 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 |
| E-mail(s) |
gpliu@fudan.edu.cn
|
| 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 |
|
| Relations |
| BioSample |
SAMN13348381 |
| SRA |
SRX7199976 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
