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| Status |
Public on Dec 24, 2009 |
| Title |
ES_input |
| Sample type |
SRA |
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| Source name |
Embryonic stem cells (total chromatin)
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| Organism |
Mus musculus |
| Characteristics |
cell line: LF2
chip antibody: none
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| Treatment protocol |
none
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| Growth protocol |
standard passaging
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and ChIP-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band-isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Total input DNA
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| Data processing |
Enrichment analysis was performed using QuEST software (http://mendel.stanford.edu/sidowlab/downloads/quest/)
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| Submission date |
Dec 04, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Anton Valouev |
| Organization name |
Stanford University
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| Department |
Pathology
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| Lab |
Sidow Lab
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| Street address |
300 Pasteur Dr.
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94035 |
| Country |
USA |
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| Platform ID |
GPL9185 |
| Series (1) |
| GSE18776 |
Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells |
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| Relations |
| SRA |
SRX015833 |
| BioSample |
SAMN00007546 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM480164_ESC_Input.bed.gz |
251.3 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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