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Sample GSM489991 Query DataSets for GSM489991
Status Public on Dec 22, 2010
Title Ezh2 RIP-seq biological replicate
Sample type SRA
 
Source name embryonic stem cells
Organism Mus musculus
Characteristics strain: 129X(M.castaneusX129)
cell type: embryonic stem cell
antibody: Ezh2
Growth protocol Mouse embryonic stem cells were routinely growed and maintained in T25 or T75 flasks with LIF supplemented in the culture medium.
Extracted molecule total RNA
Extraction protocol Cell nuclei were isolated, nuclear lysate was prepared and incubated with an anti-Ezh2 antibody. Afterwards, the RNA-protein complexes were immunoprecipitated with protein A agarose beads and the RNA fraction was extracted using Trizol reagent. Template switching method was used for the library construction per manufacturer's recommendation (Clontech's SMART cDNA Library Construction Manual).
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina Genome Analyzer II
 
Description RIP against Ezh2
library strategy: RIP-seq
library source: RNA
library selection: RIP
Data processing Image processing and base calling were performed using the Illumina RTA pipeline.
Preprocessing: 3' adapter sequences were identified using cross_match and trimmed if a match of at least 5 bp was found. Reads matching mtDNA or rRNA sequences, reads < 12 bp long, reads containing N's, and homopolymer reads were removed. Alignment: reads were aligned to the mouse genome (mm9) using shortQueryLookup with a maximum of 1 error and no indels. Frequencies of unique reads were then tabulated.
 
Submission date Dec 23, 2009
Last update date May 15, 2019
Contact name Mark L Borowsky
E-mail(s) borowsky@molbio.mgh.harvard.edu
Organization name MGH
Department Molecular Biology
Street address 185 Cambridge Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL9250
Series (1)
GSE17064 Genome-wide identification of Polycomb-associated RNAs by RIP-seq
Relations
SRA SRX018720
BioSample SAMN00010865

Data table header descriptions
SEQUENCE
COUNT

Data table
SEQUENCE COUNT
AAAAAAAAAAAC 3
AAAAAAATGCAGCGAGCGGACATTCTGATCGCTGCA 3
AAAAAACCCCTAACTCTCTCCTGCTTCCTCTCTTTC 3
AAAAAAGATGTATTTATTTTATCTATATGAGTGCTC 3
AAAAAATAAATTAAAAATTAAAAACAATTTGAAGCT 3
AAAAAATCATCAGCTTTCATCTAATGTGCCTCGTTT 4
AAAAAATGGAAGCACTTTGGAGAGAGCC 3
AAAAAATGTTCTGTCTAAAAACTTCTCCTTAGCTCA 5
AAAAACAAAACATTTTACAAACATTGTTTCTCTAAT 3
AAAAACAAACAAACAAACAAACAAACAAACAAGAAA 3
AAAAACAAACAACGACAACAACAACAAAAATCCCAC 6
AAAAACAAATAAATAAAAATAAAATTGAACAGGGCT 4
AAAAACAAATCAACCGGGCCGGCG 5
AAAAACAAATCTTACTACTAGACTCATAATTGCCTT 4
AAAAACACAAACTAAACAGAGATACATTGAAACTAA 5
AAAAACACACACATACAAGTCAAATTAATCTAGGTC 3
AAAAACACTGGAGACAGGACTATGCAGTCAGGAGCA 3
AAAAACATCCCTAACTCTCCTAGACTTGATCTGGTT 3
AAAAACATGAGGTGGAGAAATAATTAAGGAAGACCA 4
AAAAACATTCTAATTTAGATCTCTGCATGTATCTAT 3

Total number of rows: 173239

Table truncated, full table size 6495 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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