|
| Status |
Public on Nov 08, 2012 |
| Title |
Dyak_WPP_CTCF_ChIPSeq_1, 2 and 3 |
| Sample type |
SRA |
| |
|
| Source name |
white prepupae
|
| Organism |
Drosophila yakuba |
| Characteristics |
developmental stage: white prepupae
antibody name: CTCF-C
antibody manufacturer: Renkawitz Lab
antibody lot/batch#: N/A
antibody catalog: Custom
fraction: ChIP
|
| Treatment protocol |
No Treatment
|
| Growth protocol |
The four sequenced inbred fly lines for the different Drosophila species are grown in room temperature on standard fly food. The white prepupa whole animals are collected within 15 min time interval
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After chromatin immuno-precipitation, the DNA is purified in 30ul of water. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to multiple drosophila genomes using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the QuEST 2.0 algorithm (http://mendel.stanford.edu/SidowLab/downloads/quest/)
|
| |
|
| Submission date |
Sep 30, 2010 |
| 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 |
GPL11000 |
| Series (1) |
| GSE24449 |
Genome-wide comparative ChIP-seq data of CTCF and RNA-seq data in Drosophila white prepupa on Illumina Genome Analyzer |
|
| Relations |
| SRA |
SRX027395 |
| BioSample |
SAMN00113737 |
| Named Annotation |
GSM602333_dyak_combined_signal_wpp_CTCF_QuEST_CDP_scores.wig.gz |
| Named Annotation |
GSM602333_dyak_peak_region.bed.gz |
