|
| Status |
Public on Jul 02, 2014 |
| Title |
293Trex_N3.input |
| Sample type |
SRA |
| |
|
| Source name |
293T-Rex
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 293T-Rex
transgene: N3 (empty vector)
epitope tag: Flag-HA-OneSTrEP (N-terminal)
antibody: none
|
| Treatment protocol |
Expression of the transgenes was induced by doxycycline treatment for 24 hours
|
| Growth protocol |
293T-REx stable lines transfected with HA-tagged PRC1 subunits or an empty vector were grown in standard conditions (DMEM 10% FBS) and kept in selection with zeocin
K562 cells were grown in standard conditions (RPMI 10% FBS)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Method for DNA: isolation of nuclei, lysis and sonication, IP, cross link reversal, qiaquick PCR purification column. Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Trimmed (3') sequences to 40 nts
Mapped to hg19 using bowtie -v2 -m1
Duplicates were removed with samtools rmdup
Wig coverage was calculated with IGVtools extending the reads to 200 nts
Wigs were normalized to 10,000,000 sequenced reads using a shell script
Genome_build: hg19
Supplementary_files_format_and_content: Normalized WIGs
|
| |
|
| Submission date |
May 25, 2012 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Roberto Bonasio |
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Bonasio
|
| Street address |
3400 Civic Center Blvd - SCTR 9-111
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE38273 |
ChIP-seq for SCML2 and SCML2 mutants in 293T-REx and K562 cells |
| GSE38275 |
ChIP-seq and RIP-seq for SCML2 and SCML2 mutants in 293T-REx and K562 cells |
|
| Relations |
| SRA |
SRX149701 |
| BioSample |
SAMN00998596 |
