title: WT_MI_D1_1_3

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 122”.
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 2522 (Illumina) in rapid mode

value: MI day1

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.30a)


title: GV_control_b_RNA

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:
ployA 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: transcriptome

tag: treatment

value: IVM 90min

tag: cell number


title: Human_Morula_c_Ribo

description:
ribosome-binding RNA
T&T-seq

source_name: embryo

value: morula

value: translatiome


title: Primary breast cancer, sample 16

type: RNA

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50-60

department: Medical Oncology

country: Netherlands

institute: Erasmus Medical Centre

description:
EMC204_16
1156.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: local

tag: survival time (months)


title: Z3EVp_YOX1_0_rep1

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-YOX1-3V5-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: strain

tag: genotype

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


title: Z3EVp_YOX1_0_rep3


title: Primary breast cancer, sample 17

description:
EMC204_17
1160.CEL

value: other


title: Human_Morula_b_Ribo

description:
ribosome-binding RNA
T&T-seq


title: Z3EVp_YHP1_60_rep2

description:
MATa ura3∆0 his3∆1 lyp∆0 can1∆::STE2pr-SpHIS5 URA3::Z4pr-YHP1-3V5-KanMx HAP1+::NatMX::pACT1-Z3EV-ENO2term
TPM.inducible.yhp1.xlsx

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-YHP1-3V5-KanMx HAP1+::NatMX::pACT1-Z3EV-ENO2term


title: Z3EVp_YHP1_60_rep3


title: WT_MI_D1_1_32

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 125”.
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 2525 (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: operation

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 2.7.33a)


title: Human_Morula_a_Ribo

description:
ribosome-binding RNA
T&T-seq


title: WT_MI_D1_1_29

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 121”.
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 2521 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.29a)


title: WT_MI_D1_1_28

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 120”.
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 2520 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.28a)


title: Human_Morula_c_RNA

description:
ployA RNA
T&T-seq


title: WT_MI_D1_1_27

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 119”.
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 2519 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.27a)


title: Z3EVp_YHP1_60_rep1


title: Primary breast cancer, sample 15

description:
EMC204_15
1155.CEL


title: Primary breast cancer, sample 14

description:
EMC204_14
1154.CEL


title: WT_MI_D1_1_26

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 118”.
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 2518 (Illumina) in rapid mode

value: MI day1

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.26a)


title: Z3EVp_YHP1_20_rep3


title: Human_1MII_c_Ribo

description:
ribosome-binding RNA
T&T-seq

value: MII


title: Primary breast cancer, sample 13

description:
EMC204_13
1150.CEL


title: Human_Morula_a_RNA

description:
ployA RNA
T&T-seq

value: transcriptome


title: Z3EVp_YHP1_20_rep1


title: WT_MI_D1_1_25

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 117”.
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 2517 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.25a)


title: Human_Morula_b_RNA

description:
ployA RNA
T&T-seq

value: morula


title: Human_1MII_b_Ribo

description:
ribosome-binding RNA
T&T-seq

value: translatiome


title: Primary breast cancer, sample 11

description:
EMC204_11
1145.CEL


title: Z3EVp_yhp1_13A_60_rep3

description:
MATa ura3∆0 his3∆1 lyp∆0 can1∆::STE2pr-SpHIS5 URA3::Z4pr-yhp1-13A-3V5-KanMx HAP1+::NatMX::pACT1-Z3EV-ENO2term
TPM.inducible.yhp1.xlsx

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-yhp1-13A-3V5-KanMx HAP1+::NatMX::pACT1-Z3EV-ENO2term


title: WT_MI_D1_1_23

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 115”.
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 2515 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.23a)


title: Primary breast cancer, sample 10

description:
EMC204_10
1144.CEL

value: other


title: WT_MI_D1_1_21

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 113”.
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 2513 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.21a)


title: Human_10MII_b_Ribo

description:
ribosome-binding RNA
T&T-seq


title: Primary breast cancer, sample 6

description:
EMC204_6
1139.CEL

value: brain+other


title: Z3EVp_yhp1_13A_20_rep3


title: WT_MI_D1_1_22

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 114”.
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 2514 (Illumina) in rapid mode

value: ishchemic + border

value: single-cardiomyocyte

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.22a)


