|
| Status |
Public on Mar 04, 2021 |
| Title |
H3K27ac ChIP_TFE3_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
SW872 liposarcoma cells ATCC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SW872
antibody: H3K27ac
transduction: TFE3
|
| 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.
|
| |
|
| 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 |
SAMN18133073 |
| SRA |
SRX10234732 |
