumina three prime adapter sequences and retaining a minimum read length of 18bp after clipping. Meanwhile, Clipped reads were aligned using mapper.pl to Rat genome (rn4) and miRBase_v18 (rno sequences) . The joint command is: mapper.pl in_file.fastq -e -h -i -j -k adapter -l 18 -m -p rn4_index -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v, , where rn4_index is the index built through bowtie."	"The mapper.pl in miRDeep2 tool was employed to remove the Illumina three prime adapter sequences and retaining a minimum read length of 18bp after clipping. Meanwhile, Clipped reads were aligned using mapper.pl to Rat genome (rn4) and miRBase_v18 (rno sequences) . The joint command is: mapper.pl in_file.fastq -e -h -i -j -k adapter -l 18 -m -p rn4_index -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v, , where rn4_index is the index built through bowtie."	"The mapper.pl in miRDeep2 tool was employed to remove the Illumina three prime adapter sequences and retaining a minimum read length of 18bp after clipping. Meanwhile, Clipped reads were aligned using mapper.pl to Rat genome (rn4) and miRBase_v18 (rno sequences) . The joint command is: mapper.pl in_file.fastq -e -h -i -j -k adapter -l 18 -m -p rn4_index -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v, , where rn4_index is the index built through bowtie."	"The mapper.pl in miRDeep2 tool was employed to remove the Illumina three prime adapter sequences and retaining a minimum read length of 18bp after clipping. Meanwhile, Clipped reads were aligned using mapper.pl to Rat genome (rn4) and miRBase_v18 (rno sequences) . The joint command is: mapper.pl in_file.fastq -e -h -i -j -k adapter -l 18 -m -p rn4_index -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v, , where rn4_index is the index built through bowtie."	"The mapper.pl in miRDeep2 tool was employed to remove the Illumina three prime adapter sequences and retaining a minimum read length of 18bp after clipping. Meanwhile, Clipped reads were aligned using mapper.pl to Rat genome (rn4) and miRBase_v18 (rno sequences) . The joint command is: mapper.pl in_file.fastq -e -h -i -j -k adapter -l 18 -m -p rn4_index -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v, , where rn4_index is the index built through bowtie."	"The mapper.pl in miRDeep2 tool was employed to remove the Illumina three prime adapter sequences and retaining a minimum read length of 18bp after clipping. Meanwhile, Clipped reads were aligned using mapper.pl to Rat genome (rn4) and miRBase_v18 (rno sequences) . The joint command is: mapper.pl in_file.fastq -e -h -i -j -k adapter -l 18 -m -p rn4_index -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v, , where rn4_index is the index built through bowtie."	"The mapper.pl in miRDeep2 tool was employed to remove the Illumina three prime adapter sequences and retaining a minimum read length of 18bp after clipping. Meanwhile, Clipped reads were aligned using mapper.pl to Rat genome (rn4) and miRBase_v18 (rno sequences) . The joint command is: mapper.pl in_file.fastq -e -h -i -j -k adapter -l 18 -m -p rn4_index -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v, , where rn4_index is the index built through bowtie."	"The mapper.pl in miRDeep2 tool was employed to remove the Illumina three prime adapter sequences and retaining a minimum read length of 18bp after clipping. Meanwhile, Clipped reads were aligned using mapper.pl to Rat genome (rn4) and miRBase_v18 (rno sequences) . The joint command is: mapper.pl in_file.fastq -e -h -i -j -k adapter -l 18 -m -p rn4_index -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v, , where rn4_index is the index built through bowtie."	"The mapper.pl in miRDeep2 tool was employed to remove the Illumina three prime adapter sequences and retaining a minimum read length of 18bp after clipping. Meanwhile, Clipped reads were aligned using mapper.pl to Rat genome (rn4) and miRBase_v18 (rno sequences) . The joint command is: mapper.pl in_file.fastq -e -h -i -j -k adapter -l 18 -m -p rn4_index -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v, , where rn4_index is the index built through bowtie."	"The mapper.pl in miRDeep2 tool was employed to remove the Illumina three prime adapter sequences and retaining a minimum read length of 18bp after clipping. Meanwhile, Clipped reads were aligned using mapper.pl to Rat genome (rn4) and miRBase_v18 (rno sequences) . The joint command is: mapper.pl in_file.fastq -e -h -i -j -k adapter -l 18 -m -p rn4_index -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v, , where rn4_index is the index built through bowtie."
