|
| Status |
Public on Jan 18, 2018 |
| Title |
c57_drg_3_day_3 |
| Sample type |
SRA |
| |
|
| Source name |
c57 drg 3 day 3
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: dorsal root ganglion
timepoint (days post sni): 3d
developmental stage: adult
gender: male
|
| Treatment protocol |
Mice were anesthetized with isoflurane (2–4%) and SNI surgery performed; the tibial and common peroneal branches of the sciatic nerve were tightly ligated with a silk suture and transected distally while the sural nerve was left intact (10924808, 16542774).
|
| Growth protocol |
Experiments were performed in adult (9-10 weeks old) male C57BL/6J mice (Jackson laboratory, Maine, USA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Nugen Ovation RNA Ultra Low Input (500 pg) +TruSeq Nano
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
c57 drg 3 day replicate 3
|
| Data processing |
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq and using mm10 RefSeq as reference
Normalization (TMM), quantitation (FPKM) and differential expression analysis using edgeR and limma voom.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values
|
| |
|
| Submission date |
Aug 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Giovanni Coppola |
| E-mail(s) |
gcoppola@ucla.edu
|
| Phone |
310-794-4172
|
| Organization name |
UCLA
|
| Department |
Psychiatry and Neurology
|
| Lab |
Neurogenetics
|
| Street address |
1524 Gonda, 695 Charles Young Drive South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE102721 |
Mechanistic differences in neuropathic pain modalities revealed by correlating behavior with global expression profiling (RNA-Seq) |
| GSE102937 |
Mechanistic differences in neuropathic pain modalities revealed by correlating behavior with global expression profiling |
|
| Relations |
| BioSample |
SAMN07511344 |
| SRA |
SRX3097588 |
