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| Status |
Public on Oct 29, 2022 |
| Title |
TDNV_4W_H_i |
| Sample type |
SRA |
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| Source name |
DRG
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| Organism |
Mus musculus |
| Characteristics |
tissue: DRG
cell line: primary
cell type: Nociceptors
time: 4 week
Sex: M
treatment: Ipsilateral
batch: 1
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| Treatment protocol |
spared nerve injury (SNI) at 3 days (3D) or 4 weeks (4W). Ipsilateral lumbar DRG (L3-L5) were compared to their contralateral counterparts in paired samples.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cold saline perfusion, lumbar DRG dissection and dissociation, FACS into lysis buffer (NEBnext)
NEB/SMARTER
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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 |
Reads were mapped to the GRCm38 (mm10) Mouse Genome using STAR alignment (Dobin et al 2013). Samtools was used to sort, index, and merge BAM files (Li et al 2009). Quality control (QC) was performed with both FastQC and Samtools prior to gene counting with HTSeq (Andrews 2010, Li et al 2009, Anders et al 2015).
Counts were corrected for effective library size in R using DESeq2 (Love et al 2014). Normalized gene counts were fitted to a negative binomial distribution. A batch effect was introduced during sample collection, and a model that included this batch effect was fitted to every gene. The significance of the model's coefficients was assessed using the Wald test.
Assembly: GRCm38 (mm10)
Supplementary files format and content: csv files contained count data (toc) from samples that pass quality control along with column data (colData), for use with DESeq2
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| Submission date |
Oct 24, 2022 |
| Last update date |
Oct 29, 2022 |
| Contact name |
Allison M Barry |
| E-mail(s) |
allimariebarry@gmail.com
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| Organization name |
University of Oxford
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| Department |
Nuffield Department of Clinical Neurosciences
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| Street address |
John Radcliffe Hospital, Headley Way
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| City |
Oxford |
| ZIP/Postal code |
OX39DU |
| Country |
United Kingdom |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE216444 |
Deep RNA-seq of male and female murine sensory neuron subtypes after nerve injury |
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| Relations |
| BioSample |
SAMN31431000 |
| SRA |
SRX18007885 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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