title: WT_MI_D1_1_24

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 116”.
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 2516 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.24a)


title: WT_MI_D1_1_20

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 112”.
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 2512 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.20a)


title: Human_1MII_c_RNA

description:
ployA RNA
T&T-seq


title: Z3EVp_yhp1_13A_60_rep1


title: Primary breast cancer, sample 7

description:
EMC204_7
1140.CEL


title: Primary breast cancer, sample 8

description:
EMC204_8
1142.CEL


title: Human_10MII_a_Ribo

description:
ribosome-binding RNA
T&T-seq


title: WT_MI_D1_1_2

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 111”.
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 2511 (Illumina) in rapid mode

value: MI day1

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.19a)


title: Z3EVp_yhp1_13A_20_rep2


title: Z3EVp_YHP1_20_rep2

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-YHP1-3V5-KanMx HAP1+::NatMX::pACT1-Z3EV-ENO2term


title: Z3EVp_yhp1_13A_60_rep2


title: Human_1MII_a_RNA

description:
ployA RNA
T&T-seq

value: MII

value: transcriptome


title: Primary breast cancer, sample 5

description:
EMC204_5
1137.CEL


title: Human_1MII_a_Ribo

description:
ribosome-binding RNA
T&T-seq


title: Primary breast cancer, sample 4

description:
EMC204_4
1133.CEL


title: Primary breast cancer, sample 3

description:
EMC204_3
1132.CEL


title: Primary breast cancer, sample 2

description:
EMC204_2
1058.CEL


title: Z3EVp_yhp1_13A_20_rep1


title: Human_1MII_b_RNA

description:
ployA RNA
T&T-seq


title: WT_MI_D1_1_19

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 110”.
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 2510 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.18a)


title: Z3EVp_yhp1_13A_0_rep1


title: Z3EVp_yhp1_13A_0_rep3


title: Human_1GV_c_Ribo

description:
ribosome-binding RNA
T&T-seq

value: GV

value: translatiome


title: WT_MI_D1_1_16

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 107”.
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 2507 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.15a)


title: Human_1GV_b_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)


title: Human_10MII_b_RNA

description:
ployA RNA
T&T-seq


title: WT_MI_D1_1_18

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 109”.
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 2509 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.17a)


title: Z3EVp_yhp1_13A_0_rep2

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.

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-yhp1-13A-3V5-KanMx HAP1+::NatMX::pACT1-Z3EV-ENO2term


title: WT_MI_D1_1_14

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 105”.
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 2505 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.13a)


title: Human_10MII_a_RNA

description:
ployA RNA
T&T-seq


title: Z3EVp_YHP1_0_rep3


title: PC12 cells,  OGD/R+miR-483-5p group, rep 2

city: shenzhen

first: Qiang

last: Zhang

state: Guangdong

address: 628 Zhenyuaan Rd.

department: Emergency medicine

institute: The seventh Affiliated Hospital of Sun Yat sen University

data_processing:
The sequencing was conducted by Illumina HiSeq 2000 followed by Trinity de novo assembly into unigenes (the reference library constructed by non-trasngenic control fish), and, then Soapnuke software (ver. 1.5.2) is used to filter the data. Bowtie software (ver. 2.3.3.1) is used to align effective sequences with the reference genome of corresponding species, Cufflinks software (ver. 2.2.1) is used to assemble transcripts to obtain new transcripts.
Finally, FPKM data was generated with the Rsem (rnaseq by expectation maximization ver. 1.3.1) software to represent the expression levels.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: PC12 cells

growth_protocol: PC12 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C，Highly differentiated  PC12 cell line was achieved after treatment with  nerve growth factor (50ng/ml,Gibco,Lot No.2218553 ）for 48 hours.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent according to the manufacturer’s protocol. 1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x100 paired end flow cell.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells seeded in culture plates were exposed to hypoxia conditions for 4 hours with 1% O2, 5% CO2, and 94% N2 in a glucose-free medium. Cells were then incubated with a normal culture medium and reoxygenated for 6 hours before sequencing.

tag: cell line

value: PC12 cells

tag: cell type

value: adrenal medullary chromaffin differentiated cell line

value: PC12 cells were transfected with miR-483-5p mimics,after 48h,the cells was performed with OGD/R treatment.


