|
| Status |
Public on Apr 23, 2024 |
| Title |
KDH1_a48_1 |
| Sample type |
SRA |
| |
|
| Source name |
S2 cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2 cells
treatment: KD H1
chip antibody: αhrp48
|
| 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 |
SAMN33872248 |
| SRA |
SRX19758093 |
