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Sample GSM318444 Query DataSets for GSM318444
Status Public on Dec 01, 2008
Title RNAP2_mES_rep1
Sample type SRA
 
Source name RNAP2 IP
Organism Mus musculus
Characteristics embryonic stem cells
Treatment protocol Ref. to manuscript
Growth protocol V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for one passage off of MEFs, on gelatinized tissue-culture plates. Mouse embryonic fibroblasts were prepared and cultured from DR-4 strain mice.
Extracted molecule genomic DNA
Extraction protocol Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description V6.5 murine ES cells were cultured as described in Boyer et al., Nature 2006.
Antibody:RNAP2 8WG16
Data processing Images analysis and base calling was done using solexa pipeline and reads aligned to both mouse NCBI build 36 using ELAND. For ChIP-Seq, sequences from all lanes were extended 200bp (maximum fragment length accounting for ~100bp of primer sequence), and allocated into 25 bp bins. Genomic bins containing statistically significant ChIP-seq enrichment were identified by comparison to a Poissonian background model, using a p-value threshold of 10-9. Additionally, we used an empirical background model obtained from identical Solexa sequencing of DNA from whole cell extract (WCE) from matched cell samples (>5X normalized enrichment across the entire region).
 
Submission date Sep 05, 2008
Last update date May 15, 2019
Contact name Stuart Levine
E-mail(s) levine@wi.mit.edu
URL http://web.wi.mit.edu/young/
Organization name Whitehead Institute
Lab Young
Street address Nine Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL9185
Series (1)
GSE12680 Divergent transcription from active promoters
Relations
SRA SRX003119
BioSample SAMN02195746

Data table header descriptions
SEQUENCE
COUNT count

Data table
SEQUENCE COUNT
GTGGATGTTTCTCATTTTCCATTAT 120
TATCGGAAGAGCTCGT 71
ATGGCGACCGCTGCTGCTGTTGCTT 68
ACCTAAGCCACAGCAGCAGCGGGCG 64
GGAAGGTGGCCGGCTGTCCCCCGCC 61
AGTGGATGTTTCTCATTTTCCATTA 58
GATGGCGACCGCTGCTGCTGTTGCT 57
GAAGGTGGCCGGCTGTCCCCCGCCC 52
GTGATTTTCAGTTTTCTCTCCATAT 52
GCATAATTTGTGGTAGTGGGGGGCT 48
AAGTGGATGTTTCTCATTTTCCATT 44
CCCACTGAAGGACCTGGAATATGGC 43
AGTTACAATGAAAAACACATTCGTT 42
GACCTAAGCCACAGCAGCAGCGGGC 41
GATGTTTCTCATTTTCCATTATTTT 41
GACCGCTGCTGCTGTGGCTTATGTC 40
TGATTTTCAGTTTTCTCTCCATATT 39
GTTTTCTTGCCATATTTCACGTCCT 39
CATATTTCACGTCCTACAGTGGACA 35
AGATGGCGACCGCTGCTGCTGTTGC 34

Total number of rows: 4597970

Table truncated, full table size 123895 Kbytes.




Supplementary data files not provided
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Processed data included within Sample table
Raw data are available in SRA
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