title: PC12 cells,OGD/R group, rep 3

value: OGD/R

value: performed with OGD/R treatment.


title: PC12 cells,  OGD/R+miR-483-5p group, rep 1

value: PC12 cells were transfected with miR-483-5p mimics,after 48h, the cells was performed with OGD/R treatment.


title: WT_MI_D1_1_15

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 106”.
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 2506 (Illumina) in rapid mode

value: MI day1

value: ishchemic + border

value: single-cardiomyocyte

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.14a)


title: Human_10GV_b_Ribo

description:
ribosome-binding RNA
T&T-seq


title: WT_MI_D1_1_17

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 108”.
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 2508 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.16a)


title: Z3EVp_YHP1_0_rep2

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-YHP1-3V5-KanMx HAP1+::NatMX::pACT1-Z3EV-ENO2term


title: Primary breast cancer, sample 1

description:
EMC204_1
1026.CEL

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

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

value: other


title: PC12 cells,OGD/R group ,rep 2


title: PC12 cells,  OGD/R+miR-483-5p group, rep 3


title: Human_1GV_a_Ribo

description:
ribosome-binding RNA
T&T-seq

value: GV

value: translatiome


title: Primary breast cancer, sample 12

description:
EMC204_12
1148.CEL


title: Z3EVp_YHP1_0_rep1


title: WT_MI_D1_1_13

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 104”.
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 2504 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.12a)


title: Human_10GV_a_Ribo

description:
ribosome-binding RNA
T&T-seq


title: Human_1GV_c_RNA

description:
ployA RNA
T&T-seq

value: transcriptome


title: PC12 cells,OGD/R  group ,rep 1

value: PC12 cells


title: ctrl_yox1_9A_60_rep2

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

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


title: WT_MI_D1_1_11

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 102”.
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 2502 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.10a)


title: PC12 cells,control group,rep 3

value: adrenal medullary chromaffin differentiated cell line

value: control group


title: WT_MI_D1_1_12

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 103”.
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 2503 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.11a)


title: ctrl_yox1_9A_60_rep3


title: Spatial_Csrp3OE_MI_day14

description: Visium (10X Genomics)

data_processing:
Raw data was processed using Space Ranger (version 1.2.1)
Each barcode.tsv.gz, features.tsv.gz and matrix.mtx.gz files genereted using Space Ranger.

source_name: Heart

extract_protocol:
Frozen samples were embedded in OCT (TissueTek Sakura) and cryosectioned at −14ºC (Leica CM1860). Sections were placed on chilled Visium Spatial Gene Expression Slides (2000233, 10X Genomics), and adhered by warming the back of the slide. Tissue sections were then fixed in chilled methanol and stained according to the Visium Spatial Gene Expression User Guide (CG000239 Rev D, 10X Genomics).
Libraries were prepared according to the Visium Spatial Gene Expression User Guide (CG000239 Rev D, 10X Genomics)

value: MI day14_Csrp3OE

value: heart

value: 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.


title: WT_MI_D1_1_10

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 101”.
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 2501 (Illumina) in rapid mode

value: MI day1

value: ishchemic + border

value: single-cardiomyocyte

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.9a)


title: S2_RTnTag_m6A_preTagRT_n2_(210511_NK_dm_658)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: RT&Tag for m6A in S2 cells, preTagRT unbiotinylated oligo(dT), replicate 2

library_source: genomic

data_processing:
Genome_build: UCSC dm6
1. We used trim-galore 0.6.4_dev with parameters "-q 20 --length 20" to trim adapters from 50bp or 100bp single-end reads. 2. We used hisat2 2.1.0 with parameters "--max-intronlen 5000" to map the trimmed reads to the reference sequence for Drosophilia melanogaster, dm6 from UCSC. 3. We used deepTools 3.3.1 bedCoverage to with parameters "--normalizeUsing CPM" to make bigwig files (Supplementary file .bw).

