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| Status |
Public on Apr 20, 2010 |
| Title |
4.71 yr old H3K4me3_NeuN-_rep1 #6n |
| Sample type |
SRA |
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| Source name |
prefrontal cortex
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| Organism |
Homo sapiens |
| Characteristics |
population: NeuN-
age: 4.71
chip antibody: H3K4me3
cell type: neurons from prefrontal cortex
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| Growth protocol |
Samples used in the study were postmortem tissues from prefrontal cortex BA10.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIPed DNA was first blunt-ended by End-it DNA Repair Kit (Epicentre) at RT for 1hr. Reaction was cleaned by column (Qiagen), and DNA was A-tailed by exo- Klenow DNA Polymerase (Epicentre) at RT for 1hr. Reaction was again cleaned by column, and DNA was ligated to Genomic Adpater Oligo Mix (Illumina) by Fast-link DNA Ligation Kit (Epicentre) at RT for 2 hours followed by 16°C O/N. Reaction was cleaned by column, and ligated DNA was amplified using PfuUltra II Fusion HS DNA Polymerase (Stratagene) with 250µM dNTPs and 1µL of each of the Genomic PCR Primers (Illimina) in 100µL volume with the following cycling conditions: 95°C 1min; 15 cycles of 95°C 50sec, 65°C 1min, 72°C 30sec; 72°C 5min. PCR product was cleaned and volume reduced by column before loading onto a 1.8% agarose gel. Typically a strong smear of 160-230bp (including 92bp from the Illumina primers) was observed.
30sec; 72°C 5min. PCR product was cleaned and volume reduced by column before loading onto a 1.8% agarose gel. Typically a strong smear of 160-230bp (including 92bp from the Illumina primers) was observed.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Chromatin IP against H3K4me3
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| Data processing |
mapped to hg18
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| Submission date |
Apr 01, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Hennady Shulha |
| Organization name |
Boston University
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| Department |
BME
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| Street address |
44 Cummington st
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE21172 |
Developmental Regulation and Individual Differences of Neuronal Epigenomes in the Prefrontal Cortex |
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| Relations |
| SRA |
SRX019343 |
| BioSample |
SAMN00011727 |
| Named Annotation |
GSM529971_6n.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM529971_6n.wig.gz |
51.8 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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