|
| Status |
Public on Jan 26, 2015 |
| Title |
PB_E-DS20403 |
| Sample type |
SRA |
| |
|
| Source name |
human mobilized peripheral blood derived erythroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
ChIP: AcH3
cell type: human erythroblasts
|
| Growth protocol |
hESC line H1 were grown on irradiated MEFs and passaged onto matrigel coated plates for MEF free growth in MEF conditioned medium. Erythroblasts from hESCs were derived by embryoid body method. Embryoid bodies were dissociated and cultured in erythroid inducing media. FL and PB derived erythroid cells were obtained by culturing mononuclear cells from FL and CD34+ cells from mobilized PB in the same erythroid inducing media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibody at 4 °C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross-linking in the immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. 20-50 ng of ChIP DNA was end-repaired, followed by the addition of adenine, ligated to Illumina adapters and made into a Solexa library for sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Peak: Peak detection was performed using Hotspot pipeline. http://www.uwencode.org/proj/hotspot-ptih/
Alighment: Bowtie aligner (version 0.12.7), http://bowtie-bio.sourceforge.net/index.shtml standard params for Hi-Seq lanes: bowtie -p 4 --mm -n 3 -v 3 -k 2 --phred33-quals, standard params for GAII lanes: bowtie -p 4 --mm -n 3 -v 3 -k 2 --phred64-quals
Genome Build:
PB_E-DS20403.peaks.fdr0.01.hg19.bed: hg19
|
| |
|
| Submission date |
Jan 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kai-Hsin Chang |
| Organization name |
University of Washington
|
| Street address |
1705 NE Pacific St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE35375 |
Epigenetic modifications and chromosome conformations of the beta globin locus throughout development |
|
| Relations |
| SRA |
SRX117980 |
| BioSample |
SAMN00779284 |
| Named Annotation |
GSM867106_PB_E-DS20403.peaks.fdr0.01.hg19.bed.gz |
