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Sample GSM1199305 Query DataSets for GSM1199305
Status Public on Aug 01, 2013
Title ChIP-Seq Klf4 in NMuMG cells Biological replicate 1
Sample type SRA
 
Source name Normal murine mammary epithelial (NMuMG) cells
Organism Mus musculus
Characteristics chip antibody: Klf4 (SC-20691, Santa Cruz)
cell type: immortalized yet non-transformed murine mammary epithelial cells
Treatment protocol ChIP experiments were performed starting with 70 mg of chromatin and 5 mg of anti-Klf4 (SC-20691, Santa Cruz).
Growth protocol NMuMG cells were cultured in DMEM/10% FBS.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted as described in Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, et al. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genetics 39: 457–466.
The ChIP libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102–1001) according to Illumina’s instructions. DNA libraries were sequenced on an Illumina Genome Analyzer 2 following the manufacturer’s protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Data processing 2007 M. musculus genome assembly (mm9) was used as a basis for all analyses.
Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads).
Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
All quantifications were based on alignments weighted by the inverse of the number of query hits, ensuring that the total weight of a read did not exceed one.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using custom Perl scripts; Scores represent weights in 100bp windows
 
Submission date Aug 01, 2013
Last update date May 15, 2019
Contact name Neha Tiwari
Organization name University of Basel
Street address Mattenstrasse 28
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL9250
Series (2)
GSE49445 ChIP-Seq of Klf4 in NMuMG normal murine mammary gland epithelial cells.
GSE49451 Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8).
Relations
BioSample SAMN02298685
SRA SRX330635

Supplementary file Size Download File type/resource
GSM1199305_Klf4_rep1.wig.gz 12.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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