|
| Status |
Public on Aug 04, 2019 |
| Title |
T cell input (ChIP-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Pheripheral blood T cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral blood
disease state: Healthy T cells
treatment: N/A
chip antibody: none
|
| Treatment protocol |
CUTLL1 cells were treated with gamma-secretase inhibitor (1 uM) for 72 hours or BET inhibitor (JQ1, 500 nM) for 24h or CDK7 inhibitor (THZ1, 100 mM) for 24 hours.
|
| Growth protocol |
CUTLL1 cells were grown in RPMI medium with 10% FBS ; Primary T-ALL cells isolated from the peripheral blood of T-ALL patients were xenogroafted in immunocompromised NOD SCID gamma mice (NSG) . Following xenograft, and when the tumor bueden in pheripheral blood reached 80%, the mice were sacrificed and the spleen was harvested and splenocytes were used for the Chip-Seq analysis; Healthy T cells were purchased from Lonza (catlog no: 2W-200)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
libraries were prepared using Kapa Hyper prep kit (Catalog no: KK8500) following manufacturer's guidelines
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Read alignment: Reads were aligned against the reference sequence hg19 with bowtie2 (version 2.3.1) with standard parameters and only uniquely mapped reads were kept with MAPQ > 20.
Deduplication: Aligned reads were filtered for duplicated reads using picard-tools version 2.6.0.
Peak-calling: Peak calling for CTCF and H3K27ac was performed using MACS2 (version 2.0.1) using narrow (CTCF) and broad (--broad; H3K27ac) option (sepcial parameters: --no-model).
Differential binding: To identify differentially bound peaks, we performed diffBind (version 2.2.12) analysis, using the normalization option DBA_EDGER.
Bigwig: For visualization purposes, we generated fold-enrichment bigwig files by applying MACS2 (version 2.0.1) bdgcmp over input (-m FE)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, peak (bed)
|
| |
|
| Submission date |
Jul 24, 2019 |
| Last update date |
Aug 04, 2019 |
| Contact name |
Andreas Kloetgen |
| Organization name |
Helmholtz Centre for Infection Research
|
| Department |
Department for Computational Biology of Infection Research
|
| Street address |
Inhoffenstr 7
|
| City |
Braunschweig |
| State/province |
NI |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE115893 |
Dynamic 3D chromosomal landscapes in acute leukemia [ChIP-Seq] |
| GSE115896 |
Dynamic 3D chromosomal landscapes in acute leukemia |
|
| Relations |
| BioSample |
SAMN12348807 |
| SRA |
SRX6578930 |
