GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM7141028 Query DataSets for GSM7141028
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.
BioSample SAMN34060638
SRA SRX19857910

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