|
| Status |
Public on May 08, 2024 |
| Title |
NTG Meninges female bio rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Lyve1+ Meningeal lymphatic endothelial cells
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Chronic NTG
age: 3 months
tissue: Lyve1+ Meningeal lymphatic endothelial cells
genotype: Rpl22HA/+;Lyve1Cre
|
| Treatment protocol |
mice were treated with either 10 mg/kg NTG or vehicle every other day for 9 days, for 5 total injections. Mice were euthanized 60 minutes after the final injection.
|
| Growth protocol |
meninges dissected from 3 month old mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
whole tissue was lysed using Lysing Matrix D beads. Hemagglutinin positive Ribosomes were immunoprecipitated using anti-HA conjugated magnetic beads. RNA was extracted using Qiagen RNeasy Kit. See methods for additional information
|
| Label |
biotin
|
| Label protocol |
Total RNA (10 ng) was used to synthesize fragmented and labeled double-stranded cDNA (ds-cDNA) and hybridized onto Thermo Fisher arrays. The Thermo Fisher® GeneChip™ 3’ IVT Pico Kit Manual Workflow User Guide was followed to prepare the samples. Briefly, the GeneChip™ Pico Kit (Thermo Fisher) was used to generate ds-cDNA from total RNA. Following synthesis of ds-cDNA, the cDNA is converted to biotinylated ds-cDNA hybridization targets for unbiased coverage of the transcriptome.
|
| |
|
| Hybridization protocol |
The GeneChip™ Hybridization, Wash, and Stain Kit was used to prepare the ds-cDNA samples for hybridization. Fragmented and labeled ds-cDNA was added to a hybridization cocktail (50 ng/µl fragmented and labeled ds-cDNA final concentration, 50 pM control oligonucleotide B2, BioB, BioC, BioD and cre hybridization controls, 7 % DMSO, 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20). Thermo Fisher Clariom S Mouse arrays were hybridized for 16 hours at 45°C in the GeneChip Hybridization Oven 645 (Affymetrix). The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 450 (Affymetrix).
|
| Scan protocol |
The arrays were scanned with the GeneChip Scanner 3000 7G Plus with autoloader. GeneChip Command Console Software (AGCC) was used for washing, staining and scanning control of the instrumentation
|
| Description |
Ribosome bound mRNA from Lyve1+ Meningeal lymphatic endothelial cells from dorsal meningeal tissue from female Lvye1 Cre RiboTag mice, Treated with NTG
|
| Data processing |
Transcriptome Analysis Console Software v 4.0 was used for basic data analysis and quality control. Signal intensity was generated using SST-RMA algorithm. Biological level data analysis was performed using Partek Genome Suite software. Gene level expression were summarized from the corrected intensities and then quantile normalized prior to secondary analysis.
Quantile normalized gene level expression values from GeneBASE
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| |
|
| Submission date |
May 03, 2024 |
| Last update date |
May 08, 2024 |
| Contact name |
Nathan Nelson-Maney |
| E-mail(s) |
nathan_nelson-maney@med.unc.edu
|
| Phone |
5088689508
|
| Organization name |
UNC Chapel Hill
|
| Department |
Cell Biology and Physiology
|
| Lab |
Caron Lab
|
| Street address |
111 mason farm road
|
| City |
Chapel Hill |
| State/province |
North Carolina |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL33894 |
| Series (1) |
| GSE266558 |
Meningeal lymphatic CGRP signaling governs pain via cerebrospinal fluid efflux and neuroinflammation in migraine models |
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