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Sample GSM2574899 Query DataSets for GSM2574899
Status Public on Oct 21, 2020
Title GTT11_T
Sample type SRA
 
Source name thymus
Organism Mus musculus
Characteristics tissue: thymus
cell type: regulatory T-cell
gender: female
genotype: Tnfrsf11a (Rank) Foxn1 knock-out
pregnancy status: pregnant
Extracted molecule polyA RNA
Extraction protocol Equal numbers of Tregs (280 cells) were sorted from the thymus and placenta of E17.5 pregnant Bl6 females, mated with syngeneic Bl6 males. To increase robustness, the 280 placental Tregs were purified from 5 individual placentas per pregnant female (56 Tregs/placenta). Cells were sorted directly into a cell lysis buffer consisting of a 0.2% (vol/vol) Triton X-100 solution and an RNase inhibitor.
For the generation of full-length cDNA, the Smart-seq2 protocol (Picelli, S. et al, Nat Protoc. 2014 Jan;9(1):171-81. doi:10.1038/nprot.2014.006) was used.
The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina).
For sequencing, libraries were pooled, diluted and sequenced on Illumina HiSeq 3000 using 50 bp single-read chemistry.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description Thymic Tregs; mice ID GTT11: Pregnant RANK FOXN1 KO
Data processing Illumina HiSeq Control Software (HCS) HD 3.4.0.38 and 3.3.52 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.3 and 2.7.7.
BCL to BAM file conversion and demultiplexing with Illumina2bam 1.17 (http://wtsi-npg.github.io/illumina2bam/) and custom programmes based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.1a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.11 package DESeq2 1.28.1, running under R 4.0.2.
Genome_build: UCSC mm10 based on GRCm38
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format
 
Submission date Apr 11, 2017
Last update date Oct 22, 2020
Contact name Christoph Bock
E-mail(s) cbock@cemm.oeaw.ac.at
Organization name CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL21493
Series (1)
GSE97666 RNA-seq analysis of regulatory T cells in thymus, placenta, spleen and white adipose tissue of pregnant mice
Relations
BioSample SAMN06710976
SRA SRX2733590

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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