|
| Status |
Public on Dec 27, 2021 |
| Title |
P21_nr_1_a |
| Sample type |
SRA |
| |
|
| Source name |
Visual cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Visual cortex
|
| Treatment protocol |
Mice were anesthetized in an isoflurane chamber, decapitated, and the brain was immediately removed and submerged in Hibernate A
|
| Growth protocol |
Mouse breeding and husbandry procedures were carried out in accordance with UCLA's animal care and use committee protocol number 2009-031-31A, at University of California, Los Angeles. Mice were given food and water ad libitum, and lived in a 12-hr day/night cycle with up to four adult animals per cage. Only virgin male C57BL/6J wild-type mice were used in this study.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Extracted brains were placed on a metal mold and the slice containing V1 was isolated by inserting blade 0.5 mm posterior to lambda suture. A second blade was inserted 1.5 mm anterior (2 spaces on the mold). This slice was removed and lowered to Hibernate A in a 60cc petri dish which was placed on top of a ruler under a dissecting scope. Midline was lined up with a ruler and the first cut was bilaterally 3.2 mm out from the midline. The second cut was 1 mm medial to the first cut. The cortex was peeled off the underlying white matter. The V1 piece with a total of 1 mm cortex depth by 1.5 mm thickness was transferred to a dish containing 600 ul of RNAlater (Thermo Fisher Cat# AM7020) and kept on ice until dissections were complete. Dissected tissues were then kept in RNAlater at 4C overnight, and transferred to -20C the next day, where they were kept up to 1 month prior to being processed for snRNA-seq.
Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina NovaSeq™ 6000 Sequencing System (S2) to a depth of ~30,000 reads per cell.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
15 mice bio rep 1, lib rep 1
|
| Data processing |
Sample demultiplexing using Cell Ranger v3.1.0 10X Genomics
Sample alignment to the mouse reference transcriptome (Ensembl 92, GRCm38.92), which was converted to a pre-mRNA reference package by following Cell Ranger guidelines.
Genome_build: GRCm38.92
Supplementary_files_format_and_content: CSV files containing counts gene expression matrix and metadata from all 35 samples
|
| |
|
| Submission date |
Dec 27, 2021 |
| Last update date |
Dec 28, 2021 |
| Contact name |
Salwan Butrus |
| E-mail(s) |
[email protected]
|
| Organization name |
UC Berkeley
|
| Department |
Chemical and Biomolecular Engineering
|
| Lab |
Karthik Shekhar
|
| Street address |
Stanley Hall Rm
|
| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE190940 |
Vision-dependent specification of cell types and function in the developing cortex |
|
| Relations |
| BioSample |
SAMN24437381 |
| SRA |
SRX13510705 |
