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GSE201891

GSE GEO
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MECP2-related pathways are dysregulated in a cortical organoid model of Myotonic dystrophy [scRNA-Seq]

Organism: Homo sapiens
Platform: GPL24676
Samples: 5
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Apr 29 2022
Last Updated: Jul 01 2022
Status: Public on Jun 30 2022
Contact: Gene,,Yeo (UCSD)

Relations

SubSeries of: GSE201898 BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA833424

Summary

As cortical organoids consist of a heterogeneous population of cell-types, 6-month-old DM1 and Rett syndrome cortical organoids were subjected to single cell RNA-seq (scRNA-seq) analysis to determine which cell type(s) CELF2’s RNA targets are expressed in. Unsupervised clustering was implemented on the combined dataset of 8595 cells from control, DM600, and DM1200 cortical organoids that consisted of ~2865 cells per organoid line and ~17,575 reads per cell to identify genotype-specific clusters at 6-months post-differentiation. Uniform Manifold Approximation and Projection (UMAP) for dimension reduction revealed clear differences between control and DM1 organoids. From the expression of established cell-type specific gene markers, smaller sub-clusters were combined to represent four major cell classes: neural progenitors, intermediate neural progenitors, glutamatergic cortical neurons, and glial cells.

Overall Design

Gene expression profile at single cell level of cortical organoids differentiated from myotonic dystrophy 1(DM1200 and Dm600) and Rett Syndrome (MECP2) patient stem cells as well as 2 neurotypical control stem cells (MECP2_KO and MECP2_WT)

Analysis (3 steps)

View Data Processing
Processing steps for GSE201891
  1. Alignment, cell barcode processing, umis processing, abundance measurements: cellranger count (version 3.0.2)
  2. MD tags were added to alignments with samtools calmd --threads 15 -rb possorted_genome_bam.bam refdata-cellranger-hg19-3.0.0/fasta/genome.fa > possorted_genome_bam_MD.bam
  3. Reads were split based on the CB:Z tag, resulting in one BAM file per barcode.

Supplementary Files (7)

GSE201891_CellType_table_DM_forGEO.csv.gz Download
GSE201891_CellType_table_MECP2_forGEO.csv.gz Download
GSE201891_DM_Ctrl_barcode_qc_clustering_CellType.csv.gz Download
GSE201891_DM_Ctrl_gene_features.csv.gz Download
GSE201891_MECP2_barcode_qc_clustering_CellType.csv.gz Download
GSE201891_MECP2_gene_features.csv.gz Download
GSE201891_RAW.tar Download
GEO Samples (5)
GSM6077644 GSM6077645 GSM6077646 GSM6077647 GSM6077648

Dataset Citations (1)

MECP2-related pathways are dysregulated in a cortical organoid model of myotonic dystrophy.
PMID 35767654 · 2022 · Science translational medicine
Kathryn H Morelli, Wenhao Jin, Shashank Shathe, Assael A Madrigal, Krysten L Jones, Joshua L Schwartz, Tristan Bridges, Jasmine R Mueller, Archana Shankar, Isaac A Chaim, John W Day, Gene W Yeo

SRA Experiments (5) and Runs (5)

Total: 58829 MB
SRX15048734 SRP372866 RNA-Seq SINGLE
GSM6077644: Control_6M; Homo sapiens; RNA-Seq
Sample: SRS12794689
BioProject: PRJNA833424
BioSample: SAMN27988116
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Cortical Organoids
cell type: Cortical Organoids
age: 6 months post-differentiation
Original files (1)
Cortical Organoids
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR18972865 316914348 32008349148 15514.9 Control_6M_possorted_genome_bam.bam, SRR18972865, SRR18972865.lite SRA
SRX15048735 SRP372866 RNA-Seq SINGLE
GSM6077645: DM1200_6M; Homo sapiens; RNA-Seq
Sample: SRS12794690
BioProject: PRJNA833424
BioSample: SAMN27988115
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Cortical Organoids
cell type: Cortical Organoids
age: 6 months post-differentiation
Original files (1)
Cortical Organoids
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR18972864 273723831 27646106931 13309.19 DM1200_6M_possorted_genome_bam.bam, SRR18972864, SRR18972864.lite SRA
SRX15048736 SRP372866 RNA-Seq SINGLE
GSM6077646: DM600_6M; Homo sapiens; RNA-Seq
Sample: SRS12794691
BioProject: PRJNA833424
BioSample: SAMN27988114
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Cortical Organoids
cell type: Cortical Organoids
age: 6 months post-differentiation
Original files (1)
Cortical Organoids
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR18972863 314420098 31756429898 13496.53 DM600_6M_possorted_genome_bam.bam, SRR18972863, SRR18972863.lite SRA
SRX15048737 SRP372866 RNA-Seq SINGLE
GSM6077647: MECP2_KO; Homo sapiens; RNA-Seq
Sample: SRS12794692
BioProject: PRJNA833424
BioSample: SAMN27988113
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Cortical Organoids
cell type: Cortical Organoids
age: 6 months post-differentiation
Original files (1)
Cortical Organoids
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR18972862 141219373 13839498554 7012.22 MECP2_KO_possorted_genome_bam.bam, SRR18972862, SRR18972862.lite SRA
SRX15048738 SRP372866 RNA-Seq SINGLE
GSM6077648: MECP2_WT; Homo sapiens; RNA-Seq
Sample: SRS12794693
BioProject: PRJNA833424
BioSample: SAMN27988112
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Homo sapiens
Sample attributes
source_name: Cortical Organoids
cell type: Cortical Organoids
age: 6 months post-differentiation
Original files (1)
Cortical Organoids
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR18972861 187365368 18361806064 9495.82 MECP2_WT_possorted_genome_bam.bam, SRR18972861, SRR18972861.lite SRA

Linked Publications (1)

MECP2-related pathways are dysregulated in a cortical organoid model of myotonic dystrophy.
Science translational medicine · 2022

Data Files (6)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— Control_6M_possorted_genome_bam.bam RNA-Seq 15.2 GB link
— DM1200_6M_possorted_genome_bam.bam RNA-Seq 13.0 GB link
— DM600_6M_possorted_genome_bam.bam RNA-Seq 13.2 GB link
— MECP2_KO_possorted_genome_bam.bam RNA-Seq 6.8 GB link
— MECP2_WT_possorted_genome_bam.bam RNA-Seq 9.3 GB link
— SRR18972861.lite RNA-Seq 9.3 GB link