!Series_title	"Investigation of therapeutic response markers for acupuncture in Parkinson's disease: An exploratory pilot study"
!Series_geo_accession	"GSE178470"
!Series_status	"Public on Jun 19 2021"
!Series_submission_date	"Jun 18 2021"
!Series_last_update_date	"Oct 06 2021"
!Series_pubmed_id	"34574038"
!Series_summary	"Introduction: In our previous study, we demonstrated that acupuncture improved gait disturbances, such as hypometric gait, in patients with Parkinson’s disease (PD). To investigate specific genes that indicate a therapeutic response to acupuncture, we analyzed transcriptome alterations following acupuncture using blood samples collected in our previous clinical trial."
!Series_summary	"Methods: We reanalyzed the clinical data of patients and selected a representative patient with PD for transcriptomic analysis following acupuncture. We examined the expression changes of PD biomarker genes known to be consistently dysregulated in both the brain and blood in patients with PD. We validated these gene expression changes using quantitative real-time polymerase chain reaction (qPCR) in the blood of five other patients with PD who received acupuncture treatment."
!Series_summary	"Results: After acupuncture treatment, the transcriptomic alterations in the representative patient were similar to those induced by dopaminergic therapy. Among PD biomarkers, ankyrin repeat domain 22 (ANKRD22), which is upregulated after dopaminergic therapy, and synapsin 1 (SYN1), which is the common gene to indicate synaptic dysfunction in PD, were upregulated following acupuncture. These alterations correlated with changes of gait parameters in patients with PD.alterations following acupuncture using blood samples collected in our previous clinical trial."
!Series_summary	"Conclusion: This is the first report on gene expression changes and improvement of gait disturbance in patients with PD following acupuncture. Our data suggest that ANKRD22 and SYN1 can be used as biomarkers for therapeutic response to acupuncture in patients with PD, especially those with gait disturbance.alterations following acupuncture using blood samples collected in our previous clinical trial."
!Series_overall_design	"We performed RNA sequencing analysis of the representative patient with PD of the greatest therapeutic effect on gait after acupuncture (5 and 8 sessions)."
!Series_type	"Expression profiling by high throughput sequencing"
!Series_contributor	"Sang-Min,,Park"
!Series_contributor	"Gunhyuk,,Park"
!Series_contributor	"Sangsoo,,Park"
!Series_contributor	"Horyong,,Yoo"
!Series_contributor	"Jung-Hee,,Jang"
!Series_sample_id	"GSM5392193 GSM5392194 GSM5392195 "
!Series_contact_name	"Sang-Min,,Park"
!Series_contact_email	"smpark@cnu.ac.kr"
!Series_contact_laboratory	"Systems Physiology"
!Series_contact_department	"College of Pharmacy"
!Series_contact_institute	"Chungnam National University"
!Series_contact_address	"Youseong-Daero"
!Series_contact_city	"Daejeon"
!Series_contact_zip/postal_code	"34054"
!Series_contact_country	"South Korea"
!Series_supplementary_file	"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE178nnn/GSE178470/suppl/GSE178470_gene_count.txt.gz"
!Series_platform_id	"GPL18573"
!Series_platform_taxid	"9606"
!Series_sample_taxid	"9606"
!Series_relation	"BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA739172"

!Sample_title	"Patient_before_acupuncture"	"Patient_after_5_sessions_of_acupuncture"	"Patient_after_8_sessions_of_acupuncture"
!Sample_geo_accession	"GSM5392193"	"GSM5392194"	"GSM5392195"
!Sample_status	"Public on Jun 19 2021"	"Public on Jun 19 2021"	"Public on Jun 19 2021"
!Sample_submission_date	"Jun 18 2021"	"Jun 18 2021"	"Jun 18 2021"
!Sample_last_update_date	"Jun 19 2021"	"Jun 19 2021"	"Jun 19 2021"
!Sample_type	"SRA"	"SRA"	"SRA"
!Sample_channel_count	"1"	"1"	"1"
!Sample_source_name_ch1	"Whole blood"	"Whole blood"	"Whole blood"
!Sample_organism_ch1	"Homo sapiens"	"Homo sapiens"	"Homo sapiens"
!Sample_characteristics_ch1	"treatment: untreated"	"treatment: treated with 5 sessions of acpuncture"	"treatment: treated with 8 sessions of acpuncture"
!Sample_treatment_protocol_ch1	"Acupuncture treatment was given to the participants on the dorsal side for 2 days per week for 4 weeks."	"Acupuncture treatment was given to the participants on the dorsal side for 2 days per week for 4 weeks."	"Acupuncture treatment was given to the participants on the dorsal side for 2 days per week for 4 weeks."
