|
| Status |
Public on Jan 01, 2018 |
| Title |
ATAC-seq_5F_F8-shLuc-rep2 |
| 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) and puromycin was added at 0.35 ug/mL (ThermoFisher). Cultures were maintained at a density of <1 x106 cells/ml, and media were changed every 3-4 days. AGM tissue was microdissected from E10.5 embryos and dissociated to single cells. AGM hematopoietic cells were sorted for immunophenotypic markers cKit+VE-cadherin+CD45+CD41+.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ATAC-seq analysis using the Illumina NextSeq500, ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference human (hg19) or mouse (mm9) genome were retained for downstream data analysis.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) or mouse genome assembly mm9 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, mm9
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) |
| GSE89416 |
ATAC-seq analysis in 5F cells and AGM cells with EZH1 depletion |
| GSE89418 |
EZH1 as a key epigenetic barrier to definitive haematopoiesis during embryonic development |
|
| Relations |
| BioSample |
SAMN05967261 |
| SRA |
SRX2319388 |
