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Sample GSM4186931 Query DataSets for GSM4186931
Status Public on Feb 19, 2020
Title Shh-IUE Cortex E16.5_RE-4
Sample type SRA
Source name ShhN IUE E16.5 Cortex
Organism Mus musculus
Characteristics strain: CD1
tissue: Cortex
developmental stage: Embryonic day 16.5
Treatment protocol E16.5 wild type and ShhN-IUE (ShhN plasmid were electroporated at E13.5, and the cortex was harvested at E16.5) 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.
Extracted molecule total RNA
Extraction protocol The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C).
The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-seq libraries, following the manufacturer’s instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Description ShhN IUE brain
Data processing cellranger mkfastq demultiplexes raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, barcode counting, and UMI counting.
Stringtie (vetrsion: 1.3.0) was used to count the read numbers mapped to each gene, and standardrized the counts using TMM (Trimmed mean of M values)
cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the feature-barcode matrices and analysis on the combined data.
Finally, Seurat (V3) were used for the following dimensionality reduction, clustering, and gene expression.
Genome_build: mm10
Submission date Nov 21, 2019
Last update date Feb 19, 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
Platform ID GPL21273
Series (2)
GSE140816 Regulating lineage progression of cortical neural stem cells by extrinsic signaling molecule SHH [single-cell RNA-seq]
GSE140817 Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog
BioSample SAMN13348381
SRA SRX7199976

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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