|
| Status |
Public on Nov 13, 2015 |
| Title |
664b_H3K9me2_2 |
| Sample type |
SRA |
| |
|
| Source name |
Neural progenitor cells
|
| Organism |
Danio rerio |
| Characteristics |
cell type: cells derived from retina and midbrain cell populations
chip antibody: anti-H3K9me2 (AbCam)
strain: AB
genotype/variation: 664b mutant
|
| Treatment protocol |
Head region cells were cross-linked using 1% formaldehyde for 15min and quenched by treating with 0.125M glycine for 10min.
|
| Growth protocol |
ChIP assays were performed in duplicate using cells derived from ~100 zebrafish heads at 48 hpf essentially as previously described.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sonication was performed using on a Bioruptor instrument (Diagenode) using 7 cycles of 30s “ON”, 30s “OFF” on the “High” setting.
ChIP was performed using the Millipore EZ-ChIP kit according to the manufacturer protocol. ChIP DNA was sequenced by Illumina Hi-Seq sequencer with multiplex.
An anti-H3K9me2 (AbCam) and an isotype control (AbCam) antibodies were used at 2μg per sample.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
664b_H3K9me2_ChIPSeq
|
| Data processing |
ChIP-seq reads were aligned to the Zv9 genome assembly using Bowtie2 with default setting
Data were filtered using samtools to keep only uniquely mapped reads
peaks were called using MACS2 version 2.1 with p value threshold at 0.01
Genome_build: Zv9
Supplementary_files_format_and_content: bedGraph file with score representing the read count within the corresponding region
|
| |
|
| Submission date |
Nov 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yue Li |
| E-mail(s) |
gorillayue@gmail.com
|
| Organization name |
Massachusetts Institute of Technology
|
| Street address |
32 Vassar Street, 32-D528
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE63225 |
G9a and ZNF644 physically associate to suppress progenitor gene expression during neurogenesis |
|
| Relations |
| BioSample |
SAMN03177354 |
| SRA |
SRX758209 |
