!Series_title	"Gene expression from tuft cells under scopolamine treatment"
!Series_geo_accession	"GSE138365"
!Series_status	"Public on Nov 01 2019"
!Series_submission_date	"Oct 03 2019"
!Series_last_update_date	"Jan 21 2020"
!Series_pubmed_id	"31913277"
!Series_summary	"In our study, we investigated the effect of muscarinic receptor blockade on murine intestinal stem cell activity and differentiation. Following pharmacologic (scopolamine) and genetic muscarinic receptor interruption (M3R-KO, M1R-KO; Vil-Cre x M3R fl/fl, Vil-Cre x M1R fl/fl mice, respectively), we observe a selective, significant expansion of DCLK1-positive tuft cells. This is primarily sensed by endocrine Prox1-positive cells (Prox1-CreERT2 x M3R fl/fl mice), while Lgr5-positive ISCs respond with a reduction of their cellular activity (Lgr5-EGFP-IRES-CreERT2 x M3R fl/fl mice). To characterize expanding tuft cells in more detail, adult BAC transgenic DCLK1-DTR-ZSgreen reporter mice generated in our lab were treated with scopolamine or sodium chloride as controls (Sham) for 7d and live jejunal EPC-positive/ZSgreen-positive cells sorted. Extracted total RNA from sorted ZSgreen-positive cells of scopolamine- and sham-treated mice was sequenced. Further analysis revealed that expanding tuft cells orchestrate an increase in mucosal acetylcholine, which maintained intracellular signaling pathways such as p-ERK/ERK 1/2 or TCF-1/7. Finally, acute irradiation injury was employed to investigate the importance of this regulatory circuit for tissue homeostasis. Indeed, tissue injury in Vil-Cre x M3R fl/fl mice resulted in a severe reduction of epithelial DCLK1-positive tuft cells, concomitant to reduced mucosal Ach levels as well as intracellular PI3K-/p-ERK levels. Therefore, DCLK1-positive tuft cells appear essential for the maintenance of a regular intestinal cholinergic niche."
!Series_overall_design	"Bulk gene expression data are presented for sorted DCLK1-DTR-ZSgreen-positive cells from scopolamine treated mice (n=4) or sham treated mice (n=4)."
!Series_type	"Expression profiling by high throughput sequencing"
!Series_contributor	"Moritz,,Middelhoff"
!Series_contributor	"Henrik,,Nienhüser"
!Series_contributor	"H,C,Maurer"
!Series_contributor	"Timothy,C,Wang"
!Series_sample_id	"GSM4106036 GSM4106037 GSM4106038 GSM4106039 GSM4106040 GSM4106041 GSM4106042 GSM4106043 "
!Series_contact_name	"Hans,Carlo,Maurer"
!Series_contact_department	"II. Medizinische Klinik"
!Series_contact_institute	"Klinikum rechts der Isar"
!Series_contact_address	"Ismaninger Str. 22"
!Series_contact_city	"Munich"
!Series_contact_state	"Bavaria"
!Series_contact_zip/postal_code	"81675"
!Series_contact_country	"Germany"
!Series_supplementary_file	"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE138nnn/GSE138365/suppl/GSE138365_TC-Scopolamine-Experiment-RawCounts.txt.gz"
!Series_platform_id	"GPL24247"
!Series_platform_taxid	"10090"
!Series_sample_taxid	"10090"
!Series_relation	"BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA575638"
!Series_relation	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP224064"

