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Series GSE140816 Query DataSets for GSE140816
Status Public on Feb 19, 2020
Title Regulating lineage progression of cortical neural stem cells by extrinsic signaling molecule SHH [single-cell RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose:To asses changes in gene expression profiles of single cell from the E16.5 wild type littermate controls cortex, and ShhN IUE (ShhN palsmid were electroporated to wild type mice cortex at E13.5 and the cortex were dissected at E16.5) mice.
Methords: E16.5 wild type and ShhN-IUE cortices were carefully dissected under a fluorescent stereoscope, and incubated in 4 ml of papain solution for 20 min at 37℃, The cortical tissues were gently triturated, filtered through a 40 mm strainer, and washed with HBSS to obtain the single cell suspension. The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-seq libraries, following the manufacturer’s instructions. The cDNA libraries were purified, quantified using Agilent 2100 Bioanalyzer, and sequenced on the Illumina Hiseq4000
Results: 7834 cells (2368 median genes per cell) captured for the Control cortex. And 8538 cells with 2422 median genes per cell captured for Shh-IUE mice.
Overall design scRNA-seq: Individual cells were sampled from mice cortices of E16.5 wild type mice and ShhN IUE mice.
Contributor(s) Zhang Y, Liu G, Guo T, Liang XG, Du H, Yang L, Bhaduri A, Li X, Xu Z, Zhang Z, Li Z, He M, Tsyporin J, Kriegstein AR, Rubenstein JL, Yang Z, Chen B
Citation(s) 32234482
Submission date Nov 21, 2019
Last update date May 20, 2020
Contact name Guoping Liu
Phone 18521006300
Organization name Fudan University
Street address 138 Yi Xue Yuan Road
City Shanghai
ZIP/Postal code 200032
Country China
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (8)
GSM4186924 WT Cortex E16.5_RC-1
GSM4186925 WT Cortex E16.5_RC-2
GSM4186926 WT Cortex E16.5_RC-3
This SubSeries is part of SuperSeries:
GSE140817 Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog
BioProject PRJNA591016
SRA SRP231176

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE140816_CTL_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE140816_CTL_genes.tsv.gz 212.7 Kb (ftp)(http) TSV
GSE140816_CTL_matrix.mtx.gz 84.2 Mb (ftp)(http) MTX
GSE140816_EXP_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSE140816_EXP_genes.tsv.gz 212.7 Kb (ftp)(http) TSV
GSE140816_EXP_matrix.mtx.gz 83.7 Mb (ftp)(http) MTX
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Raw data are available in SRA
Processed data are available on Series record

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