|
| Status |
Public on Jun 13, 2023 |
| Title |
CH12_SNSseq_Rif1KO_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
CH12
|
| Organism |
Mus musculus |
| Characteristics |
cell line: CH12
genotype: Rif1KO
|
| Growth protocol |
CH12 cells cultured in complete RPMI medium wit IL4/CD40/TGF beta stimulation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
short nascent DNA was enriched via size selection and lamda exonuclease digestion
Libraries were prepared following standard Illumina protocols
Genomic DNA was extracted and short nascent DNA was enriched via size selection and lamda exonuclease digestion
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
SNS-seq
|
| Data processing |
library strategy: SNS-seq
Reads were quality and adaptor trimmed with trim_galore v0.6.4 and cutadapt v2.6 with a length filter of 18bp
Trimmed reads were aligned to the mouse genome (mouse genome build UCSC mm9) using bowtie v1.2.3
rreplicate peak sets for each condition were overlapped with BEDTools intersect 2.27.1 using default parameters retaining only those peaks that were found in both replicates
retained peaks were then clustered by genome-wide median interpeak distance with ClusterScan 0.2.1 using -n 2 and only peaks that are part of a cluster were retained
filtered peak sets were then merged merged with BEDTools merge 2.27.1
Assembly: mm9
Supplementary files format and content: CH12_unstimulated_IS.bed is a BED file containing the genomic positions of the merged initiation sites for Rif1KO and WT
|
| |
|
| Submission date |
Apr 03, 2023 |
| Last update date |
Jun 13, 2023 |
| Contact name |
Tobias Neumann |
| Organization name |
IMP
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE228879 |
RIF1 regulates replication origin activity and early replication timing in B cells [SNS-seq] |
| GSE228880 |
RIF1 regulates early replication timing in murine B cells. |
|
| Relations |
| BioSample |
SAMN34060638 |
| SRA |
SRX19857910 |
