title: 293FT_single_e_RNA

description:
T&T-seq
T&T-seq validation_TPM.xlsx

tag: cell line

value: translatome

value: single 293FT cell


title: WT_MI_D1_2_11

status: Public on Jul 25 2022

type: SRA

city: Tokyo

first: Shintaro

last: Yamada

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

library_source: transcriptomic

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 182”.
ReadCounts file generated using featureCounts.

molecule: total RNA

organism: Mus musculus

source_name: Cardiomyocyte

growth_protocol: All the animal experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines for animal experiments of the University of Tokyo (Approved Number P14-106). All of wild type C57BL/6 male mice were purchased from CLEA JAPAN. All mouse were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 12-h light/dark cycle with ad libitum access to food and water.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2582 (Illumina) in rapid mode

treatment_protocol: Myocardial infarction (MI) was induced as previously described. Mice were anaesthetized by inhalation of 2% isoflurane. MI was induced by ligation of the left anterior descending artery. Mice that failed to develop MI or died within one week after the operation were excluded from the analysis.

tag: strain

tag: operation

value: MI day1

tag: region

value: ishchemic + border

tag: tissue

value: single-cardiomyocyte

tag: name in supplementary file

tag: genome build

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.90a)


title: WT_MI_D1_2_1

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 180”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2580 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.88a)


title: WT_MI_D1_2_13

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 184”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2584 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.92a)


title: WT_MI_D1_2_10

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 181”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2581 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.89a)


title: 293FT_single_e_Ribo

city: beijing

first: Wenqi

last: Hu

state: beijing

address: Room D110, Medical Science Building, School of Medicine, Tsinghua University

country: China

institute: Tsinghua University

description:
T&T-seq
T&T-seq validation_TPM.xlsx

data_processing:
For T&T-seq data,  sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Trim galore (v0.6.4) with parameters  -q 20 --phred33 --stringency 3 -j 32 --length 50 -e 0.1.
For T&T-seq data,reads were mapped to hg38 or mm10 whole genome using Hisat2 (v2.1.0) with default parameters.
gene count was calculated using Featurecounts (v1.6.5) with parameters -T 32 -O -t exon -M --extraAttributes gene_name
transcripts per million(TPM) was calculated by customize R script
Assembly: hg38 or mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Library strategy: Ribo-seq

organism: Homo sapiens

growth_protocol: oocytes were collect from 4-6 weeks C57BL/6 female mice, human oocytes were collected form donors underwent ART treatment.

extract_protocol:
For the transcriptome of T&T-seq mRNAs were directly reverse transcribed after lysing . For the translatome of T&T-seq, ribosome binding RNAs are purifed by RiboLace beads.
For T&T-seq, RNA libraries were prepared for sequencing using Single Cell Full Length mRNA-Amplification Kit (N712, Vazyme) ,TruePrep DNA Library Prep Kit V2 for Illumina (TD502, Vazyme) and TruePrep® Index Kit V2 for Illumina (TD202, Vazyme).

treatment_protocol: For IVM experiments, oocytes was injected with Trim21 mRNA and OOSP2 antibody or IgG and cultured for 2 hours

tag: type

value: transcriptome

tag: treatment

tag: cell number


title: MI_D1_IZ_1_41

description:
Smart-seq2
ReadCounts.xlsx

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.027 with the parameters “--cut_tail --cut_tail_window_size 1 --cut_tail_mean_quality 30 --length_required 30”
The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.2b)
The reads aligned to exon were counted using featureCounts
For nonCM RNA-seq, raw data was processed using Cell Ranger (version 4.0.0)
For spatial transcriptome, raw data was processed using Space Ranger (version 1.2.1)
Genome_build: For single-cardiomyocyte RNA-seq, the reference transcript data and the gene annotation file for mouse was downloaded from GENCODE (release 23, https://www.gencodegenes.org/)
Genome_build: For nonCM RNA-seq, the reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz.
Genome_build: For spatial transcrptome, the reference transcript data and the gene annotation file for mouse was downloaded from https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-mm10-2020-A.tar.gz.
Supplementary_files_format_and_content: ReadCounts file generated using featureCounts.
Supplementary_files_format_and_content: Each barcode.tsv.gz, features.tsv.gz and matrix.mtx.gz files genereted using Cell Ranger or Space Ranger.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described7. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2500 (Illumina) in rapid mode

treatment_protocol: Myocardial infarction (MI) was induced as previously described25. Mice were anaesthetized by inhalation of 2% isoflurane. MI was induced by ligation of the left anterior descending artery. Mice that failed to develop MI or died within one week after the operation were excluded from the analysis.

