{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Vasileios Bekiaris"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16691"],"description":["This experiment was designed to explore the transcriptional programs of γδT17 and γδT1 cells isolated from the lamina propria and peripheral lymph nodes. For this purpose, we sorted intestinal γδT17 (RORγtGFP+TbetAmCyan+) and γδT1 (TbetAmCyan+) cells, as well as γδT17 (RORγtGFP+) and γδT1 (TbetAmCyan+) cells from peripheral lymph nodes and performed bulk RNA-seq to identify subset- and tissue-specific gene expression programs in wild-type mice."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Equimolar amounts of each library were sequenced on a NextSeq 500 instrument controlled by the NextSeq Control Software (NCS) v2.2.0, using a 75 Cycles High Output Kit with the dual index, single-read (SR) run parameters. Image analysis and base calling were done by the Real Time Analysis Software (RTA) v2.4.11. The resulting .bcl files were converted into .fastq files with the CASAVA Software v1.8.2.","Sample Collection - Lymphocytes were isolated from small intestine, colon lamina propria and peripheral lymph nodes of wild type mice that transgenically expressed GFP and AmCyan under the control of the RORγt or Tbet promoters respectively (RORγtGFPTbetAMCYAN), 4 mice were pooled in each biological repeat, n=3. Subsequently cells were sorted as GFP+ (RORγt+), AmCyan+ (Tbet+) or GFP+AmCyan+ (RORγt+Tbet+) using a FACSAriaIII sorter and collected directly in RNAprotect Cell Reagent (Qiagen).","Nucleic Acid Extraction - Total RNA was extracted from sorted cells according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored and shipped in buffer RNAlater at 2-8 °C. After pelleting by centrifugation for 5 minutes at 5,000 x g, the RNAlater was replaced by 350 µl buffer RLT Plus and the samples were homogenized by vortexing for 30 sec. Genomic DNA contamination was removed using gDNA Eliminator spin columns. Next one volume of 70 % ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).","Library Construction - The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 500 pg total-RNA. Double stranded cDNA was amplified by LD PCR (12 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Vasileios Bekiaris"],"additional_accession":[]},"is_claimable":false,"name":"Bulk RNA-seq of murine γδT17 and γδT1 cells from the lamina propria and peripheral lymph nodes of wild-type mice","description":"This experiment was designed to explore the transcriptional programs of γδT17 and γδT1 cells isolated from the lamina propria and peripheral lymph nodes. For this purpose, we sorted intestinal γδT17 (RORγtGFP+TbetAmCyan+) and γδT1 (TbetAmCyan+) cells, as well as γδT17 (RORγtGFP+) and γδT1 (TbetAmCyan+) cells from peripheral lymph nodes and performed bulk RNA-seq to identify subset- and tissue-specific gene expression programs in wild-type mice.","dates":{"release":"2026-03-14T00:00:00Z","modification":"2026-03-14T02:03:46.983Z","creation":"2026-02-26T14:27:29.512Z"},"accession":"E-MTAB-16691","cross_references":{"ENA":["ERP189679"],"Biostudies":["E-MTAB-16692","E-MTAB-16690","E-MTAB-16689"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}