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Sample GSM7906813 Query DataSets for GSM7906813
Status Public on Jan 10, 2024
Title EAE, ND6, rep 1
Sample type SRA
 
Source name Spinal cord
Organism Mus musculus
Characteristics tissue: Spinal cord
disease state: EAE
cell type: Various
genotype: Nd6
Extracted molecule polyA RNA
Extraction protocol Mice were perfused with actinomycin D and triptolide in ice cold HBSS, spinal cords were extracted and underwent mechanical dissociation in digestion buffer. After myelin removal, cells were used for library preparation.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, the cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The barcoded processing and gene counting were made using the Cell Ranger software v7.1.0 [Zheng2017] and post-alignment processing and visualisation was performed using Seurat v4.3.0.1 [Stuart2019]. Data was normalised using Sctransform [Hafemeister2019].
The clustering was performed using SLM; ClustAssess was used for identifying stable clusters; the identification of markers was performed per cluster vs its complement.
The visualisation and community accessible overview were complied using ShinyCell [Ouyang2021]
Assembly: GRCm38 (Ensembl 93 from pre-built Cell Ranger reference 3.1.0)
Supplementary files format and content: count matrix containing raw gene expression (csv)
 
Submission date Nov 17, 2023
Last update date Jan 10, 2024
Contact name Irina Mohorianu
E-mail(s) data-submissions@stemcells.cam.ac.uk
Organization name University of Cambridge
Department Wellcome-MRC Cambridge Stem Cell Institute
Street address Puddicombe Way
City Cambridge
ZIP/Postal code CB2 0AW
Country United Kingdom
 
Platform ID GPL24247
Series (2)
GSE248173 Mitochondrial complex I activity in microglia sustains neuroinflammation [scRNA-seq II]
GSE248175 Mitochondrial complex I activity in microglia sustains neuroinflammation
Relations
BioSample SAMN38302560
SRA SRX22560647

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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