title: WT_MI_D1_1_55

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 150”.
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 2550 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.58a)


title: GV_abOOSP2_f_Ribo

status: Public on Jul 25 2022

type: SRA

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:
ribosome-binding RNA
T&T-seq

library_source: transcriptomic

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 miniRibo-seq  sequenced reads were treated by Cutadapt (v1.18) with parameters -j 16  -a AAAAAAAAAA -u 3 --discard-untrimmed -m 25 -M 40
For T&T-seq data,reads were mapped to hg38 or mm10 whole genome using Hisat2 (v2.1.0) with default parameters. For miniRibo-seq, reads were mapped to  mm10 whole genome using STAR (v2.7.1a) with parameters --outFilterType BySJout --runThreadN 16 --outFilterMismatchNmax 2  --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --outFilterMultimapNmax1 --outFilterMatchNmin 16 --alignEndsType EndToEnd --outSAMattrIHstart 0
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
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

molecule: total RNA

organism: Homo sapiens

source_name: oocyte

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 miniRibo-seq,total RNAs were digested by Rnase cocktail. Ribosome protected RNA fragment are separated by PAGE-gel and recovered by isopropanol precipitation. 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). For miniRibo-seq, RNA libraries were prepared for sequencing using SMARTer® smRNA-Seq Kit for Illumina (635030, TAKARA)

treatment_protocol: One replicate was OOSP2 protein or  OOSP2 antibody treated for 90 minutes

tag: Stage

value: GV

tag: type

value: translatiome

tag: treatment

value: IVM +abOOSP2 90min

tag: cell number


title: GV_abOOSP2_e_Ribo

description:
ribosome-binding RNA
T&T-seq


title: WT_MI_D1_1_58

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

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 153”.
ReadCounts file generated using featureCounts.

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 2553 (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 2.7.61a)


title: Primary breast cancer, sample 44

type: RNA

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50-60

department: Medical Oncology

country: Netherlands

institute: Erasmus Medical Centre

description:
EMC204_44
1230.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: brain+other

tag: survival time (months)


title: GV_abOOSP2_d_Ribo

description:
ribosome-binding RNA
T&T-seq


title: Primary breast cancer, sample 43

description:
EMC204_43
1217.CEL

value: other


title: WT_MI_D1_1_54

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 149”.
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 2549 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.57a)


title: WT_MI_D1_1_53

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 148”.
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 2548 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.56a)


title: WT_MI_D1_1_57

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 152”.
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 2552 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.60a)


title: Primary breast cancer, sample 42

description:
EMC204_42
1210.CEL


title: GV_abOOSP2_c_Ribo

description:
ribosome-binding RNA
T&T-seq


title: Primary breast cancer, sample 46

description:
EMC204_46
1238.CEL

value: local


title: WT_MI_D1_1_52

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 147”.
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 2547 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.55a)


title: GV_abOOSP2_b_Ribo

description:
ribosome-binding RNA
T&T-seq


title: MI_D1_IZ_1_8

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: WT_MI_D1_1_51

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 146”.
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 2546 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.54a)


title: Primary breast cancer, sample 45

description:
EMC204_45
1237.CEL


title: MI_D1_IZ_1_7

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_IZ_1_6

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_IZ_1_10

description:
Smart-seq2
ReadCounts.xlsx


title: GV_abOOSP2_a_Ribo

description:
ribosome-binding RNA
T&T-seq


title: Primary breast cancer, sample 40

description:
EMC204_40
1207.CEL


title: WT_MI_D1_1_50

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 145”.
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 2545 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.53a)


title: WT_MI_D1_1_5

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 144”.
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 2544 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.52a)


title: GV_abOOSP2_f_RNA

description:
ployA RNA
T&T-seq

value: GV

value: transcriptome


title: MI_D1_IZ_1_9

description:
Smart-seq2
ReadCounts.xlsx

value: MI day1


title: Primary breast cancer, sample 38

description:
EMC204_38
1199.CEL


title: MI_D1_IZ_1_5

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_IZ_1_4

description:
Smart-seq2
ReadCounts.xlsx


title: WT_MI_D1_1_49

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 143”.
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 2543 (Illumina) in rapid mode

