|
| Status |
Public on Jun 28, 2023 |
| Title |
pair8_L |
| Sample type |
SRA |
| |
|
| Source name |
Primary preadipocytes from subcutaneous adipose tissue
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary preadipocytes from subcutaneous adipose tissue
pair: pair8
status: lower BMI MZ sibling
|
| 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 |
polyA RNA |
| Extraction protocol |
Cells were washed once with PBS before lysing with TriZol (Invitrogen 15596026) and RNA was purified using the Direct-Zol RNA Mini-Prep (Zymo Research R2061).
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
pair8_L
|
| Data processing |
Reads were aligned to hg19 with STAR v2.7.0e, using the 2-pass method and the following parameters: --outFilterMultimaNmax 1, --outFilterMismatchNmas 6, --alignIntronMin 20, --alignIntronMax 500000, --chimSegmentMin 15.
Gene counts were obtained using the featureCounts function of Subread v1.6.4 and the gencode v19 annotation.
We corrected the log2-transformed gene transcripts per million mapped reads (TPMs) for pair ID (as a random effect), age, sex, and median 3' bias, using the lme4 v1.1 R package.
Assembly: hg19
Supplementary files format and content: geneCounts_allSamples.txt: tab-delimited file includes raw counts for each sample
Supplementary files format and content: geneTPMs_normalized_corrected.txt: tab-delimited file includes the log2-transformed TPMs 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) |
| GSE235362 |
Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes [RNA-Seq] |
| GSE235363 |
Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes |
|
