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GSE136911

GSE GEO
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small RNA Seq of Subcutaneous adipose tissue from endothelial-AGO1-knockout (EC-AGO1-KO) mice and wild-type (WT) littermates fed 16 week of high fat high sucrose diet

Organism: Mus musculus
Platform: GPL17021
Samples: 9
Experiment Types:
Non-coding RNA 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/PRJNA564029 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP220437

Summary

Purpose:to reveal the changes in small RNA, esp. microRNA to correlate with transcriptome changes occuring due to EC-AGO1-KO and further explain the observed phenotype. Methods: Subcutaneous adipose tissue were harvested.Small RNA library was prepared and for sequencing. Results: We found substantial changes in miRNA due to EC-AGO1-KO. Conclusions: Our study represents the detailed analysis of Ago1 regulated small RNA transcriptomes in subcutaneous adipose tissue between WT and KO mice. We conclude that small RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

Overall Design

Three biological replica, each collected from an individual mice, per genotype were processed.

Analysis (2 steps)

View Data Processing
Processing steps for GSE136911
  1. miRDeep2 0.0.8 was used to count the number of microRNAs
  2. The numbers are then manually normalized into FPKM values

Supplementary Files (1)

GSE136911_RAW.tar Download
GEO Samples (9)
GSM4061761 GSM4061762 GSM4061763 GSM4061764 GSM4061765 GSM4061766 GSM4061767 GSM4061768 GSM4061769

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: 5308 MB
SRX6804750 SRP220437 miRNA-Seq SINGLE
GSM4061761: WT rep1 miRNA; Mus musculus; miRNA-Seq
Sample: SRS5349668
BioProject: PRJNA564029
BioSample: SAMN12698316
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: adipose tissue
age: 24 weeks
diet: fed high fat high sucrose diet for 16 weeks starting from 8-week-old
genotype: WT
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071167 17934197 896709850 552.54 WT_1_SAT_S52_R1_001.fastq.gz, SRR10071167, SRR10071167.sralite SRA
SRX6804751 SRP220437 miRNA-Seq SINGLE
GSM4061762: WT rep2 miRNA; Mus musculus; miRNA-Seq
Sample: SRS5349669
BioProject: PRJNA564029
BioSample: SAMN12698315
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: adipose tissue
age: 24 weeks
diet: fed high fat high sucrose diet for 16 weeks starting from 8-week-old
genotype: WT
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071168 14757263 737863150 458.52 WT_2_SAT_S51_R1_001.fastq.gz, SRR10071168, SRR10071168.sralite SRA
SRX6804752 SRP220437 miRNA-Seq SINGLE
GSM4061763: WT rep3 miRNA; Mus musculus; miRNA-Seq
Sample: SRS5349670
BioProject: PRJNA564029
BioSample: SAMN12698314
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: adipose tissue
age: 24 weeks
diet: fed high fat high sucrose diet for 16 weeks starting from 8-week-old
genotype: WT
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071169 20178001 1008900050 625.98 WT_3_SAT_S74_R1_001.fastq.gz, SRR10071169, SRR10071169.sralite SRA
SRX6804753 SRP220437 miRNA-Seq SINGLE
GSM4061764: Hete rep1 miRNA; Mus musculus; miRNA-Seq
Sample: SRS5349671
BioProject: PRJNA564029
BioSample: SAMN12698313
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: adipose tissue
age: 24 weeks
diet: fed high fat high sucrose diet for 16 weeks starting from 8-week-old
genotype: Hete KO
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071170 27222889 1361144450 851.87 AGO_1_Hete_SAT_S54_R1_001.fastq.gz, SRR10071170, SRR10071170.sralite SRA
SRX6804754 SRP220437 miRNA-Seq SINGLE
GSM4061765: Hete rep2 miRNA; Mus musculus; miRNA-Seq
Sample: SRS5349672
BioProject: PRJNA564029
BioSample: SAMN12698321
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: adipose tissue
age: 24 weeks
diet: fed high fat high sucrose diet for 16 weeks starting from 8-week-old
genotype: Hete KO
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071171 11471126 573556300 356.64 AGO_2_Hete_SAT_S56_R1_001.fastq.gz, SRR10071171, SRR10071171.sralite SRA
SRX6804755 SRP220437 miRNA-Seq SINGLE
GSM4061766: Hete rep3 miRNA; Mus musculus; miRNA-Seq
Sample: SRS5349673
BioProject: PRJNA564029
BioSample: SAMN12698320
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: adipose tissue
age: 24 weeks
diet: fed high fat high sucrose diet for 16 weeks starting from 8-week-old
genotype: Hete KO
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071172 20615006 1030750300 638.71 AGO_3_Hete_SAT_S55_R1_001.fastq.gz, SRR10071172, SRR10071172.sralite SRA
SRX6804756 SRP220437 miRNA-Seq SINGLE
GSM4061767: Homo rep1 miRNA; Mus musculus; miRNA-Seq
Sample: SRS5349674
BioProject: PRJNA564029
BioSample: SAMN12698319
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: adipose tissue
age: 24 weeks
diet: fed high fat high sucrose diet for 16 weeks starting from 8-week-old
genotype: Homo KO
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071173 19076753 953837650 591.75 AGO_1_Homo_SAT_S59_R1_001.fastq.gz, SRR10071173, SRR10071173.sralite SRA
SRX6804757 SRP220437 miRNA-Seq SINGLE
GSM4061768: Homo rep2 miRNA; Mus musculus; miRNA-Seq
Sample: SRS5349675
BioProject: PRJNA564029
BioSample: SAMN12698318
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: adipose tissue
age: 24 weeks
diet: fed high fat high sucrose diet for 16 weeks starting from 8-week-old
genotype: Homo KO
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071174 16493456 824672800 508.8 AGO_2_Homo_SAT_S57_R1_001.fastq.gz, SRR10071174, SRR10071174.sralite SRA
SRX6804758 SRP220437 miRNA-Seq SINGLE
GSM4061769: Homo rep3 miRNA; Mus musculus; miRNA-Seq
Sample: SRS5349676
BioProject: PRJNA564029
BioSample: SAMN12698317
Platform: ILLUMINA
Instrument: Illumina HiSeq 2500
Organism: Mus musculus
Sample attributes
source_name: Subcutaneous adipose tissue
strain: adipose tissue
age: 24 weeks
diet: fed high fat high sucrose diet for 16 weeks starting from 8-week-old
genotype: Homo KO
Original files (1)
Subcutaneous adipose tissue
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071175 23552456 1177622800 723.12 AGO_3_Homo_SAT_S58_R1_001.fastq.gz, SRR10071175, SRR10071175.sralite SRA