!Sample_data_processing	"quantifier.pl scripts in miRDeep2 is used to obtain the counts (and normalized counts, Reads Per Kilobase of mature miRNA reads per Megabase of all mature reads, RPKM)of known miRNAs, using command: quantifier.pl -p precursors_rno.fa -m mature_rno.fa -r reads_collapsed.fa -y output_file -t rno."	"quantifier.pl scripts in miRDeep2 is used to obtain the counts (and normalized counts, Reads Per Kilobase of mature miRNA reads per Megabase of all mature reads, RPKM)of known miRNAs, using command: quantifier.pl -p precursors_rno.fa -m mature_rno.fa -r reads_collapsed.fa -y output_file -t rno."	"quantifier.pl scripts in miRDeep2 is used to obtain the counts (and normalized counts, Reads Per Kilobase of mature miRNA reads per Megabase of all mature reads, RPKM)of known miRNAs, using command: quantifier.pl -p precursors_rno.fa -m mature_rno.fa -r reads_collapsed.fa -y output_file -t rno."	"quantifier.pl scripts in miRDeep2 is used to obtain the counts (and normalized counts, Reads Per Kilobase of mature miRNA reads per Megabase of all mature reads, RPKM)of known miRNAs, using command: quantifier.pl -p precursors_rno.fa -m mature_rno.fa -r reads_collapsed.fa -y output_file -t rno."	"quantifier.pl scripts in miRDeep2 is used to obtain the counts (and normalized counts, Reads Per Kilobase of mature miRNA reads per Megabase of all mature reads, RPKM)of known miRNAs, using command: quantifier.pl -p precursors_rno.fa -m mature_rno.fa -r reads_collapsed.fa -y output_file -t rno."	"quantifier.pl scripts in miRDeep2 is used to obtain the counts (and normalized counts, Reads Per Kilobase of mature miRNA reads per Megabase of all mature reads, RPKM)of known miRNAs, using command: quantifier.pl -p precursors_rno.fa -m mature_rno.fa -r reads_collapsed.fa -y output_file -t rno."	"quantifier.pl scripts in miRDeep2 is used to obtain the counts (and normalized counts, Reads Per Kilobase of mature miRNA reads per Megabase of all mature reads, RPKM)of known miRNAs, using command: quantifier.pl -p precursors_rno.fa -m mature_rno.fa -r reads_collapsed.fa -y output_file -t rno."	"quantifier.pl scripts in miRDeep2 is used to obtain the counts (and normalized counts, Reads Per Kilobase of mature miRNA reads per Megabase of all mature reads, RPKM)of known miRNAs, using command: quantifier.pl -p precursors_rno.fa -m mature_rno.fa -r reads_collapsed.fa -y output_file -t rno."	"quantifier.pl scripts in miRDeep2 is used to obtain the counts (and normalized counts, Reads Per Kilobase of mature miRNA reads per Megabase of all mature reads, RPKM)of known miRNAs, using command: quantifier.pl -p precursors_rno.fa -m mature_rno.fa -r reads_collapsed.fa -y output_file -t rno."	"quantifier.pl scripts in miRDeep2 is used to obtain the counts (and normalized counts, Reads Per Kilobase of mature miRNA reads per Megabase of all mature reads, RPKM)of known miRNAs, using command: quantifier.pl -p precursors_rno.fa -m mature_rno.fa -r reads_collapsed.fa -y output_file -t rno."
!Sample_data_processing	"The txt files for miRNA expression from mirDeep2 were used for further analysis."	"The txt files for miRNA expression from mirDeep2 were used for further analysis."	"The txt files for miRNA expression from mirDeep2 were used for further analysis."	"The txt files for miRNA expression from mirDeep2 were used for further analysis."	"The txt files for miRNA expression from mirDeep2 were used for further analysis."	"The txt files for miRNA expression from mirDeep2 were used for further analysis."	"The txt files for miRNA expression from mirDeep2 were used for further analysis."	"The txt files for miRNA expression from mirDeep2 were used for further analysis."	"The txt files for miRNA expression from mirDeep2 were used for further analysis."	"The txt files for miRNA expression from mirDeep2 were used for further analysis."
