|
| Status |
Public on Sep 24, 2013 |
| Title |
p300 ChIP-Seq for control_n1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Human Kidney Embryonic Cell line HEK293
genotype/variation: pCI1-EGFP
chip antibody: anti-p300 [affinity purified p300 from our lab (ref, Byun et al, Nature Comm. 3, 633, 2012)]
|
| Growth protocol |
HEK293 cells and the cells expressing HSP70K71E were proliferated with RPMI1640, 10% FBS, 25 mM HEPES, 1X PS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP'd DNA was extracted accordingly in previous publication (Byun et al, ELL faciliates RNA polymerase II pause site entry and release. Nature Communications 3, 633 2012.
ChIP-Seq samples were sequenced on GAIIx with 36bp length using Illumina TruSeq v3 Chemistry, Allthe samples have good quality with over 93% of bases having Q30 or above. Library complexity is measured by uniquely aligned reads using picard's markduplicate utility.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
T2p300
ChIP'd DNA
|
| Data processing |
PhiX was used for sequencing control and illumina TruSeq V3 was used for sequencing chemistry.
The basic calling is analyzed by illumina RTA 1.8. 70.0 and allignment was used by illumina Casava 1.8.2
An unthresholded hotspot is determined as a contiguous union of 250 bp window whose z-scores are greater than 2.
Once a hotspot is called, the z-scoreof the hotspot is given by the maximum z-score of the constituent tags.
More detailed steps for ChIP-Seq data analysis were described in the manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files
|
| |
|
| Submission date |
Sep 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jung S Byun |
| E-mail(s) |
byunjs@mail.nih.gov
|
| Phone |
3014352890
|
| Organization name |
NCI/NIH
|
| Lab |
Genetics Branch
|
| Street address |
37 convent drive, Bldg 37, Rm 1042
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE51117 |
Genome wide ChIP-Seq profiles of p300 and CBP in control and cells expressing HSP70K71E |
| GSE51118 |
p300 is a preferred client protein for Nuclear Chaperones |
|
| Relations |
| BioSample |
SAMN02362716 |
| SRA |
SRX359406 |
