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Sample GSM1689018 Query DataSets for GSM1689018
Status Public on Sep 17, 2015
Title GATA1 G1E-ER4 24h [Replicate 2]
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 24 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 AB 5500xl Genetic Analyzer
 
Description Replicate 2
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) bxp12@psu.edu
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 GPL15907
Series (1)
GSE68964 Genome-wide binding of GATA1 and TAL1 determined at high resolution
Relations
BioSample SAMN03699976
SRA SRX1030245

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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