|
| Status |
Public on Jul 02, 2014 |
| Title |
293Trex_N3-SCML2AdRBR.SCML2.b3 |
| Sample type |
SRA |
| |
|
| Source name |
293T-Rex
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 293T-Rex
transgene: N3-SCML2A∆RBR (256-330)
epitope tag: Flag-HA-OneSTrEP (N-terminal)
antibody: SCML2 (in-house)
|
| Treatment protocol |
Expression of the transgenes was induced by doxycycline treatment for 48 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 |
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 |
mapped to mm9 with BOWTIE -m4 -v2 --best
1nt resolution bedgraphs were generated with the BEDtools bamToBed and genomeCoverageBed utilities after extending each read to 200
coverage was normalized to FP10M (fragments per 10 million reads sequenced)
bigWig files were generated with bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: FP10M-normalized bigWigs
|
| |
|
| Submission date |
Jul 02, 2014 |
| 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 |
| BioSample |
SAMN02900482 |
| SRA |
SRX644716 |
