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Sample GSM6945824 Query DataSets for GSM6945824
Status Public on Oct 17, 2023
Title IKO_MNP_D18_Rep2
Sample type SRA
 
Source name Motor neuron progenitor cells
Organism Homo sapiens
Characteristics cell type: d18 hiPSC-derived motor neuron progenitor cells
cell line: ISL1-/-
treatment: untreated
Treatment protocol Detailed in "characteristics: Treatment" to specify different treatments on samples.
Growth protocol Cardiac progenitors cells were differentiated from WTC11 hiPSC lines by the WNT modulation protocol. In brief, 6 uM CHIR were added for 48hours, followed by 5 uM IWP4 for 48 hours. Cells were then grown RPMI with B27 supplement minus insulin until day 10, then with RPMI with B27 plus insulin
Extracted molecule total RNA
Extraction protocol Single cell suspensions were loaded into the Chromium controller (10X genomics) microfluidic chip for single cell droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (PN- 1000121) and Chromium i7 Multiplex Kit (PN-120262).
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description scRNA-seq of total RNA in cell type
Data processing Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger Suite v3.1.0 from 10X genomics
Additional filtering, quality control and doublet removal was done using Seurat v3 according to specifications in the tutorials (https://satijalab.org/seurat/pbmc3k_tutorial.html)
Assembly: hg19
Supplementary files format and content: normalized gene-cellbarcode expression matrix in csv format
 
Submission date Jan 20, 2023
Last update date Oct 17, 2023
Contact name Deepak Srivastava
Organization name J David Gladstone Institutes
Department GICD
Lab Deepak Srivastava
Street address 1650 Owens St
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL18573
Series (2)
GSE195476 The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5
GSE223339 Single cell RNA-sequencing (scRNA-seq) of ISL1 knockout (KO) or knockdown and NKX2.5 KO compared to WT in cardiac progenitors (CPs); scRNA-seq of ISL1 KO compared to WT in motor neuron progenitors (MNPs)
Relations
BioSample SAMN32811722
SRA SRX19103452

Supplementary file Size Download File type/resource
GSM6945824_Sample16_IKO_MNP_D18_Rep2_matrix.csv.gz 17.5 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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