|
| Status |
Public on Apr 27, 2015 |
| Title |
H3K27ac_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
G1E cells, an erythroid progenitor model
|
| Organism |
Mus musculus |
| Characteristics |
treatment: none
cell type: Derived from Gata1 knock out ES cells; immortalized as a model for erythroid progenitors
strain: 129
developmental stage: model for adult erythropoiesis
antibody: H3K27ac
|
| Treatment protocol |
See Treatment column for Samples
|
| Growth protocol |
http://stokes.chop.edu/web/weiss/G1Ecells.html
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation of H3K27ac occupied segments using anti-H3K27ac (Abcam Cat# Ab4729) using published methods (Welch et al. 2004)
TruSeq ChIP Sample Prep Kit (Illumina)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
local id 535
|
| Data processing |
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm9 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle generated with MACS using parameters --nomodel --shiftsize=120--format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Peaks called with Sicer V1.1 using parameters mm9 1 200 150 0.74 600 0.01
Filter blacklist regions from peaks, and convert to broadpeak format (see UCSC Genome Browser for format specs)
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle file with read coverage, peak file in broad peak format
|
| |
|
| Submission date |
Sep 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ross Hardison |
| E-mail(s) |
rch8@psu.edu
|
| Organization name |
Pennsylvania State University
|
| Street address |
303 Wartik Lab
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE61349 |
Epigenetic and genetic features that lead to discovery of enhancer function |
|
| Relations |
| BioSample |
SAMN03079637 |
| SRA |
SRX710370 |
