|
| Status |
Public on Jul 13, 2021 |
| Title |
CoKO Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
CD69+CD4+CD8+ Adult thymocytes_CoKO
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
age: 6 weeks
genotype/variation: Foxa1fl/flFoxa2fl/fl CD4Cre+
tissue: Adult thymus
cell type: CD69+CD4+CD8+ Adult thymocytes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Thymocyte suspensions were prepared from adult (6 week old) Foxa1fl/flFoxa2fl/fl.CD4Cre-tg+ (Foxa1/2coKO) and Foxa1fl/flFoxa2fl/fl.Cre- (control) thymus. Cells were stained with anti-CD69, anti-CD4 and anti-CD8 and facs sorted to purify CD69+CD4+CD8+ cells. RNA was extracted from this CD69+CD4+CD8+ cells defined as DP.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
UCLGNS1204-DP3_S11
|
| Data processing |
Base Calling was done using RTA v(2.4.1.1)
Alignment was done using TopHat v(2.0.7)
Peak Calling was performed using Picard
The Bioconductor package DESeq2 was used to generate normalised estimates of transcript abundance
Genome_build: mm10
Supplementary_files_format_and_content: comma separated file including RPKM values for each Sample.
|
| |
|
| Submission date |
Mar 25, 2021 |
| Last update date |
Jul 13, 2021 |
| Contact name |
Tessa Crompton |
| Organization name |
UCL
|
| Department |
Immunobiology
|
| Street address |
30 Guilford Street
|
| City |
London |
| ZIP/Postal code |
WC1N 1EH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE169602 |
The pioneer transcription factors Foxa1 and Foxa2 regulate alternative RNA splicing during positive selection in the thymus |
|
| Relations |
| BioSample |
SAMN18489537 |
| SRA |
SRX10442179 |
