|
| Status |
Public on Feb 24, 2020 |
| Title |
hSTAT5B, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
CD8+ T-cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N
tissue: Lymph node
genotype: hSTAT5B +/T
|
| Treatment protocol |
CD8+ T-cells were sorted using magnisort kit (eBioscience)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lymph nodes were isolated and kept on ice, single-cell suspensions were inclubated with CD8 antibody and magnetic bead, isolated CD8 T-cells were flash-frozen in Trizol reagent, RNA was harvested
1µg of total RNA per sample was taken for cDNA library synthesis using SENSE mRNA-Seq Library preparation kit according to the manufacturers recommendations.
50 bp single-end 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 |
| |
|
| Description |
expression profile of hSTAT5B CD8+ T-cell, replicate 1
|
| Data processing |
Alignment to genome version GRCm37 using transcriptome guided alignment with TopHat version 1.4.1.
Adapter trimming and removing of low quality bases was performed using cutadapt.
Counting of reads was done using htseq-count (HTSeq version 0.6.1p1), mode union.
Genome_build: GRCm37/mm9
Supplementary_files_format_and_content: raw count file (tab delimited)
|
| |
|
| Submission date |
Jan 19, 2017 |
| Last update date |
Feb 24, 2020 |
| Contact name |
Ha T T Pham |
| E-mail(s) |
ha.pham@lbicr.lbg.ac.at
|
| Organization name |
Ludwig Boltzmann Institute for Cancer Research
|
| Lab |
Richard Moriggl
|
| Street address |
SCHWARZSPANIERSTR 17
|
| City |
Wien |
| ZIP/Postal code |
A1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE93847 |
STAT5BN642H is a driver mutation for T-cell neoplasia (RNA-Seq) |
| GSE104577 |
STAT5BN642H is a driver mutation for T-cell neoplasia |
|
| Relations |
| BioSample |
SAMN06242182 |
| SRA |
SRX2505202 |
