|
| Status |
Public on Jun 12, 2017 |
| Title |
shLuc -Glucose H3K9ac ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
Hep3B cells_ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: anti-H3K9ac, Active Motif, 39917
cell line: Hep3B
shRNA: Luc
|
| Treatment protocol |
glucose starvation in DMEM medium without glucose, then treat with glucose (4.5g/L)
|
| Growth protocol |
culture in DME/F12 medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-IT High Sensitivity kit (Active motif) according to the manufacturer’s manual
Prepared using DNA Library preparation kit (KAPA, KK8232), as per the manufacturer’s protocol. In brief, DNA was fragmented to a median size of 150bp by sonication. Fragmented DNA ends were polished and 5′-phosphorylated. After addition of 3′-A to the ends, indexed Y-adapters were ligated and the samples were PCR amplified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
BCL files containing the sequence data were converted into “.fastq.gz” files and individual sample libraries were demultiplexed using CASAVA 1.8.2 with no mismatches.
3 nts from both ends were trimmed off and aligned to hg19 human assembly by Bowtie2.
sam files converted to bam files
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated by bamcompare in Deeptools and normailzed to 1X genome coverage
|
| |
|
| Submission date |
Feb 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xian Zhang |
| E-mail(s) |
zhangxian1987@gmail.com
|
| Organization name |
MSKCC
|
| Street address |
580 main st apt 138
|
| City |
New York |
| ZIP/Postal code |
10044 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE66340 |
H3K9ac occupancy of Nedd4- or control-knockdown Hep3B cells |
| GSE66342 |
Gene expression profiling and H3K9ac occupancy in Nedd4 knockdown Hep3B cells |
|
| Relations |
| BioSample |
SAMN03378741 |
| SRA |
SRX892618 |