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: RT&Tag

tag: antibody

value: m6A Megabase cat# AP60500

value: S2 cell line


title: WT_MI_D1_1_1

data_processing:
Raw sequencing reads from single-cardiomyocyte RNA sequencing libraries were trimmed to remove adapter sequences and low-quality bases using fastp-0.20.038 with the parameters “--cut_tail --cut_tail_window_size 10 --cut_tail_mean_quality 30 --length_required 100”.
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 2500 (Illumina) in rapid mode

value: The clean reads were aligned to the mouse genome (mm10) using STAR (version 2.7.8a)


title: S2_RTnTag_m6A_coTagRT_n2_(210511_NK_dm_662)

description: RT&Tag for m6A in S2 cells, coTagRT unbiotinylated oligo(dT), replicate 2


title: Human_10GV_a_RNA

description:
ployA RNA
T&T-seq

value: GV

value: transcriptome


title: S2_RTnTag_m6A_preTagRT_n1_(210511_NK_dm_650)

description: RT&Tag for m6A in S2 cells, preTagRT unbiotinylated oligo(dT), replicate 1


title: PC12 cells,control group,rep 2

value: PC12 cells


title: ctrl_yox1_9A_20_rep3

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


title: Spatial_shCsrp3_MI_day14

description: Visium (10X Genomics)

value: MI day14_shCsrp3


title: ctrl_yox1_9A_20_rep1


title: Human_1GV_a_RNA

description:
ployA RNA
T&T-seq


title: ctrl_yox1_9A_20_rep2


title: Spatial_shCsrp3_MI_day1

description: Visium (10X Genomics)

value: MI day1_shCsrp3


title: PC12 cells,control group,rep 1

value: adrenal medullary chromaffin differentiated cell line

value: control group


title: FSF1_TERT_12

city: Grand Rapids

first: Peter

middle: W

last: Laird

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

data_processing:
Pooled lbraries were sequenced using 2x50 bp sequencing on the Illumina NovaSeq 6000 sequencer at the Van Andel Research Institute. Data were demultplexed using Bcl2fastq v1.9.0.
Adapter removal performed using Trimgalore v0.6.0 with options --paired -q 20
Alignment to hg38 performed using STAR v2.7.8a with options --twopassMode Basic --quantMode GeneCounts
Data were filtered in R for a minimum of 0.36 counts per million in >6 samples to generate the filtered expression matrix
RNAseq differential expression analysis was performed in R (v4.1.1) using standard edgeR and DESeq2 workflow
Genome_build: GRCh38

source_name: Skin, sacrum

extract_protocol:
RNA was isolated from frozen cell pellets using the AllPrep DNA/RNA Mini Kit (Qiagen 80204), then stored at -80°C before analysis.
RNA Libraries were prepared from 100 ng of total RNA with the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems KK8401).

tag: subexperiment

value: TERT immortalization

value: 16 fetal weeks

value: female

value: ambient

value: TERT

tag: subculture

tag: growth protocol

value: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.

tag: treatment protocol

value: Low-PD primary fibroblasts were transduced with purified lentiviral particles containing expression vectors encoding human Telomerase Reverse Transcriptase (TERT) and hygromycin resistance marker. Following selection with 250ug/ml hygromycin B, cells were serially cultured in perpetuity, in triplicate.


title: Spatial_Csrp3OE_MI_day1

description: Visium (10X Genomics)

value: MI day1_Csrp3OE

value: heart

value: 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.


title: ctrl_yox1_9A_60_rep1


title: S2_RTnTag_m6A_coTagRT_n1_(210511_NK_dm_654)

description: RT&Tag for m6A in S2 cells, coTagRT unbiotinylated oligo(dT), replicate 1

value: m6A Megabase cat# AP60500

value: S2 cell line


title: Human_1GV_b_RNA

description:
ployA RNA
T&T-seq

tag: Stage

value: GV

tag: type

value: transcriptome

tag: treatment

tag: cell number


title: Human_10GV_b_RNA

description:
ployA RNA
T&T-seq


title: FSF1_TERT_11


title: ctrl_yox1_9A_0_rep3

tag: strain

tag: genotype

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


title: ctrl_yox1_9A_0_rep2


title: S2_RTnTag_m6A_IgGcontrol_coTagRT_n1_(210511_NK_dm_651)

description: RT&Tag for IgG in S2 cells, coTagRT unbiotinylated oligo(dT), replicate 1

value: IgG Abcam cat# ab172730


title: ctrl_yox1_9A_0_rep1


title: FSF1_TERT_10


title: ctrl_YOX1_60_rep3

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

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


title: S2_RTnTag_m6A_IgGcontrol_preTagRT_n1_(210511_NK_dm_647)

