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

PRJNA527139: Deconvolution of Transcriptional Networks Identifies TCF4 as a Master Regulator in Schizophrenia

Source: NCBI / GSE128333
Submission Date: Mar 14 2019
Release Date: Sep 17 2019
Update Date: Sep 17 2019

Summary: We report the data generated upon knockdown of TCF4 in hiPSC-derived neural progenitor cells and glutamatergic neurons.

Overall Design: Examination of TCF4 knockdown to probe its contribution to schizophrenia.

GEN Datasets:
GEND000017
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Cell Line:
Development Stage:
Protocol
Growth Protocol: The hiPSC line used for deriving neurons was generated by Sendai virus method at Rutgers University Cell and DNA Repository (RUCDR)-NIMH Stem Cell Center from cryopreserved lymphocytes (CPLs) of a 29-year-old male SCZ patient (cell ID: 07C65853) from the MGS collection. The NorthShore University HealthSystem Institutional Review Board (IRB) approved the study. hiPSCs were cultured using the feeder-free method in Geltrex (Thermofisher)-coated plates in mTeSR1 medium (StemCell). The media were changed daily, and cell were passaged as clumps every 5 days using ReLeSR (StemCell) in the presence of 5 μm ROCK inhibitor (R&D Systems). hiPSCs were characterized by positive IF staining of pluripotent stem cell markers OCT4, TRA-1-60, NANOG, and SSEA4.
Treatment Protocol: -
Extract Protocol: Total RNAs were extracted from homogenized cell lysate using the RNeasy Plus mini kit (Qiagen)
Library Construction Protocol: RNA libraries were prepared for sequencing using standard Illumina protocols.
Sequencing
Molecule Type: rRNA- 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
Deconvolution of transcriptional networks identifies TCF4 as a master regulator in schizophrenia.
Science advances . 2019-09-11 [PMID: 31535015]