value: ischemic


title: Primary breast cancer, sample 83

type: RNA

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50-60

department: Medical Oncology

country: Netherlands

institute: Erasmus Medical Centre

description:
EMC204_83
2430.CEL

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol on Affymetrix scanner 3000

data_processing: MAS5 parameters from affy R package, available at www.bioconductor.org using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 600.

label: biotin

source_name: Snap frozen primary breast tumor

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted with RNABee (Campro, Veenendaal, the Netherlands) according to the manufacturer procedure

tag: site of relapse (brain or other)

value: other

tag: survival time (months)


title: Primary breast cancer, sample 79

description:
EMC204_79
2427.CEL


title: WT_MI_D1_1_9

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 179”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2579 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.87a)


title: 293FT_single_d_RNA

description:
T&T-seq
T&T-seq validation_TPM.xlsx

data_processing:
For T&T-seq data,  sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Trim galore (v0.6.4) with parameters  -q 20 --phred33 --stringency 3 -j 32 --length 50 -e 0.1.
For T&T-seq data,reads were mapped to hg38 or mm10 whole genome using Hisat2 (v2.1.0) with default parameters.
gene count was calculated using Featurecounts (v1.6.5) with parameters -T 32 -O -t exon -M --extraAttributes gene_name
transcripts per million(TPM) was calculated by customize R script
Assembly: hg38 or mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA


title: MI_D1_IZ_1_40

description:
Smart-seq2
ReadCounts.xlsx


title: Primary breast cancer, sample 76

description:
EMC204_76
2422.CEL


title: WT_MI_D1_1_80

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 178”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2578 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.86a)


title: 293FT_single_d_Ribo

description:
T&T-seq
T&T-seq validation_TPM.xlsx


title: MI_D1_IZ_1_39

description:
Smart-seq2
ReadCounts.xlsx


title: Primary breast cancer, sample 77

description:
EMC204_77
2424.CEL


title: MI_D1_IZ_1_42

description:
Smart-seq2
ReadCounts.xlsx


title: WT_MI_D1_1_8

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 177”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2577 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.85a)


title: WT_MI_D1_1_79

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 176”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2576 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.84a)


title: 293FT_single_c_RNA

description:
T&T-seq
T&T-seq validation_TPM.xlsx


title: 293FT_single_c_Ribo

description:
T&T-seq
T&T-seq validation_TPM.xlsx


title: 293FT_single_b_RNA

description:
T&T-seq
T&T-seq validation_TPM.xlsx


title: MI_D1_IZ_1_36

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_IZ_1_38

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_IZ_1_37

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_IZ_1_35

description:
Smart-seq2
ReadCounts.xlsx


title: WT_MI_D1_1_77

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 174”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2574 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.82a)


title: WT_MI_D1_1_78

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 175”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2575 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.83a)


title: Primary breast cancer, sample 74

description:
EMC204_74
2420.CEL


title: 293FT_single_a_RNA

description:
T&T-seq
T&T-seq validation_TPM.xlsx

value: translatome

value: single 293FT cell


title: 293FT_single_b_Ribo

description:
T&T-seq
T&T-seq validation_TPM.xlsx


title: MI_D1_IZ_1_34

description:
Smart-seq2
ReadCounts.xlsx

value: MI day1


title: Primary breast cancer, sample 72

description:
EMC204_72
2418.CEL


title: Primary breast cancer, sample 75

description:
EMC204_75
2421.CEL


title: Primary breast cancer, sample 70

description:
EMC204_70
2415.CEL

value: brain


title: 293FT_single_a_Ribo

description:
T&T-seq
T&T-seq validation_TPM.xlsx


title: WT_MI_D1_1_76

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 173”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2573 (Illumina) in rapid mode

