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GSE130238

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Nested oscillatory dynamics in cortical organoids model early human brain network development

Organism: Homo sapiens
Platform: GPL20301
Samples: 4
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Apr 24 2019
Last Updated: Aug 18 2020
Status: Public on Apr 25 2019
Contact: Jing,,Gu (UC San Diego)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA534424 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP193683

Summary

We characterized the different cell types and their differential gene expression patterns in 1, 3, 6, and 10 month-old cortical organoids.

Overall Design

Profling of single cell RNA-Seq for 1, 3, 6, and 10 month-old human cortical organoids

Analysis (3 steps)

View Data Processing
Processing steps for GSE130238
  1. base-calling: cellranger mkfastq (version 2.1.1)
  2. alignment, cell barcode processing, umi processing, feature-barcode matrix generation: cellranger count (version 2.1.1)
  3. Supplementary files including lists of barcodes, genes, and feature-barcode matrix were generated by Cell Ranger v2.1.1.

Supplementary Files (1)

GSE130238_RAW.tar Download
GEO Samples (4)
GSM3734294 GSM3734295 GSM3734296 GSM3734297

Dataset Citations (1)

Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development.
PMID 31474560 · 2019 · Cell stem cell
Cleber A Trujillo, Richard Gao, Priscilla D Negraes, Jing Gu, Justin Buchanan, Sebastian Preissl, Allen Wang, Wei Wu, Gabriel G Haddad, Isaac A Chaim, Alain Domissy, Matthieu Vandenberghe, Anna Devor, Gene W Yeo, Bradley Voytek, Alysson R Muotri

SRA Experiments (4) and Runs (4)

Total: 37393 MB
SRX5728924 SRP193683 RNA-Seq PAIRED
GSM3734294: 1 month cortical organoids; Homo sapiens; RNA-Seq
Sample: SRS4666811
BioProject: PRJNA534424
BioSample: SAMN11490178
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Cortical organoids
cell line: WT - iPSC
passage: 37
age of organoid: 1 month
reprogramming strategy: Retroviral
Original files (1)
Cortical organoids
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8948931 282806072 35067952928 16581.3 1M_cortical_organoids_R1.fastq.gz, 1M_cortical_organoids_R2.fastq.gz,… SRA
SRX5728925 SRP193683 RNA-Seq PAIRED
GSM3734295: 3 month cortical organoids; Homo sapiens; RNA-Seq
Sample: SRS4666812
BioProject: PRJNA534424
BioSample: SAMN11490177
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Cortical organoids
cell line: WT - iPSC
passage: 37
age of organoid: 3 month
reprogramming strategy: Retroviral
Original files (1)
Cortical organoids
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8948932 136833052 16967298448 7932.69 3M_cortical_organoids_R1.fastq.gz, 3M_cortical_organoids_R2.fastq.gz,… SRA
SRX5728926 SRP193683 RNA-Seq PAIRED
GSM3734296: 6 month cortical organoids; Homo sapiens; RNA-Seq
Sample: SRS4666813
BioProject: PRJNA534424
BioSample: SAMN11490176
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Cortical organoids
cell line: WT - iPSC
passage: 37
age of organoid: 6 month
reprogramming strategy: Retroviral
Original files (1)
Cortical organoids
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8948933 114443912 14191045088 6517.87 6M_cortical_organoids_R1.fastq.gz, 6M_cortical_organoids_R2.fastq.gz,… SRA
SRX5728927 SRP193683 RNA-Seq PAIRED
GSM3734297: 10 month cortical organoids; Homo sapiens; RNA-Seq
Sample: SRS4666814
BioProject: PRJNA534424
BioSample: SAMN11490175
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: Cortical organoids
cell line: WT - iPSC
passage: 37
age of organoid: 10 month
reprogramming strategy: Retroviral
Original files (1)
Cortical organoids
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8948934 112754126 13981511624 6360.81 10M_cortical_organoids_R1.fastq.gz, 10M_cortical_organoids_R2.fastq.g… SRA

Linked Publications (1)

Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development.
Cell stem cell · 2019

Potentially Related Publications (1)

This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.

Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development.
Cell stem cell · 2019

Data Files (8)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— 10M_cortical_organoids_R1.fastq.gz RNA-Seq 6.2 GB link
— 1M_cortical_organoids_R1.fastq.gz RNA-Seq 16.2 GB link
— 3M_cortical_organoids_R1.fastq.gz RNA-Seq 7.7 GB link
— 6M_cortical_organoids_R1.fastq.gz RNA-Seq 6.4 GB link
— SRR8948931_GSM3734294 RNA-Seq 16.2 GB link
— SRR8948932_GSM3734295 RNA-Seq 7.7 GB link
— SRR8948933_GSM3734296 RNA-Seq 6.4 GB link
— SRR8948934_GSM3734297 RNA-Seq 6.2 GB link