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Status |
Public on Dec 27, 2023 |
Title |
ID18024_adipose_0yr |
Sample type |
SRA |
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Source name |
adipose
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Organism |
Papio anubis |
Characteristics |
tissue: adipose animal id: 18024 treatment: LCLF time: 0yr
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Treatment protocol |
The animals were feeding a high cholesterol, high fat diet for two years, switching from a low cholesterol, low fat diet.
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Extracted molecule |
total RNA |
Extraction protocol |
Approximately 10 mg of each frozen tissue sample was homogenized in 1ml QIAzol Lysis Reagent (79306, QIAGEN) using BeadBug 6 Microtube Homogenizer (D1036, Benchmark Scientific) with 1.5mm Zirconium beads (D1032-15, Benchmark Scientific). RNA was immediately extracted from the homogenate using QIAGEN RNeasy Universal Kit (73404, QIAGEN). RNA concentration and quality was measured using Agilent RNA 6000 Nano Kit and RNA 6000 Pico Kit (5067-1511 & 5067-1513, Agilent) on Agilent 2100 Bioanalyzer. TruSeq RNA Library Preparation Kit v2 (RS-122-2001, RS-122-2002, Illumina); TruSeq stranded mRNA Library Preparation Kit (20020595, Illumina) 96 libraries from 16 animals in batch 1 were performed using TruSeq RNA Library Preparation Kit v2 (RS-122-2001, RS-122-2002, Illumina) and were sequenced 50 base pairs, single-end using the Illumina HiSeq4000 according to manufacturer instructions with the goal of achieving at least 15 million reads per sample. Each sequencing lane contained 24 multiplexed samples from different RNA extraction batches. 498 libraries from 83 animals in batch 2 were performed using TruSeq stranded mRNA Library Preparation Kit (20020595, Illumina) and were sequenced 50 base pairs, paired-end using the Illumina NovaSeq6000 according to manufacturer instructions with the goal of achieving at least 30 million reads per sample. Each sequencing lane contained 84 multiplexed samples from different RNA extraction batches. Samples from the same animal were always in the same RNA extraction, library preparation, and sequencing batches. Samples from different animals were randomized in every processing step to avoid potential batch effects.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Data processing |
RNA-seq data were aligned to the baboon reference genome Panubis1.0 with STAR v2.7.7a. FASTQC was used to confirm that the reads were of high quality. Gene-level expression quantification was performed using featureCounts. Quality controls were performed on two levels using a similar pipeline for GTEx. On the sample level, we first identified and removed sample swaps and contaminations where a sample was not matched to its genotype or contained a mixture of two or more samples using verifyBamID. We removed outlier samples based on expression profile using PCA. We checked sex correctness by examining gene expression for genes on the Y chromosome for each sample. On the gene level, gene expression values for all samples from a given tissue were normalized using the following procedure: 1) read counts were normalized between samples using trimmed mean of M-values (TMM); 2) genes were selected based on expression thresholds of ≥0.1 TPM in ≥10% of samples, and > 3 reads (unnormalized) in ≥10% of samples for both diet conditions; 3) expression values for each gene were inverse normal transformed across samples. After the quality controls, we obtained 570 high-quality RNA samples and 20,224 genes for downstream analyses. Assembly: Panubis1.0 Supplementary files format and content: raw count matrix of all samples (n=588) Supplementary files format and content: raw count matrix of post-QC samples (n=570)
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Submission date |
Mar 14, 2023 |
Last update date |
Dec 27, 2023 |
Contact name |
Wenhe Lin |
E-mail(s) |
wenhelin@uchicago.edu
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Organization name |
University of Chicago
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Street address |
920 E 58th St
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City |
Chicago |
State/province |
Illinois |
ZIP/Postal code |
60637 |
Country |
USA |
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Platform ID |
GPL33248 |
Series (1) |
GSE227346 |
Dynamic complexity of genetic regulatory effects in response to a high cholesterol, high fat diet in baboons |
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Relations |
BioSample |
SAMN33760999 |
SRA |
SRX19678635 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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