|
| Status |
Public on Dec 01, 2020 |
| Title |
SW872 Empty Vector replicate 1 (atacseq) |
| Sample type |
SRA |
| |
|
| Source name |
SW872 liposarcoma cells ATCC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SW872 liposarcoma cells
|
| Growth protocol |
SW872 cells were stably transduced and plated
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 cells were trypsinized, pelleted, and subjected to tranposition via Tn5 Transposae (Nextera) according to the manufacturer's instructions
Transposed DNA fragments were PCR amplified using the Nextera XT Index Kit per the manufacturer's instruction of generate indexed libraries
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
accessible DNA
SW872_EV_1
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: narrowPeak
|
| |
|
| Submission date |
Jun 18, 2020 |
| Last update date |
Dec 01, 2020 |
| 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 |
GPL20301 |
| Series (2) |
| GSE152733 |
The TAZ-CAMTA1 and YAP-TFE3 fusion proteins modulate the basal TAZ/YAP transcriptional program by recruiting the Ada2a-containing histone acetyltransferase complex [atacseq] |
| GSE152780 |
The TAZ-CAMTA1 and YAP-TFE3 fusion proteins modulate the basal TAZ/YAP transcriptional program by recruiting the Ada2a-containing histone acetyltransferase complex |
|
| Relations |
| BioSample |
SAMN15313613 |
| SRA |
SRX8572501 |
