|
| Status |
Public on Sep 05, 2016 |
| Title |
DCKO DN3_1 |
| Sample type |
SRA |
| |
|
| Source name |
thymus
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pre-T cell, lymphocyte
genotype: Zfp36l1fl/fl, Zfp36l2fl/fl, CD2cre
strain: C57BL/6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells FACS sorted from thymus as described in summary above (methods). RNA was extracted using RNeasy Micro Kit
20-200 ng of RNA used to make libraries using TruSeq Stranded Total RNA and rRNA Removal Mix – Gold from Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
KV9
|
| Data processing |
Libraries were sequenced by Hiseq 2000 in 100bp single-end reads
Basecalling was done using Illumina default pipeline
Reads were trimmed to remove adapter sequences using Trim Galore
Reads were mapped using Tophat (version 2.0.12) to the GRCm38 mouse assembly
Read counts for each gene were generated in htseq-count: transcripts from the same gene were collapsed into a single transcript containing all exons
Differences in the abundance of transcripts between DCKO and control samples were calculated in the R/Bioconductor program DESeq2 (version 1.6.3).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw and normalised read counts for each sample, and output from DESeq2 analysis
|
| |
|
| Submission date |
Mar 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Turner |
| E-mail(s) |
martin.turner@babraham.ac.uk
|
| Organization name |
Babraham Institute
|
| Department |
Lymphocyte Signalling and Development
|
| Lab |
Dr. Martin Turner
|
| Street address |
Babraham Hall
|
| City |
Cambridge |
| ZIP/Postal code |
CB22 3AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE79174 |
RNAseq of pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice. |
| GSE79179 |
Pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice |
|
| Relations |
| BioSample |
SAMN04549418 |
| SRA |
SRX1630336 |