description: RT&Tag for IgG in S2 cells, preTagRT unbiotinylated oligo(dT), replicate 1


title: Spatial_MI_day14_3

description: Visium (10X Genomics)

tag: operation

value: MI day14

tag: region


title: FSF1_TERT_7

value: TERT immortalization

value: 16 fetal weeks


title: Spatial_MI_day7_2

description: Visium (10X Genomics)

value: MI day7

tag: tissue

tag: name in supplementary file


title: S2_RTnTag_m6A_IgGcontrol_coTagRT_n2_(210511_NK_dm_659)

description: RT&Tag for IgG in S2 cells, coTagRT unbiotinylated oligo(dT), replicate 2


title: ctrl_YOX1_20_rep3


title: S2_RTnTag_MSL2_preTagRT_n1_(201221_NK_dm_287)

description: RT&Tag for MSL2 in S2 cells, preTagRT unbiotinylated oligo(dT), replicate 1

value: MSL2 gift from Mitzi Kuroda


title: ctrl_YOX1_20_rep2


title: Spatial_MI_day1_3

description: Visium (10X Genomics)

value: MI day1

tag: genome build


title: FSF1_TERT_8

value: female

value: ambient

value: TERT

value: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.

value: Low-PD primary fibroblasts were transduced with purified lentiviral particles containing expression vectors encoding human Telomerase Reverse Transcriptase (TERT) and hygromycin resistance marker. Following selection with 250ug/ml hygromycin B, cells were serially cultured in perpetuity, in triplicate.


title: Spatial_MI_day7_3

description: Visium (10X Genomics)

value: heart

value: 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.


title: FSF1_TERT_9


title: S2_RTnTag_MSL2_coTagRT_n2_(210820_NK_dm_904)

description: RT&Tag for MSL2 in S2 cells, coTagRT unbiotinylated oligo(dT), replicate 2

tag: cell type

value: S2 cell line


title: FSF1_TERT_6


title: ctrl_YOX1_60_rep2


title: ctrl_YOX1_60_rep1


title: S2_RTnTag_MSL2_preTagRT_n2_(210211_NK_dm_388)

description: RT&Tag for MSL2 in S2 cells, preTagRT unbiotinylated oligo(dT), replicate 2

tag: antibody


title: ctrl_YOX1_20_rep1


title: FSF1_TERT_5

tag: subexperiment


title: Spatial_MI_day1_2

description: Visium (10X Genomics)


title: Spatial_MI_day14_2

description: Visium (10X Genomics)


title: S2_RTnTag_m6A_IgGcontrol_preTagRT_n2_(210511_NK_dm_655)

description: RT&Tag for IgG in S2 cells, preTagRT unbiotinylated oligo(dT), replicate 2


title: CM_MI_day14_RZ_2

description: Chromium (10X Genomics)

data_processing:
Raw data was processed using Cell Ranger (version 4.1.1)
Each barcode.tsv.gz, features.tsv.gz and matrix.mtx.gz files genereted using Cell Ranger.

source_name: cardiomyocyte

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 (IZ+BZ vs RZ) 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). Nuclei were isolated immediately after the collection of cardiomyocytes using Minute™ Detergent-Free Single Nuclei Isolation Kit (NI-024, Invent Biotechnologies, USA) according to the manufacturer’s instruction.
Single-nucleus cDNA libraries were generated using 5,000 isolated nuclei by the Chromium 3′ v3 chemistry kit (10x Genomics) according to the manufacturer’s instruction.

value: remote

value: cardiomyocyte

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2033-A.tar.gz.


title: S2_RTnTag_IgG_preTagRT_n2_(210211_NK_dm_386)

value: IgG Abcam cat# ab172730


title: Spatial_MI_day1_1

description: Visium (10X Genomics)


title: S2_RTnTag_IgG_preTagRT_n1_(201221_NK_dm_285)


title: ctrl_YOX1_0_rep3

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


title: FSF1_TERT_2

value: TERT immortalization

value: 16 fetal weeks

tag: subculture


title: CM_MI_day14_IZ+BZ_2

description: Chromium (10X Genomics)

value: MI day14

value: ishchemic + border

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2031-A.tar.gz.


