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Sample GSM417015 Query DataSets for GSM417015
Status Public on Nov 25, 2009
Title GATA-1_ChIPSeq
Sample type SRA
 
Source name MEL86 erythroid cell line expressing metabolically biotinylated GATA-1 (MEL Bio-GATA-1)
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Induced MEL bioGATA-1 cells
chip antibody: GATA-1
Growth protocol MEL-bioGATA-1 cells were cultured in 5% CO2 at 37°C in DMEM+ 10% FCS+1% L-Glutamine+ 2% Pen/Strep. Erythrocyte differentiation of MEL cells was induced with 1.7% (v/v) for 24 hrs.
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description Streptavidin pull down of metabolically biotinylated GATA-1
Data processing Alignment: Sequence reads were obtained and mapped to the mouse genome (UCSC, mm8) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
 
Submission date Jun 12, 2009
Last update date May 15, 2019
Contact name Laura Riva
E-mail(s) lriva@mit.edu
Organization name MIT
Department Biological Engineering
Lab Fraenkel Lab
Street address 77 Massachusetts Avenue
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL9185
Series (1)
GSE16594 Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis
Relations
SRA SRX015120
BioSample SAMN00007204

Supplementary file Size Download File type/resource
GSM417015_GATA1.aligned.txt.gz 68.9 Mb (ftp)(http) TXT
GSM417015_GATA1.peaks.txt.gz 55.3 Kb (ftp)(http) TXT
GSM417015_readme.aligned.txt.gz 212 b (ftp)(http) TXT
GSM417015_readme.peaks.txt.gz 257 b (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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