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Sample GSM7422898 Query DataSets for GSM7422898
Status Public on Jun 07, 2023
Title twi, pooled CD45+ cells
Sample type SRA
 
Source name brain
Organism Mus musculus
Characteristics strain: C57Bl/6
tissue: brain
age: Postnatal Day 21
cell type: CD45+
genotype: galc-/-
treatment: none
Extracted molecule total RNA
Extraction protocol brain tissues were collected inot RPMI media and enzymatically dissociated using collagenase/dispase and DNAase (1h/37C). Following this, the cellular suspension was filtered (70uM) and then separated on a 70/30 Percoll gradient where leukocytes were collected at tht interphase. CD45+ cells were collected by flowcyotmetry (FACSARIA II, Becton-Dickinson).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). CD4+ cells were resuspended in a master mix that was 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.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description 10X Genomics
Data processing The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date May 24, 2023
Last update date Jun 07, 2023
Contact name Stephen Crocker
E-mail(s) crocker@uchc.edu
Phone 8606798750
Organization name University of Connecticut School of Medicine
Department Neuroscience
Street address 263 Farmington Ave.
City Farmington
State/province Connecticut
ZIP/Postal code 06030
Country USA
 
Platform ID GPL21493
Series (1)
GSE233320 Gene expression profile at single cell level of CD45+ cells isolated from twitcher (twi) mouse brain (postnatal day 21)
Relations
BioSample SAMN35345447
SRA SRX20502035

Supplementary file Size Download File type/resource
GSM7422898_SC17003_barcodes.tsv.gz 5.8 Kb (ftp)(http) TSV
GSM7422898_SC17003_genes.tsv.gz 212.7 Kb (ftp)(http) TSV
GSM7422898_SC17003_matrix.mtx.gz 5.1 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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