 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 04, 2013 |
| Title |
Insv ChIP, 6.5-12h |
| Sample type |
SRA |
| |
|
| Source name |
w[1118] embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: wt, w[1118]
developmental stage: 6.5-12h
chip antibody: Insensitive
|
| Growth protocol |
embryos were aged and collected at 25 degrees
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
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 II |
| |
|
| Data processing |
Mapping to the Drosophila dm3 genome, using Bowtie, parameters –v 2 –m 1, (i.e. allowing 2 mismatches and only using uniquely mapping reads)
Peak calling using Quest, comparing Insv ChIP to IgG control for each time point. The following parameters were used: bandwidth = 30, region size = 300 ChIP enrichment = 10, ChIP to background enrichment = 2.5, ChIP extension enrichment = 3
Genome_build: dm3
Supplementary_files_format_and_content: 2 bed files with Insv peaks, one for 2.5-6h and one for 6.5-12h.
|
| |
|
| Submission date |
Feb 08, 2013 |
| Last update date |
Apr 18, 2013 |
| Contact name |
Jakub Orzechowski Westholm |
| E-mail(s) |
orzechoj@mskcc.org
|
| Organization name |
Memorial Sloan-Kettering Cancer Center
|
| Department |
Developmental Biology
|
| Lab |
Eric Lai
|
| Street address |
1275 York Avenue, Box 252
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL9061 |
| Series (2) |
| GSE44176 |
Genome wide binding of Insensitive in w[1118] embryos |
| GSE44178 |
The BEN domain is a novel sequence-specific DNA binding domain conserved in neural transcriptional repressors |
|
| Relations |
| BioSample |
SAMN02052096 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1080116_insv_6.5_12h.fasta.gz |
104.2 Mb |
(ftp)(http) |
FASTA |
| GSM1080116_insv_late.bed.gz |
46.5 Kb |
(ftp)(http) |
BED |
| Raw data provided as supplementary file |
| Processed data provided as supplementary file |
|
|
|
|
 |
