KEY RESOURCES TABLE
| Resource Type | Specific Reagent or Resource | Source or Reference | Identifiers | Additional Information |
|---|---|---|---|---|
| Add additional rows as needed for each resource type | Include species and sex when applicable. | Include name of manufacturer, company, repository, individual, or research lab. Include PMID or DOI for references; use “this paper” if new. | Include catalog numbers, stock numbers, database IDs or accession numbers, and/or RRIDs. RRIDs are highly encouraged; search for RRIDs at https://scicrunch.org/resources. | Include any additional information or notes if necessary. |
| Commercial Assay Or Kit | Affymetrix Rat Expression Set 230 A Microarray Chip | Affymetrix (now ThermoFisher, Waltham, MA) | ||
| Commercial Assay Or Kit | Illumina RatRef- 12v1 Beadchip | Illumina, San Diego, CA | ||
| Commercial Assay Or Kit | TRIzol reagent | Invitrogen, Calsbad, CA | Catalog #15596018 | |
| Commercial Assay Or Kit | RNeasy RNA purification columns | Qiagen (sold via ThermoFisher, Waltham, MA), Valencia, CA | ||
| Commercial Assay Or Kit | TruSeq library preparation kit | Illumina, San Diego, CA | ||
| Commercial Assay Or Kit | AllPrep DNA RNA miRNA Universal Kit 50 | Qiagen, Valencia, CA | Catalog #: 80224 | |
| Commercial Assay Or Kit | Illumina TruSeq Stranded mRNA Library Preparation kit | Illumina, San Diego, CA | Catalog #s RS-122-2101, RS-122-2102 | |
| Commercial Assay Or Kit | Kapa’s library quantification kit for Illumina Sequencing platforms | Kapa Biosystems,Wilmington MA | Catalog # KK4835 | |
| Commercial Assay Or Kit | QIAshredder kit | Qiagen, Valencia, CA | Catalog #79654 | |
| Commercial Assay Or Kit | RNeasy Mini Kit | Qiagen, Valencia, CA | Catalog #74104 | |
| Commercial Assay Or Kit | iScript cDNA Synthesis Kit | Biorad, Hercules, CA | Catalog #1708891 | |
| Commercial Assay Or Kit | iQTM SYBR® Green Supermix | Biorad, Hercules, CA | ||
| Deposited Data; Public Database | MBNI_AffymetrixRae230_F4 Dataset | Gene Expression Omnibus, ref: this paper | GSE140596 | |
| Deposited Data; Public Database | MBNI_AffymetrixRgU34A_F6 Dataset | Gene Expression Omnibus, ref: PMID: 21864320 | GSE29552 | |
| Deposited Data; Public Database | MBNI_AffymetrixRae230_F15 Dataset | Gene Expression Omnibus, ref: this paper | GSE140595 | |
| Deposited Data; Public Database | MBNI_IlluminaRatRef12v1_F15 Dataset | Gene Expression Omnibus, ref: this paper | GSE140594 | |
| Deposited Data; Public Database | MBNI_RNASeq_F29 Dataset | Gene Expression Omnibus, ref: this paper | GSE140597 | |
| Deposited Data; Public Database | Alabama_Nimblegen_F34 Dataset | Gene Expression Omnibus, ref: PMID: 25791846 | GSE88874 | |
| Deposited Data; Public Database | MBNI_RNASeq_F37 Dataset | Gene Expression Omnibus, ref: this paper | GSE140598 | |
| Deposited Data; Public Database | MBNI_RNASeq_F43 Dataset | Gene Expression Omnibus, ref: this paper | GSE140287 | |
| Deposited Data; Public Database | Flinders Sensitive Line vs. Flinders Resistant Line Affymetrix Rat Expression Set 230 Microarray Dataset | Gene Expression Omnibus, ref: PMID: 20830301 | GSE20388 | |
