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. Author manuscript; available in PMC: 2020 Jan 15.
Published in final edited form as: Cell Rep. 2019 Dec 10;29(11):3751–3765.e5. doi: 10.1016/j.celrep.2019.11.026

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Biological Samples
Human whole heart tissue lysate Novus Biologicals NB820–59217
Chemicals, Peptides, and Recombinant Proteins
Synthetic Peptides LAPITSDPTEATAVGAVEASFK[13C(6)15N(2)] Thermo Fisher Scientific Standard Peptides https://www.thermofisher.com/us/en/home/life-science/protein-biology/peptides-proteins/custom-peptide-synthesis-services.html
CLAAALIVLTESGR[13C(6)15N(4)]
AAIAPPSPPCDITCLESFR[13C(6)15N(4)]
APHVEFLRPLTDLQVR[13C(6)15N(4)]
QCQGQAAQEAAGGGR[13C(6)15N(4)]
DSGLVGLAVCNTPHER[13C(6)15N(4)]
VGPVSAVGVTAPGK[13C(6)15N(2)]
DSEGDTPSLINWPSSK[13C(6)15N(2)]
LLGADSATVFNIQEPEEETANQIYWFK
VLDIANVLFHLEQVEHPQR[13C(6)15N(4)]
YSTGSDSASFPHTTPSMCLNPDLEGPPLELTK[13C(6)15N(2)]
AITQLLCETEGR[13C(6)15N(4)]
RTDSHEDTGILDFSSLLK[13C(6)15N(2)]
ANLSSSTGNVEDSFEGFR[13C(6)15N(4)
Deposited Data
Quantitative shotgun proteomics data on human iPSC-cardiomyocyte differentiation This Study ProteomeXchange PXD013426
Targeted mass spectrometry data on isoform peptide verification This Study ProteomeXchange PXD015544
RNA sequencing data on human iPSC-cardiomyocyte differentiation This Study NCBI GEO GSE137920
Experimental Models: Cell Lines
Human induced pluripotent stem cells Stanford Cardiovascular Institute Biobank (Burridge et al., 2014; Lee et al., 2019; Kitani et al., 2019). N/A
Software and Algorithms
GRCh38.89 Ensembl http://www.ensembl.org/
STAR v.2.5.0a Ballouz et al., 2018 https://github.com/alexdobin/STAR
rMATS-Turbo v.0.1 Shen et al., 2014 rnaseq-mats.sourceforge.net
limma v.3.34.3 Ritchie et al., 2015 http://bioconductor.org
Comet v.2017.01 rev.0 Eng et al., 2015 http://comet-ms.sourceforge.net
ProteoWizard msconvert v.3.0.11392 Adusumilli and Mallick, 2017 http://proteowizard.sourceforge.net
Percolator v.3.0 The et al., 2016 http://crux.ms
MSFragger v.20171106 Kong et al., 2017 https://msfragger.nesvilab.org
R v.3.4.4 The R Foundation https://www.r-project.org/
JCAST v.0.1.0 This study https://github.com/ed-lau/jcast
Other
RNA sequencing data on human heart ENCODE (ENCODE Project Consortium, 2012) ENCSR436QDU ENCSR391VGU
RNA sequencing data on human liver ENCODE (ENCODE Project Consortium, 2012) ENCSR226KML ENCSR504QMK
RNA sequencing data on human lung ENCODE (ENCODE Project Consortium, 2012) ENCSR425RGZ ENCSR406SAW
RNA sequencing data on human pancreas ENCODE (ENCODE Project Consortium, 2012) ENCSR671IYC
ENCSR586SYA
RNA sequencing data on human adrenal gland ENCODE (ENCODE Project Consortium, 2012) ENCSR801MKV ENCSR754WLW
RNA sequencing data on human transverse colon ENCODE (ENCODE Project Consortium, 2012) ENCSR800WIY ENCSR403SZN
RNA sequencing data on human ovary ENCODE (ENCODE Project Consortium, 2012) ENCSR841ADZ ENCSR042GYH
RNA sequencing data on human esophagus ENCODE (ENCODE Project Consortium, 2012) ENCSR098BUF ENCSR750ETS
RNA sequencing data on human testis ENCODE (ENCODE Project Consortium, 2012) ENCSR029KNZ
ENCSR344MQK
RNA sequencing data on human prostate ENCODE (ENCODE Project Consortium, 2012) ENCSR495HDM ENCSR701TST
RNA sequencing data on human spleen ENCODE (ENCODE Project Consortium, 2012) ENCSR194HVU ENCSR900SGE
RNA sequencing data on human thyroid ENCODE (ENCODE Project Consortium, 2012) ENCSR113HQM ENCSR017ZLM
Mass spectrometry data on human heart, liver, lung, pancreas, adrenal gland, colon, ovary, esophagus, testis, prostate ProteomeXchange (Kim et al., 2014) PXD000561
Mass spectrometry data on human liver ProteomeXchange PXD009021
Mass spectrometry data on human testis ProteomeXchange (Sun et al., 2018) PXD009737
Mass spectrometry data on human heart ProteomeXchange (Doll et al., 2017) PXD006675
Mass spectrometry data on human heart, liver, lung, pancreas, adrenal gland, colon, ovary, esophagus, testis, prostate, spleen, thyroid ProteomeXchange (Wang et al., 2019) PXD010154