|
| Status |
Public on Oct 23, 2020 |
| Title |
GTT24_T |
| Sample type |
SRA |
| |
|
| Source name |
thymus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl6
tissue: thymus
cell type: regulatory T-cell
gender: female
genotype: Tnfrsf11a (Rank) Foxn1 knock-out
pregnancy status: non-pregnant
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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 3000/4000 using 50 bp single-read chemistry.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Thymus Treg Neutropilin-high cells: GTT24 mother (Rank KO)
GTT24_T_S13928
|
| 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 |
Oct 22, 2020 |
| Last update date |
Oct 23, 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 |
SAMN16517735 |
| SRA |
SRX9345989 |
