|
| Status |
Public on Sep 17, 2015 |
| Title |
GATA1 G1E-ER4 3h [Replicate 3] |
| Sample type |
SRA |
| |
|
| Source name |
G1E-ER4
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: GATA1 (sc265)
cell type: G1E-ER4
cell description: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)
strain: 129
|
| Treatment protocol |
3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)
|
| Growth protocol |
G1E_Hardison_protocol.pdf; http://genome.ucsc.edu/ENCODE/protocols/cell/mouse/
G1E_ER4_E2_Hardison_protocol.pdf; http://genome.ucsc.edu/ENCODE/protocols/cell/mouse/
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and GATA1(or TAL1)-DNA complexes were isolated with antibody.
ChIP-exo libraries were prepared for sequencing using standard SOLiD & Illumina protocols with a minor modification; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Replicate 3
gata1_peakpair.gff
gata1_multiGPS.gff
|
| Data processing |
For single end reads from HiSeq, basecalls were performed using CASAVA version 1.7 and for paired end reads from NextSeq, basecalls were performed using Bcl2fastq version 2.15.
ChIP-exo reads were aligned to the mm9 genome assembly using Bowtie 1.00 for SOLiD(1 mismatch allowed), and BWA (Version: BWA ALN 0.6.2 for HiSeq single end reads and Version: BWA MEM 0.7.9a for NextSeq paired end reads) with default options. Non-uniquely mapped reads were filtered out in order to remove the reads with low mapping quality.
GeneTrack peak caller; https://github.com/ialbert/chipexo/tree/master/genetrack (-s 5 -e 10)
multiGPS v0.5; http://mahonylab.org/software/multigps/ (--geninfo mm9.info --threads 4 --q 0.05 --d reb1_chipexo.distrib.txt --exclude blacklist.bed --design design_gata1 --verbose --probshared 0.99 --poissongausspb --medianscale --prlogconf -5 --memepath usr/bin --mememinw 6 --mememaxw 16 )
finding the enriched peaks from multiple biological replicates; http://atlas.bx.psu.edu/Han_etal_GATA_Method.htm
Genome_build: mm9
Supplementary_files_format_and_content: gff
|
| |
|
| Submission date |
May 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Bongsoo Park |
| E-mail(s) |
[email protected]
|
| Phone |
814-441-3861
|
| Organization name |
Penn State University
|
| Street address |
453 North Frear Building
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE68964 |
Genome-wide binding of GATA1 and TAL1 determined at high resolution |
|
| Relations |
| BioSample |
SAMN03699974 |
| SRA |
SRX1030243 |
