Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
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PRJNA445711

PRJNA445711: Novel risk variants affecting enhancers of TH1 and TREG cells in type 1 diabetes [RNA-seq]

Source: NCBI / GSE112341
Submission Date: Mar 26 2018
Release Date: Mar 26 2019
Update Date: Mar 26 2019

Summary: We generated expression profiles of TH1 and TREG cells from T1D and healthy subjects by RNA-Seq. By integrating RNA-Seq dta with other data sets, we predicted and validated serveral T1D risk SNPs.

Overall Design: Effector memory TH1 and effector memory TREG cells were isolated from 6 T1D patients and mached 5 helathy controls. Gene expression profilings were generated using RNA-Seq. By integrating RNA-Seq data, ChIP-Seq and other data sets, we predicted and validated several risk SNPs for T1D.

GEN Datasets:
GEND000018
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: TH1 and TREG cell were sorted into TRIzol-LS and total mRNA was isolated using RNeasy Micro Kit (Qiagen). Total RNA was treated with DNase (Ambion) to remove genomic DNA.
Library Construction Protocol: Libraries were prpared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to manufacturer's instructions. Bioanalyzer, KAPA qPCR were done before pooling libraries for sequencing on Illumina HiSeq2500 in paired-end mode with the read length of 75 nt.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2500
Strand-Specific: Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Risk variants disrupting enhancers of TH1 and TREG cells in type 1 diabetes.
Proceedings of the National Academy of Sciences of the United States of America . 2019-03-25 [PMID: 30910956]