| Chemicals, peptides, and recombinant proteins |
|
| Continuous single culture media |
IrvineScientific |
90164 |
| Human Serum Albumin (HSA) solution |
IrvineScientific |
9988 |
| Agencourt Ampure XP Beads |
Beckman Coulter |
A63880 |
| Nextera XT Index Kit (24 indexes, 96 samples) |
Illumina |
FC-131-1001 |
|
| Critical commercial assays |
|
| Human Chorionic Gonadotropin (hCG) assay |
Roche Diagnostics International |
21198-7 |
| SMART-Seq v4 Ultra Low Input RNA assay |
Takara-Clontech |
634890 |
| Qubit dsDNA high sensitivity fluorometric assay |
Thermo Fisher Scientific |
Q32851 |
| Nextera XT DNA library preparation assay |
Illumina |
FC-131-1024 |
| Bioanalyzer High Sensitivity DNA assay |
Agilent |
5067-4626 |
| SYBR Green MasterMix |
Thermo Fisher Scientific |
13256519 |
|
| Deposited data |
|
| Raw and process data |
This paper |
GEO: GSE133592
|
|
| Oligonucleotides |
|
| Primers for RT-qPCR, see Table S10
|
This paper |
N/A |
|
| Software and algorithms |
|
| FastQC |
Andrews, 2010 |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| Trim galore |
Krueger, 2015 |
https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| HISAT2 |
Pertea et al., 2016 |
http://daehwankimlab.github.io/hisat2/ |
| Samtools |
Li et al., 2009 |
http://samtools.sourceforge.net/ |
| Picard tools |
Broad Institute, 2010 |
ttp://broadinstitute.github.io/picard |
| StringTie |
Pertea et al., 2015 |
https://ccb.jhu.edu/software/stringtie/ |
| Python script to extract read counts from the HISAT2/StringTie outputs in a format suitable as input for the Bioconductor R package edgeR |
Pertea et al., 2015 |
https://ccb.jhu.edu/software/stringtie/dl/prepDE.py |
| edgeR |
(Robinson and Oshlack, 2010
|
https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| featureCounts |
Liao et al., 2013 |
https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts |
| Clustvis |
Metsalu and Vilo, 2015 |
https://biit.cs.ut.ee/clustvis/ |
| Plotly |
Plotly Technologies Inc |
https://plotly.com/ |
| heatmap.plus |
Day, 2012 |
https://www.rdocumentation.org/packages/heatmap.plus/versions/1.3/topics/heatmap.plus.package |
| DaMiRseq |
Chiesa et al., 2018 |
https://bioconductor.org/packages/release/bioc/html/DaMiRseq.html |
| ggplot2 |
Wickham, 2016 |
https://ggplot2.tidyverse.org/ |
| Pheatmap |
Kolde and Kolde, 2019 |
https://www.rdocumentation.org/packages/pheatmap/versions/1.0.12/topics/pheatmap |
| Cytoscape GeneMANIA |
Mostafavi et al., 2008, Warde-Farley et al., 2010
|
http://apps.cytoscape.org/apps/genemania |
| DAVID |
Huang et al., 2009a, Huang et al., 2009b
|
https://david.ncifcrf.gov/ |
| STRING |
Jensen et al., 2009 |
https://string-db.org/ |
| RnaSeqSampleSize |
Zhao et al., 2018 |
http://bioconductor.org/packages/release/bioc/html/RnaSeqSampleSize.html |
| eSNP karyotyping protocol |
Weissbein et al., 2016, Ntostis et al., 2019
|
https://github.com/daveiles/human_TEbiopsy_eSNPanalysis |
| GATK |
McKenna et al., 2010 |
https://gatk.broadinstitute.org/hc/en-us |
