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. 2020 Aug 4;32(5):107980. doi: 10.1016/j.celrep.2020.107980
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

Phospho-mTOR (Ser2448) (D9C2) XP® Rabbit mAb Cell Signaling Technology CAT: #5536; RRID: AB_10691552
Phospho-p70 S6 Kinase (Thr389) (108D2) Rabbit mAb Cell Signaling Technology CAT: #9234; RRID: AB_2269803
Phospho-eEF2 (Thr56) Antibody Cell Signaling Technology CAT: #2331; RRID:AB_10015204
Phospho-4E-BP1 (Thr37/46) (236B4) Rabbit mAb Cell Signaling Technology CAT: #2855; RRID:AB_10695878
Anti-Puromycin Antibody, clone 12D10 Merck Millipore CAT: MABE343; RRID:AB_2566826

Biological Samples

Human Muscle Present article NA
Human Muscle Morton et al., 2016; Mitchell et al., 2014; Phillips et al., 2017 NA

Chemicals, Peptides, and Recombinant Proteins

Deuterium oxide (D, 70%) Cambridge Isotope Laboratories, Inc. DLM-4-70-PK; CAS#7732-18-5
Dowex – 50WX8 – Hydrogen Form Sigma Aldrich AC335335000
PhosStop Phosphatase Inhibitor Roche 04906837001
cOmplete Mini EDTA-free Protease Inhibitor Cocktail Roche 11836170001
TRIzol Reagent ThermoFisher Scientific CAT: 15596018
CD56 Microbeads, human Miltenyi Biotec CAT: 130-097-042
Lipofectamine RNAiMAX Transfection Reagent ThermoFisher Scientific CAT: 13778030
LONG® R3 IGF-I human Sigma-Aldrich CAT: I1271
Puromycin dihydrochloride Sigma-Aldrich CAT: P8833
SYBR Select Master Mix Applied Biosystems CAT: 4472920

Critical Commercial Assays

E.Z.N.A Total RNA Isolation Kit Omega Bio-Tek SKU: R6834-01
GeneChip WT Plus Reagent Kit ThermoFisher Scientific CAT: 902280
High-Capacity cDNA Reverse Transcription Kit Applied Biosystems CAT: 4368813

Deposited Data

Raw and analyzed data This study GEO: GSE154846

Oligonucleotides

esiRNA human BCAT2 (esiRNA1) Sigma-Aldrich CAT: EHU032991
esiRNA human NID2 (esiRNA1) Sigma-Aldrich CAT: EHU083781
esiRNA human FKBP1A (esiRNA1) Sigma-Aldrich CAT: EHU106961
esiRNA human MBNL1 (esiRNA1) Sigma-Aldrich CAT: EHU086561
Primer: BCAT2 Forward: GAGCTGAAGGAGATCCAGTACG Sigma-Aldrich N/A
Primer: BCAT2 Reverse: GAGTCATTGGTAGGGAGGCG Sigma-Aldrich N/A
Primer: NID2 Forward: TGGAAGCTACAGGTGTGAGTG Sigma-Aldrich N/A
Primer: NID2 Reverse: AGGTGGGGTGATCAAGATGCAA Sigma-Aldrich N/A
Primer: MBNL1 Forward: CTGCCCAATACCAGGTCAAC Sigma-Aldrich N/A
Primer: MBNL1 Reverse: GGGGAAGTACAGCTTGAGGA Sigma-Aldrich N/A
Primer: FKBP1A Forward: GGTGGAAACCATCTCCCCAG Sigma-Aldrich N/A
Primer: FKBP1A Reverse: TCAAGCATCCCGGTGTAGTG Sigma-Aldrich N/A

Software and Algorithms

ImageJ Schneider et al., 2012 https://imagej.nih.gov
Bowtie Alignment Tool Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/index.shtml
Significance Analysis of Microarrays (SAM) implemented in the R programming environment (SAMR) Tusher et al., 2001 https://cran.r-project.org/web/packages/samr/index.html
aroma.affymetrix Bengtsson et al., 2008 https://cran.rstudio.com/web/packages/aroma.affymetrix/index.html
MEGENA Song and Zhang, 2015 https://rdrr.io/cran/MEGENA/
Bioconductor Gentleman et al., 2004 https://www.bioconductor.org/
CMap-L1000v1 database Subramanian et al., 2017 https://clue.io/
Custom CDF protocol Timmons et al., 2018 https://www.augurprecisionmedicine.com
Ciiider Gearing et al., 2019 www.ciiider.org

Other

GeneChip Human Transcriptome Array 2.0 and RT labeling kits ThermoFisher Scientific CAT: 902162
Raw and analyzed data Timmons et al., 2018, 2019 GEO: GSE154846
Human reference genome NCBI build 38, GRCh38_82p3 Genome Reference Consortium https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/