| Antibodies |
| Rabbit polyclonal anti-Iba1 |
Wako |
Cat#019–19741; lot# WDK2121; RRID:AB_2665520 |
| Mouse monoclonal anti-β-Amyloid (6E10) |
Covance |
Cat#SIG-39320; lot#D14FF01323 |
| anti-rabbit Alexa 488 |
Thermo Fisher Scientific |
Cat#A-11008; RRID:AB_143165 |
| anti-mouse Alexa 594 |
Thermo Fisher Scientific |
Cat#A-11005; RRID:AB_2534073 |
| Biological Samples |
|
|
| Deposited Data |
| Preclinical AD gene expression microarrays |
Liang et al., 2010 |
GSE9770 |
| Control gene expression microarrays |
Liang et al., 2007 |
GSE5281 |
| Viral nucleotide sequences and genomic feature annotations |
Brister et al., 2015 |
https://www.ncbi.nlm.nih.gov/genome/viruses/ |
| GRCh37 ensembl reference sequences and gene annotations |
Kersey et al., 2016 |
https://uswest.ensembl.org/info/data/ftp/index.html |
| MSBB RNA-sequences |
https://www.synapse.org/#!Synapse:syn3159438 |
syn3157743 |
| MAYO TCX RNA-sequences |
Allen et al., 2016 |
syn8612203 |
| ROSMAP RNA-sequences |
Bennett et al., 2012a, Bennett et al., 2012b
|
syn8612097 |
| MSBB Whole exome sequences |
https://www.synapse.org/#!Synapse:syn3159438 |
syn4645334 |
| MSBB Proteomics |
https://www.synapse.org/#!Synapse:syn3159438 |
syn5759470 |
| IGAP Alzheimer’s disease GWAS summary statistics |
Lambert et al., 2013 |
http://web.pasteur-lille.fr/en/recherche/u744/igap/igap_download.php |
| Brain single cell RNA-sequencing data |
Darmanis et al., 2015 |
GSE67835 |
| 1000 Genomes Phase 3 reference genotypes |
1000 Genomes Phase 3 reference genotypes |
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/ |
| UCSC hg19 “Known genes” table |
Lander et al., 2001 |
http://hgdownload.cse.ucsc.edu/goldenPath/hg19 |
| Experimental Models: Organisms/Strains |
| Mouse: B6.Cg-Mir155tm1Rsky/J |
The Jackson Laboratory |
Cat#: 007745; RRID:IMSR_JAX:007745 |
| Mouse: B6.Cg-Tg(APPswe,PSEN1dE9)85Dbo/Mmjax |
The Jackson Laboratory |
Cat#: 34832-JAX; RRID:MMRRC_034832-JAX |
| Mouse: C57BL/6J |
The Jackson Laboratory |
Cat #000664
RRID:IMSR_JAX:000664 |
| Software and Algorithms |
| MatInspector |
Cartharius et al., 2005 |
https://www.genomatix.de/online_help/help_matinspector/matinspector_help.html |
| R |
R Core Team et al., 2013 |
https://cran.r-project.org |
| Viromescan |
Rampelli et al., 2016 |
https://sourceforge.net/projects/viromescan/ |
| Bowtie2 |
Langmead et al., 2012 |
http://bowtie-bio.sourceforge.net/bowtie2 |
| STAR-RNAseq (2.4.0g1) read aligner |
Dobin et al., 2013 |
https://github.com/alexdobin/STAR |
| CIT |
Millstein et al., 2009 |
https://cran.r-project.org/package=cit |
| VEGAS |
Liu et al., 2010, Mishra et al., 2015
|
https://bioconductor.org/packages/cpvSNP/ |
| CIBERSORT |
Newman et al., 2015 |
https://cibersort.stanford.edu/ |
| miRTarBase |
Hsu et al., 2011 |
http://mirtarbase.mbc.nctu.edu.tw/php/download.php |
| SKAT |
Lee et al., 2012, Wu et al., 2016
|
https://cran.r-project.org/package=SKAT |
| Limma |
Law et al., 2014, Ritchie et al., 2015
|
https://bioconductor.org/packages/limma/ |
| MatrixEQTL |
Shabalin, 2012 |
https://cran.r-project.org/package=MatrixEQTL |
| Subread |
Liao et al., 2013, Liao et al., 2014
|
https://sourceforge.net/projects/subread/ |
| Jellyfish |
Marcais et al., 2011 |
http://www.genome.umd.edu/jellyfish.html |
| BMtagger |
Rotmistrovsky et al., 2011 |
https://sourceforge.net/projects/viromescan/ |
| Samtools |
Li et al., 2009b |
https://github.com/samtools/samtools/releases/download/ |
| BLAST |
Altschul et al., 1990 |
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ |
| edgeR |
Robinson et al., 2010 |
https://bioconductor.org/packages/edgeR/ |
| IMPUTE2 |
Howie et al., 2009, Howie et al., 2011
|
https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download |
| Other |
