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Sample GSM6890285 Query DataSets for GSM6890285
Status Public on May 31, 2023
Title WT mouse forebrain 1
Sample type SRA
 
Source name brain
Organism Mus musculus
Characteristics tissue: brain
cell line: primary cells
cell type: forebrain nuclei
genotype: wt
treatment: none
Extracted molecule total RNA
Extraction protocol Brains were removed from P16 mice. The forebrain was discected and flash frozen. Forebrains were homogenized using a Dounce homogenizer and nuclei were isolated using a Nuclear Isolation Kit (Millipore; nuc101)
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs 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
 
Description Nuclei were isolated from WT mouse forebrains at P16. RNA was sequenced using the 10X Chromium platform.
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)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date Dec 22, 2022
Last update date Jun 10, 2023
Contact name Andrew Lieberman
Organization name University of Michigan
Department Pathology
Street address 1150 W Medical Center Drive
City Ann Arbor
State/province MI
ZIP/Postal code 48105
Country USA
 
Platform ID GPL24247
Series (2)
GSE221609 The cholesterol transporter NPC1 is essential for epigenetic regulation and maturation of oligodendrocyte lineage cells snRNA-Seq
GSE221610 The cholesterol transporter NPC1 is essential for epigenetic regulation and maturation of oligodendrocyte lineage cells
Relations
BioSample SAMN32398606
SRA SRX18847394

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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