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Sample GSM6355862 Query DataSets for GSM6355862
Status Public on Jul 23, 2022
Title (Con, scRNAseq
Sample type SRA
 
Source name Spinal cord
Organism Mus musculus
Characteristics tissue: Spinal cord
genotype: (mSmn+/-, hSMN22tg/0)
age: postnatal day 4
strain: FVB
Extracted molecule total RNA
Extraction protocol Whole spinal cords were obtained from transgenic mice, and the spinal cords were stripped according to established methods and placed in ice-cold phosphate-buffered saline (PBS). The tissue was minced and dissociated with 0.25% trypsin in a centrifuge tube for 30 min at 28 °C, followed by 1 mg/mL collagenase II for 20 min, with gentle mixing every 10 min. The enzymatic reaction was terminated through the addition of 10% fetal bovine serum (FBS). The sample was filtered using a 70 µm strainer to obtain a single-cell suspension.
Using single-cell 3 ‘Library and Gel Bead Kit V3 (10× Genomics, 1000075) and Chromium Single Cell B Chip Kit (10× Genomics, 1000074), the cell suspension (300–600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10× Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% bovine serum albumin (BSA). Approximately 6000 cells were added to each channel, and the target cell recovered was estimated to be approximately 3000 cells. Captured cells were lysed, and the released RNAs were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on an S1000TM Touch Thermal Cycler (Bio Rad) at 53 °C for 45 min followed by 85 °C for 5 min, and incubated at 4 °C. The complementary DNA (cDNA) was generated and then amplified, and the quality was assessed using an Agilent 4200. According to the manufacturer’s instruction, scRNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with a pair-end 150 bp reading strategy.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing The Cell Ranger Single-Cell toolkit (version 3.0.0) provided by 10× genomics was applied to align reads and generate the gene-cell unique molecular identifier (UMI) matrix for each sample (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest). The read data were mapped using the corresponding Mus musculus reference genome. Different samples were merged using the cellranger aggr function. The obtained raw_feature_bc_matrix was loaded, and Seurat R package (v 3.2.2) was further used for downstream analyses .
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date Jul 20, 2022
Last update date Jul 24, 2022
Contact name junjie sun
E-mail(s) jjsun@ntu.edu.cn
Phone +86 515506660626
Organization name nantong university
Street address 19 Qixiu Road
City nantong
State/province jiangsu province
ZIP/Postal code 226001
Country China
 
Platform ID GPL24247
Series (1)
GSE208629 Single-cell transcriptomic data in the spinal cord of Taiwanese type I SMA mice
Relations
BioSample SAMN29843166
SRA SRX16358214

Supplementary file Size Download File type/resource
GSM6355862_Con_barcodes.tsv.gz 118.3 Kb (ftp)(http) TSV
GSM6355862_Con_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM6355862_Con_matrix.mtx.gz 118.2 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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