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GSE136910

GSE GEO
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RNA Seq of Subcutaneous adipose tissue from endothelial-AGO1-knockout (EC-AGO1-KO) mice and wild-type (WT) littermates

Organism: Mus musculus
Platform: GPL13112
Samples: 9
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Sep 05 2019
Last Updated: Jul 05 2022
Status: Public on Sep 06 2019
Contact: Sheng,,Zhong (University of California, San Diego)

Relations

SubSeries of: GSE136912 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA564027 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP220444

Summary

Purpose: to profile transcriptome changes due to EC-AGO1-deficiency Methods: Subcutaneous adipose tissue were harvested. RNA was extracted using TRIzol and library was prepared for sequencing. Results: We found genes involved in pathways promoting angiogenesis, browning, insulin sensitivity to be upregulated, and those promoting inflammation and fibrosis to be decreased in KO compared with WT mice. Conclusions:Our study represents the detailed analysis of Ago1 regulate transcriptomes in SAT between WT and KO mice. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

Overall Design

To elucidate the molecular changes underlying the observed metabolic phenotype in EC-AGO1-KO mice.

Analysis (2 steps)

View Data Processing
Processing steps for GSE136910
  1. STAR2.6.0a was used to align reads to the genome with default parameters
  2. Kallisto0.44.0 was used to quantify transcripts abundance in terms of TPM

Supplementary Files (1)

GSE136910_RAW.tar Download
GEO Samples (9)
GSM4061752 GSM4061753 GSM4061754 GSM4061755 GSM4061756 GSM4061757 GSM4061758 GSM4061759 GSM4061760

Dataset Citations (1)

Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction.
PMID 32393053 · 2020 · Circulation
Xiaofang Tang, Yifei Miao, Yingjun Luo, Kiran Sriram, Zhijie Qi, Feng-Mao Lin, Yusu Gu, Chih-Hung Lai, Chien-Yi Hsu, Kirk L Peterson, Kendall Van Keuren-Jensen, Patrick T Fueger, Gene W Yeo, Rama Natarajan, Sheng Zhong, Zhen Bouman Chen

SRA Experiments (9) and Runs (9)

