|
| Status |
Public on Aug 18, 2017 |
| Title |
1WTgA |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: WT
replicate: 1
chip antibody: rabbit gammaHAvD (Rockland, catalog# 600-401-914, lot# 33026)
cell type: S2 cells
|
| Treatment protocol |
Drosophila S2 cells were grown to 5x10^5 cell/ml and incubated for 8 days with 100μg of dsRNA against dH1 added to the culture at days 1, 4 and 7.
|
| 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)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with polyclonal αgH2Av antibodies (3mL). 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 15 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).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
2208_16505_TGACCA
IP
|
| Data processing |
Encoding is Sanger/Illumina 1.9
Quality control of FastQ sequences was assessed using the FastQC software version 0.10.1.
Reads were aligned against the dm3 UCSC genome 2012 release using Bowtie 0.12.5, allowing 2 mismatches in the read seed and considering all possible alignment sites for each read in both Immunoprecipitated and control Input samples (setting an upper limit of 10.000 to limit output file size), in order to compare enrichment proportion for genomic features with multiple copies across the genome (i.e. transposons).
Identification and removal of potential PCR-amplification artifacts was performed with sambamba v0.5.1 using the markdup option and default settings. Coverage TDF tracks were generated with the IGV software version 2.1.16.
Peak calling between IPs and their respective input control in untreated and dH1-depleted cells was performed with MACS 1.4 using options –g dm and leaving the rest as default (p-value < 1e-05).
Genome_build: dm3
Supplementary_files_format_and_content: BED files indicate chromosome, start, end and score in MACS 1.4.2 _peaks.bed output format
|
| |
|
| Submission date |
May 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Oscar Reina Garcia |
| E-mail(s) |
oscar.reina@irbbarcelona.org
|
| Organization name |
IRB Barcelona
|
| Department |
Biostatistics and Bioinformatics
|
| Street address |
C/Baldiri Reixac 10
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE99004 |
Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin [ChIP Seq] |
| GSE99016 |
Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin |
|
| Relations |
| BioSample |
SAMN07136457 |
| SRA |
SRX2831138 |
