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| Status |
Public on Feb 24, 2020 |
| Title |
hSTAT5B, replicate 1 |
| Sample type |
SRA |
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| Source name |
Lymph node
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| Organism |
Mus musculus |
| Characteristics |
cell type: CD8+ T-cells
strain: C57BL/6N
genotype: hSTAT5B +/T
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| Treatment protocol |
CD8+ T-cells were sorted using magnisort kit (eBioscience)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from purified CD8+ T-cells was isolated using AllPrep DNA/RNA mini kit (Qiagen) and subsequently subjected to RRBS and analysis.
RRBS was carried out as described earlier (Tomazou et al. Cell Rep, 2015).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
DNA methylation profile of hSTAT5B CD8+ T cells, replicate 1
STAT5B_262
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| Data processing |
Sequences were trimmed for adapters using Trimmomatic with ILLUMINACLIP settings “:2:40:7 SLIDINGWINDOW:4:15 MAXINFO:20:0.50 MINLEN:18”
Reads were aligned to the GRCm38 (mm10) assembly of the mouse genome, using BSMAP in its RRBS mapping mode
DNA methylation levels for individual CpGs were calculated using custom Python scripts
Genome_build: mm10
Supplementary_files_format_and_content: DNA methylation calls (text file, BED format: chrom, start, end, methylated/total-reads, score, strand)
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| Submission date |
Oct 03, 2017 |
| Last update date |
Feb 24, 2020 |
| Contact name |
Ha T T Pham |
| E-mail(s) |
ha.pham@lbicr.lbg.ac.at
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| Organization name |
Ludwig Boltzmann Institute for Cancer Research
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| Lab |
Richard Moriggl
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| Street address |
SCHWARZSPANIERSTR 17
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| City |
Wien |
| ZIP/Postal code |
A1090 |
| Country |
Austria |
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| Platform ID |
GPL21493 |
| Series (2) |
| GSE104557 |
STAT5BN642H is a driver mutation for T-cell neoplasia (RRBS) |
| GSE104577 |
STAT5BN642H is a driver mutation for T-cell neoplasia |
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| Relations |
| BioSample |
SAMN07735531 |
| SRA |
SRX3241534 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2803336_cpgmeth_STAT5B_262_mm10.bed.gz |
21.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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