KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Chicken anti-GFP (1:1000) | Aves | GFP-1020; RRID: AB_10000240 |
| Mouse anti-puromycin (1:1000) | Kerafast | 3RH1; RRID: AB_2620162 |
| Goat anti-Chicken, Alexa Fluor 488 (1:400) | Invitrogen | A-11039; RRID:AB_142924 |
| Donkey anti-Mouse, Alexa Fluor 647 (1:400) | Invitrogen | A-31571; RRID: AB_162542 |
| Rat anti-mouse CD45 | BD Biosciences | 550539; RRID: AB_2174426 |
| Anti-integrin beta 5 monoclonal antibody | eBioscience | 14-0497-82; RRID: AB_467288 |
| Rabbit anti-GFAP (1:1500) | Dako | Z0334; RRID: AB_10013382 |
| Chemicals, peptides, and recombinant proteins | ||
| Pentylenetetrazol (PTZ) | Sigma Aldrich | P6500 |
| Ampure XP beads | Beckman Coulter | #A63881 |
| Recombinant human/murine/rat BDNF | PeproTech | #450–02 |
| Puromycin | Tocris | #40-895-0 |
| Anisomysin | Sigma Aldrich | #A9789 |
| Tissue Tek OCT | Sakura | #4583 |
| Dulbecco’s Modified Eagle’s Medium | LifeTechnologies | 11960069 |
| Neurobasal medium | LifeTechnologies | 21103049 |
| Sodium Pyruvate | LifeTechnologies | 11360070 |
| Glutamine | LifeTechnologies | 25030081 |
| N-acetyl cysteine | Sigma Aldrich | A8199 |
| HBEGF | Sigma Aldrich | E4643 |
| Tetrodotoxin | Abcam | #120055 |
| Critical commercial assays | ||
| RNA Clean and Concentrator Kit | Zymo Research | R1014 |
| NEBNext Ultra II RNA Library Prep Kit for Illumina | New England BioLabs | NEB #7770 |
| NEBNext rRNA Depletion Kit (Human/Mouse/Rat) | New England BioLabs | NEB #E6310 |
| Deposited data | ||
| Raw and analyzed data | This paper | GEO: GSE147830 |
| Code for analysis | This paper | Bitbucket: https://bitbucket.org/jdlabteam/ptz_sal/src/master/RNASeq_analysis/ (10.5281/ZENODO.7054545) |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6J | Jackson Labs | Strain No. 000664 |
| Mouse: B6.FVB-Tg(Aldh1L1-EGFP/Rpl10a)JD130Htz | Jackson Labs (Doyle et al., 2008) | Strain No. 030247 |
| Oligonucleotides | ||
| Primers for qPCR, see Table S8 | This paper | |
| Recombinant DNA | ||
| CBA-IRES-GFP | This Paper | Packaged into AAV9 by Hope Center Viral Vectors Core at Washington University |
| GFAP-LCK-CFP-MYC | Sakers et al., 2017 | Packaged into AAV9 by Hope Center Viral Vectors Core at Washington University |
| Software and algorithms | ||
| FastQC | Version 0.11.7 | |
| Trimmomatic | Bolger et al., 2014 | Version 0.38 |
| Bowtie2 | Dobin et al., 2013 | Version 2.3.5 |
| STAR | Langmead and Salzber, 2012 | Version 2.7.0d |
| Htseq-count | Version 0.9.1 | |
| edgeR | Robinson et al., 2010 | Version 3.24.3 |
| BiNGO Tool | Maere et al., 2005 | Cytoscape |
| COMPBIO | GTAC at WUSTL | https://gtac-compbio.wustl.edu/ |
| TADA algorithm | Satterstrom et al., 2018 | |
| SFARI Gene database | Abrahams et al., 2013 | |
| FreezeFrame | Actimetrics | |
| MS-DAP | Koopmans et al. under review | Version 0.2.6.3; GitHub: https://doi.org/10.5281/ZENODO.7054911 |
| SynGO | Koopmans et al., 2019 | 1.1 |
| RStudio | RStudio Team 2020 | http://www.rstudio.com/, version 1.3.1093 |
| GraphPad Prism | GraphPad Software | Version 9.1.2 www.graphpad.com |