|
| Status |
Public on Jan 03, 2022 |
| Title |
CCI 2dpi 1 |
| Sample type |
SRA |
| |
|
| Source name |
Lumbar spinal cord microglia
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lumbar spinal cord microglia
strain: C57BL/6J
condition: CCI
timepoint or dose: 2dpi
|
| Treatment protocol |
Mice received one of 2 chronic morphine dosing strategies (fixed or escalating) or one of three peripheral nerve injuries - sciatic nerve transection (SNT), chronic constriction injury (CCI), or spared nerve injury (SNI). Controls received saline or no treatment/injury
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were perfused with ice cold PBS, caudal lumbar cord was dissection and manually dissociated then subjected to MACS myelin removal and CD11b selection. Total RNA was extracted from CD11b-positive cells using the RNeasy Micro Kit
Libraries were prepared using Smart-Seq2 and modified for sequencing using the Nextera XT DNA Sample Preparation Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped to the UCSC mouse reference genome mm10 via the Galaxy platform (http://usegalaxy.org) using HISAT2 version 2.0.5.1.
FPKM (fragments per kilobase of transcript sequence per million mapped fragments) values were obtained using Cufflinks version 2.2.1.
Reads were quantified using featureCounts version 1.4.6.p5
Differential expression analysis was conducted in R with DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including FPKM for all samples
Supplementary_files_format_and_content: excel spreadsheet with Deseq2 output for all groups
|
| |
|
| Submission date |
Jul 18, 2018 |
| Last update date |
Jan 03, 2022 |
| Contact name |
Gregory Scherrer |
| E-mail(s) |
gs25@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Anesthesiology
|
| Street address |
1050 Arastradero Rd
|
| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE117320 |
Distinct microglial transcriptional responses during opioid exposure or neuropathic pain [mouse] |
| GSE117321 |
Distinct microglial transcriptional responses during opioid exposure or neuropathic pain |
|
| Relations |
| BioSample |
SAMN09689844 |
| SRA |
SRX4404691 |
