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GSE136907

GSE GEO
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Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

Organism: Homo sapiens
Platform: GPL11154
Samples: 4
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/PRJNA564016 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP220435

Summary

Purpose: to identify the AGO1-bound miRNAs and mRNAs in human endothelial cells subject to hypoxic condition (2% oxygen) Methods: human microvascular endothelial cells was cultured under normoxia (20% oxygen) or hypoxia (2%) oxygen for 24 hours. Total RNA was extracted and RNA and small RNA libraries were prepared for Seq. Results: We found substantial changes in AGO1-bound mRNAs due to hypoxia. A portion of CLIP-seq reads also reveal direct binding to miRNA to mRNA. Conclusions: hypoxia induces profound changes in mRNAs associated with AGO1.

Overall Design

Biological replicates for each condition

Analysis (2 steps)

View Data Processing
Processing steps for GSE136907
  1. CLIPSeqTool0.1.8 was used to trim the adapaters, align the reads to the genome and perform deduplications
  2. Kallisto0.44.0 was used to quantify transcripts abundance in terms of TPM

Supplementary Files (1)

GSE136907_RAW.tar Download
GEO Samples (4)
GSM4061740 GSM4061741 GSM4061742 GSM4061743

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 (4) and Runs (8)

Total: 12537 MB
SRX6804738 SRP220435 RIP-Seq SINGLE
GSM4061740: Hypoxia-1; Homo sapiens; RIP-Seq
Sample: SRS5349656
BioProject: PRJNA564016
BioSample: SAMN12698218
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Human microvascular endothelial cells
condition: Hypoxia
antibody: AGO1
passage: Passage 3-4
Original files (1)
Human microvascular endothelial cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR10071151 9507299 389799259 310.49 ZNH_NoIndex_L008_R1.R12_AGO1_hypoxia_HighRNase_H.fastq.gz, SRR1007115… SRA
SRR10071152 65071691 2667939331 1941.32 ZNL_NoIndex_L007_R1.R12_AGO1_hypoxia_HighRNase_L.fastq.gz, SRR1007115… SRA
SRX6804739 SRP220435 RIP-Seq SINGLE
GSM4061741: Hypoxia-2; Homo sapiens; RIP-Seq
Sample: SRS5349657
BioProject: PRJNA564016
BioSample: SAMN12698217
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Human microvascular endothelial cells
condition: Hypoxia
antibody: AGO1
passage: Passage 3-4
Original files (1)
Human microvascular endothelial cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR10071153 25129743 1030319463 804.4 ZNH_NoIndex_L008_R1.R11_AGO1_hypoxia_LowRNAse_H.fastq.gz, SRR10071153… SRA
SRR10071154 12345472 506164352 378.47 ZNL_NoIndex_L007_R1.R11_AGO1_hypoxia_LowRNAse_L.fastq.gz, SRR10071154… SRA
SRX6804740 SRP220435 RIP-Seq SINGLE
GSM4061742: Normoxia-1; Homo sapiens; RIP-Seq
Sample: SRS5349658
BioProject: PRJNA564016
BioSample: SAMN12698220
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Human microvascular endothelial cells
condition: Normoxia
antibody: AGO1
passage: Passage 3-4
Original files (1)
Human microvascular endothelial cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR10071155 64439227 2642008307 1995.48 ZNH_NoIndex_L008_R1.R10_AGO1_normoxia_HighRNAse_H.fastq.gz, SRR100711… SRA
SRR10071156 38226064 1567268624 1118.38 ZNL_NoIndex_L007_R1.R10_AGO1_normoxia_HighRNAse_L.fastq.gz, SRR100711… SRA
SRX6804741 SRP220435 RIP-Seq SINGLE
GSM4061743: Normoxia-2; Homo sapiens; RIP-Seq
Sample: SRS5349659
BioProject: PRJNA564016
BioSample: SAMN12698219
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: Human microvascular endothelial cells
condition: Normoxia
antibody: AGO1
passage: Passage 3-4
Original files (1)
Human microvascular endothelial cells
Runs (2)
Run Spots Bases Size (MB) Files Link
SRR10071157 114515193 4695122913 3536.28 ZNH_NoIndex_L008_R1.R09_AGO1_normoxia_LowRNAse_H.fastq.gz, SRR1007115… SRA
SRR10071158 83313699 3415861659 2451.94 ZNL_NoIndex_L007_R1.R09_AGO1_normoxia_LowRNAse_L.fastq.gz, SRR1007115… SRA

Linked Publications (1)

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

Data Files (8)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— ZNH_NoIndex_L008_R1.R09_AGO1_normoxia_LowRNAse_H.fastq… RIP-Seq 3.5 GB link
— ZNH_NoIndex_L008_R1.R10_AGO1_normoxia_HighRNAse_H.fast… RIP-Seq 1.9 GB link
— ZNH_NoIndex_L008_R1.R11_AGO1_hypoxia_LowRNAse_H.fastq.… RIP-Seq 804.4 MB link
— ZNH_NoIndex_L008_R1.R12_AGO1_hypoxia_HighRNase_H.fastq… RIP-Seq 310.5 MB link
— ZNL_NoIndex_L007_R1.R09_AGO1_normoxia_LowRNAse_L.fastq… RIP-Seq 2.4 GB link
— ZNL_NoIndex_L007_R1.R10_AGO1_normoxia_HighRNAse_L.fast… RIP-Seq 1.1 GB link
— ZNL_NoIndex_L007_R1.R11_AGO1_hypoxia_LowRNAse_L.fastq.… RIP-Seq 378.5 MB link
— ZNL_NoIndex_L007_R1.R12_AGO1_hypoxia_HighRNase_L.fastq… RIP-Seq 1.9 GB link