|
| Status |
Public on Feb 07, 2013 |
| Title |
H293T_H3K4me3 RNAi TET2 |
| Sample type |
SRA |
| |
|
| Source name |
H293T_TET2 kd_H3K4me3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H293T
genotype/variation: TET2 knockdown (RNAi TET2)
chip antibody: H3K4me3
chip antibody vendor: Abcam
chip antibody cat. #: ab1012
chip antibody lot#: GR32764
|
| Growth protocol |
H293T cells were cultured in DMEM + serum at 37°C / 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were performed according to the Transcription ChIP kit (Diagenode) protocol and sonication was performed with a bioruptor (Diagenode). Sonicated protein-DNA complexes were isolated with antibody or HaloLink resin (Promega).The library preparation was performed using ChIP-Seq DNA sample prep kit (Illumina). Briefly, 10ng of qPCR verified ChIPed DNA was subjected to 5’ and 3’ protruding ends repair. Non-templated adenines were added to the 3’ ends of the blunted DNA fragments. DNA fragments were then size selected with a 2% agarose gel electrophoresis in order to remove all unligated adapters and to sequence 300bp fragments. 18 cycles of PCR were done to amplify the library. DNA was quantified by fluorometry using the Qubit 2.0 and its integrity was assessed with 2100 bioanalyzer (Agilent). 3 pM DNA library spiked with 1% PhiX viral DNA was clustered on cBot (Illumina), and then sequenced on HiScanSQ module (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
ChIP-Seq reads were aligned to the mm9 & h18 genomes using BWA 0.5.9
peaks were called using MACS v1.4
Genome_build: mm9 & hg18
Supplementary_files_format_and_content: wig files were generated using MACS
|
| |
|
| Submission date |
Mar 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthieu Defrance |
| Organization name |
Université Libre de Bruxelles
|
| Lab |
Cancer Epigenetics
|
| Street address |
CP614 route de Lennik 808
|
| City |
Bruxelles |
| ZIP/Postal code |
1070 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL15456 |
| Series (1) |
| GSE36620 |
TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS |
|
| Relations |
| SRA |
SRX130270 |
| BioSample |
SAMN00829063 |
