|
Status |
Public on Mar 30, 2010 |
Title |
SRS009478.1_p300_T0.fq |
Sample type |
SRA |
|
|
Source name |
Human glioblastoma T98G cells
|
Organism |
Homo sapiens |
Characteristics |
time after stimulation: T0 (minutes) cell line: T98G antibody: p300
|
Treatment protocol |
stimulation with serum (20%) and Tetradecanoyl phorbol acetate (TPA 100 ng/ml; Sigma)
|
Growth protocol |
Human glioblastoma T98G cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), penicillin (100 ug/ml), and streptomycin (100 ug/ml). Then serum starved for 2-3 days (DMEM supplemented with 0.1% FBS).
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Chromatin was prepared and ChIPs were carried out as previously described, including fragmentation by sonication (Denissov et al. 2007) (fragment size around 500 bp). For ChIP-seq all samples were prepared with Illumina's DNA sampleprep Kit (FC-102-1001) according to the manufacturer's protocol. Single ends of each sample were then sequenced on a single lane of the Illumina Genome Analyzer for 36 cycles.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer |
|
|
Description |
Chromatin IP against p300
|
Data processing |
Alignment (also enrichment): We ran the Illumina GAPipeline, ran GAPSS (www.lgtc.nl/GAPSS to remove first bps, aligned with Rmap to human NCBI build 36, and construct UCSC wiggle files) and to make wiggle file size manageable and reduce background base pairs with only a single tag aligning were not reported.
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|
|
Submission date |
Mar 23, 2010 |
Last update date |
May 15, 2019 |
Contact name |
Peter A.C. 't Hoen |
E-mail(s) |
p.a.c.hoen@lumc.nl
|
Phone |
+31 71 5269421
|
Fax |
+31 71 5268285
|
URL |
http://www.humgen.nl
|
Organization name |
Leiden University Medical Center
|
Department |
Center for Human and Clinical Genetics
|
Street address |
PO Box 9600
|
City |
Leiden |
ZIP/Postal code |
2300 RC |
Country |
Netherlands |
|
|
Platform ID |
GPL9052 |
Series (1) |
GSE21026 |
Genome-wide assessment of differential roles for p300 and CBP in transcription regulation |
|
Relations |
SRA |
SRX018278 |
BioSample |
SAMN00010214 |