|
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 |