value: ishchemic + border

value: single-cardiomyocyte

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.81a)


title: Primary breast cancer, sample 71

description:
EMC204_71
2417.CEL

value: local


title: WT_MI_D1_1_75

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 172”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2572 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.80a)


title: 293FT_1000_RNA

description:
T&T-seq
T&T-seq validation_TPM.xlsx

value: 1000 293FT cells


title: Primary breast cancer, sample 68

description:
EMC204_68
2413.CEL

value: other


title: Primary breast cancer, sample 66

description:
EMC204_66
2410.CEL


title: Primary breast cancer, sample 69

description:
EMC204_69
2414.CEL


title: Primary breast cancer, sample 67

description:
EMC204_67
2412.CEL


title: MI_D1_IZ_1_33

description:
Smart-seq2
ReadCounts.xlsx

value: ischemic


title: Primary breast cancer, sample 65

description:
EMC204_65
2406.CEL


title: MI_D1_IZ_1_32

description:
Smart-seq2
ReadCounts.xlsx


title: WT_MI_D1_1_73

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 170”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2570 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.78a)


title: MI_D1_IZ_1_29

description:
Smart-seq2
ReadCounts.xlsx


title: 293FT_100_RNA

description:
T&T-seq
T&T-seq validation_TPM.xlsx

value: 100 293FT cells


title: 293FT_100_Ribo

description:
T&T-seq
T&T-seq validation_TPM.xlsx

value: transcriptome


title: 293FT_1000_Ribo

description:
T&T-seq
T&T-seq validation_TPM.xlsx


title: MI_D1_IZ_1_31

description:
Smart-seq2
ReadCounts.xlsx


title: WT_MI_D1_1_74

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 171”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2571 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.79a)


title: Primary breast cancer, sample 63

description:
EMC204_63
2403.CEL


title: WT_MI_D1_1_71

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 168”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2568 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.76a)


title: 293FT_10_RNA

description:
T&T-seq
T&T-seq validation_TPM.xlsx

value: translatome

value: 10 293FT cells


title: MI_D1_IZ_1_30

description:
Smart-seq2
ReadCounts.xlsx

value: MI day1


title: WT_MI_D1_1_72

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 169”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2569 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.77a)


title: WT_MI_D1_1_7

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 166”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2566 (Illumina) in rapid mode

value: ishchemic + border

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.74a)


title: WT_MI_D1_1_70

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 167”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2567 (Illumina) in rapid mode

value: single-cardiomyocyte

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.75a)


title: WT_MI_D1_1_68

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 164”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2564 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.72a)


title: WT_MI_D1_1_69

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 165”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2565 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.73a)


title: MI_D1_IZ_1_28

description:
Smart-seq2
ReadCounts.xlsx

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.027 with the parameters “--cut_tail --cut_tail_window_size 1 --cut_tail_mean_quality 30 --length_required 30”
The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.2b)
The reads aligned to exon were counted using featureCounts
For nonCM RNA-seq, raw data was processed using Cell Ranger (version 4.0.0)
For spatial transcriptome, raw data was processed using Space Ranger (version 1.2.1)
Genome_build: For single-cardiomyocyte RNA-seq, the reference transcript data and the gene annotation file for mouse was downloaded from GENCODE (release 23, https://www.gencodegenes.org/)
Genome_build: For nonCM RNA-seq, the reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz.
Genome_build: For spatial transcrptome, the reference transcript data and the gene annotation file for mouse was downloaded from https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-mm10-2020-A.tar.gz.
Supplementary_files_format_and_content: ReadCounts file generated using featureCounts.
Supplementary_files_format_and_content: Each barcode.tsv.gz, features.tsv.gz and matrix.mtx.gz files genereted using Cell Ranger or Space Ranger.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described7. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2500 (Illumina) in rapid mode


title: Primary breast cancer, sample 60

description:
EMC204_60
2048.CEL

data_processing: MAS5 parameters from affy R package, available at www.bioconductor.org using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 600.

