GEO DataSets

(Submitter supplied) De novomutations and copy number variations (CNVs) inNRXN1(2p16.3) pose a significant risk for schizophrenia (SCZ). HowNRXN1CNVs impact cortical development in a cell type-specific manner and how disease genetic background modulates these phenotypes are unclear. Here, we leveraged human pluripotent stem cell-derived brain organoid models carryingNRXN1heterozygous deletions in isogenic and SCZ patient genetic backgrounds and conducted single cell transcriptomic analysis over the course of cortical brain organoid development from 3 weeks to 3.5 months. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

26 Samples

Download data: H5

(Submitter supplied) Heterozygous NRXN1 deletions constitute the most prevalent currently known single-gene mutation associated with schizophrenia, and predispose to multiple other neurodevelopmental disorders. Previous studies showed that engineered heterozygous NRXN1 deletions impaired neurotransmitter release in human neurons, suggesting a synaptic pathophysiological mechanism. Utilizing this observation for drug discovery, however, requires confidence in its robustness and validity. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL19415

30 Samples

Download data: TSV, XLSX

(Submitter supplied) We performed targeted long-read and short-read RNA sequencing to identify and quantify NRXN1 isoforms in human post-mortem dlPFC and hiPSC-neurons derived from controls and NRXN1+/- individuals.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

14 Samples

Download data: TXT

(Submitter supplied) We performed targeted long-read and short-read RNA sequencing to identify and quantify NRXN1 isoforms in human post-mortem dlPFC and hiPSC-neurons derived from controls and NRXN1+/- individuals. We also performed whole transcriptome RNA seuqencing and 10x genomics single cell sequencing to determine transcriptional changes in NRXN1+/- hiPSC-neurons compared to controls.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

60 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Single-cell sequencing of donor-derived 3D cerebral organoids comparing those from schizphrenic patients to those from healthy donors.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

7 Samples

Download data: CSV

(Submitter supplied) Background ­- Schizophrenia (SCZ) is a debilitating psychiatric disorder with a large genetic contribution; however, its neurodevelopmental substrates remain largely unknown. Modeling pathogenic processes in SCZ using human iPSC-derived neurons (iNs) has emerged as a promising strategy. Copy number variations (CNV) confer high genetic risk for SCZ, with duplication of the 16p11.2 locus increasing risk 14.5 fold. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

23 Samples

Download data: CSV, XLSX

(Submitter supplied) We used microarrays to identify the differently expressed genes in disease model for bipolar disorder and schizophrenia.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

12 Samples

Download data: CEL, CHP

(Submitter supplied) We established PCCB knockdown human induced pluripotent stem cell (hiPSC) line using CRISPR interference (CRISPRi). The established PCCB knockdown and control hiPSCs were then used to generate human forebrain organoids (hFOs). On day 60 of organoid culture, PCCB knockdown and control hFOs were randomly selected for RNA-sequencing (RNA-seq). We found that differentially expressed genes (DEGs) affected by PCCB knockdown were enriched with GABAergic synapse, synaptic vesicle cycle, neurotransmitter transport, forebrain development, axon development, synaptic organization, and calcium signaling pathways. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19415 GPL19057 GPL18573

37 Samples

Download data

(Submitter supplied) The humanized mice's frontal cortical tissues were used for transcriptomic analysis, as this brain area shows early involvement in pathophysiology of schizophrenia. We transplanted hiPSC-astrocyte progenitors from one monozygotic twin pair discordant for schizophrenia and one healthy control into neonatal mouse forebrains and analyzed mouse behavior at five and ten months, followed by gene expression profiling of the frontal cortices seven days later.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19415 GPL19057

21 Samples

Download data: TXT

(Submitter supplied) Previous studies have implicated several brain cell types in schizophrenia, but the genetic impact of astrocytes is unknown. Considering their high complexity in humans, astrocytes are likely key determinants of neurodevelopmental diseases. Human induced pluripotent stem cell (hiPSC) -derived astrocytes differentiated from five monozygotic twin pairs discordant for schizophrenia and five healthy subjects were studied for alterations related to high genetic risk and clinical manifestation of SCZ in astrocyte transcriptomics.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: TXT

(Submitter supplied) Reciprocal deletion and duplication of 16p11.2 is the most common copy number variation (CNV) associated with Autism Spectrum Disorder (ASD) and other developmental disorders, and has significant effect on brain size. We used cortical organoids derived from ASD cases to investigate neurodevelopmental pathways dysregulated by dosage changes of 16p11.2 CNV. We show that organoids recapitulate patients’ macrocephaly and microcephaly phenotypes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

108 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Rattus norvegicus; Human alphaherpesvirus 2; Merkel cell polyomavirus; Mus musculus cytomegalovirus 2; Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1; human gammaherpesvirus 4; JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus macacae; Murid gammaherpesvirus 4; Betapolyomavirus hominis

Type:

Non-coding RNA profiling by array

Platforms:

GPL11434 GPL15691

13 Samples

Download data: TXT

(Submitter supplied) Neurogenesis is a pro-survival process that comprises of dendritic and axonal growth, synaptogenesis, synaptic and neuronal pruning. These complex processes are determined by temporal gene expression during development, which is in turn tightly regulated by long non-coding RNAs and microRNAs. In this study, we investigated the processes implicated in the maturation of primary neuronal cultures based on RNA expression profiling. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL15691

9 Samples

Download data: TXT

(Submitter supplied) Neurogenesis is a pro-survival process that comprises of dendritic and axonal growth, synaptogenesis, synaptic and neuronal pruning. These complex processes are determined by temporal gene expression during development, which is in turn tightly regulated by long non-coding RNAs and microRNAs. In this study, we investigated the processes implicated in the maturation of primary neuronal cultures based on RNA expression profiling. more...

Organism:

Human alphaherpesvirus 1; Human alphaherpesvirus 2; human gammaherpesvirus 4; Mus musculus cytomegalovirus 2; Betapolyomavirus macacae; Homo sapiens; Mus musculus; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1; Merkel cell polyomavirus; Rattus norvegicus; JC polyomavirus; Murid gammaherpesvirus 4; Betapolyomavirus hominis; Human gammaherpesvirus 8

Type:

Non-coding RNA profiling by array

Platform:

GPL11434

4 Samples

Download data: TXT