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| Status |
Public on Dec 15, 2010 |
| Title |
ESC_FAIRE |
| Sample type |
SRA |
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| Source name |
Human embryonic stem cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H9 ESC
chip antibody: FAIRE
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| Treatment protocol |
hESCs were differentiated into hNECs using a previously described differentiation protocol 21. Briefly, hESC were incubated with 2mg/ml collagenase. Once detached, cells were plated in NEC differentiation media: 1:1 Neurobasal medium/D-MEM F-12 medium (Invitrogen), 0.5x B-27 supplement minus Vitamin A (50x stock, Invitrogen), 0.5x N-2 supplement (100x stock, Invitrogen), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich), 5 µg/ml bovine insulin (Sigma-Aldrich), 0.1 µg/ml recombinant human NOGGIN (Peprotech), 1x Glutamax-I supplement (100x stock, Invitrogen). Cells were differentiated for seven days, changing media every other day.
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| Growth protocol |
hESCs (H9 line, Wi-Cell) were expanded in feeder free, serum free medium, mTESR-1 from StemCell technologies. Cells were passaged 1:7 every 5-6 days by incubation with accutase (Invitrogen) long and resultant small cell clusters were subsequently re-plated on tissue culture dishes coated overnight with growth factor reduced matrigel (BD biosciences). hESCs quality was regularly tested by evaluating the expression of a panel of hESC markers (e.g. Alkaline phosphatase, OCT4) and the capacity to differentiate into cell types derived from the three germ layers.
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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 size selected on agarose gel from 200-700 bp. Then isolated DNA was PCR amplified with Illumina primers for 18 cycles. 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.
Antibodies used: p300: Santa Crux Biotechnologies (sc-585). Lot#K1609BRG1: clone JA1, a kind gift from Dr. G. CrabtreeH3K4me1: Abcam (ab8895), lot#730178H3K27ac: Abcam (ab4729), lot#733245H3K27me3: Active Motif (39536) lot#09508002H3K4me3: Active Motif (39159) lot#01609004
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
FAIRE (formaldehyde assisted isolation of regulatory elements) in crosslinked H9 ESC
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| Data processing |
All sequences were mapped by ELAND software (Illumina Inc) using the hg18 human genome assembly and analyzed by QuEST 2.4 software (Valouev et al (2008)). ChIP-seq enrichment regions were determined using settings according to QuEST recommendations. Valouev, A. et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 5, 829-834 (2008).
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| Submission date |
Sep 29, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Alvaro Rada |
| E-mail(s) |
alvaror@stanford.edu
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| Organization name |
Stanford University
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| Department |
Chemical and Systems Biology
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| Lab |
Wysocka lab
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| Street address |
269 Campus Drive, CCSR Building
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE24447 |
A unique chromatin signature uncovers early developmental enhancers in humans |
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| Relations |
| SRA |
SRX027489 |
| BioSample |
SAMN00113797 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM602298_ESC_FAIRE_aligned.bed.gz |
68.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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