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/ |