title: ctrl_YOX1_0_rep2


title: S2_RTnTag_IgG_coTagRT_n2_(210820_NK_dm_903)


title: CM_MI_day14_IZ+BZ_1

description: Chromium (10X Genomics)

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2030-A.tar.gz.


title: NFF2_LOWO2_8

source_name: Foreskin

value: Reduced oxygen

value: 0 years

value: male

value: low 3%

value: a

tag: growth protocol

value: Fibroblasts were maintained in Ham’s F12/DMEM 1:1 media supplemented with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: ctrl_YHP1_60_rep3

description:
MATa ura3∆0 his3∆1 lyp∆0 can1∆::STE2pr-SpHIS5 URA3::Z4pr-HO HAP1+::NatMX::pACT1-Z3EV-ENO2term YHP1-3V5-KanMx
TPM.inducible.yhp1.xlsx

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-HO HAP1+::NatMX::pACT1-Z3EV-ENO2term YHP1-3V5-KanMx


title: FSF1_TERT_3

value: female

value: ambient

value: TERT

value: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.

tag: treatment protocol

value: Low-PD primary fibroblasts were transduced with purified lentiviral particles containing expression vectors encoding human Telomerase Reverse Transcriptase (TERT) and hygromycin resistance marker. Following selection with 250ug/ml hygromycin B, cells were serially cultured in perpetuity, in triplicate.


title: ctrl_YHP1_60_rep2


title: FSF1_TERT_1

value: TERT immortalization

value: 16 fetal weeks


title: S2_RTnTag_H3K27me3_preTagRT_n2_(210211_NK_dm_387)

description: RT&Tag for H3K27me3 in S2 cells, preTagRT unbiotinylated oligo(dT), replicate 2

value: H3K27me3 Cell Signaling Technology cat# CST9733

value: S2 cell line


title: S2_RTnTag_H3K27me3_preTagRT_n1_(201221_NK_dm_286)

description: RT&Tag for H3K27me3 in S2 cells, preTagRT unbiotinylated oligo(dT), replicate 1


title: ctrl_YHP1_60_rep1


title: NFF2_LOWO2_7


title: CM_MI_day7_RZ_2

description: Chromium (10X Genomics)

value: MI day7

value: remote

value: cardiomyocyte

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2029-A.tar.gz.


title: S2_RTnTag_IgG_coTagRT_n1_(210820_NK_dm_883)

value: IgG Abcam cat# ab172730


title: CM_MI_day7_IZ+BZ_2

description: Chromium (10X Genomics)

value: ishchemic + border

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2027-A.tar.gz.


title: S2_RTnTag_MSL2_coTagRT_n1_(210820_NK_dm_884)

description: RT&Tag for MSL2 in S2 cells, coTagRT unbiotinylated oligo(dT), replicate 1

value: MSL2 gift from Mitzi Kuroda


title: CM_MI_day14_RZ_1

description: Chromium (10X Genomics)

value: MI day14

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2032-A.tar.gz.


title: ctrl_YHP1_20_rep3

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-HO HAP1+::NatMX::pACT1-Z3EV-ENO2term YHP1-3V5-KanMx


title: NFF2_LOWO2_6

value: Reduced oxygen

value: 0 years

value: male

value: low 3%

value: a

value: Fibroblasts were maintained in Ham’s F12/DMEM 1:1 media supplemented with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: NFF2_LOWO2_5


title: ctrl_YHP1_20_rep2


title: ctrl_YOX1_0_rep1

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


title: FSF1_TERT_4

value: TERT immortalization

value: 16 fetal weeks

value: female

value: ambient

value: TERT

value: Fibroblasts were maintained in Eagle’s MEM with Earle’s salts and non-essential amino acids with 15% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.

value: Low-PD primary fibroblasts were transduced with purified lentiviral particles containing expression vectors encoding human Telomerase Reverse Transcriptase (TERT) and hygromycin resistance marker. Following selection with 250ug/ml hygromycin B, cells were serially cultured in perpetuity, in triplicate.


