|
| Status |
Public on Nov 13, 2012 |
| Title |
Lmd2_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Lmd2_ChIPSeq
|
| Organism |
Drosophila melanogaster |
| Characteristics |
chip antibody: Lmd2 [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 |
SRX151219 |
| BioSample |
SAMN01001952 |