!Sample_data_processing	"Genome_build: rn4"	"Genome_build: rn4"	"Genome_build: rn4"	"Genome_build: rn4"	"Genome_build: rn4"	"Genome_build: rn4"	"Genome_build: rn4"	"Genome_build: rn4"	"Genome_build: rn4"	"Genome_build: rn4"
!Sample_data_processing	"Supplementary_files_format_and_content: tab-delimited text files include counts&RPKM values for each Sample"	"Supplementary_files_format_and_content: tab-delimited text files include counts&RPKM values for each Sample"	"Supplementary_files_format_and_content: tab-delimited text files include counts&RPKM values for each Sample"	"Supplementary_files_format_and_content: tab-delimited text files include counts&RPKM values for each Sample"	"Supplementary_files_format_and_content: tab-delimited text files include counts&RPKM values for each Sample"	"Supplementary_files_format_and_content: tab-delimited text files include counts&RPKM values for each Sample"	"Supplementary_files_format_and_content: tab-delimited text files include counts&RPKM values for each Sample"	"Supplementary_files_format_and_content: tab-delimited text files include counts&RPKM values for each Sample"	"Supplementary_files_format_and_content: tab-delimited text files include counts&RPKM values for each Sample"	"Supplementary_files_format_and_content: tab-delimited text files include counts&RPKM values for each Sample"
!Sample_platform_id	"GPL14844"	"GPL14844"	"GPL14844"	"GPL14844"	"GPL14844"	"GPL14844"	"GPL14844"	"GPL14844"	"GPL14844"	"GPL14844"
!Sample_contact_name	"Christine,,Nardini"	"Christine,,Nardini"	"Christine,,Nardini"	"Christine,,Nardini"	"Christine,,Nardini"	"Christine,,Nardini"	"Christine,,Nardini"	"Christine,,Nardini"	"Christine,,Nardini"	"Christine,,Nardini"
!Sample_contact_email	"christine.nardini.rsrc@gmail.com"	"christine.nardini.rsrc@gmail.com"	"christine.nardini.rsrc@gmail.com"	"christine.nardini.rsrc@gmail.com"	"christine.nardini.rsrc@gmail.com"	"christine.nardini.rsrc@gmail.com"	"christine.nardini.rsrc@gmail.com"	"christine.nardini.rsrc@gmail.com"	"christine.nardini.rsrc@gmail.com"	"christine.nardini.rsrc@gmail.com"
!Sample_contact_institute	"PICB"	"PICB"	"PICB"	"PICB"	"PICB"	"PICB"	"PICB"	"PICB"	"PICB"	"PICB"
!Sample_contact_address	"Via dei Taurini 9"	"Via dei Taurini 9"	"Via dei Taurini 9"	"Via dei Taurini 9"	"Via dei Taurini 9"	"Via dei Taurini 9"	"Via dei Taurini 9"	"Via dei Taurini 9"	"Via dei Taurini 9"	"Via dei Taurini 9"
!Sample_contact_city	"Rome"	"Rome"	"Rome"	"Rome"	"Rome"	"Rome"	"Rome"	"Rome"	"Rome"	"Rome"
!Sample_contact_zip/postal_code	"00186"	"00186"	"00186"	"00186"	"00186"	"00186"	"00186"	"00186"	"00186"	"00186"
!Sample_contact_country	"Italy"	"Italy"	"Italy"	"Italy"	"Italy"	"Italy"	"Italy"	"Italy"	"Italy"	"Italy"
!Sample_data_row_count	"0"	"0"	"0"	"0"	"0"	"0"	"0"	"0"	"0"	"0"
!Sample_instrument_model	"Illumina HiSeq 2000"	"Illumina HiSeq 2000"	"Illumina HiSeq 2000"	"Illumina HiSeq 2000"	"Illumina HiSeq 2000"	"Illumina HiSeq 2000"	"Illumina HiSeq 2000"	"Illumina HiSeq 2000"	"Illumina HiSeq 2000"	"Illumina HiSeq 2000"
!Sample_library_selection	"cDNA"	"cDNA"	"cDNA"	"cDNA"	"cDNA"	"cDNA"	"cDNA"	"cDNA"	"cDNA"	"cDNA"
!Sample_library_source	"transcriptomic"	"transcriptomic"	"transcriptomic"	"transcriptomic"	"transcriptomic"	"transcriptomic"	"transcriptomic"	"transcriptomic"	"transcriptomic"	"transcriptomic"
!Sample_library_strategy	"RNA-Seq"	"RNA-Seq"	"RNA-Seq"	"RNA-Seq"	"RNA-Seq"	"RNA-Seq"	"RNA-Seq"	"RNA-Seq"	"RNA-Seq"	"RNA-Seq"
!Sample_relation	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02854488"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02854489"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02854491"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02854495"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02854494"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02854490"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02854492"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02854497"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02854493"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02854496"
!Sample_relation	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX595727"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX595728"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX595729"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX595730"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX595731"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX595732"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX595733"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX595734"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX595735"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX595736"
!Sample_supplementary_file_1	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1412nnn/GSM1412027/suppl/GSM1412027_RAT_RA_T0_1.txt.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1412nnn/GSM1412028/suppl/GSM1412028_RAT_RA_T0_2.txt.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1412nnn/GSM1412029/suppl/GSM1412029_RAT_AP_1h_1.txt.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1412nnn/GSM1412030/suppl/GSM1412030_RAT_AP_1h_2.txt.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1412nnn/GSM1412031/suppl/GSM1412031_RAT_PLA_1h_1.txt.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1412nnn/GSM1412032/suppl/GSM1412032_RAT_PLA_1h_2.txt.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1412nnn/GSM1412033/suppl/GSM1412033_RAT_AP_34d_1.txt.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1412nnn/GSM1412034/suppl/GSM1412034_RAT_AP_34d_2.txt.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1412nnn/GSM1412035/suppl/GSM1412035_RAT_PLA_34d_1.txt.gz"	"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1412nnn/GSM1412036/suppl/GSM1412036_RAT_PLA_34d_2.txt.gz"
!series_matrix_table_begin
"ID_REF"	"GSM1412027"	"GSM1412028"	"GSM1412029"	"GSM1412030"	"GSM1412031"	"GSM1412032"	"GSM1412033"	"GSM1412034"	"GSM1412035"	"GSM1412036"
!series_matrix_table_end
