|
| Status |
Public on May 15, 2018 |
| Title |
SCF+IL7_1 |
| Sample type |
SRA |
| |
|
| Source name |
SCF+IL7_Pro-T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Pro-T cells
treatment: stimulated with Scf+Il7
|
| Treatment protocol |
Prior to RNA extraction, cells were left unstimulated for 18h, followed by 8h stimulation with indicated cytokines
|
| Growth protocol |
pro-T cells were grown in the presence of DL4, Scf and Il7
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Maxwell 16 LEV simplyRNA Cells Kit according to manufacturers instructions (Promega)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with TopHat2
count reads with htseq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts
|
| |
|
| Submission date |
May 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sofie Demeyer |
| E-mail(s) |
sofie.demeyer@kuleuven.vib.be
|
| Organization name |
KULeuven / VIB
|
| Department |
Center for Cancer Biology
|
| Lab |
Laboratory of Molecular Biology of Leukemia
|
| Street address |
Herestraat 49 / bus 912
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE98899 |
A systems biology approach in understanding oncogenic cooperation between TAL1 expression and PTEN deletion in T-cell acute lymphoblastic leukaemia |
|
| Relations |
| BioSample |
SAMN07109626 |
| SRA |
SRX2821714 |
