|
| Status |
Public on Jun 08, 2020 |
| Title |
ATACseq_Sub5_ABD_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
subcutaneous abdominal fat
|
| Organism |
Homo sapiens |
| Characteristics |
body type: apple
cell type: adipocytes
fat depot: subcutaneous abdominal fat
Sex: female
|
| Treatment protocol |
The technical replicates for ATAC-seq: For each subject, the cells were cultured, harvested and counted. From there, 2 aliquots (with the same number of cells) were separated and proceed in parallel. Lysis, DNA isolation and library prep were then performed separately but in the same time. They were run in the same lane during sequencing.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fat biospsies were collected, adipocytes were isolated by centrifugation. Nuclei were used for tagmentation using Nextera DNA Library Preparation Kit (Illumina).DNA was purified with MinElute PCR Purification Kit (Qiagen).
Tagmented DNA was amplified with Kapa HiFi Hot Start Kit (Kapa Biosystems) using 16 PCR cycles. Amplified libraries were purified with Agencourt AMPure XP (Beckman Coulter). Fragment distribution of libraries was assessed with Agilent Bioanalyzer.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
technical replicate 2
|
| Data processing |
Burrows-Wheeler Alignment (BWA) tool (v07.10)
BAM files were generated with SAMtools (v0.1.19)
“Peaks” were predicted using the Model-based Analysis of ChIP-Seq (MACS2) tool (v2.0.10)
To remove the artifacts from the predicted peaks, we used the blacklisted genomic regions of the Encyclopedia of DNA Elements (ENCODE)
Fragment length was set to 150 nucleotides by the makeTagDirectory program of the Hypergeometric Optimization of Motif EnRichment (HOMER) package (v4.2)
Coverage (bedgraph) files were created by the makeUCSCfile.pl program of HOMER
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph
|
| |
|
| Submission date |
Jan 10, 2020 |
| Last update date |
Jun 08, 2020 |
| Contact name |
Adeline Divoux |
| E-mail(s) |
[email protected]
|
| Phone |
4073037100
|
| Organization name |
Adventhealth
|
| Department |
Translational Research Institute
|
| Street address |
301 E. Princeton St
|
| City |
orlando |
| State/province |
FL |
| ZIP/Postal code |
32804 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE143449 |
Transcriptomic signatures and chromatin structure in adipocytes isolated from premenauposal women subcutaneous fat [ATAC-seq] |
| GSE143450 |
Transcriptomic signatures and chromatin structure in adipocytes isolated from premenauposal women subcutaneous fat |
|
| Relations |
| BioSample |
SAMN13825222 |
| SRA |
SRX7540641 |