title: NFF2_LOWO2_4


title: S2_RTnTag_H3K27me3_coTagRT_n1_(210820_NK_dm_886)

description: RT&Tag for H3K27me3 in S2 cells, coTagRT unbiotinylated oligo(dT), replicate 1

value: H3K27me3 Cell Signaling Technology cat# CST9733

value: S2 cell line


title: CM_MI_day7_IZ+BZ_1

description: Chromium (10X Genomics)

value: MI day7

value: ishchemic + border

value: cardiomyocyte

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2026-A.tar.gz.


title: NFF2_LOWO2_3

value: Reduced oxygen

value: 0 years

value: male

value: low 3%


title: CM_MI_day1_RZ_2

description: Chromium (10X Genomics)

value: MI day1

value: remote

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2025-A.tar.gz.


title: CM_MI_day1_RZ_1

description: Chromium (10X Genomics)

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2024-A.tar.gz.


title: 55644

city: Vienna

first: Angelos

last: Athanasiou

address: Veterinaerplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

data_processing:
Removal of the 8-bp Unique Molecular Identifiers (UMIs) from the 5’ end of the raw reads using scripts of the Computational Genomics Analysis Tools (CGAT) collection and addition of UMIs to the header of the reads for the ease of later processing steps.
Removal of adapters from the 3' end using the adapter trimmer Cutadapt.
Removal of the 2 bp long spacer sequence CA preceding each read.
Mapping of trimmed reads against the human reference genome (GRCh38) using the Spliced Transcripts Alignment to a Reference (STAR) aligner. No mismatch was allowed within the first 25 bp of the reads; a single mismatch was allowed in total.
Removal of PCR duplicates by deduplication and utilization of UMI tools to count the sequences.
Assignment of the biotypes of the remaining reads based on the annotation of mirBase (version 21), the Genomic tRNA Database and the GENCODE project (release 22). Sequence molecules mapping to multiple genomic locations were assigned by a weighting approach (molecule number/number of annotated locations). miRNAs expressed from different genomic locations were collapsed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file containing counts of each miRNA molecule

source_name: human blood plasma

extract_protocol:
miRNeasy Serum/Plasma Kit (Qiagen)
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (New England Biolabs)

value: plasma


title: CM_MI_day7_RZ_1

description: Chromium (10X Genomics)

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2028-A.tar.gz.


title: ctrl_YHP1_20_rep1

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-HO HAP1+::NatMX::pACT1-Z3EV-ENO2term YHP1-3V5-KanMx


title: 55645


title: NFF2_LOWO2_2

value: a

value: Fibroblasts were maintained in Ham’s F12/DMEM 1:1 media supplemented with 10% v/v fetal bovine serum. Triplicate cultures derived from the same parent plate or vial obtained from Coriell were maintained in parallel through replicative senescence, which was defined in this study as drastically slowed growth (inability to reach near-confluence at 14 days after previous passage) or viable fraction of cells falling below 60%. Passaging occurred as cells became approximately 90% confluent.


title: CM_MI_day1_IZ+BZ_2

description: Chromium (10X Genomics)

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2023-A.tar.gz.


title: S2_RTnTag_H3K27me3_coTagRT_n2_(210820_NK_dm_906)

description: RT&Tag for H3K27me3 in S2 cells, coTagRT unbiotinylated oligo(dT), replicate 2

value: H3K27me3 Cell Signaling Technology cat# CST9733

value: S2 cell line


title: ctrl_yhp1_13A_60_rep2

description:
MATa ura3∆0 his3∆1 lyp∆0 can1∆::STE2pr-SpHIS5 URA3::Z4pr-HO HAP1+::NatMX::pACT1-Z3EV-ENO2term yhp1-13A-3V5-KanMx
TPM.inducible.yhp1.xlsx

value: MATa ura3delta0 his3delta1 lypdelta0 can1delta::STE2pr-SpHIS5 URA3::Z4pr-HO HAP1+::NatMX::pACT1-Z3EV-ENO2term yhp1-13A-3V5-KanMx


title: CM_MI_day1_IZ+BZ_1

description: Chromium (10X Genomics)

value: ishchemic + border

value: cardiomyocyte

value: The reference transcript data and the gene annotation file for mouse was downloaded from  https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2022-A.tar.gz.


title: NFF2_LOWO2_1

value: Reduced oxygen

value: 0 years

value: male

value: low 3%


title: NFF2_AMBO2_8

value: ambient