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| Status |
Public on Apr 23, 2024 |
| Title |
IP KDH1 1 |
| Sample type |
SRA |
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| Source name |
S2 cells
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2 cells
chip antibody: αRNAPII
treatment: KD H1
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1.8% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Twin Sonication System (Diagenode).
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (Illumina)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
1845_2022
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| Data processing |
NGMerge was used to automatically detect and remove sequencing adapters using options -a -n 18 -v
FastQ files were aligned to the dm3 genome using Bowtie2 v2.2.2 with options -N 1 -k 1.
Duplicated reads for generation of TDF tracks were identified and removed with sambamba 0.8.0. TDF tracks were generated with IGVTools2 and options count -z 5 -w 25 -e 250.
Peak calling between IP and Input samples was performed independently for individual and pooled replicates per group using MACS 1.4.2 with default options (duplicate removal) and genome=dm. Candidate called peaks from pooled replicates were defined as final peaks if they presented overlap with peaks identified in both their respective individual replicates.
Final peaks in all conditions were used to perform a Differential Binding analysis using the DiffBind package version 2.10.0, using functions: dba.count with options score=DBA_SCORE_RPKM_FOLD,bLog=TRUE,bRemoveDuplicates=TRUE,bScaleControl=TRUE; dba.contrast with options categories=DBA_CONDITION,block=DBA_REPLICATE,minMembers=2 and dba.analyze with options method=DBA_DESEQ2,bFullLibrarySize=TRUE,bSubControl=FALSE. Peaks were selected as significant based on a raw pvalue of 0.05 (column DiffBind.rej).
Peaks were annotated to dm3 genomic features using homer2 with the anntatePeaks function and default options.
Assembly: dm3
Supplementary files format and content: BED files with final peak calling results (pooled called peaks also present in both individual replicate peak calls)
Supplementary files format and content: Excel XLSX with DiffBind results
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| Submission date |
Dec 05, 2023 |
| Last update date |
Apr 23, 2024 |
| Contact name |
Oscar Reina Garcia |
| E-mail(s) |
oscar.reina@irbbarcelona.org
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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 |
GPL25244 |
| Series (2) |
| GSE228142 |
Linker histone H1 regulates homeostasis of heterochromatin associated cRNAs |
| GSE249374 |
Linker histone H1 regulates homeostasis of heterochromatin associated cRNAs [ChIP-Seq 3] |
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| Relations |
| BioSample |
SAMN38671853 |
| SRA |
SRX22777802 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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