| Deposited Data; Public Database | bHR vs. bLR Bmp4 qPCR Dataset | FigShare, ref: this paper | https://doi.org/10.1101/774034 | |
| Deposited Data; Public Database | bHR vs. bLR Exome Sequencing Dataset | NCBI Bioproject, https://www.ncbi.nlm.nih.gov/bioproject/, ref: PMID: 31182603 | PRJNA521139 | |
| Deposited Data; Public Database | Rat Genome Database | https://rgd.mcw.edu, ref: PMID: 25355511 | accessed 08/08/2019, RRID:SCR_006444 | |
| Deposited Data; Public Database | GO2MSIG | http://www.bioinformatics.org/go2msig/, ref: PMID: 24884810 | accessed 6/2017, RRID:SCR_018359 | |
| Deposited Data; Public Database | Hipposeq | https://hipposeq.janelia.org, ref: PMID: 27113915 | accessed 05/11/2018, RRID:SCR_015730 | |
| Deposited Data; Public Database | string-db | https://string-db.org/cgi/input.pl, ref: PMID: 25352553 | accessed 04/2018, RRID:SCR_005223 | |
| Deposited Data; Public Database | Interactive web dashboard for viewing bHR vs. bLR differential expression | https://mbni.org/dashboard/huzefak/hrlrMetaAnalysis/, ref: this paper | ||
| Deposited Data; Public Database | Custom chip definition files (.cdf) | http://nmg-r.bioinformatics.nl/NuGO_R.html, http://mbni.org/customcdf/22.0.0/entrezg.download/ , ref: PMID: 16284200 | rae230arnentrezgcdf_19.0.0, rgu34arnentrezgcdr_19.0.0, rat2302rnentrezgcdf_22.0.0 | |
| Deposited Data; Public Database | R package org.Rn.eg.db | http://bioconductor.org/packages/org.Rn.eg.db/ | version 3.4.1, RRID:SCR_018358 | |
| Deposited Data; Public Database | NCBI Genome Remapping Service | https://www.ncbi.nlm.nih.gov/genome/tools/remap | accessed 8/8/2019 | |
| Deposited Data; Public Database | mousebrain.org | mousebrain.org, ref: PMID: 30096314 | accessed 04/09/2018, RRID:SCR_018356 | |
| Deposited Data; Public Database | Pubmed | https://www.ncbi.nlm.nih.gov/pubmed/ | ||
| Organism/Strain | Selectively-bred High Responder rats, species: Rattus Norvegicus, sex: male | Laboratory of Dr. Huda Akil & Dr. Stanley Watson Jr., ref: PMID: 16502134, this paper | ||
| Organism/Strain | Selectively-bred Low Responder rats, species: Rattus Norvegicus, sex: male | Laboratory of Dr. Huda Akil & Dr. Stanley Watson Jr., ref: PMID: 16502134, this paper | ||
| Sequence-Based Reagent | Custom-designed qPCR primers targeting Bmp4 (Rattus Norvegicus) | Laboratory of Dr. Huda Akil & Dr. Stanley Watson Jr., ref: this paper | ACC# NM_012827.2; forward primer: 5’-CCCTGGTCAACTCCGTTAAT-3’, start = 1214; reverse primer: 5’-AACACCACCTTGTCGTACTC-3’, start = 1319 | |
| Sequence-Based Reagent | Custom-designed qPCR primers targeting Gapdh (Rattus Norvegicus) | Laboratory of Dr. Huda Akil & Dr. Stanley Watson Jr., ref: this paper | ACC# NM_017008.4; forward primer: 5’- GTTTGTGATGGGTGTGAACC-3’, start = 459; reverse primer: 5’-TCTTCTGAGTGGCAGTGATG-3’, start = 628 | |
| Software; Algorithm | Noldus Ethovision | Noldus, Leesburg, VA | ||
| Software; Algorithm | R Studio | CRAN: The Comprehensive R Archive Network, https://cran.r-project.org | v.1.0.153 | |
| Software; Algorithm | R | CRAN: The Comprehensive R Archive Network, https://cran.r-project.org | v.3.2.2 | |
