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| Status |
Public on May 01, 2015 |
| Title |
ROW |
| Sample type |
SRA |
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| Source name |
S2 cells
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| Organism |
Drosophila melanogaster |
| Characteristics |
type: IP
cell line: S2 cells
chip antibody: rabbit αROW
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| Growth protocol |
S2 cells were grown on Schneider’s insect Medium (Sigma) supplemented with 100 μg/ml streptomycin (Gibco), 100 units/ml penicilin (Gibco) and 10% FBS (Gibco)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with polyclonal αWOC, αROW, αZ4, αDsk2 and αHP1c antibodies. Finally DNA was purified by standard phenol extraction.
10 ng DNA, quantified by Qubit dsDNA HS Assay Kit (Invitrogen) was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 18 cycles was performed using TruSeqRNA Sample Prep Kit (Illumina) according to manufacturer’s recommendations. Purified libraries were quantified by Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution was evaluated using Bioanalyzer DNA 1000 assay (Agilent).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
genomic DNA
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| Data processing |
Basecalling was performed using CASAVA version 1.8
Quality control of FastQ sequences was assessed using the FastQC software version 0.9.3.
ChIP-seq reads were aligned to the dm3 genome assembly using Bowtie 0.12.5, rejecting reads aligning to more than one genomic location, allowing up to 2 mismatches in the first 28 bases of the reads and no gapped alignments.
Aligned reads were filtered with the htSeqTools R package. PCR artifacts were detected and removed with the filterDuplicateReads function using a FDR of 1%. Strand shift bias was removed using the alignPeaks function with the default options.
A first step for peak calling was done using the enrichedRegions function from the htSeqTools package to find genomic regions with coverage above 10 reads, comparing the proportion of reads inside/outside of each region between each IP sample and the Input with a logistic regression likelihood-ratio test. Enriched regions were defined as those with a Benjamini–Yekutieli adjusted P-value below 0.05.
In a second step, we used the function enrichedPeaks from htSeqTools to define peaks (i.e. putative binding sites) as locations within the enriched regions with a coverage difference between IP and Input above 30 reads for WOC/ROW/Z4 and 20 reads for HP1c/Dsk2.
After peak calling, we used the mergeRegions function from htSeqTools to merge adjacent peaks closer than 300bp.
Genome_build: dm3
Supplementary_files_format_and_content: BED files include chromosome, start and end of the identified peaks in the dm3 Drosophila melanogaster genome.
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| Submission date |
Jul 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Oscar Reina Garcia |
| E-mail(s) |
[email protected]
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| Organization name |
IRB Barcelona
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| Department |
Biostatistics and Bioinformatics
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| Street address |
C/Baldiri Reixac 10
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| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
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| Platform ID |
GPL11203 |
| Series (2) |
| GSE49102 |
dDsk2 stabilizes dHP1c binding at TSS [ChIP-Seq] |
| GSE49104 |
dDsk2 stabilizes dHP1c binding at TSS |
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| Relations |
| BioSample |
SAMN02261605 |
| SRA |
SRX326966 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1193811_ROW.bed.gz |
68.6 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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