|
| Status |
Public on Aug 16, 2013 |
| Title |
S2_Input, replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
S2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: S2
fraction: input DNA
replicate: 1
transcription factor: NA
antibody name: NA
antibody manufacturer: NA
antibody catalog number: NA
|
| 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.
Libraries were prepared according to ChIP-seq library kit instruction Nextera DNA prep kit is FC-121-103
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
NA
NA
|
| 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 SPP and IDR
Wig files were generated using MACS2
Genome_build: dm3
Supplementary_files_format_and_content: bed (columns are: chrom; chromStart; chromEnd; name; score; strand; signalValue; pValue; qValue; peak; Ref to: http://code.google.com/p/phantompeakqualtools/) and wig
|
| |
|
| Submission date |
Aug 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin P. White |
| E-mail(s) |
kpwhite@uchicago.edu
|
| 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 (1) |
| GSE49899 |
Diverse patterns of genome-wide DNA targeting by transcriptional regulators in Drosophila melanogaster |
|
| Relations |
| BioSample |
SAMN02318066 |
| SRA |
SRX335520 |