!Sample_title	"WH001"	"WH002"	"WH003"	"WH004"	"WH005"	"WH006"	"WH007"	"WH008"
!Sample_geo_accession	"GSM4106036"	"GSM4106037"	"GSM4106038"	"GSM4106039"	"GSM4106040"	"GSM4106041"	"GSM4106042"	"GSM4106043"
!Sample_status	"Public on Nov 01 2019"	"Public on Nov 01 2019"	"Public on Nov 01 2019"	"Public on Nov 01 2019"	"Public on Nov 01 2019"	"Public on Nov 01 2019"	"Public on Nov 01 2019"	"Public on Nov 01 2019"
!Sample_submission_date	"Oct 03 2019"	"Oct 03 2019"	"Oct 03 2019"	"Oct 03 2019"	"Oct 03 2019"	"Oct 03 2019"	"Oct 03 2019"	"Oct 03 2019"
!Sample_last_update_date	"Nov 01 2019"	"Nov 01 2019"	"Nov 01 2019"	"Nov 01 2019"	"Nov 01 2019"	"Nov 01 2019"	"Nov 01 2019"	"Nov 01 2019"
!Sample_type	"SRA"	"SRA"	"SRA"	"SRA"	"SRA"	"SRA"	"SRA"	"SRA"
!Sample_channel_count	"1"	"1"	"1"	"1"	"1"	"1"	"1"	"1"
!Sample_source_name_ch1	"tuft_cells"	"tuft_cells"	"tuft_cells"	"tuft_cells"	"tuft_cells"	"tuft_cells"	"tuft_cells"	"tuft_cells"
!Sample_organism_ch1	"Mus musculus"	"Mus musculus"	"Mus musculus"	"Mus musculus"	"Mus musculus"	"Mus musculus"	"Mus musculus"	"Mus musculus"
!Sample_characteristics_ch1	"treatment: scopolamine"	"treatment: scopolamine"	"treatment: scopolamine"	"treatment: scopolamine"	"treatment: sham"	"treatment: sham"	"treatment: sham"	"treatment: sham"
!Sample_characteristics_ch1	"ncell_sorted: 3000"	"ncell_sorted: 4000"	"ncell_sorted: 4000"	"ncell_sorted: 4000"	"ncell_sorted: 3000"	"ncell_sorted: 4000"	"ncell_sorted: 4000"	"ncell_sorted: 4000"
!Sample_characteristics_ch1	"mouse_id: M-8463"	"mouse_id: M-8466"	"mouse_id: M-8468"	"mouse_id: N-0593"	"mouse_id: M-8465"	"mouse_id: N-0556"	"mouse_id: N-0564"	"mouse_id: N-0595"
!Sample_molecule_ch1	"total RNA"	"total RNA"	"total RNA"	"total RNA"	"total RNA"	"total RNA"	"total RNA"	"total RNA"
!Sample_extract_protocol_ch1	"Qiagen RNAeasy Plus Micro Kit"	"Qiagen RNAeasy Plus Micro Kit"	"Qiagen RNAeasy Plus Micro Kit"	"Qiagen RNAeasy Plus Micro Kit"	"Qiagen RNAeasy Plus Micro Kit"	"Qiagen RNAeasy Plus Micro Kit"	"Qiagen RNAeasy Plus Micro Kit"	"Qiagen RNAeasy Plus Micro Kit"
!Sample_extract_protocol_ch1	"Clontech Ultra Low v4 kit to amplify total RNA. Nextera XT protocol using the resulting cDNA for library preparation."	"Clontech Ultra Low v4 kit to amplify total RNA. Nextera XT protocol using the resulting cDNA for library preparation."	"Clontech Ultra Low v4 kit to amplify total RNA. Nextera XT protocol using the resulting cDNA for library preparation."	"Clontech Ultra Low v4 kit to amplify total RNA. Nextera XT protocol using the resulting cDNA for library preparation."	"Clontech Ultra Low v4 kit to amplify total RNA. Nextera XT protocol using the resulting cDNA for library preparation."	"Clontech Ultra Low v4 kit to amplify total RNA. Nextera XT protocol using the resulting cDNA for library preparation."	"Clontech Ultra Low v4 kit to amplify total RNA. Nextera XT protocol using the resulting cDNA for library preparation."	"Clontech Ultra Low v4 kit to amplify total RNA. Nextera XT protocol using the resulting cDNA for library preparation."