extract_protocol: Total RNA was extracted with RNABee (Campro, Veenendaal, the Netherlands) according to the manufacturer procedure

value: other


title: MI_D1_IZ_1_26

description:
Smart-seq2
ReadCounts.xlsx

value: ischemic


title: MI_D1_IZ_1_27

description:
Smart-seq2
ReadCounts.xlsx


title: Primary breast cancer, sample 61

description:
EMC204_61
2063.CEL

value: brain+other


title: MI_D1_IZ_1_25

description:
Smart-seq2
ReadCounts.xlsx


title: HepG2_RNASeq_siHNF4a_2_rep2

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

country: Italy

institute: fondazione Istituto italiano di tecnologia

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Assembly: hg19
Supplementary files format and content: differential expression results (DESeq2) and eRPKM after 48h YAP overexpression and after knock-down of HNF4a using two different siRNAs (siHNF4a_1 and 2)

source_name: HepG2 pSLIK YAPs127a cells transfected with siRNA HNF4a (#2)

growth_protocol: RPMI, 10% FBS. Medium renewal: twice per week

extract_protocol:
Total RNA was extracted with Quick RNA miniprep kit following manufacturer instructions (Zymo Research).
Libraries were prepared with QuantSeq 3‘ mRNA-Seq Library Prep Kit for Illumina (FWD) following manufacturer instructions (Lexogen)

treatment_protocol: Doxycycline 2µg/ml for 48h. siRNA transfection with Lipofectamine RNAi-MAX in antibiotics-free medium according to manufacturer instructions (Life Technologies)

value: Liver

value: transfected with siHNF4a_2


title: MI_D1_IZ_1_24

description:
Smart-seq2
ReadCounts.xlsx


title: Primary breast cancer, sample 64

description:
EMC204_64
2405.CEL


title: 293FT_10_Ribo

description:
T&T-seq
T&T-seq validation_TPM.xlsx

data_processing:
For T&T-seq data,  sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by Trim galore (v0.6.4) with parameters  -q 20 --phred33 --stringency 3 -j 32 --length 50 -e 0.1.
For T&T-seq data,reads were mapped to hg38 or mm10 whole genome using Hisat2 (v2.1.0) with default parameters.
gene count was calculated using Featurecounts (v1.6.5) with parameters -T 32 -O -t exon -M --extraAttributes gene_name
transcripts per million(TPM) was calculated by customize R script
Assembly: hg38 or mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Library strategy: Ribo-seq

extract_protocol:
For the transcriptome of T&T-seq mRNAs were directly reverse transcribed after lysing . For the translatome of T&T-seq, ribosome binding RNAs are purifed by RiboLace beads.
For T&T-seq, RNA libraries were prepared for sequencing using Single Cell Full Length mRNA-Amplification Kit (N712, Vazyme) ,TruePrep DNA Library Prep Kit V2 for Illumina (TD502, Vazyme) and TruePrep® Index Kit V2 for Illumina (TD202, Vazyme).

value: transcriptome


title: HepG2_RNASeq_siHNF4a_2_rep3


title: Primary breast cancer, sample 62

description:
EMC204_62
2208.CEL


title: HepG2_RNASeq_siHNF4a_1_rep3

source_name: HepG2 pSLIK YAPs127a cells transfected with siRNA HNF4a (#1)

value: transfected with siHNF4a_1


title: WT_MI_D1_1_67

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 163”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2563 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.71a)


title: HepG2_RNASeq_siHNF4a_1_rep2


title: Primary breast cancer, sample 59

description:
EMC204_59
2037.CEL


title: MI_D1_IZ_1_22

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_IZ_1_23

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_IZ_1_21

description:
Smart-seq2
ReadCounts.xlsx


title: WT_MI_D1_1_65

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 161”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2561 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.69a)


title: Primary breast cancer, sample 56

description:
EMC204_56
1630.CEL


title: WT_MI_D1_1_64

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 160”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2560 (Illumina) in rapid mode

value: MI day1

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.68a)


title: Primary breast cancer, sample 54

description:
EMC204_54
1544.CEL


title: Primary breast cancer, sample 58

description:
EMC204_58
2001.CEL


title: HepG2_RNASeq_siHNF4a_2_rep1


title: Primary breast cancer, sample 53

description:
EMC204_53
1513.CEL


title: HepG2_RNASeq_siCTRL_rep3

source_name: HepG2 pSLIK YAPs127a cells transfected with siRNA CTRL

value: transfected with siRNA CTRL


title: Primary breast cancer, sample 55

description:
EMC204_55
1619.CEL

value: local


title: WT_MI_D1_1_63

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 159”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2559 (Illumina) in rapid mode