value: ishchemic + border

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.51a)


title: GV_abOOSP2_e_RNA

description:
ployA RNA
T&T-seq

value: IVM +abOOSP2 90min


title: Primary breast cancer, sample 39

description:
EMC204_39
1205.CEL


title: Primary breast cancer, sample 41

description:
EMC204_41
1208.CEL


title: WT_MI_D1_1_48

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 142”.
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 2542 (Illumina) in rapid mode

value: single-cardiomyocyte

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.50a)


title: Primary breast cancer, sample 37

description:
EMC204_37
1195.CEL

value: other


title: GV_abOOSP2_d_RNA

description:
ployA RNA
T&T-seq


title: MI_D1_IZ_1_3

description:
Smart-seq2
ReadCounts.xlsx


title: MI_D1_IZ_1_2

description:
Smart-seq2
ReadCounts.xlsx


title: GV_abOOSP2_b_RNA

description:
ployA RNA
T&T-seq


title: GV_abOOSP2_c_RNA

description:
ployA RNA
T&T-seq


title: GV_abOOSP2_a_RNA

description:
ployA RNA
T&T-seq


title: Primary breast cancer, sample 35

description:
EMC204_35
1193.CEL


title: WT_MI_D1_1_45

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 139”.
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 2539 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.47a)


title: Primary breast cancer, sample 32

description:
EMC204_32
1187.CEL


title: Z3EVp_yox1_9A_60_rep2

city: Worcester

first: Jennifer

last: Benanti

state: MA

address: 364 Plantation St., LRB 525

department: Molecular, Cell and Cancer Biology

country: USA

institute: University of Massachusetts Medical School

description:
MATa ura3∆0 his3∆1 lyp∆0 can1∆::STE2pr-SpHIS5 URA3::Z4pr-yox1-9A-3V5-KanMx HAP1+::NatMX::pACT1-Z3EV-ENO2term
TPM.inducible.yox1.xlsx

data_processing:
aligned to Saccharomyces_cerevisiae R64-1-1 genome, with R64-1-1.90 annotation, by STAR(v2.5.3a) aligner.
Gene expression were quantified with featureCounts v1.5.2, measuring exon reads for each gene_id.
TPM was calculated
Genome_build: R64-1-1
Supplementary_files_format_and_content: TPM was calculated

organism: Saccharomyces cerevisiae

growth_protocol: RNA was purified from asynchronous cells growing in rich medium (YM-1 with 2% dextrose) without estradiol addition (0 minutes), and 20 or 60 minutes following the addition of estradiol.

extract_protocol:
Total RNA was purified using an acid-phenol extraction protocol.
polyA depletion and library construction were performed by BGI Americas.

treatment_protocol: 1μM estradiol was added for 20 or 60 minutes, as indicated.

tag: genotype

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-yox1-9A-3V5-KanMx HAP1+::NatMX::pACT1-Z3EV-ENO2term


title: Z3EVp_yox1_9A_60_rep3


title: Primary breast cancer, sample 36

description:
EMC204_36
1194.CEL

value: brain+other


title: Primary breast cancer, sample 33

description:
EMC204_33
1189.CEL


title: WT_MI_D1_1_44

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 138”.
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 2538 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.46a)


title: Primary breast cancer, sample 34

description:
EMC204_34
1192.CEL


title: GV_OOSP2_d_Ribo

description:
ribosome-binding RNA
T&T-seq

value: translatiome

value: IVM +hRecOOSP2 90min


title: HepG2_RNASeq_siHNF4a_1_rep1

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 (#1)

