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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 01, 2017 |
| Title |
Casnaive-162 |
| Sample type |
SRA |
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| Source name |
CAST/Ei_DRG_Naive
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| Organism |
Mus musculus |
| Characteristics |
strain: CAST/Ei
tissue: dorsal root ganglia
treatment: none (naive)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
After dissection, the naïve or IVA DRG neurons were filtered through a 35um mesh and resuspended in 2ml of complete media before being layered on a Percoll solution (density of 1.040) as described in (Delree et al., 1989) to remove myelin debris. The lower 5ml fraction was washed in PBS and the pellet was resuspended in C1 cell wash buffer. Cells were counted and resuspended at a concentration of 310 cells per ul, stained for viability on ice for 30 minutes and then captured by the C1 from Fluidigm using the large chip. Cells were imaged at 4X magnification. Cell lysis, reverse transcription and pre-amplification were performed on the C1 as described by the manufacturer.
cDNA was diluted and library prepared for Illumina sequencing using the Nextera kit and according to the Fluidigm protocol. Libraries were sequenced on a NextSeq 500 using a high-output 150 cycles chip. Up to 192 cells were sequenced at once and cells from all conditions were combined on each sequencing run.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were mapped to the mm10 mouse genome using Bowtie2.
Duplicate reads removed using samtools.
Reads were summarized on a gene annotation using RsubReads.
Genome_build: mm10
Supplementary_files_format_and_content: matrix of counts for each cell (as column) and each gene (as row)
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| Submission date |
May 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kenneth S. Kosik |
| Organization name |
UCSB
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| Department |
NRI
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| Lab |
Kosik
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| Street address |
UC Santa Barbara
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| City |
Santa Barbara |
| State/province |
California |
| ZIP/Postal code |
93106 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE98415 |
Single cell sequencing of primary dorsal root ganglia from CAST/Ei or C57BL/6 mouse highlights strain differences in cellular populations. |
| GSE98417 |
Enhanced neuronal regeneration in the CAST/Ei mouse strain is linked to expression of differentiation markers after injury |
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| Relations |
| BioSample |
SAMN06858441 |
| SRA |
SRX2774336 |
| 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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