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Sample GSM378632 Query DataSets for GSM378632
Status Public on Mar 09, 2009
Title H9 hESC Hpa II MethylSeq
Sample type SRA
 
Source name H9 hESC
Organism Homo sapiens
Characteristics cell type: H9 hESC
Extracted molecule genomic DNA
Extraction protocol In Methyl-seq, 5 µg genomic DNA was digested with HpaII or MspI. Fragments were made into next-gen sequencing libraries by using adapters and reagents from Illumina's Library Construction Kit. After an initial round of PCR, DNA bands (fragments with adapters) of 100-350 bp were isolated by gel extraction (Supplemental Fig. 2). Size-selected libraries were then PCR-amplified prior to sequencing. For meDIPSeq, 5 µg genomic DNA was digested with MspI and immunoprecipitated with anti-methylcytosine antibody (Calbiochem); fragments were made into Illumina libraries as described above.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina Genome Analyzer
 
Description please supplementary file GSE14966_sequence_annotations.txt.gz on Series record for sequence information
methylation call, Library5, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)
Data processing Usable sequence reads were mapped to CCGG sites predicted in silico. Sites with four or more MspI tags occurring in either the forward or reverse direction were retained in the analysis. These assayable sites were then grouped with neighboring sites that were within 35-75 bp. Regions therefore represent any number of digestion sites (between 2 and 18) that have neighboring sites within 35-75 bp of each other. Methylation calls were made by using HpaII tag data from all assayable cut sites. The larger of either the forward read count or reverse read count for each site was averaged across each region. Regions that had an average of zero or one reads per digestion site were called methylated, and regions with more than one sequence read per site were considered unmethylated.
 
Submission date Mar 09, 2009
Last update date Jun 11, 2013
Contact name Rami Rauch
E-mail(s) rrauch@stanford.edu
Organization name Stanford U
Street address 300 Pasteaur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5317
Country USA
 
Platform ID GPL9052
Series (2)
GSE14966 Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
GSE29071 High-throughput sequencing of ES cell lines, ES-derived cells, and fetal and normal livers
Relations
BioSample SAMN02197870

Data table header descriptions
SEQUENCE
COUNT methylation call, 0=unmethylated (tag average>1), 1=methylated (tag average<=1)

Data table
SEQUENCE COUNT
1 1
2 0
3 0
4 1
5 0
6 0
7 1
8 1
9 1
10 1
11 1
12 1
13 0
14 0
15 0
16 0
17 0
18 0
19 0
20 0

Total number of rows: 90612

Table truncated, full table size 697 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record
Processed data provided as supplementary file
Raw data provided as supplementary file

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