|
| Status |
Public on Feb 17, 2020 |
| Title |
S2 R1 input |
| Sample type |
SRA |
| |
|
| Source name |
WT S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: WT
cell line: S2 cells
type: Input
replicate: 1
chip antibody: none
|
| Treatment protocol |
Cells were treated with 1mM CuSo4 for 24h.
|
| Growth protocol |
S2 cells were grown on Schneider’s insect Medium (Biowest) supplemented with 100 μg/ml streptomycin (Gibco), 100 units/ml penicilin (Gibco) and 10% FBS (Gibco). dBigH1::FLAG and dBigH1ΔED::FLAG cells were maintained in Schneider's insect medium (Biowest) supplmented with 0.3 mg/ml Hygromycin B (Sigma) and for performing the experiments cells were grown on the same medium as S2 cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with polyclonal αdBigH1 and αH1 antibodies. Finally DNA was purified by standard phenol extraction.
3-5 ng DNA, quantified by Qubit dsDNA HS Assay Kit (Invitrogen) was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 10 cycles was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) 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 2500 |
| |
|
| Description |
genomic DNA
1887_28918_ATCACG
|
| Data processing |
FastQ files were aligned against the dm3 genome using Bowtie 0.12.5, allowing for 2 mismatches and reporting only unique hit alignments.
FastQC v011 was used to perform a quality control overview of FastQ files, aligned BAM files, and also for multiple hits and unaligned sequences.
Binary tracks for all reads in TDF format were generated with IGVTools 2.
Immunoprecipitation assessment (Gini coverage inequality) and PCA/MDS plots were genered using htSeqTools (Planet et al. 2012).
Peak Calling with the Drosophila default options was performed for IP vs their respective Input control sample usinc MACS 1.4.2 with options -g dm
Genome_build: dm3
Supplementary_files_format_and_content: BED files in MACS 1.4.2 format for ChIP vs Input peak calling
|
| |
|
| Submission date |
Feb 26, 2019 |
| Last update date |
Feb 17, 2020 |
| Contact name |
Oscar Reina Garcia |
| E-mail(s) |
[email protected]
|
| 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 |
GPL17275 |
| Series (2) |
| GSE127225 |
The embryonic linker histone dBigH1 compromises the functional epigenetic state of active chromatin [ChIP2] |
| GSE127227 |
The embryonic linker histone dBigH1 compromises the functional epigenetic state of active chromatin |
|
| Relations |
| BioSample |
SAMN11024457 |
| SRA |
SRX5436038 |
