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Sample GSM7474612 Query DataSets for GSM7474612
Status Public on Jun 30, 2023
Title snRNA-seq of Mut
Sample type SRA
Source name Spinal cord
Organism Mus musculus
Characteristics tissue: Spinal cord
genotype: Mut
age: 9-month-old
Sex: male
Extracted molecule nuclear RNA
Extraction protocol The frozen ventral horn of L3-L5 spinal cord was used for isolation the nuclei. The spinal cord was taken from the 9-month-old male mice, and quickly placed straightly in the embedding mold. Then the spinal cord was quickly frozen with OCT in liquid nitrogen. Removed the ventral white matter in microtome until the gray matter appears and removed the white matter on both sides carefully. Then taking the gray matter at the depth of 1/2 before the confluence of the gray matter of two sides and put the gray matter into the EP tube for liquid nitrogen quick freezing again. Then the nuclei were extracted
For snRNA-seq, the single cell 3′ GEM, Library & Gel Bead Kit V3.1 (10× Genomics, 1000075) and Chromium Single Cell B Chip Kit (10× Genomics, 1000074) were used. To generate single-nuclei gel beads in emulsion, the nuclei suspension was loaded onto the Chromium single cell controller (10× Genomics). Then suspended the single nuclei in PBS (containing 0.04% BSA). Captured cells were lysed to release their RNA and barcoded through reverse transcription in individual GEMs. The reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min. The cDNA was kept at 4°C and then amplified for sequencing.
For snATAC-seq, incubating the nuclei with Tn5 transposase. Then the nuclei suspension was loaded into the Chromium microfluidic chip E with 10x Genomics reagents and barcoded with a 10x Genomics Chromium Controller (10x Genomics, Pleasanton, CA). DNA fragments were subsequently amplified, and the sequencing libraries were constructed with reagents from a Chromium Single Cell ATAC reagent kit (10x Genomics; PN-1000110, PN-1000156, PN-1000084) according to the manufacturer’s instructions. After preliminary quantification and quality inspection, libraries were then pooled and loaded on an Illumina NovaSeq with 2 x 50 paired-end kits.
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Using cellranger to preprocess the data.
Assembly: mm10
Submission date Jun 13, 2023
Last update date Jun 30, 2023
Contact name Dan Zhang
Organization name Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Street address No. 1 West Beichen Road, Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
Platform ID GPL24247
Series (1)
GSE234783 Functional identification of protocadherin alpha 9 (PCDHA9) as a candidate causative gene for amyotrophic lateral sclerosis
BioSample SAMN35722397
SRA SRX20666618

Supplementary file Size Download File type/resource
GSM7474612_snRNA-seq_of_Mut.tar.gz 108.3 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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