KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Serpina3n | R&D systems | Cat# AF4709 |
| α-tubulin | Sigma | Cat# T9026 |
| β-actin | Cell Signaling Technology | Cat# 4967L |
| CD68 | Abcam | Cat# ab125212 |
| IBA1 | WAKO | Cat# 019–19741 |
| Chemicals | ||
| Trizol | Trizol | Trizol |
| RNeasy Mini Kit | RNeasy Mini Kit | RNeasy Mini Kit |
| Critical Commercial Assays | ||
| AbsoluteIDQ p180 kit | Biocrates | https://www.biocrates.com/products/research-products/absoluteidq-p180-kit |
| cBot and HiSeq 3000/4000 PE Cluster Kit | Illumina | RRID: SCR_010233 |
| TruSeq RNA Sample Prep Kit v2 | Illumina | RRID: SCR_010233 |
| HiSeq 3000/4000 sequencing kit | Illumina | RRID: SCR_010233 |
| HCS v3.3.52 collection software | Illumina | RRID: SCR_010233 |
| Mouse Serpina3 ELISA kit | Cusabio | Cat# CSB-E13727m |
| RNAscope® Multiplex Fluorescent Reagent Manual Assay Kit v2 | ACD | Cat #323100 |
| Deposited Data | ||
| Raw data and analysis for brain transcriptomics | This paper | https://www.synapse.org/ Synapse ID: syn15682620 |
| Raw data and analysis for serum metabolomics | This paper | https://www.synapse.org/ Synapse ID: syn15682634 |
| Mayo Clinic human brain RNA-seq raw data | (Allen et al., 2016) | https://www.synapse.org/ Synapse ID: syn5550404 |
| ROSMAP human brain RNA-seq raw data | (Bennett et al., 2018) | https://www.synapse.org/ Synapse ID: syn3219045 |
| Human brain proteomics raw data | (Ping et al., 2018) | https://www.synapse.org/ Synapse ID: syn10183278 |
| Mouse reference genome mm10 | Genome Reference Consortium | http://useast.ensembl.org/Musmusculus/Info/Annotation |
| Experimental Models: Organisms/Strains | ||
| Mouse/apoE2-TR (B6.129P2-Apoetm1(APOE2)Mae N9) | Taconic Biosciences | RRID: IMSR_TAC:1547 |
| Mouse/apoE3-TR (B6.129P2-Apoetm2(APOE3)Mae N8) | Taconic Biosciences | RRID: IMSR_TAC:1548 |
| Mouse/apoE4-TR (B6.129P2-Apoetm3(APOE4)Mae N8) | Taconic Biosciences | RRID: IMSR_TAC:1549 |
| Oligonucleotides | ||
| Mouse Serpina3n | ACD | Cat #430191 |
| DapB | ACD | Cat #310043 |
| Ppib | ACD | Cat #313911 |
| Software and Algorithms | ||
| RTA version 2.7.3 | Illumina | RRID: SCR_010233 |
| R version 3.4.2 | R Core Team | https://www.R-project.org/ |
| MAP-RSeq version 2.1.1 | (Kalari et al., 2014) | http://bioinformaticstools.mayo.edu/research/maprseq/ |
| TopHat version 2.1.0 | (Kim et al., 2013) | https://ccb.jhu.edu/software/tophat/index.shtml |
| Bowtie version 1.1.2 | (Langmead et al., 2009) | https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.2/ |
| RSeQC version 2.6.2 | (Wang et al., 2012) | http://rseqc.sourceforge.net/ |
| featureCounts version 1.4.6-p5 | (Liao et al., 2014) | http://subread.sourceforge.net |
| CQN version 1.24.0 | (Hansen et al., 2012) | https://bioconductor.org/packages/release/bioc/vignettes/cqn/ |
| Partek Genomics Suite version 6.6 | Partek | http://www.partek.com/ |
| Ingenuity Pathway Analysis version 2019–05–15 | Qiagen | https://www.qiagenbioinformatics.com/products/ingenuitypathway-analysis |
| WGCNA version 1.61 | (Langfelder and Horvath, 2008) | https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/ |
| anRichment version 0.82–1 | (Langfelder and Horvath, 2008) | https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/GeneAnnotation/index.html |
| VisANT version 5.51 | (Hu et al., 2013) | http://visant.bu.edu/home2.htm |
| MATLAB | MathWorks | https://www.mathworks.com/products/matlab.html |
| Prism 7.0 | GraphPad Software | http://www.graphpad.com/ |
| Other | ||
| Resource website | This paper | http://www.gbulab.com/ |