Chemicals, Peptides, and Recombinant Proteins |
DMEM, GlutaMAX Supplement, pyruvate |
GIBCO |
Cat#31966021 |
Dermal Cell Basal Medium |
ATCC |
Cat#ATCC PCS-200-030 |
Fetal Bovine Serum |
GE Healthcare Bio-Sciences |
Cat#SV30160.03 |
Pen/strep stock, 10,000/10,000, 100ml |
Lonza |
Cat#LO DE17-602E |
Hydrogen Peroxide Solution |
Sigma Aldrich |
Cat#216763-100ML-D |
Doxorubicin hydrochloride |
Tebu-bio |
Cat#BIA-D1202-1 |
25% Glutaraldehyde solution |
Thermo Fisher Scientific |
Cat#MERC8.20603.1000 |
16% Formaldehyde (w/v), Methanol-free |
Thermo Fisher Scientific |
Cat#28906 |
Diamidino-2-phenylindole (DAPI) |
Sigma-Aldrich |
Cat#D9542 |
Critical Commercial Assays |
Beta-Galactosidase Staining Kit |
BioVision |
Cat#K802 |
Click-iT EdU Alexa Fluor 488 Imaging kit |
Thermo Fisher Scientific |
Cat#C10337
|
Isolate II RNA Mini Kit |
Bioline |
Cat#BIO-52073 |
High-Capacity cDNA Reverse Transcription kit |
Applied Biosystems |
Cat#4368813 |
Universal Proble Library System |
Roche |
Cat#04683633001 |
SENSIFast Probe no-ROX One-step Kit |
Bioline |
Cat#BIO-76001 |
RNAeasy mini kit |
QIAGEN |
Cat#74104 |
Truseq RNA Sample Preparation kit |
Illumina |
Cat#RS-122-2001 or RS-122-2002 |
HiSeq PE Cluster Kit v4 – cBot |
Illumina |
Cat#PE-401-4001 |
HiSeq SBS Kit v4 (50 cycles) |
Illumina |
Cat#FC-401-4002 |
Deposited Data |
Self-generated RNA-seq datasets of IRIS in fibroblasts, melanocytes and keratinocytes |
ArrayExpress database |
ArrayExpress: E-MTAB-5403 |
Experimental Models: Cell Lines |
Human foreskin fibroblasts HCA2 |
O. Pereira-Smith (University of Texas Health Science Center, San Antonio) |
N/A |
Human foreskin fibroblasts BJ |
ATCC |
Cat#CRL-2522 |
Mouse Embryonic Fibroblasts (MEFs) |
Self-produced |
N/A |
Mouse primary skin microvascular endothelial cells |
Cellbiologics |
Cat#C57-6064 |
Human Epidermal Keratinocytes Neonatal Foreskin |
ATCC |
Cat#PCS-200-010 |
Human Epidermal Melanocytes Neonatal |
ATCC |
Cat#PCS-200-012 |
Oligonucleotides |
Sets of primers for qPCR |
IDT |
Table S1 |
Software and Algorithms |
SRA Toolkit 2.6.2 |
GitHub |
https://github.com/ncbi/sra-tools |
FastQC software v0.11.5 |
Babraham Institute |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
Trimmommatic 0.36 |
Usadellab |
http://www.usadellab.org/cms/?page=trimmomatic |
STAR-2.5.1b |
GitHub |
https://github.com/alexdobin/STAR/releases |
DESeq2 |
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
MetaRNaseq |
CRAN |
https://cran.r-project.org/web/packages/metaRNASeq/index.html |
Consensus Path DB-human |
Max Planck Institute |
http://cpdb.molgen.mpg.de/ |
R and associated R-packages (pheatmap, ggplot2, ggfortify, RcolorBrewer, VennDiagram) |
Bioconductor, CRAN |
https://cran.r-project.org/web/packages/ |
ImageJ |
NIH – public domain |
https://imagej.nih.gov/ij/download.html |