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Status |
Public on Aug 01, 2013 |
Title |
ChIP-Seq Klf4 in NMuMG cells Biological replicate 1 |
Sample type |
SRA |
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Source name |
Normal murine mammary epithelial (NMuMG) cells
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Organism |
Mus musculus |
Characteristics |
chip antibody: Klf4 (SC-20691, Santa Cruz) cell type: immortalized yet non-transformed murine mammary epithelial cells
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Treatment protocol |
ChIP experiments were performed starting with 70 mg of chromatin and 5 mg of anti-Klf4 (SC-20691, Santa Cruz).
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Growth protocol |
NMuMG cells were cultured in DMEM/10% FBS.
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer II |
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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
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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 |
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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). |
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Relations |
BioSample |
SAMN02298685 |
SRA |
SRX330635 |