| Software; Algorithm | All code used to analyze the genomics data in this paper | Github Repository: https://github.com/isabellie4/PhenotypeProject | ||
| Software; Algorithm | All code used to analyze the genomics data in this paper | Github Repository: https://github.com/hagenaue/bHRbLR_MetaAnalysisProject | ||
| Software; Algorithm | Robust multi-array average (RMA) | ref: PMID: 12582260 | ||
| Software; Algorithm | R package affy | https://www.bioconductor.org/packages/release/bioc/html/affy.html, ref: PMID: 14960456 | version 1.54.0, RRID:SCR_012835 | |
| Software; Algorithm | R package metafor | https://cran.r-project.org/web/packages/metafor/index.html, ref: DOI: 10.18637/jss.v036.i03 | version 2.0-0, RRID:SCR_003450 | |
| Software; Algorithm | R package multtest | https://www.bioconductor.org/packages/release/bioc/html/multtest.html, ref: DOI: 10.1007/0-387-29362-0_15 | version 2.32.0, RRID:SCR_001255 | |
| Software; Algorithm | Positional Gene Enrichment (PGE) Analysis | http://silico.biotoul.fr/pge/ , ref: PMID: 18346969 | RRID:SCR_018360 | |
| Software; Algorithm | R package fgsea | https://bioconductor.org/packages/release/bioc/html/fgsea.html, ref: DOI: 10.1101/060012 | version 1.2.1 | |
| Software; Algorithm | R package BrainInABlender | https://github.com/hagenaue/BrainInABlender, ref: PMID: 30016334 | version 0.0.0.9000 | |
| Software; Algorithm | R package limma | https://bioconductor.org/packages/release/bioc/html/limma.html, ref: PMID: 25605792 | version 3.28.21, RRID:SCR_010943 | |
| Software; Algorithm | R package preprocessCore | https://www.bioconductor.org/packages/release/bioc/html/preprocessCore.html, ref: S8 | version 1.34.0 | |
| Software; Algorithm | Tophat2 | https://ccb.jhu.edu/software/tophat/index.shtml, ref: PMID: 23618408 | RRID:SCR_013035 | |
| Software; Algorithm | Bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml, ref: PMID: 22388286 | RRID:SCR_005476 | |
| Software; Algorithm | Cufflinks | http://cole-trapnell-lab.github.io/cufflinks/, ref: PMID: 22383036 | RRID:SCR_014597 | |
| Software; Algorithm | CuffDiff | http://cole-trapnell-lab.github.io/cufflinks/, ref: PMID: 22383036 | RRID:SCR_001647 | |
| Software; Algorithm | Cuffmerge | https://www.genepattern.org/modules/docs/Cuffmerge, ref: PMID: 22383036 | RRID:SCR_015688 | |
| Software; Algorithm | SubRead aligner | http://subread.sourceforge.net, ref: PMID: 23558742 | RRID:SCR_009803 | |
| Software; Algorithm | featureCounts | http://subread.sourceforge.net, ref: PMID: 24227677 | RRID:SCR_012919 | |
| Software; Algorithm | R package compute.es | https://cran.r-project.org/web/packages/compute.es/index.html | version 0.2-2 | |
| Software; Algorithm | R package GEOQuery | https://www.bioconductor.org/packages/release/bioc/html/GEOquery.html, ref: PMID: 17496320 | version 2.42.0, RRID:SCR_000146 | |
| Other | The Genomic Services Laboratory at HudsonAlpha | (now called HudsonAlpha Discovery), Huntsville, AL, https://gsl.hudsonalpha.org/index | ||
| Other | University of Michigan DNA Sequencing Core | Ann Arbor, MI, https://seqcore.brcf.med.umich.edu |