|
| Status |
Public on Feb 07, 2013 |
| Title |
H3K4me3 embryo ChIP, replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
8-16hr embryo ChIP; Iso1 strain; H3K4me3 antibody
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Iso1
developmental stage: Embryo, 8-16hr
tissue: Whole embryo
antibody: anti-H3K4me3
|
| Growth protocol |
Embryos were collected at 8-16 hours after egg laying. For wing discs, wandering 3rd instar larvae were manually removed from Drosophila culture. Larvae were inverted in PBS to expose imaginal discs. Imaginal discs dissected off before fixation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin lysates were clarified from homogenized and sonicated tissues; protein-DNA complexes were isolated with antibody. DNA fragments recovered following chromatin IP prepared for Illumina sequencing using the Epicentre Nextera DNA Sample Prep Kit (Cat. # GA0911). Briefly, up to 12.5 ng DNA was included in the high molecular weight (HMW) tagmentation reaction (5 minutes at 55 degrees Celsius). Tagmented DNA was purified using a Qiagen MinElute column. Addition of barcoded PCR-compatible sites and library enrichment were performed using 12 cycles of PCR. Amplified DNA was purified using the Qiagen MinElute PCR Purification Kit. Library fragments of approximately 225 bp were gel purified and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a HiSeq2000 according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
H3K4me3 embryo ChIP, replicate 2
H3K4me3_E8-16.bedGraph
H3K4me3_E8-16.bed
|
| Data processing |
The Raw images were first processed with the Casava 1.7.0.
Base-called sequences with confidence metrics were obtained using OLB-1.9.0. All multiplexed samples were demultiplexed using Casava 1.7.0
The BWA program was used to align the sequence reads to the Drosophila melanogaster (v5.32) genome, allowing up to 2 edit distance in the seed region and 3 in the full read length. Tags that aligned to more than one location were excluded from our analysis for both ChIP sample and the corresponding control sample (input chromatin). Only properly aligned reads with mapping quality more than 30 were kept.
Peaks were called using MACS (v2), on merged replicates, using bandwidth of 100 and a p-value cutoff of 1E-5
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph files were generated using SPP from sorted bam file, which was generated by SAM/bowtie, under 100 bp step
|
| |
|
| Submission date |
Jun 08, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin P. White |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Chicago
|
| Department |
Institute for Genomics and Systems Biology
|
| Street address |
900 E. 57th STR. 10th FL.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60615 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE38594 |
Genome-wide binding of Yki and GAF in embryos and wing imaginal discs [ChIP-Seq] |
| GSE43130 |
Genome-wide binding of Yki and GAF in embryos and wing imaginal discs |
|
| Relations |
| SRA |
SRX152097 |
| BioSample |
SAMN01041477 |
