|
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 |