|
| Status |
Public on Oct 04, 2019 |
| Title |
SNI_2dpi |
| Sample type |
SRA |
| |
|
| Source name |
trigeminal nuclei
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL
age: > 6 wks
genotype/variation: spared nerve injury
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trigeminal ganglia were harvested and incubated in RNAlater (ThermoFisher) at 4oC overnight. Tissues were then transferred and stored at -80oC until use. Tissues were homogenized using a glass dounce homogenizer on ice. Neuronal nuclei were isolated using rabbit anti-NeuN antibody (Abcam) followed by anti-rabbit IgG microbeads (Miltenyi Biotec) and LS column (Miltenyi Biotec).
Libraries construction were performed either with the Drop-seq protocol from the McCarroll lab (for Drop-seq runs) or with method from 10x Genomics for 10x Chromium runs.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
spared nerve injury was performed on the infraorbital nerve. Nuclei were isolated for snRNA-seq 2 days after injury.
D2-10x.csv
|
| Data processing |
bcl2fastq (v2.17) was used for basecalling
Sequence reads were processed using the Drop-seq cookbook (v 1.12) from the McCarroll lab (http://mccarrolllab.com/dropseq/) for Drop-seq libraries. Sequence reads from 10x libraries were processed using Cell Ranger 2.1.0 from 10x Genomics (https://www.10xgenomics.com/)
Reads were aligned using STAR (v 2.5.3a) to a pre-mRNA mm10 genome.
Seurat package (v2 and v3) was used for downstream data analysis in R as described by the Satija lab (http://satijalab.org/seurat/)
Genome_build: mm10
Supplementary_files_format_and_content: csv files with cell barcodes and corresponding gene expression counts; only nuclei meeting minimum threshold of transcripts are included for analysis
|
| |
|
| Submission date |
May 15, 2019 |
| Last update date |
Oct 04, 2019 |
| Contact name |
Minh Q Nguyen |
| Organization name |
NIDCR/NIH
|
| Street address |
9000, Rockville Pike
|
| City |
Bethesda |
| State/province |
MARYLAND |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE131272 |
Stereotyped transcriptomic transformation of somatosensory neurons in response to injury |
|
| Relations |
| BioSample |
SAMN11654450 |
| SRA |
SRX5836840 |