value: ishchemic + border

value: single-cardiomyocyte

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.67a)


title: WT_MI_D1_1_62

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 158”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2558 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.66a)


title: HepG2_RNASeq_siCTRL_rep2


title: WT_MI_D1_1_66

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 162”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2562 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.70a)


title: HepG2_RNASeq_siCTRL_rep1


title: HepG2_RNASeq_48h_doxy_rep3

source_name: HepG2 pSLIK YAPs127a cells treated with dodycycline 2µg/ml for 48h

value: treated with docycycline (2ug/ml) for 48h


title: MI_D1_IZ_1_18

description:
Smart-seq2
ReadCounts.xlsx

value: ischemic


title: MI_D1_IZ_1_19

description:
Smart-seq2
ReadCounts.xlsx


title: Primary breast cancer, sample 52

description:
EMC204_52
1491.CEL

value: brain+other


title: WT_MI_D1_1_61

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 157”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2557 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.65a)


title: MI_D1_IZ_1_17

description:
Smart-seq2
ReadCounts.xlsx


title: WT_MI_D1_1_60

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 156”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2556 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.64a)


title: Primary breast cancer, sample 51

description:
EMC204_51
1484.CEL

value: other


title: HepG2_RNASeq_48h_doxy_rep2

value: Liver


title: MI_D1_IZ_1_16

description:
Smart-seq2
ReadCounts.xlsx


title: Primary breast cancer, sample 49

description:
EMC204_49
1294.CEL


title: WT_MI_D1_1_6

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 155”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2555 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.63a)


title: Primary breast cancer, sample 50

description:
EMC204_50
1458.CEL


title: HepG2_RNASeq_48h_doxy_rep1


title: HepG2_RNASeq_NT_rep3

source_name: HepG2 pSLIK YAPs127a cells

value: not treated


title: WT_MI_D1_1_59

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 154”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2554 (Illumina) in rapid mode

value: MI day1

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.62a)


title: MI_D1_IZ_1_15

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_IZ_1_14

description:
Smart-seq2
ReadCounts.xlsx


title: HepG2_RNASeq_NT_rep2


title: Primary breast cancer, sample 48

description:
EMC204_48
1243.CEL

value: brain


title: HepG2_RNASeq_NT_rep1


title: MI_D1_IZ_1_13

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_IZ_1_12

description:
Smart-seq2
ReadCounts.xlsx


title: WT_MI_D1_1_56

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 151”.
ReadCounts file generated using featureCounts.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricle as previously described. Enzymatic dissociation using Langendorff perfusion was performed with 35 mL enzyme solution (type 2 collagenase 1 mg/mL [Worthington], protease type XIV 0.05 mg/mL [Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM; pH 7.4) pre-heated to 37 °C, at a rate of 3 mL/min. To neutralize enzymatic activity, fetal bovine serum (FBS) was added to the solution to a final concentration of 0.2% (v/v). After perfusion of digestion buffer, left ventricle was cut according to each sectional region (IR, RR) and cardiomyocytes were subsequently isolated. Cell suspensions were filtered through a 100-μm nylon mesh cell strainer and centrifuged at 100 g for 2 min, after which the supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%; pH 7.4) containing a low concentration of calcium (0.1 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥80% for all time points) were collected immediately with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cardiomyocyte cDNA libraries were generated using the Smart-seq2 protocol26 and the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad), and the distribution of cDNA fragment lengths was assessed using LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward: TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse: TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold. The sequencing libraries were subjected to paired-end 51-bp RNA sequencing on a HiSeq 2551 (Illumina) in rapid mode

value: ishchemic + border

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.59a)


title: MI_D1_IZ_1_11

description:
Smart-seq2
ReadCounts.xlsx

value: single-cardiomyocyte


title: Primary breast cancer, sample 47

description:
EMC204_47
1240.CEL