|
| Status |
Public on Sep 08, 2013 |
| Title |
R2_dZn1_DP |
| Sample type |
SRA |
| |
|
| Source name |
DP thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Ikaros-ZnF1-/-
age: 4 week
Sex: Female
tissue: Thymus
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cell suspensions were prepared from whole thymus of 4 week old mice. CD4+ CD8+ double positive cells were sorted on a FACSAriaII cell sorter. Total RNA was purified from Tri-Reagent LS using Qiagen RNEasy MinElute columns according to manufacturer protocol.
Illumina RNA TruSeq Sample Prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base calling was performed using HCS 1.3.8, RTA 1.10.36, Recipe Fragments 1.3.1/HiScanSQ 1.1.1 software bundle.
Reads were aligned to the mouse genome (mm9) using Tophat with the following parameters:-p 8 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-stranded- --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2
Per base report of genome coverage (BedGraph) was obtained using the Bedtools suite.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph file values represent per base coverage of the genome, and was imported to UCSC Genome Browser to provide a visual representation of genome coverage
|
| |
|
| Submission date |
May 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Teresita Arenzana |
| Organization name |
UCLA
|
| Department |
Microbiology, Immunology, and Molecular Genetics
|
| Lab |
Stephen Smale
|
| Street address |
675 Charles E. Young Dr. S., MRL 6-535
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE33693 |
Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros |
| GSE47496 |
Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (RNA-seq: sorted DP thymocytes) |
|
| Relations |
| Reanalyzed by |
GSE80797 |
| BioSample |
SAMN02183406 |
| SRA |
SRX288050 |