Total: 48998 MB
SRX6804874 SRP220444 RNA-Seq PAIRED
GSM4061752: WT rep1; Mus musculus; RNA-Seq
Sample: SRS5349792
BioProject: PRJNA564027
BioSample: SAMN12698309
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: C57BL/6
tissue: Subcutaneous adipose tissue
age: 24 weeks
genotype: WT
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071341 45948931 7535624684 5145.09 WT_1_SAT_S26_R1_001.fastq.gz, WT_1_SAT_S26_R2_001.fastq.gz, SRR100713… SRA
SRX6804875 SRP220444 RNA-Seq PAIRED
GSM4061753: WT rep2; Mus musculus; RNA-Seq
Sample: SRS5349793
BioProject: PRJNA564027
BioSample: SAMN12698308
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: C57BL/6
tissue: Subcutaneous adipose tissue
age: 24 weeks
genotype: WT
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071342 48221163 7908270732 5495.52 WT_2_SAT_S23_R1_001.fastq.gz, WT_2_SAT_S23_R2_001.fastq.gz, SRR100713… SRA
SRX6804876 SRP220444 RNA-Seq PAIRED
GSM4061754: WT rep3; Mus musculus; RNA-Seq
Sample: SRS5349794
BioProject: PRJNA564027
BioSample: SAMN12698307
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: C57BL/6
tissue: Subcutaneous adipose tissue
age: 24 weeks
genotype: WT
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071343 54652435 8962999340 6171.7 WT_3_SAT_S20_R1_001.fastq.gz, WT_3_SAT_S20_R2_001.fastq.gz, SRR100713… SRA
SRX6804877 SRP220444 RNA-Seq PAIRED
GSM4061755: Hete rep1; Mus musculus; RNA-Seq
Sample: SRS5349795
BioProject: PRJNA564027
BioSample: SAMN12698306
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: C57BL/6
tissue: Subcutaneous adipose tissue
age: 24 weeks
genotype: Hete KO
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071344 53122925 8712159700 5916.99 AGO_1_Hete_SAT_S21_R1_001.fastq.gz, AGO_1_Hete_SAT_S21_R2_001.fastq.g… SRA
SRX6804878 SRP220444 RNA-Seq PAIRED
GSM4061756: Hete rep2; Mus musculus; RNA-Seq
Sample: SRS5349796
BioProject: PRJNA564027
BioSample: SAMN12698305
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: C57BL/6
tissue: Subcutaneous adipose tissue
age: 24 weeks
genotype: Hete KO
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071345 51645837 8469917268 5764.9 AGO_2_Hete_SAT_S24_R1_001.fastq.gz, AGO_2_Hete_SAT_S24_R2_001.fastq.g… SRA
SRX6804879 SRP220444 RNA-Seq PAIRED
GSM4061757: Hete rep3; Mus musculus; RNA-Seq
Sample: SRS5349797
BioProject: PRJNA564027
BioSample: SAMN12698304
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: C57BL/6
tissue: Subcutaneous adipose tissue
age: 24 weeks
genotype: Hete KO
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071346 42611296 6988252544 4765.67 AGO_3_Hete_SAT_S27_R1_001.fastq.gz, AGO_3_Hete_SAT_S27_R2_001.fastq.g… SRA
SRX6804880 SRP220444 RNA-Seq PAIRED
GSM4061758: Homo rep1; Mus musculus; RNA-Seq
Sample: SRS5349798
BioProject: PRJNA564027
BioSample: SAMN12698303
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: C57BL/6
tissue: Subcutaneous adipose tissue
age: 24 weeks
genotype: Homo KO
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071347 44405835 7282556940 4952.24 AGO_1_Homo_SAT_S19_R1_001.fastq.gz, AGO_1_Homo_SAT_S19_R2_001.fastq.g… SRA
SRX6804881 SRP220444 RNA-Seq PAIRED
GSM4061759: Homo rep2; Mus musculus; RNA-Seq
Sample: SRS5349799
BioProject: PRJNA564027
BioSample: SAMN12698311
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: C57BL/6
tissue: Subcutaneous adipose tissue
age: 24 weeks
genotype: Homo KO
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071348 47913819 7857866316 5363.55 AGO_2_Homo_SAT_S25_R1_001.fastq.gz, AGO_2_Homo_SAT_S25_R2_001.fastq.g… SRA
SRX6804882 SRP220444 RNA-Seq PAIRED
GSM4061760: Homo rep3; Mus musculus; RNA-Seq
Sample: SRS5349800
BioProject: PRJNA564027
BioSample: SAMN12698310
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: C57BL/6
tissue: Subcutaneous adipose tissue
age: 24 weeks
genotype: Homo KO
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071349 48898267 8019315788 5422.08 AGO_3_Homo_SAT_S22_R1_001.fastq.gz, AGO_3_Homo_SAT_S22_R2_001.fastq.g… SRA

Linked Publications (1)

Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction.
Circulation · 2020

Data Files (10)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— AGO_1_Hete_SAT_S21_R1_001.fastq.gz RNA-Seq 5.8 GB link
— AGO_1_Homo_SAT_S19_R1_001.fastq.gz RNA-Seq 4.8 GB link
— AGO_2_Hete_SAT_S24_R1_001.fastq.gz RNA-Seq 5.6 GB link
— AGO_2_Homo_SAT_S25_R1_001.fastq.gz RNA-Seq 5.2 GB link
— AGO_3_Hete_SAT_S27_R1_001.fastq.gz RNA-Seq 4.7 GB link
— AGO_3_Homo_SAT_S22_R1_001.fastq.gz RNA-Seq 5.3 GB link
— SRR10071346 RNA-Seq 4.7 GB link
— WT_1_SAT_S26_R1_001.fastq.gz RNA-Seq 5.0 GB link
— WT_2_SAT_S23_R1_001.fastq.gz RNA-Seq 5.4 GB link
— WT_3_SAT_S20_R1_001.fastq.gz RNA-Seq 6.0 GB link