|
| Status |
Public on May 11, 2020 |
| Title |
H3K27ac_HiChIP_MED14-dTAG_2h_dTAG7_A |
| Sample type |
SRA |
| |
|
| Source name |
H3K27ac_HiChIP_MED14-dTAG_2h_dTAG7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KBM7
cell type: chronic myeloid leukemia cell line
genotype/variation: MED14-dTAG
treatment: 2h 500nM dTAG7
chip antibody: H3K27ac (Abcam ab4729)
|
| Treatment protocol |
15mio cells were treated for 2h with 500nM dTAG7 or DMSO and then fixed with 1% MeOH-free PFA for 10min at room temperature.
|
| Growth protocol |
KBM7 cells were grown in IMDM medium supplemented with 10% FBS and 1% Pen/Strep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin contacts were generated and pulldown performed as previously described (PMID: 27643841).
Library construction using Illumina Tn5.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
conversion and demultiplexing: Illumina2bam
FASTQ files were in silico digested by looking for the restriction enzyme religations sites GATCGATC. Only the 5 prime part of a read is kept after removing the remainder of a read when cut at the restriction site. All non cut reads are kept.
All filtered reads are then mapped to human genome assembly hg19 with bowtie2 (version 2.2.3) using options --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder
The human genome was insilico digested with MboI enzyme and mapped reads are assigned to the insilico digested genome fragments. Read pairs are tagged as valid if they had the correct orientation and are on different fragments.
Genome_build: hg19
Supplementary_files_format_and_content: hic generation: .hic files were generated with the 'pre' tool from juicer tools (version 1.8.9).
|
| |
|
| Submission date |
Oct 28, 2019 |
| Last update date |
May 12, 2020 |
| Contact name |
Georg E Winter |
| Organization name |
CeMM - Research Institute for Molecular Medicine of the Austrian Academy of Sciences
|
| Street address |
Lazarettgasse 14, AKH BT25.3
|
| City |
Wien |
| State/province |
Austria |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE139466 |
Selective Mediator-dependence of cell type-specifying transcription [HiChIP] |
| GSE139468 |
Selective Mediator dependence of cell-type-specifying transcription |
|
| Relations |
| BioSample |
SAMN13139825 |
| SRA |
SRX7064290 |
