|
Status |
Public on Nov 13, 2012 |
Title |
Lmd1_ChIPSeq |
Sample type |
SRA |
|
|
Source name |
Lmd1_ChIPSeq
|
Organism |
Drosophila melanogaster |
Characteristics |
chip antibody: Lmd1 [Cunha et al. 2010 PLoS Genet 6(7): e1001014] cell type: sorted primary mesodermal developmental stage: 2 hour embryo collection spanning late stage 11 to early stage 12
|
Growth protocol |
Embryos were collected spanning a two-hour window from stage 11 through early stage 12; following embryo collection, cells were dissociated on ice and fixed in 1.8% formaldehyde (15 min) prior to cell sorting
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Immunoprecipiated DNA was end-repaired (END-IT kit from Epicentre), A-tailed (Epicentre), ligated with barcoded Illumina paired-end Y-linker, PCR-amplified for 16 cycles and library fragments of 300-500 bp were selected on 2% agarose E-gel and gel-purified.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Basecalls performed using CASAVA version 1.8.1 ChIP-seq reads were aligned to the dm3 genome assembly using Burrows-Wheeler Aligner Genome_build: dm3 Supplementary_files_format_and_content: wig files: peaks were called using MACS with the following setting: p-value (10-5) and mfold (2) Supplementary_files_format_and_content: bed file: dm3 genomic coordinates for the overlap of regions called enriched by MACS from Lmd1_ChIPSeq compared to input and Lmd2_ChIPSeq compared to input
|
|
|
Submission date |
Jun 01, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Brian Busser |
Organization name |
NHLBI/NIH
|
Lab |
LDSB
|
Street address |
10 Center Drive
|
City |
Bethesda |
State/province |
Md |
ZIP/Postal code |
20892 |
Country |
USA |
|
|
Platform ID |
GPL13304 |
Series (1) |
GSE38402 |
Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network |
|
Relations |
SRA |
SRX151218 |
BioSample |
SAMN01001951 |