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GSE136908

GSE GEO
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RNA Seq of HMVEC under hypoxia

Organism: Homo sapiens
Platform: GPL11154
Samples: 8
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/PRJNA564026 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP220436

Summary

Purpose: to profile transcriptome changes due to EC-AGO1-deficiency Methods: We had HMVECs subjected to normoxia (20%) or hypoxia (2%) for 0, 12, 24, and 48 hr in biological replicates. Total RNA was extracted with mirVana total RNA isolation kit (Life Technologies). RNA-seq was performed. 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 HMVEC under Hx. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. To elucidate the molecular changes underlying the observed metabolic phenotype in EC-AGO1-KO mice.

Overall Design

Biological replicates for each condition

Analysis (2 steps)

View Data Processing
Processing steps for GSE136908
  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)

GSE136908_RAW.tar Download
GEO Samples (8)
GSM4061744 GSM4061745 GSM4061746 GSM4061747 GSM4061748 GSM4061749 GSM4061750 GSM4061751

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 (8) and Runs (8)

Total: 8759 MB
SRX6804742 SRP220436 RNA-Seq SINGLE
GSM4061744: 0h rep1; Homo sapiens; RNA-Seq
Sample: SRS5349660
BioProject: PRJNA564026
BioSample: SAMN12698301
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Human microvascular endothelial cells
time point: 0h
condition: hypoxia
genotype: Passage 3-4
Original files (1)
Human microvascular endothelial cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071159 30956411 3095641100 957.32 JK_A1_R1_merged.fastq.gz, SRR10071159, SRR10071159.sralite SRA
SRX6804743 SRP220436 RNA-Seq SINGLE
GSM4061745: 0h rep2; Homo sapiens; RNA-Seq
Sample: SRS5349661
BioProject: PRJNA564026
BioSample: SAMN12698300
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Human microvascular endothelial cells
time point: 0h
condition: hypoxia
genotype: Passage 3-4
Original files (1)
Human microvascular endothelial cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071160 34291292 3429129200 1060.61 JK_A2_R1_merged.fastq.gz, SRR10071160, SRR10071160.sralite SRA
SRX6804744 SRP220436 RNA-Seq SINGLE
GSM4061746: 12h rep1; Homo sapiens; RNA-Seq
Sample: SRS5349662
BioProject: PRJNA564026
BioSample: SAMN12698299
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Human microvascular endothelial cells
time point: 12h
condition: hypoxia
genotype: Passage 3-4
Original files (1)
Human microvascular endothelial cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071161 36501776 3650177600 1134.1 JK_A3_R1_merged.fastq.gz, SRR10071161, SRR10071161.sralite SRA
SRX6804745 SRP220436 RNA-Seq SINGLE
GSM4061747: 12h rep2; Homo sapiens; RNA-Seq
Sample: SRS5349663
BioProject: PRJNA564026
BioSample: SAMN12698298
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Human microvascular endothelial cells
time point: 12h
condition: hypoxia
genotype: Passage 3-4
Original files (1)
Human microvascular endothelial cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071162 39045345 3904534500 1207.61 JK_A4_R1_merged.fastq.gz, SRR10071162, SRR10071162.sralite SRA
SRX6804746 SRP220436 RNA-Seq SINGLE
GSM4061748: 24h rep1; Homo sapiens; RNA-Seq
Sample: SRS5349664
BioProject: PRJNA564026
BioSample: SAMN12698297
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Human microvascular endothelial cells
time point: 24h
condition: hypoxia
genotype: Passage 3-4
Original files (1)
Human microvascular endothelial cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071163 35114741 3511474100 1083.6 JK_N1_R1_merged.fastq.gz, SRR10071163, SRR10071163.sralite SRA
SRX6804747 SRP220436 RNA-Seq SINGLE
GSM4061749: 24h rep2; Homo sapiens; RNA-Seq
Sample: SRS5349665
BioProject: PRJNA564026
BioSample: SAMN12698296
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Human microvascular endothelial cells
time point: 24h
condition: hypoxia
genotype: Passage 3-4
Original files (1)
Human microvascular endothelial cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071164 32139955 3213995500 995.16 JK_N2_R1_merged.fastq.gz, SRR10071164, SRR10071164.sralite SRA
SRX6804748 SRP220436 RNA-Seq SINGLE
GSM4061750: 48h rep1; Homo sapiens; RNA-Seq
Sample: SRS5349666
BioProject: PRJNA564026
BioSample: SAMN12698295
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Human microvascular endothelial cells
time point: 48h
condition: hypoxia
genotype: Passage 3-4
Original files (1)
Human microvascular endothelial cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071165 38967379 3896737900 1206.82 JK_N3_R1_merged.fastq.gz, SRR10071165, SRR10071165.sralite SRA
SRX6804749 SRP220436 RNA-Seq SINGLE
GSM4061751: 48h rep2; Homo sapiens; RNA-Seq
Sample: SRS5349667
BioProject: PRJNA564026
BioSample: SAMN12698294
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Human microvascular endothelial cells
time point: 48h
condition: hypoxia
genotype: Passage 3-4
Original files (1)
Human microvascular endothelial cells
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR10071166 36084677 3608467700 1113.35 JK_N4_R1_merged.fastq.gz, SRR10071166, SRR10071166.sralite SRA

Linked Publications (1)

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

Data Files (16)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— JK_A1_R1_merged.fastq.gz RNA-Seq 957.3 MB link
— JK_A2_R1_merged.fastq.gz RNA-Seq 1.0 GB link
— JK_A3_R1_merged.fastq.gz RNA-Seq 1.1 GB link
— JK_A4_R1_merged.fastq.gz RNA-Seq 1.2 GB link
— JK_N1_R1_merged.fastq.gz RNA-Seq 1.1 GB link
— JK_N2_R1_merged.fastq.gz RNA-Seq 995.2 MB link
— JK_N3_R1_merged.fastq.gz RNA-Seq 1.2 GB link
— JK_N4_R1_merged.fastq.gz RNA-Seq 1.1 GB link
— SRR10071159_GSM4061744 RNA-Seq 957.0 MB link
— SRR10071160_GSM4061745 RNA-Seq 1.0 GB link
— SRR10071161_GSM4061746 RNA-Seq 1.1 GB link
— SRR10071162_GSM4061747 RNA-Seq 1.2 GB link
— SRR10071163_GSM4061748 RNA-Seq 1.1 GB link
— SRR10071164_GSM4061749 RNA-Seq 995.0 MB link
— SRR10071165_GSM4061750 RNA-Seq 1.2 GB link
— SRR10071166_GSM4061751 RNA-Seq 1.1 GB link