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

tag: cell line

value: transfected with siHNF4a_1


title: GV_OOSP2_c_Ribo

description:
ribosome-binding RNA
T&T-seq

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 miniRibo-seq  sequenced reads were treated by Cutadapt (v1.18) with parameters -j 16  -a AAAAAAAAAA -u 3 --discard-untrimmed -m 25 -M 40
For T&T-seq data,reads were mapped to hg38 or mm10 whole genome using Hisat2 (v2.1.0) with default parameters. For miniRibo-seq, reads were mapped to  mm10 whole genome using STAR (v2.7.1a) with parameters --outFilterType BySJout --runThreadN 16 --outFilterMismatchNmax 2  --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --outFilterMultimapNmax1 --outFilterMatchNmin 16 --alignEndsType EndToEnd --outSAMattrIHstart 0
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
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

extract_protocol:
For miniRibo-seq,total RNAs were digested by Rnase cocktail. Ribosome protected RNA fragment are separated by PAGE-gel and recovered by isopropanol precipitation. 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). For miniRibo-seq, RNA libraries were prepared for sequencing using SMARTer® smRNA-Seq Kit for Illumina (635030, TAKARA)

value: GV


title: WT_MI_D1_1_47

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 141”.
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 2541 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.49a)


title: WT_MI_D1_1_42

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 136”.
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 2536 (Illumina) in rapid mode

value: MI day1

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.44a)


title: Z3EVp_yox1_9A_60_rep1


title: MI_D1_IZ_1_1

description:
Smart-seq2
ReadCounts.xlsx

value: ischemic


title: GV_OOSP2_b_Ribo

description:
ribosome-binding RNA
T&T-seq


title: WT_MI_D1_1_46

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 140”.
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 2540 (Illumina) in rapid mode

value: ishchemic + border

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.48a)


title: Z3EVp_yox1_9A_20_rep3


title: GV_OOSP2_a_Ribo

description:
ribosome-binding RNA
T&T-seq


title: Z3EVp_yox1_9A_20_rep2


title: Primary breast cancer, sample 31

description:
EMC204_31
1186.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


title: WT_MI_D1_1_41

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 135”.
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 2535 (Illumina) in rapid mode

value: single-cardiomyocyte

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.43a)


title: GV_OOSP2_d_RNA

description:
ployA RNA
T&T-seq

value: transcriptome


title: WT_MI_D1_1_43

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 137”.
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 2537 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.45a)


title: WT_MI_D1_1_40

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 134”.
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 2534 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.42a)


title: GV_OOSP2_c_RNA

description:
ployA RNA
T&T-seq


title: Z3EVp_yox1_9A_20_rep1

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-yox1-9A-3V5-KanMx HAP1+::NatMX::pACT1-Z3EV-ENO2term


title: Primary breast cancer, sample 29

description:
EMC204_29
1184.CEL

value: other


title: WT_MI_D1_1_39

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 132”.
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 2532 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.40a)


title: Primary breast cancer, sample 27

description:
EMC204_27
1181.CEL


title: Z3EVp_yox1_9A_0_rep2


title: Z3EVp_yox1_9A_0_rep1


title: GV_OOSP2_a_RNA

description:
ployA RNA
T&T-seq

value: IVM +hRecOOSP2 90min


title: GV_control_d_Ribo

description:
ribosome-binding RNA
T&T-seq

value: translatiome

value: IVM 90min


title: Z3EVp_YOX1_60_rep3

description:
MATa ura3∆0 his3∆1 lyp∆0 can1∆::STE2pr-SpHIS5 URA3::Z4pr-YOX1-3V5-KanMx HAP1+::NatMX::pACT1-Z3EV-ENO2term
TPM.inducible.yox1.xlsx

