|
Status |
Public on Mar 04, 2021 |
Title |
H3K27ac ChIP_Input_Empty Vector_Rep1 |
Sample type |
SRA |
|
|
Source name |
SW872 liposarcoma cells ATCC
|
Organism |
Homo sapiens |
Characteristics |
cell line: SW872 antibody: none transduction: empty vector
|
Growth protocol |
SW872 cells were stably transduced and grown to 90% confluence 48 hrs before collection (except CAMTA1 collected at sub-confluence)
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Cells were cross-linked and prepared using the SimpleChIP Enzymatic Chromatin IP KIt according to manufacturer's instructions. Flag tagged proteins were immunoprecipated with the anti-DYKDDDDK rabbit monoclonal antibody (Cell Signaling) The SimpleChIP ChIP-seq DNA Library Prep Kit for Illumina was used to prepare the DNA library according to manufacturer's instructions
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
BCL basecalls were converted to FASTQ with Illumina 'bcl2fastq" fastq data were processed using the 'bcbio-nextgen.py' pipeline in "chip-seq" mode. Genome build was "GRCh37". reads were trimmed with "atropos", aligned with 'bwa', and peaks called with 'macs2' running in "narrowPeak" mode. Peaks with FDR p-value < 0.05 were accepted.
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|
|
Submission date |
Mar 03, 2021 |
Last update date |
Mar 05, 2021 |
Contact name |
Michael S Chimenti |
E-mail(s) |
michael-chimenti@uiowa.edu
|
Organization name |
University of Iowa
|
Department |
Iowa Institute of Human Genetics
|
Street address |
431 Newton Road
|
City |
Iowa City |
State/province |
IA |
ZIP/Postal code |
52245 |
Country |
USA |
|
|
Platform ID |
GPL24676 |
Series (1) |
GSE168201 |
The TAZ-CAMTA1 and YAP-TFE3 fusion proteins modulate the basal TAZ/YAP transcriptional program by recruiting the Ada2a-containing histone acetyltransferase complex [ChIP-seq] |
|
Relations |
BioSample |
SAMN18132848 |
SRA |
SRX10234709 |