|
| Chemicals, peptides, and recombinant proteins |
|
| PEBBLES PCB Mixture |
Superfund Research Center at The University of Iowa |
P42 ES013661 |
|
| Critical commercial assays |
|
| AllPrep DNA/RNA/miRNA Universal Kit |
Qiagen |
80224 |
| EZ DNA Methylation-Lightning Kit |
Zymo Research |
D5031 |
| Accel-NGS Methyl-Seq DNA Library Kit |
Swift Biosciences |
30096 |
| Methyl-Seq Combinatorial Dual Indexing Kit |
Swift Biosciences |
38096 |
| Bioanalyzer Eukaryotic Total RNA Nano Assay |
Agilent |
5067–1511 |
| KAPA mRNA HyperPrep Kit |
Roche |
08098123702 |
| NEXTFLEX Unique Dual Index Barcodes |
PerkinElmer |
NOVA-514150
NOVA-514152 |
|
| Deposited data |
|
| Raw sequencing data and processed count matrices |
This paper |
GEO: GSE180979
|
| Custom code |
This paper |
https://github.com/ben-laufer/PCB-Placenta-and-Brain
http://10.5281/zenodo.5037818
|
|
| Experimental models: Organisms/strains |
|
| Mice: C57BL/6J |
The Jackson Laboratory |
000664 |
|
| Software and algorithms |
|
| CpG_Me |
Laufer et al. (2020)
|
https://github.com/ben-laufer/CpG_Me10.5281/zenodo.5030083
|
| Trim Galore |
Babraham Bioinformatics |
https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
|
| Cutadapt |
Martin (2011)
|
https://cutadapt.readthedocs.io/en/stable/
|
| FastQ Screen |
Wingett and Andrews (2018)
|
https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
|
| Bismark |
Krueger and Andrews (2011)
|
https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
|
| Bowtie 2 |
Langmead and Salzberg (2012)
|
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
| Samtools |
Li et al. (2009)
|
http://www.htslib.org
|
| Picard |
Broad Institute |
https://broadinstitute.github.io/picard/
|
| MultiQC |
Ewels et al. (2016)
|
https://multiqc.info
|
| R |
https://www.r-project.org/
|
| DMRichR |
Laufer et al. (2020)
|
https://github.com/ben-laufer/DMRichR10.5281/zenodo.5030057
|
| Dmrseq |
Korthauer et al. (2018)
|
https://bioconductor.org/packages/release/bioc/html/dmrseq.html
|
| Bsseq |
Hansen et al. (2012)
|
https://bioconductor.org/packages/release/bioc/html/bsseq.html
|
| ComplexHeatmap |
Gu etal. (2016)
|
https://jokergoo.github.io/ComplexHeatmap-reference/book/
|
| GOfuncR |
Grote (2020); Prüfer et al. (2007)
|
https://www.bioconductor.org/packages/release/bioc/html/GOfuncR.html
|
| Rrvgo |
Sayols (2020)
|
http://bioconductor.org/packages/release/bioc/html/rrvgo.html
|
| HOMER |
Heinz et al. (2010)
|
http://homer.ucsd.edu/homer/
|
| Memes |
Bailey et al. (2009); McLeay and Bailey (2010); Nystrom (2021); Yin et al. (2017)
|
http://www.bioconductor.org/packages/release/bioc/html/memes.html
|
| ChIPseeker |
Yu et al. (2015a)
|
https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
|
| LOLA |
Sheffield and Bock (2015)
|
https://bioconductor.org/packages/release/bioc/html/LOLA.html
|
| STAR |
Dobin et al. (2013)
|
https://github.com/alexdobin/STAR
|
| edgeR |
Robinson et al. (2010)
|
https://bioconductor.org/packages/release/bioc/html/edgeR.html
|
| Limma-voom |
Law et al. (2014)
|
https://bioconductor.org/packages/release/bioc/html/limma.html
|
| variancePartition |
Hoffman and Roussos (2021)
|
https://bioconductor.org/packages/release/bioc/html/variancePartition.html
|
| regioneR |
Gel et al. (2016)
|
https://bioconductor.org/packages/release/bioc/html/regioneR.html
|
| GAT |
Heger et al. (2013)
|
https://github.com/AndreasHeger/gat
|
| ComplexUpset |
Conway et al. (2017); Krassowski (2020); Lex et al. (2014)
|
https://cran.r-project.org/web/packages/ComplexUpset/index.html
|
| enrichR |
Chen et al. (2013); Jawaid (2021); Kuleshov et al. (2016); Xie et al. (2021)
|
https://cran.r-project.org/web/packages/enrichR/index.html
|
|
| Other |
|
| TissueLyser II |
Qiagen |
85300 |
| E220 Focused-ultrasonicator |
Covaris |
500239 |
