|
| Status |
Public on May 16, 2022 |
| Title |
ETV6-NCOA2 CD34_control |
| Sample type |
SRA |
| |
|
| Source name |
CD34 positive cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD34 positive cells
genotype/variation: Expression of ETV6-NCOA2
sort: GFP
chip antibody: H3
|
| Treatment protocol |
Each CD34 biological replicate composed of three different cord blood units
|
| Growth protocol |
Samples 1-2: The cells were cultured for five days in-vitro (SCF, Flt3L, and TPO) , sorted for GFP positive. Sample 3: bone marrow samples from ETV6-NCOA2 patients were transplanted into NSGS mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CD34 positive cells were isolated using magnetic beads from fresh cord blood (For each biological replicate, at least three different cord blood samples were mixed). The cell were retrovirally infected with ETV6-NCOA2 or empty vector and cultured in IMDM supplemented with hSCF, hTPO, hFlt3L (100 ng/ml) for 5 days. The positive cells were sorted (GFP+). ETV6-NCOA2 patient derived xenografts were sorted from bone marrow of the sick mice (human CD45+). We extracted DNA from the samples and performed H3K27Ac ChIP sequencing.
In-house ChIP-Seq protocol, Libraries were evaluated by Qubit and BioAnalyzer. Sequencing libraries were constructed with barcodes to allow multiplexing of y samples on one lane.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CD34 positive cells transduced with ETV6-NCOA2 after five days culture in-vitro
|
| Data processing |
Reads were demultiplexed
Adapters were trimmed using the cutadapt tool
The reads were aligned uniquely to the human genome (hg19)
Bound regions were detected using MACS2 (version 2.0.10.20131216)
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files of MACS2 peaks (bed)
|
| |
|
| Submission date |
Nov 17, 2020 |
| Last update date |
May 16, 2022 |
| Contact name |
Gilgi Friedlander |
| Organization name |
Weizmann Institute of Science
|
| Street address |
Hertzel st
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE161624 |
ChIP sequencing of ETV6-NCOA2 H3K27Ac profile in T/M mixed-phenotype acute leukemia |
| GSE162338 |
ETV6-NCOA2 expression in CD34 positive cord blood cells |
|
| Relations |
| BioSample |
SAMN16816785 |
| SRA |
SRX9520828 |
