|
| Status |
Public on Oct 24, 2019 |
| Title |
Control Si CTCF Ab |
| Sample type |
SRA |
| |
|
| Source name |
SLK cell line
|
| Organism |
Homo sapiens |
| Characteristics |
hci_id: 11237X4
knockdown: control KD
antibody: CTCF Ab IP
|
| Growth protocol |
Bac16 KSHV infected iSLK cells (iSLK/Bac16) were maintained in 1.2 mg/ml hygromycin, 250µg/ml G-418 and 1µg/ml puromycin, inDMEM containing 10% charcoal stripped FBS (Sigma) and 1% glutamine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen DNA isolation kit after immunoprecipitation with each antibody
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were aligned to hg19 + kshv (GQ994935) using Novoalign.
Coverage tracks (reads per million mapped) were generated using USeq 8.8.1.
Enriched peaks were called using MACS2
Peaks were annotated with USeq FindNeighboringGenes
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig coverage files from Useq
|
| |
|
| Submission date |
Sep 27, 2019 |
| Last update date |
Oct 24, 2019 |
| Contact name |
Chris Stubben |
| Organization name |
Huntsman Cancer Institute
|
| Department |
University of Utah
|
| Street address |
2000 Cir of Hope Dr
|
| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84103 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE138105 |
Effect of CTCF and Rad21 knockdown on cell and KSHV gene expression |
|
| Relations |
| BioSample |
SAMN12861969 |
| SRA |
SRX6916365 |
