|
| Status |
Public on Apr 23, 2014 |
| Title |
Yki S2 ChIP input |
| Sample type |
SRA |
| |
|
| Source name |
S2 cell line ChIP; Input
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: S2 (embryo cell line)
cell line: S2
chip antibody: no antibody (input control)
|
| Growth protocol |
S2 cells were grown in schneiders medium and fixed with formaldehyde for ChIP (formaldehyde added direcly to culture media).
|
| 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 |
Yki embryo ChIP, replicate 1
|
| 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: peak file was generated using SPP from sorted bam file, which was generated by SAM/bowtie, under 100 bp step
|
| |
|
| Submission date |
Apr 23, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jason Grundstad |
| E-mail(s) |
jgrundstad@uchicagoedu
|
| Phone |
7738347359
|
| Organization name |
University of Chicago
|
| Department |
Division of Biological Sciences
|
| Lab |
Kevin White - IGSB
|
| Street address |
900 E 57th St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE46305 |
Genome-wide binding of Yki in S2 cells |
|
| Relations |
| BioSample |
SAMN02055431 |
| SRA |
SRX271405 |
