REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit Antibody against GAPDH	Sigma	Cat# G9545; RRID: AB_796208
Rabbit Antibody against lamin B1	Life Technologies	Cat# PA5-19468; RRID: AB_10985414
Rabbit Antibody against PDI	Cell Signaling Technology	Cat# mAb3501; RRID: AB
Rabbit Antibody against REDD1/DDIT4	Novus Biologicals	Cat# NBP1-77321SS; RRID: AB_11036185
Rabbit Antibody against Phospho-eIF2 alpha	Sigma	Cat# SAB4504388
Rabbit Antibody against 4EBP1	Bethyl Laboratories	Cat# A300-501; RRID: AB_2277825
Rabbit Antibody against HIF-1	Abcam	Cat# Ab51608; RRID: AB_880418
Mouse mAb against S6 Ribosomal Protein	Cell Signaling Technology	Cat# 2317; RRID: AB_2238583
Rabbit Antibody against Phospho-S6 Ribosomal Protein (Ser235/236)	Cell Signaling Technology	Cat# 4858S; RRID: AB_916156
Rabbit Antibody against Actin	Sigma	Cat# A2066; RRIB: AB_476693
Rabbit Antibody against Na/K ATPase	Santa Cruz	Cat# SC58626; RRIB: AB_781529
DIG specific FAB fragments (Fluorescein)	Roche	Cat# 11207741910; RRID: AB_514498
Goat anti-rabbit antibody (HRP)	Dako	Cat# P0448; RRID: AB_2617138
Goat anti-Rabbit IgG H&L (IRDye® 800CW) preadsorbed	Abcam	Cat# Ab216773
Goat anti mouse	Dako	Cat# P0447; RIID: AB_2617137
Digoxigenin Antibody (9H27L19)	Thermo Fisher	Cat# 700772; RIID: AB_1024571
Biological Samples
T cells, peripheral blood	healthy volunteers	N/A
Chemicals, Peptides, and Recombinant Proteins
Recombinant IFNα	Thermo Fisher	Cat# PHC4014
Recombinant TNFα	Thermo Fisher	Cat# PHC3015
Actinomycin D	Sigma	Cat# A1410
Ficoll-Hypaque Plus	GE Healthcare	Cat# GE17-1440-02
Imidazolo-oxindole PKR inhibitor C16	Sigma	Cat# I9785
Desferrioxamine	Sigma	Cat# D9533
EIF2AK4 (ID 440275) Trilencer-27 Human siRNA	Origene	Cat# SR318498
GSK2606414	Merck	Cat# 516535
ER Tracker™ Red	Thermo Fisher	Cat# E34250
deionized Formamide	Sigma	Cat# F9037
Dextran	Sigma	Cat# D8906
Hering Sperm DNA	Invitrogen	Cat#15634017
ProLong Gold Antifade Mountant with DAPI	Molecular Probes	Cat# P36931
Nuclei Ez Prep kit	Sigma	Cat# NUC101
TRI Reagent	Sigma	Cat# T9424
Agencurt AMPure XP beads	Beckman	Cat# A63880
Critical Commercial Assays
TACS Annexin V-FITC Apoptosis Detection Kit	R&D	Cat# 4830-250-K
Pan T cell isolation kit	Miltenyi Biotec	Cat# 130-096-535
High-Capacity cDNA Reverse Transcription Kit	Applied Bioscience	Cat# 4368814
QuantiTect SYBR Green RT-PCR Kit	QIAGEN	Cat# 204243
PureLink® miRNA Isolation Kit	Ambion	Cat# K157001
TGIRT Template-Switching RNA-seq Kit	InGex	Cat #TGIRTKit25
5′DNA Adenylation Kit	NEB	Cat# E2610S
Thermostable 5′ AppDNA/RNA Ligase	NEB	Cat# M0319S
Phusion High Fidality PCR Master Mix	Life Technologies	Cat# F-531S
NextSeq® 500/550 Mid Output Kit v2 (150 cycles)	Illumina	Cat# FC-404-2001
mTOR SAB target list H96 qPCR set	BioRad	N/A
Unfolded protein response SAB target list qPCR set	BioRad	N/A
Deposited Data
TGRIT sequencing data	BioProject NCBI	submission ID: SUB2812477, BioProject NCBI: PRJNA391929
Experimental Models: Cell Lines
Neo-NHDFs (neonatal Normal Human Dermal Fibroblasts)	Gift from Kim Midwood	N/A
HeLa	Gift from Clare Jolly	N/A
Oligonucleotides
Please see Table S7
Software and Algorithms
cutadapt v1.11	https://cutadapt.readthedocs.io/	Martin, 2011
hisat2 v2.0.4	https://ccb.jhu.edu/software/hisat2/index.shtml	Kim et al., 2015
R	https://www.r-project.org/	R Development Core Team, 2011
DESeq2	https://bioconductor.org/packages/release/bioc/html/DESeq2.html	Love et al., 2014
gplots package	https://cran.r-project.org/web/packages/gplots/gplots.pdf	N/A
R library ggplots2	https://cran.r-project.org/web/packages/ggplot2/index.html	N/A
GraphPad Prism 7.01	https://www.graphpad.com/scientific-software/prism/	N/A
ImageJ 1.49	https://imagej.nih.gov/ij/	N/A
Other
GtRNAdb 2.0	http://gtrnadb.ucsc.edu/	Lowe and Chan 2016
Ensembl ncRNA compilation (GRCh37/75)	http://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/	N/A