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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

Data Files (4)

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