|
| Status |
Public on Dec 01, 2023 |
| Title |
CD34_CHD7_Input |
| Sample type |
SRA |
| |
|
| Source name |
CD34+ cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: mobilized peripheral blood
cell type: CD34 positive cells
antibody: None
|
| Treatment protocol |
None.
|
| Growth protocol |
Human mobilized peripheral CD34+ cells were thawed and grown in StemSpan SFEM media supplemented with 2% pen/strep and 1% StemSpan CC100 cocktail (Stem Cell Technologies) for 5 days. Cells were fixed and collected on day 5 for ChIP-seq.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CD34+ cells were fixed in 1% formaldehyde for 10 minutes and lysed to collect nuclei for sonication, followed by ChIP with antibody.
Library synthesis was performed using TruSeq ChIP Library Prep Kit (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Ordered from Fred Hutchinson Cancer Research Center
|
| Data processing |
Reads were aligned to human reference genome hg19 using Bowtie Version 0.12.9 with parameters -n 2 -S -k 2 -m 2 -best
Regions enriched for CHD7 were identified using SICER with parameters -w 200 -I 200 -g 400 -e 1e1
Regions enriched for histone H3K27ac were identified using MACS with input control and parameters -p 1e-9 -keep-dup=auto
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Alignment and bed files of binding peaks
|
| |
|
| Submission date |
Jul 07, 2016 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Leonard Zon |
| E-mail(s) |
zon@enders.tch.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Department |
Oncology/Hematology
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE84130 |
CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation [CD34 ChIP-seq] |
| GSE84131 |
CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation |
|
| Relations |
| BioSample |
SAMN05363828 |
| SRA |
SRX1901614 |
