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Status |
Public on Jun 28, 2023 |
Title |
pair6_H |
Sample type |
SRA |
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|
Source name |
Primary preadipocytes from subcutaneous adipose tissue
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Organism |
Homo sapiens |
Characteristics |
cell type: Primary preadipocytes from subcutaneous adipose tissue pair: pair6 status: higher BMI MZ sibling
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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|
Description |
pair6_H
|
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
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|
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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 |
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