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| Status |
Public on Feb 26, 2015 |
| Title |
H3K4me3.MN.WT [ChIP-Seq] |
| Sample type |
SRA |
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| Source name |
Differentiated motor neuron
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| Organism |
Mus musculus |
| Characteristics |
genotype: WT
ip antibody: H3K4me3
antibody source: Abcam #ab8580
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| Growth protocol |
mESCs were grown in standard ESC medium containing Lif, 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021). ESCs were differentiated in ANDFK medium (Advanced DMEM/F12 : Neurobasal (1:1) Medium, 15% Knockout Serum Replacement, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 2 of differentiation. Patterning of embryoid bodies was induced by supplementing the media on Day 2 with 1 μM all-trans-Retinoic acid (RA, Sigma) and 0.5 μM smoothened agonist (SAG, Calbiochem).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed in ChIP buffer (50 mM Tris-HCl pH 7.9, 150 mM NaCl, 1% Triron X-100, 0.5% NP-40, 5 mM EDTA pH 8.0, 1 mM PMSF and protease inhibitor) and chromatin was sonicated to ~200 bp with a Diagenode Bioruptor
Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters. Fragments of 300±100 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Q5 polymerase (NEB M0530).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
biological replicates fastq files were merged
mapped to mm9 with BOWTIE -m4 -v2
duplicate reads were filtered
1nt resolution bedgraphs were generated with the BEDtools bamToBed and genomeCoverageBed utilities after extending each read to 200
coverage was normalized to FP10M (fragments per 10 million reads sequenced)
bigWig files were generated with bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: FP10M-normalized bigWigs
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| Submission date |
Aug 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Danny Reinberg |
| E-mail(s) |
reinbd01@nyumc.org
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| Phone |
212-263-9036
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| Organization name |
NYU School of Medicine / HHMI
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| Street address |
522 First Avenue, 2nd floor Rm 211
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| City |
New York City |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE60232 |
CTCF functions as a chromatin insulator in the HoxA cluster during neurogenesis [ChIP-Seq] |
| GSE60240 |
CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation |
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| Relations |
| BioSample |
SAMN02979100 |
| SRA |
SRX672424 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1468401_H3K4me3.MN.WT.bw |
299.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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