|
| Status |
Public on Feb 23, 2015 |
| Title |
BRD4 G1E rep1 |
| Sample type |
SRA |
| |
|
| Source name |
G1E_BRD4 G1E
|
| Organism |
Mus musculus |
| Characteristics |
cell type: GATA1 null erythroblasts (G1E)
gata1 transgene: none
treated with: none
chip antibody: BRD4
chip antibody vendor: Bethyl
chip antibody cat. #: A301-985A
chip antibody lot #: Lot# 1
|
| Treatment protocol |
10mM JQ1 was added to a final concentration of 250nM. 10mM E2 was added to a final concentration 100nM.
|
| Growth protocol |
G1E cells were grown in IMDM +20% FBS, glutamine, penicillin/streptomycin, MTG, and Epoetin alpha in a standard tissue culture incubator at 37 degree with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation was performed as described (Kadauke et al. Cell 2012). Cells were fixed in 1% formaldehyde for 10 minutes with gentle shaking at room temperature. Sonication employed a Diagenode Bioruptor (High signal, 30 seconds on/30 seconds off, for 30 minutes). IPs were performed using protein A/G sepharose beads. Beads were washed in high salt buffer and eluted in buffer containing bicarbonate and SDS. Crosslinks were reversed by heating to 65 degrees overnight. DNA was purified on Qiagen miniprep columns.
Libraries were prepared using the protocol as outlined for Illumina's TruSeq ChIP Sample Prep Kit ( IP-202-1012), except that the libraries were size selected using Agencourt SPRIselect beads for an average size of ~300-325bp prior to PCR amplification. Library quality was assessed using the Aglient Bioanalzyer 2100 and libraries were sequenced on the Illumina HiSeq2000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
#422 BRD4 G1E rep1
|
| 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 and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file with read coverage, mapped reads in bam format
|
| |
|
| Submission date |
Oct 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Aaron James Stonestrom |
| E-mail(s) |
aaron.stonestrom@gmail.com
|
| Organization name |
Children's Hospital of Philadelphia
|
| Department |
Hematology
|
| Lab |
Gerd A. Blobel
|
| Street address |
315 ARC 3615 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE62736 |
Functions of BET proteins in GATA1-mediated transcription [ChIP-seq] |
| GSE62737 |
Functions of BET proteins in GATA1-mediated transcription |
|
| Relations |
| BioSample |
SAMN03144744 |
| SRA |
SRX744016 |