!Sample_molecule_ch1	"total RNA"	"total RNA"	"total RNA"
!Sample_extract_protocol_ch1	"The PAXgene Blood miRNA Kit (Qiagen, Hilden, Germany) was used for total RNA isolation from whole blood samples of a representative patient before acupuncture, and after 5 sessions and 8 sessions of acupuncture treatment."	"The PAXgene Blood miRNA Kit (Qiagen, Hilden, Germany) was used for total RNA isolation from whole blood samples of a representative patient before acupuncture, and after 5 sessions and 8 sessions of acupuncture treatment."	"The PAXgene Blood miRNA Kit (Qiagen, Hilden, Germany) was used for total RNA isolation from whole blood samples of a representative patient before acupuncture, and after 5 sessions and 8 sessions of acupuncture treatment."
!Sample_extract_protocol_ch1	"Library construction for control and test RNAs was performed using the QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen Inc., Austria)."	"Library construction for control and test RNAs was performed using the QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen Inc., Austria)."	"Library construction for control and test RNAs was performed using the QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen Inc., Austria)."
!Sample_taxid_ch1	"9606"	"9606"	"9606"
!Sample_data_processing	"Illumina Casava1.8 software used for basecalling."	"Illumina Casava1.8 software used for basecalling."	"Illumina Casava1.8 software used for basecalling."
!Sample_data_processing	"Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2."	"Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2."	"Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2."
!Sample_data_processing	"Read count extraction and nomalization were performed using edgeR."	"Read count extraction and nomalization were performed using edgeR."	"Read count extraction and nomalization were performed using edgeR."
!Sample_data_processing	"Genome_build: hg19"	"Genome_build: hg19"	"Genome_build: hg19"
!Sample_data_processing	"Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample"	"Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample"	"Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample"
!Sample_platform_id	"GPL18573"	"GPL18573"	"GPL18573"
!Sample_contact_name	"Sang-Min,,Park"	"Sang-Min,,Park"	"Sang-Min,,Park"
!Sample_contact_email	"smpark@cnu.ac.kr"	"smpark@cnu.ac.kr"	"smpark@cnu.ac.kr"
!Sample_contact_laboratory	"Systems Physiology"	"Systems Physiology"	"Systems Physiology"
!Sample_contact_department	"College of Pharmacy"	"College of Pharmacy"	"College of Pharmacy"
!Sample_contact_institute	"Chungnam National University"	"Chungnam National University"	"Chungnam National University"
!Sample_contact_address	"Youseong-Daero"	"Youseong-Daero"	"Youseong-Daero"
!Sample_contact_city	"Daejeon"	"Daejeon"	"Daejeon"
!Sample_contact_zip/postal_code	"34054"	"34054"	"34054"
!Sample_contact_country	"South Korea"	"South Korea"	"South Korea"
!Sample_data_row_count	"0"	"0"	"0"
!Sample_instrument_model	"Illumina NextSeq 500"	"Illumina NextSeq 500"	"Illumina NextSeq 500"
!Sample_library_selection	"cDNA"	"cDNA"	"cDNA"
!Sample_library_source	"transcriptomic"	"transcriptomic"	"transcriptomic"
!Sample_library_strategy	"RNA-Seq"	"RNA-Seq"	"RNA-Seq"
!Sample_relation	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19775067"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19775066"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19775064"
!Sample_supplementary_file_1	"NONE"	"NONE"	"NONE"
!series_matrix_table_begin
"ID_REF"	"GSM5392193"	"GSM5392194"	"GSM5392195"
!series_matrix_table_end