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-YOX1-3V5-KanMx HAP1+::NatMX::pACT1-Z3EV-ENO2term


title: Primary breast cancer, sample 30

description:
EMC204_30
1185.CEL


title: GV_control_c_Ribo

description:
ribosome-binding RNA
T&T-seq

value: GV


title: Primary breast cancer, sample 28

description:
EMC204_28
1183.CEL


title: Z3EVp_YOX1_60_rep2


title: WT_MI_D1_1_37

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 130”.
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 2530 (Illumina) in rapid mode

value: MI day1

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.38a)


title: WT_MI_D1_1_36

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 129”.
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 2529 (Illumina) in rapid mode

value: ishchemic + border

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.37a)


title: Primary breast cancer, sample 26

description:
EMC204_26
1178.CEL


title: Primary breast cancer, sample 24

description:
EMC204_24
1170.CEL


title: Primary breast cancer, sample 23

description:
EMC204_23
1169.CEL


title: GV_control_b_Ribo

description:
ribosome-binding RNA
T&T-seq


title: Z3EVp_YOX1_60_rep1


title: Z3EVp_yox1_9A_0_rep3


title: GV_OOSP2_b_RNA

description:
ployA RNA
T&T-seq


title: WT_MI_D1_1_4

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 133”.
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 2533 (Illumina) in rapid mode

value: single-cardiomyocyte

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.41a)


title: WT_MI_D1_1_35

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 128”.
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 2528 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.36a)


title: WT_MI_D1_1_38

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 131”.
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 2531 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.39a)


title: WT_MI_D1_1_34

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 127”.
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 2527 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.35a)


title: Z3EVp_YOX1_20_rep3

data_processing:
aligned to Saccharomyces_cerevisiae R64-1-1 genome, with R64-1-1.90 annotation, by STAR(v2.5.3a) aligner.
Gene expression were quantified with featureCounts v1.5.2, measuring exon reads for each gene_id.
TPM was calculated
Genome_build: R64-1-1
Supplementary_files_format_and_content: TPM was calculated

extract_protocol:
Total RNA was purified using an acid-phenol extraction protocol.
polyA depletion and library construction were performed by BGI Americas.


title: GV_control_a_Ribo

description:
ribosome-binding RNA
T&T-seq


title: Z3EVp_YOX1_20_rep2


title: WT_MI_D1_1_33

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 126”.
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 2526 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.34a)


title: Primary breast cancer, sample 21

description:
EMC204_21
1166.CEL

value: other


title: GV_control_d_RNA

description:
ployA RNA
T&T-seq

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 miniRibo-seq  sequenced reads were treated by Cutadapt (v1.18) with parameters -j 16  -a AAAAAAAAAA -u 3 --discard-untrimmed -m 25 -M 40
For T&T-seq data,reads were mapped to hg38 or mm10 whole genome using Hisat2 (v2.1.0) with default parameters. For miniRibo-seq, reads were mapped to  mm10 whole genome using STAR (v2.7.1a) with parameters --outFilterType BySJout --runThreadN 16 --outFilterMismatchNmax 2  --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --outFilterMultimapNmax1 --outFilterMatchNmin 16 --alignEndsType EndToEnd --outSAMattrIHstart 0
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
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

extract_protocol:
For miniRibo-seq,total RNAs were digested by Rnase cocktail. Ribosome protected RNA fragment are separated by PAGE-gel and recovered by isopropanol precipitation. 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). For miniRibo-seq, RNA libraries were prepared for sequencing using SMARTer® smRNA-Seq Kit for Illumina (635030, TAKARA)

value: transcriptome


title: GV_control_c_RNA

description:
ployA RNA
T&T-seq


title: WT_MI_D1_1_31

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 124”.
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 2524 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.32a)


title: Z3EVp_YOX1_20_rep1


title: GV_control_a_RNA

description:
ployA RNA
T&T-seq


title: Z3EVp_YOX1_0_rep2


title: Primary breast cancer, sample 20

description:
EMC204_20
1165.CEL


title: Primary breast cancer, sample 25

description:
EMC204_25
1173.CEL

value: brain


title: WT_MI_D1_1_30

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 123”.
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 2523 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.31a)


title: Primary breast cancer, sample 22

description:
EMC204_22
1167.CEL


title: Primary breast cancer, sample 19

description:
EMC204_19
1164.CEL

value: local


title: MI_D1_IZ_1_20

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

value: ischemic


title: Primary breast cancer, sample 18

description:
EMC204_18
1162.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