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| Status |
Public on Aug 19, 2022 |
| Title |
Control 5 |
| Sample type |
SRA |
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| Source name |
Lumber spine
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Intervertebral disc
strain: Sprague-Dawley
Sex: male
age: 8 weeks old
treatment: Uninjured
timepoint: 8 weeks
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| Treatment protocol |
Rats (n=8, male Sprague-Dawley, 8 weeks) underwent surgery for retroperitoneal exposure of the L4-L6 -lumbar spine. The L4-5 and L5-6 IVDs each received a single stab injury via a 27G needle and allowed to recover postoperatively for either 2 (n=4) or 8 weeks (n=4)
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| Growth protocol |
n/a
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| Extracted molecule |
total RNA |
| Extraction protocol |
Intervertebrals discs (IVDs) were harvested and tissue was isolated at room temperature; tissue was then immediately transferred into the digestion medium 0.3% pronase and 0.2% Typle 2 collagenase (< 4h total) to obtain IVD cells at 37 degrees Celsius. Once the IVDs were digested into a single cell suspension, the cells were immediately put on ice and expedited to the Genome Technology and Access Center at Washington University in St. Louis.
The input samples were submitted to the Washington University Genome Technology Access Center to obtain and sequence the cDNA libraries (10XGenomics, 3’v3.1; Illumina NovaSeq S4) according to established protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
fastq files were coverted to filtered.feature.bc.matrix.h5 files for each sample by the Washington University Genome Technology Access Center
.h5 files were read into Partek Flow software for analysis
For CON and Stab samples, only cells with <10% mitochondrial features, gene counts of 500-3000 and UMI (unique molecular identifier) counts between 500-30,000 were determined to be of sufficient quality to include in the analyses (Partek FlowTM, Partek Inc).
Under these selection criteria, the total number of cells from rat samples was 42,560 and 51,365 for CON and LDP at 2 weeks post-surgery, 27,064 and 28,293 for CON and LDP at 8 weeks post-surgery, respectively.
In order to identify resident cell populations, we first performed Principal Com-ponents Analysis (PCA) on pooled data from n=4 CON samples at 2 weeks, and then again for the 8 weeks samples.
The percentage of cells mapped to each cluster was evaluated for each tissue sample at both 2 and 8 weeks post-surgery as a test of inter-subject variability and appropriate-ness of the clustering scheme.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include count values for each gene sorted by cluster for each sample
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| Submission date |
Aug 16, 2022 |
| Last update date |
Aug 19, 2022 |
| Contact name |
Sade Williams Clayton |
| E-mail(s) |
sade@wustl.edu
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| Organization name |
Washington University in St. Louis
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| Department |
Biomedical Engineering
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| Street address |
1 Brookings Dr
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63130 |
| Country |
USA |
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| Platform ID |
GPL25947 |
| Series (1) |
| GSE211407 |
Single Cell RNA-Sequence Analyses Reveal Uniquely Expressed Genes and Heterogeneous Immune Cell Involvement in the Rat Model of Intervertebral Disc Degeneration |
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| Relations |
| BioSample |
SAMN30351844 |
| SRA |
SRX17109168 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6469634_C5.txt.gz |
22.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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