!Sample_taxid_ch1	"10090"	"10090"	"10090"	"10090"	"10090"	"10090"	"10090"	"10090"
!Sample_data_processing	"RTA (Illumina) was used for base calling and"	"RTA (Illumina) was used for base calling and"	"RTA (Illumina) was used for base calling and"	"RTA (Illumina) was used for base calling and"	"RTA (Illumina) was used for base calling and"	"RTA (Illumina) was used for base calling and"	"RTA (Illumina) was used for base calling and"	"RTA (Illumina) was used for base calling and"
!Sample_data_processing	"bcl2fastq (version 2.20) was used to convert BCL to fastq format, coupled with adaptor trimming."	"bcl2fastq (version 2.20) was used to convert BCL to fastq format, coupled with adaptor trimming."	"bcl2fastq (version 2.20) was used to convert BCL to fastq format, coupled with adaptor trimming."	"bcl2fastq (version 2.20) was used to convert BCL to fastq format, coupled with adaptor trimming."	"bcl2fastq (version 2.20) was used to convert BCL to fastq format, coupled with adaptor trimming."	"bcl2fastq (version 2.20) was used to convert BCL to fastq format, coupled with adaptor trimming."	"bcl2fastq (version 2.20) was used to convert BCL to fastq format, coupled with adaptor trimming."	"bcl2fastq (version 2.20) was used to convert BCL to fastq format, coupled with adaptor trimming."
!Sample_data_processing	"Pseudoalignment was carried out to a kallisto index created from the murine GRCm38 transcriptome using kallisto (0.44.0) and"	"Pseudoalignment was carried out to a kallisto index created from the murine GRCm38 transcriptome using kallisto (0.44.0) and"	"Pseudoalignment was carried out to a kallisto index created from the murine GRCm38 transcriptome using kallisto (0.44.0) and"	"Pseudoalignment was carried out to a kallisto index created from the murine GRCm38 transcriptome using kallisto (0.44.0) and"	"Pseudoalignment was carried out to a kallisto index created from the murine GRCm38 transcriptome using kallisto (0.44.0) and"	"Pseudoalignment was carried out to a kallisto index created from the murine GRCm38 transcriptome using kallisto (0.44.0) and"	"Pseudoalignment was carried out to a kallisto index created from the murine GRCm38 transcriptome using kallisto (0.44.0) and"	"Pseudoalignment was carried out to a kallisto index created from the murine GRCm38 transcriptome using kallisto (0.44.0) and"
!Sample_data_processing	"estimated counts and transcripts per kilobase million (TPM) per gene were computed from the kallisto output using the tximport R package."	"estimated counts and transcripts per kilobase million (TPM) per gene were computed from the kallisto output using the tximport R package."	"estimated counts and transcripts per kilobase million (TPM) per gene were computed from the kallisto output using the tximport R package."	"estimated counts and transcripts per kilobase million (TPM) per gene were computed from the kallisto output using the tximport R package."	"estimated counts and transcripts per kilobase million (TPM) per gene were computed from the kallisto output using the tximport R package."	"estimated counts and transcripts per kilobase million (TPM) per gene were computed from the kallisto output using the tximport R package."	"estimated counts and transcripts per kilobase million (TPM) per gene were computed from the kallisto output using the tximport R package."	"estimated counts and transcripts per kilobase million (TPM) per gene were computed from the kallisto output using the tximport R package."
