|
| Status |
Public on Jan 01, 2018 |
| Title |
ChIP-seq_5F_BirA-Only_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Human MSCiPS1-derived 5F hematopoietic cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Hematopoietic cells
|
| Treatment protocol |
NA
|
| Growth protocol |
MSCiPS1 human induced pluripotent stem cells were differentiated to CD34+ hematopoietic cells and transduced with 5 transcription factors (5F). Human 5F cells were cultured in SFEM with 50 ng/ml SCF, 50 ng/ml FLT3, 50 ng/ml TPO, 50 ng/ml IL6, and 10 ng/ml IL3 (all R&D Systems). Dox was added at 2 μg/ml (Sigma). Puromycin was added at 0.35 ug/mL (ThermoFisher) and G418 was added at 750 ug/mL (Gibco). Media were changed every 3-4 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq analysis using the Illumina NextSeq500, 10-20 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 |
| |
|
| Description |
Streptavidin Dynabeads or Antibodies: ThermoFisher 65601, lot:123612210
|
| Data processing |
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v0.12.7 with the following parameters: -v 2 -m 3 --strata --best. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by NextSeq500.
Genome_build: hg19
Supplementary_files_format_and_content: wig file, and peak bed file
|
| |
|
| Submission date |
Nov 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Melissa Kinney |
| E-mail(s) |
melissa.kinney@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE89417 |
ChIP-seq analysis of EZH1, H3K4me3 and H3K27me3 in 5F cells |
| GSE89418 |
EZH1 as a key epigenetic barrier to definitive haematopoiesis during embryonic development |
|
| Relations |
| BioSample |
SAMN05967254 |
| SRA |
SRX2319395 |
