NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4947336 Query DataSets for GSM4947336
Status Public on Jan 01, 2021
Title Kap1 for over expression of ESC, Replicate 2
Sample type SRA
 
Source name ESC
Organism Mus musculus
Characteristics cell type: ESC
strain: 129Sv
genotype: Dcaf11 Over expression
chip antibody: Kap1 (Abcam no. ab22553)
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and Kap1-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Description Normalized tag counts
Data processing ChIP-seq reads were first removed adapters and low-quality base calls by trim_galore (version 0.4.2) using the default parameters.
Chip-seq reads were aligned to the mouse genome (mm9) using Bowtie2 v.2.3.5 with the parameters –no-mixed --no-discordant.
ChIP-seq peaks were called with MACS2 with the parameters –nomodel --keep-dup all --SPMR over input files
Genome_build: mm9
Supplementary_files_format_and_content: Signal track for each sample were generated using the “bamCoverage” function of deeptools and were normalized by calculating the reads per kilobase of transcript per million mapped reads (RPKM)
 
Submission date Nov 27, 2020
Last update date Jan 03, 2021
Contact name Yixin Huang
E-mail(s) 1710944@tongji.edu.cn
Organization name Tongji University
Street address Siping Road
City Shanghai
ZIP/Postal code 200092
Country China
 
Platform ID GPL24247
Series (2)
GSE132746 Dcaf11 facilitates telomere elongation in early embryos and embryonic stem cells (ESCs) through activating the Zscan4-mediated alternative lengthening telomere (ALT) mechanism
GSE162232 Kap1 ChIP-seq Analysis of Wild Type(WT) and Dcaf11 overexpresion(OE) ESCs
Relations
BioSample SAMN16935281
SRA SRX9596425

Supplementary file Size Download File type/resource
GSM4947336_OE.2_Kap1.bw 228.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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