|
| Status |
Public on Mar 12, 2019 |
| Title |
P8a cerebellum |
| Sample type |
SRA |
| |
|
| Source name |
Total cerebellum cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
developmental stage: postnatal day 8
tissue: cerebellum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were sheared in 1×Hank’s balanced salt solution (HBSS) and digested for 15-20 min in 0.25% trypsin solution
All procedures followed the guidelines provided by 10x Genomics, Inc Dissociated cells in each sample were partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) in a limiting dilution to lower multiplet rate. Then, single-cell GEMs were incubated with reverse-transcription reagents, including several primers for cell and transcript barcoding in cDNA synthesis, followed by cDNA amplification and library construction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Basecalls performed using CellRanger 2.1
reads were aligned to the mm10 genome assembly using cellranger 2.1 with the following configurations…
cellranger count --id=result --transcriptome=/ion/luozg_group/pengjian/2_refdata/1_mm/refdata-cellranger-mm10-1.2.0 --fastqs=/ion/luozg_group/pengjian/1_rawdata --sample=P0 \ ##P8a or P8b
--expect-cells=5000
Data were filtered using the following specifications…filtering out outliers with extremely low (less than 1000) and high (more than 6500) gene numbers
Cluster were perform using Seurat in R
26 bp Read1 (10× cell barcode and UMI), 8 bp i7 Index (sample index), and 98 bp Read2 (insert)is biological,otherwise is technical
Genome_build: mm10
Supplementary_files_format_and_content: [.csv] raw counts
|
| |
|
| Submission date |
Nov 09, 2018 |
| Last update date |
Mar 12, 2019 |
| Contact name |
Peng Jian |
| E-mail(s) |
jpeng@ion.ac.cn
|
| Organization name |
University of Chinese Academy of Sciences
|
| Department |
Institute of Neuroscience
|
| Street address |
320 Yue Yang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE122357 |
Single-Cell Transcriptomes Reveal Molecular Specializations of Neuronal Cell Types in the Developing Cerebellum |
|
| Relations |
| BioSample |
SAMN10229739 |
| SRA |
SRX4870265 |
