NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7113518 Query DataSets for GSM7113518
Status Public on Apr 23, 2024
Title KDH1_a36_1
Sample type SRA
 
Source name S2 cells
Organism Drosophila melanogaster
Characteristics cell line: S2 cells
treatment: KD H1
chip antibody: αhrp36
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)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description ChIP_10.05_KDH1_a36_peaks_filtered.bed
ChIP_10.05_KDH1_a48_peaks_filtered.bed
ChIP_10.05_LZ_a36_peaks_filtered.bed
ChIP_10.05_LZ_a48_peaks_filtered.bed
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.
Assembly: dm3
Supplementary files format and content: bed
 
Submission date Mar 23, 2023
Last update date Apr 23, 2024
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 GPL25244
Series (2)
GSE228068 Linker histone H1 regulates homeostasis of heterochromatin associated cRNAs [ChIP-seq 2]
GSE228142 Linker histone H1 regulates homeostasis of heterochromatin associated cRNAs
Relations
BioSample SAMN33872249
SRA SRX19758092

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap