|
| Status |
Public on Feb 20, 2020 |
| Title |
ChIP-seq_G1E-ER4_24hr_H3K27ac_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse G1E-ER4 cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse G1E-ER4 cells
chip antibody: H3K27ac, Abcam, ab4729, GR132150-4
|
| Treatment protocol |
Cells were treated with 10-7 M β-estradiol to induce erythroid differentiation.
|
| Growth protocol |
G1E-ER4 cells were cultured in IMDM medium containing 15% FBS, 50 ng/mL recombinant SCF, and 2 U/ml recombinant human erythropoietin (EPO).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq analysis using the Illumina NextSeq500, 5 ng of ChIP DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads were aligned to mouse (mm10) genome assembly using Bowtie2 with default parameters.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm.
The wig files were generated by a moving window of size 200bp. The tag count in the window was further normalized by total read count for ChIP-seq data generated by NextSeq500.
Genome_build: mm10
Supplementary_files_format_and_content: wig file and peak bed file
|
| |
|
| Submission date |
Oct 18, 2019 |
| Last update date |
Feb 20, 2020 |
| Contact name |
Jian Xu |
| E-mail(s) |
Jian.Xu@stjude.org
|
| Phone |
9015955208
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Pathology
|
| Street address |
262 Danny Thomas Place, MS 345
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE139111 |
ChIP-seq analysis of H3K4me3, H3K27ac and CTCF in undifferentiated and differentiated G1E-ER4 cells |
| GSE139117 |
Analysis of CRE-mediated chromatin interactions by CAPTURE2.0 |
|
| Relations |
| BioSample |
SAMN13060830 |
| SRA |
SRX7024015 |
