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/ |