 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 01, 2023 |
| Title |
G1ER_CHD7-KO_50K_2 [ATAC-seq] |
| Sample type |
SRA |
| |
|
| Source name |
G1ER_CHD7-KO_50K
|
| Organism |
Mus musculus |
| Characteristics |
cell line: G1ER
tissue source: erythroblasts
genotype: Chd7-/-
cell number: 50,000
time: 2 hours
|
| Treatment protocol |
None
|
| Growth protocol |
Wild type and CHD7 knockout G1ER cells were grown and maintained in IMDM media containing heat-inactivated FBS (16%), pen/strep (2%), monothioglycerol (6.2 mL per 500 mL), EPO (2U/mL) and SCF conditioned media (0.6%).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell lysates were treated with transposase (Illumina Nextera kit, 15028252) for 1-2 hours at 37C. Following transposition, DNA was purified using MinElute PCR purification kit (Qiagen, 28004).
Libraries were constructed according to Illumina protocol using transposase treated DNA, NEB PCR master mix, SYBR green, universal and library-specific Nextera index primers. Libraries were analyzed on an Agilent Bioanalyzer and sequenced using Illumina Hiseq 2500.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
AC8_E9_50K_2HR_GCTACGCT
|
| Data processing |
All ATAC-Seq datasets were aligned to build version GRCm38/mm9 of the mouse genome using Bowtie2 (version 2.2.1) (Langmead et al., 2012) with the following parameters: --end-to-end, -N0, -L20. We used the MACS2 version 2.1.0 (Zhang et al., 2008) peak finding algorithm to identify regions of ATAC-Seq peaks, with the following parameter --nomodel --shift -100 --extsize 200. A q-value threshold of enrichment of 0.05 was used for all datasets.
Genome_build: GRCm38/mm10
|
| |
|
| Submission date |
Apr 24, 2019 |
| Last update date |
Jan 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 |
GPL17021 |
| Series (2) |
| GSE84131 |
CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation |
| GSE130280 |
CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN11492671 |
| SRA |
SRX5732376 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3735209_AC8_E9_50K_2HR_GRCm38_peaks.narrowPeak.gz |
296.7 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
