|
| Status |
Public on Oct 07, 2021 |
| Title |
IF8 |
| Sample type |
SRA |
| |
|
| Source name |
visual cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
age: post natal day 14
Sex: female
genotype: Ip3r2 ko
|
| Growth protocol |
12 hour light/dark cycle with ad lib access to standard mouse chow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mice anesthetized with Ketamine/ Xylazine injection, then brain microdissection in cold PBS, snap freeze in ethanol+CO2. stored at -80C until use. On day of experiment, tissue digested to release single nucleus suspension, then immunostained against Neun, and FACS sorted to obtain Neun negative nuclei. Immediately proceeded to 10x chromium protocol, barcoding and cDNA preparation. cDNA stored at -30C until all samples collected. Libraries prepared from all samples at the same time.
10X chromium kit following manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
from single nucleus barcode
|
| Data processing |
BCL files from sequencer were demultiplexed by cellranger "mkfastq" function (v3.1.0)
Resulting FASTQ files were mapped by cellranger "count" function to mouse mm10 genome with gene annotations that came with cellranger to get the BAM file.
Genome_build: mm10
|
| |
|
| Submission date |
Dec 23, 2020 |
| Last update date |
Oct 07, 2021 |
| Contact name |
Nicola Allen |
| Organization name |
Salk Institute
|
| Street address |
10010 North Torrey Pines Rd
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE163775 |
Activity-dependent modulation of synapse-regulating genes in astrocytes |
|
| Relations |
| BioSample |
SAMN17147690 |
| SRA |
SRX9724366 |