Linked Publications (1)

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

Data Files (18)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— AGO_1_Hete_SAT_S54_R1_001.fastq.gz miRNA-Seq 851.9 MB link
— AGO_1_Homo_SAT_S59_R1_001.fastq.gz miRNA-Seq 591.8 MB link
— AGO_2_Hete_SAT_S56_R1_001.fastq.gz miRNA-Seq 356.6 MB link
— AGO_2_Homo_SAT_S57_R1_001.fastq.gz miRNA-Seq 508.8 MB link
— AGO_3_Hete_SAT_S55_R1_001.fastq.gz miRNA-Seq 638.7 MB link
— AGO_3_Homo_SAT_S58_R1_001.fastq.gz miRNA-Seq 723.1 MB link
— SRR10071167_GSM4061761 miRNA-Seq 552.0 MB link
— SRR10071168_GSM4061762 miRNA-Seq 458.0 MB link
— SRR10071169_GSM4061763 miRNA-Seq 625.0 MB link
— SRR10071170_GSM4061764 miRNA-Seq 851.0 MB link
— SRR10071171_GSM4061765 miRNA-Seq 356.0 MB link
— SRR10071172_GSM4061766 miRNA-Seq 638.0 MB link
— SRR10071173_GSM4061767 miRNA-Seq 591.0 MB link
— SRR10071174_GSM4061768 miRNA-Seq 508.0 MB link
— SRR10071175_GSM4061769 miRNA-Seq 723.0 MB link
— WT_1_SAT_S52_R1_001.fastq.gz miRNA-Seq 552.5 MB link
— WT_2_SAT_S51_R1_001.fastq.gz miRNA-Seq 458.5 MB link
— WT_3_SAT_S74_R1_001.fastq.gz miRNA-Seq 626.0 MB link