|
Status |
Public on Oct 16, 2012 |
Title |
U2OS.KD.SIRT3.r2 |
Sample type |
SRA |
|
|
Source name |
U2OS_KD_SIRT3
|
Organism |
Homo sapiens |
Characteristics |
cell line: U2OS cell type: human osteosarcoma cells genotype/variation: stable SIRT3 knockdown (KD); retroviral expression of shRNAs against SIRT3 chip antibody: SIRT3 chip antibody vendor: Santa Cruz chip antibody cat. #: P-19 chip antibody lot #: L0409
|
Growth protocol |
U2OS cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum
|
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 T4 DNA ligase (Enzymatics). 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 |
|
|
Description |
120918.TI.chip.8
|
Data processing |
Trimmed (3') sequences to 36 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 BigWigs were generated with the wigToBigWig script from UCSC Genome_build: hg19 Supplementary_files_format_and_content: normalized bigWigs
|
|
|
Submission date |
Sep 19, 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 (1) |
GSE41000 |
SIRT3 functions in the nucleus in the control of stress-related gene expression. |
|
Relations |
SRA |
SRX188793 |
BioSample |
SAMN01179555 |