 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 23, 2021 |
| Title |
human SOD1(G93A) (mutant) 1 |
| Sample type |
SRA |
| |
|
| Source name |
Brainstem
|
| Organism |
Mus musculus |
| Characteristics |
strain: 002726 B6SJL-Tg
tissue: brainstem
genotype: SOD1(G93A)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each tissue was finely dissected and incubated in Hibernate A without calcium (BrainBits, Springfield, IL, USA) supplemented with 12 mg papain (Worthington, Lakewood, NJ, USA). This solution is then transferred to a shaker-incubator (set to 30 °C and 60 rpm) for 30 min. After 30 min, using a Pasteur pipette, the solution is triturated three times to release cells from the tissue remnants, and transferred to a new collection tube. The media containing the cells is then gently added to the OptiPrep density gradient (Sigma Aldrich, St. Louis, MO, USA) and centrifuged at 800 g for 15 min at 22 °C. The layers consisting of cells were collected, and this solution was passed through a 40-μm strainer (Fisher Scientific, Hampton, NH, USA). The cells were counted and suspended at a concentration of 100 cells/μl in 0.01% BSA-PBS.
Drop-Seq Laboratory Protocol version 3.1
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads corresponding to low quality barcodes with quality score less than 10 was removed using DropSeq Tools version 1.12. Next, any occurrence of the SMART adapter sequence or polyA tails found in the reads was trimmed
Cleaned reads were converted back to fastq format and were aligned to the mouse reference genome mm10 using STAR-2.5.0c
A percentage of the Chemgenes barcoded beads which contain the UMIs and cell barcodes were anticipated to have synthesis errors, which were assessed using the function DetectBeadSynthesisErrors in DropSeq Tools.
A digital gene expression matrix for each sample was generated using DropEst (Petukhov et al., 2018), where each row is the read count of a gene and each column is a unique single cell.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jun 22, 2021 |
| Last update date |
Jun 24, 2021 |
| Contact name |
Xia Yang |
| E-mail(s) |
xyang123@ucla.edu
|
| Organization name |
University of California, Los Angeles
|
| Department |
Integrative Biology and Physiology
|
| Lab |
2000ABC Terasaki Life Sciences Bld
|
| Street address |
610 Charles E. Young Drive East
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE178693 |
Single-cell RNA-seq analysis of the brainstem of mutant SOD1 mice reveals perturbed cell types and pathways of amyotrophic lateral sclerosis |
|
| Relations |
| BioSample |
SAMN19814251 |
| SRA |
SRX11199714 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5396157_Mutant1.tar.gz |
3.3 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
