|
| Status |
Public on Mar 10, 2023 |
| Title |
R366 E11.5 Medial cortex |
| Sample type |
SRA |
| |
|
| Source name |
E11.5 Medial cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
development stage: E11.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The medial cortex was dissociated at E11.5 for Single-cell RNA sequencing. And we using AnnexinV and PI co-staining protocol to sort AnnexinV positive, PI negative and AnnexinV, PI double negative cells for bulk RNA sequencing.
The Single-cell RNA sequencing libraries were prepared for sequencing following the manufacturer’s recommendations for the DNBelab C Series High-throughput Single-cell System (BGI-research). The bulk RNA sequencing libraries were applied to modify smart-seq2 protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
The sequencing data were processed using an open-source pipeline (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software)
Fastq reads were filtered using Trimmomatic to discard low-quality reads and trim poor-quality bases.The remaining clean reads were aligned to GRCm38 (mm10) genome. STAR with default parameter settings was used for alignment to generate BAM files. Gene-counting tools, featureCounts were used to generate TPM(transcripts per million) gene counts per cell/sample.
Seurat R package (v4) was used for standard Single-cell RNA sequencing data analysis.
Assembly: mm10
Supplementary files format and content: Matrix table with gene TPM for every gene and every sample; WT_all_cell_20220427.rds. rds are serialized R objects of the Bioconductor class ExpressionSet that contains the final data used to generate the results. It can be imported into R with readRDS(“WT_all_cell_20220427.rds”). It contains the gene counts, sample metadata, and feature metadata for single cells that passed quality control.
|
| |
|
| Submission date |
May 17, 2022 |
| Last update date |
Mar 10, 2023 |
| Contact name |
Zhenhua Chen |
| E-mail(s) |
czh@genetics.ac.cn
|
| Organization name |
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
|
| Department |
State Key Laboratory of Molecular Development Biology
|
| Lab |
Wu
|
| Street address |
West Beichen Road, Olympic Village, Beijing
|
| City |
Beijing |
| State/province |
China |
| ZIP/Postal code |
100000 |
| Country |
China |
| |
|
| Platform ID |
GPL28457 |
| Series (1) |
| GSE203163 |
Identifying endogenous superior and inferior neural progenitor cells |
|
| Relations |
| BioSample |
SAMN28488223 |
| SRA |
SRX15302952 |
