|
| Status |
Public on Jun 28, 2023 |
| Title |
pair2_L_D1 |
| Sample type |
SRA |
| |
|
| Source name |
Primary preadipocytes from subcutaneous adipose tissue
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary preadipocytes from subcutaneous adipose tissue
treatment: adipogenic differentiation, 24 hours
pair: pair2
status: lower BMI MZ sibling
|
| Treatment protocol |
For the adipogenic differentiation (D1 samples), preadipocytes were grown to 100% confluency and the differentiation was initiated using the PromoCell Preadipocyte Differentiation Medium (PromoCell C-27436) for 24 hours
|
| Growth protocol |
Preadipocytes were seeded into PromoCell Preadipocyte Growth Medium (PromoCell C-27410) with 1% Penicillin-Streptomycin and maintained in a monolayer at <90% confluency at 37°C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following the omni-ATAC protocol, cells were treated with DNase I, trypsinized, and DNA was tagmented and purified with the Qiagen minElute kit.
Illumina sequencing adapters were added to the tagmented DNA samples to create the sequencing libraries.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
pair2_L_D1
|
| Data processing |
Reads were aligned to hg19 with Bowtie2 v2.2.9 using the following parameters: --k 4, -X 2000 --local.
Unpaired unmapped reads, duplicate reads, sex chromosome reads, and reads with MAPQ < 30 were filtered out
We called consensus peaks on all samples combined, using MACS2 v2.2.7.1 and peaks not in blacklisted regions, with an FDR<0.05 and counts per million mapped reads (CPM) >=1 in >=10% of samples were retained
Peak counts were obtained using the featureCounts function of Subread v1.6.4 and the ATAC-seq peaks called from MACS2
We performed a differential accessiblity (DA) analysis between the PAd and D1 time points using limma v3.34.9 and the voom method. We used the duplicateCorrelation function in limma to account for the repeated measures from the same individual. We included age, sex and fraction of reads in peaks (FRiP) in the model. We tested for PAd vs. D1 DA in the lower and higher BMI sibling subgroups separately. We used an FDR<0.05 as the cutoff to define significant DA peaks for these comparisons.
100-kb bin counts were obtained using the featureCounts function of Subread v1.6.4 and 100-kb genomic bins with blacklisted regions removed
The preadipocyte A compartment counts were obtained using the featureCounts function of Subread v1.6.4 and A compartments called in the preadipocytes
We corrected the log2-transformed ATAC peak bins per million mapped reads (BPMs), 100-kb BPMs, and A compartment BPMs for pair ID (as a random effect), age, sex, and fraction of reads in peaks (FRiP), using the lme4 v1.1 R package.
Assembly: hg19
Supplementary files format and content: peakCounts_allSamples.txt: tab-delimited file includes raw counts for each sample
Supplementary files format and content: DApeaks_PAdvD1.txt: tab-delimited file includes the differentially accessible (DA) peaks called in the lower and higher BMI siblings separately, with positive log2 fold-change (FC) corresponding to peaks that are more accessible at D1 and negative log2FC corresponding to peaks that are more accessible in PAd
Supplementary files format and content: peakTPMs_normalized_corrected_allSamples.txt: tab-delimited file includes the log2-transformed BPMs corrected for covariates and technical factors
Supplementary files format and content: binTPMs_100kbBins_normalized_corrected_PAdsamples.txt: tab-delimited file includes the PAd log2-transformed 100-kb bin BPMs corrected for covariates and technical factors
Supplementary files format and content: AcompTPMs_normalized_corrected_PAdsamples.txt: tab-delimited file includes the log2-transformed PAd A compartment BPMs corrected for covariates and technical factors
|
| |
|
| Submission date |
Jun 20, 2023 |
| Last update date |
Jun 28, 2023 |
| Contact name |
Kristina Marie Garske |
| E-mail(s) |
kmgarske@ucla.edu, kg8086@princeton.edu
|
| Organization name |
Princeton University
|
| Department |
Lewis-Sigler Institute for Integrative Genomics; Ecology & Evolutionary Biology
|
| Lab |
Julien Ayroles
|
| Street address |
Carl Icahn Lab, South Drive, Princeton University
|
| City |
Princeton |
| State/province |
New Jersey |
| ZIP/Postal code |
08540 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE235361 |
Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes [ATAC-Seq] |
| GSE235363 |
Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes |
|
