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Sample GSM3494230 Query DataSets for GSM3494230
Status Public on Nov 27, 2019
Title E18 cerebral cortex
Sample type SRA
Source name superficial cerebral cortex cell
Organism Mus musculus
Characteristics strain: C57BL/6
developmental stage: E18
tissue: cerebral cortex
Extracted molecule total RNA
Extraction protocol Samples were sheared in 1×Hank’s balanced salt solution (HBSS) and digested for 15 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=CR --expect-cells=5000
Data were filtered using the following specifications…filtering out outliers with extremely low (less than 200) 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: raw counts; column head (E18_cerebral cortex.csv) is barcode sequence (16bp) for each cell ID, each row represents the genes that had detected
Submission date Nov 28, 2018
Last update date Nov 28, 2019
Contact name Peng Jian
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)
GSE123035 Single-Cell Transcriptomes of Cerebral Cortex in Embryonic 18 Days
BioSample SAMN10492159
SRA SRX5075305

Supplementary file Size Download File type/resource
GSM3494230_E18_cerebral_cortex.csv.gz 13.8 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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