!Sample_data_processing	"Genome_build: Mouse GRCm38"	"Genome_build: Mouse GRCm38"	"Genome_build: Mouse GRCm38"	"Genome_build: Mouse GRCm38"	"Genome_build: Mouse GRCm38"	"Genome_build: Mouse GRCm38"	"Genome_build: Mouse GRCm38"	"Genome_build: Mouse GRCm38"
!Sample_data_processing	"Supplementary_files_format_and_content: tab-delimited text file containing raw read count values per gene for each sample"	"Supplementary_files_format_and_content: tab-delimited text file containing raw read count values per gene for each sample"	"Supplementary_files_format_and_content: tab-delimited text file containing raw read count values per gene for each sample"	"Supplementary_files_format_and_content: tab-delimited text file containing raw read count values per gene for each sample"	"Supplementary_files_format_and_content: tab-delimited text file containing raw read count values per gene for each sample"	"Supplementary_files_format_and_content: tab-delimited text file containing raw read count values per gene for each sample"	"Supplementary_files_format_and_content: tab-delimited text file containing raw read count values per gene for each sample"	"Supplementary_files_format_and_content: tab-delimited text file containing raw read count values per gene for each sample"
!Sample_platform_id	"GPL24247"	"GPL24247"	"GPL24247"	"GPL24247"	"GPL24247"	"GPL24247"	"GPL24247"	"GPL24247"
!Sample_contact_name	"Hans,Carlo,Maurer"	"Hans,Carlo,Maurer"	"Hans,Carlo,Maurer"	"Hans,Carlo,Maurer"	"Hans,Carlo,Maurer"	"Hans,Carlo,Maurer"	"Hans,Carlo,Maurer"	"Hans,Carlo,Maurer"
!Sample_contact_department	"II. Medizinische Klinik"	"II. Medizinische Klinik"	"II. Medizinische Klinik"	"II. Medizinische Klinik"	"II. Medizinische Klinik"	"II. Medizinische Klinik"	"II. Medizinische Klinik"	"II. Medizinische Klinik"
!Sample_contact_institute	"Klinikum rechts der Isar"	"Klinikum rechts der Isar"	"Klinikum rechts der Isar"	"Klinikum rechts der Isar"	"Klinikum rechts der Isar"	"Klinikum rechts der Isar"	"Klinikum rechts der Isar"	"Klinikum rechts der Isar"
!Sample_contact_address	"Ismaninger Str. 22"	"Ismaninger Str. 22"	"Ismaninger Str. 22"	"Ismaninger Str. 22"	"Ismaninger Str. 22"	"Ismaninger Str. 22"	"Ismaninger Str. 22"	"Ismaninger Str. 22"
!Sample_contact_city	"Munich"	"Munich"	"Munich"	"Munich"	"Munich"	"Munich"	"Munich"	"Munich"
!Sample_contact_state	"Bavaria"	"Bavaria"	"Bavaria"	"Bavaria"	"Bavaria"	"Bavaria"	"Bavaria"	"Bavaria"
!Sample_contact_zip/postal_code	"81675"	"81675"	"81675"	"81675"	"81675"	"81675"	"81675"	"81675"
!Sample_contact_country	"Germany"	"Germany"	"Germany"	"Germany"	"Germany"	"Germany"	"Germany"	"Germany"
!Sample_data_row_count	"0"	"0"	"0"	"0"	"0"	"0"	"0"	"0"
!Sample_instrument_model	"Illumina NovaSeq 6000"	"Illumina NovaSeq 6000"	"Illumina NovaSeq 6000"	"Illumina NovaSeq 6000"	"Illumina NovaSeq 6000"	"Illumina NovaSeq 6000"	"Illumina NovaSeq 6000"	"Illumina NovaSeq 6000"
!Sample_library_selection	"cDNA"	"cDNA"	"cDNA"	"cDNA"	"cDNA"	"cDNA"	"cDNA"	"cDNA"
!Sample_library_source	"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"
!Sample_relation	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12905805"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12905804"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12905803"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12905802"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12905801"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12905800"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12905799"	"BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12905798"
!Sample_relation	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6943902"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6943903"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6943904"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6943905"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6943906"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6943907"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6943908"	"SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6943909"
!Sample_supplementary_file_1	"NONE"	"NONE"	"NONE"	"NONE"	"NONE"	"NONE"	"NONE"	"NONE"
!series_matrix_table_begin
"ID_REF"	"GSM4106036"	"GSM4106037"	"GSM4106038"	"GSM4106039"	"GSM4106040"	"GSM4106041"	"GSM4106042"	"GSM4106043"
!series_matrix_table_end
