|
| Status |
Public on Aug 21, 2023 |
| Title |
ChIPmentation_HSC_LMO2_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bone Marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone Marrow
cell type: CD34+ HSPC
cell subset: HSC
chip antibody: LMO2 (Abcam)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching, cells were lysed and nuclei frozen. Nuclei were sonicated using a Bioruptor Pico to generate chromatin fragments.
Antibody bound chromatin was collected and crosslinked, before library construction using the KAPA HiFi HotStart Ready Mix and size selection using AMPure XP beads.
ChIPmentation/ Low input ChIP seq using tagmentation
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Coverage_LMO2_HSC.bw
LMO2_HSC_peaks.narrowPeak
|
| Data processing |
ChipSeq reads were trimmed using TrimGalore. Adaptors were removed using CutAdapt. The reads were aligned to hg38 using BWA.
ChipSeq reads were sorted, indexed using Samtools. Dupicate reads were removed using Picard. Replicates were merged using Samtools.
ChipSeq peak calling was done using MACS 2.0 with a p value of 1e-5
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak: BED6+4 files containing peaks called from merged replicates with macs2 using p-value of 1 x 10-5 and the IgG track as the control.
Library strategy: ChIPmentation
|
| |
|
| Submission date |
May 01, 2023 |
| Last update date |
Aug 21, 2023 |
| Contact name |
Julie Thoms |
| E-mail(s) |
j.thoms@unsw.edu.au
|
| Organization name |
UNSW Sydney
|
| Department |
Adult Cancer Program
|
| Street address |
Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St
|
| City |
Randwick |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE231422 |
Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [ChIPmentation] |
| GSE231486 |
Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC |
|
| Relations |
| BioSample |
SAMN34505677 |
| SRA |
SRX20176880 |
