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Sample GSM3464551 Query DataSets for GSM3464551
Status Public on Mar 12, 2019
Title P8b 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 SAMN10229741
SRA SRX4870267

Supplementary file Size Download File type/resource
GSM3464551_P8b.csv.gz 20.2 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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