title: WT_sham2_CM_37

description: WT sham1 CM


title: WT_sham2_CM_36

status: Public on Mar 03 2022

type: SRA

city: Tokyo

first: Seitaro

last: Nomura

state: Select a State or Province

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

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

description: WT sham1 CM

library_source: transcriptomic

data_processing:
RefSeq transcripts (coding and non-coding) were downloaded from the UCSC Genome Browser (http://genome.ucsc.edu).
Reads were mapped to the mouse genome (mm9) with the parameters “-g 1 -p 8 mm9—no-coverage-search” using TopHat (Trapnell et al., 2009).
FPKM was calculated with reads mapped to the nuclear genome (Trapnell et al., 2010).
All genes expressed at an FPKM value of ≥10 in at least one of the samples were used to for subsequent analysis.
Genome_build: mm9
Supplementary_files_format_and_content: csv

molecule: total RNA

organism: Mus musculus

source_name: cardiomyocytes

growth_protocol: C57BL/6N mice were purchased from CLEA Japan, Inc. Female and male mice were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 19-h light/dark cycle with ad libitum access to food and water. All experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines of the University of Tokyo for animal experiments.

extract_protocol:
Cardiomyocytes were isolated using Langendorff perfusion from the left ventricular free wall. 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). 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 after isolation from 2 mice with a 0.2–2-µL pipette (sample volume, 0.5 µL) and incubated in lysis buffer.
Single-cell cDNA libraries were generated using the Smart-seq2 protocol. For the cDNA libraries constructed by Smart-seq2, the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2 for cardiomyocytes) 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.

treatment_protocol: Sham surgery was performed in mice randomly selected from among those weighing 20–23 g at the age of 9–11 weeks.

tag: cell type

value: cardiomyocytes

tag: strain

tag: operation

value: sham

tag: tissue

value: heart

tag: name in supplementary file

tag: molecule subtype

value: Full length

tag: protocol


title: Sp193_Af_6h

city: Jena

first: Sascha

last: Schäuble

address: Beutenbergstraße 11a

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

data_processing:
quality control with FastQC (v0.11.7)
quality trimming of raw data with bbduk from the BBMap (v37.44)
read alignment STAR Aligner (v2.5.2b)
read counting with featureCounts (v1.20.6)
Genome_build: Ensembl annotation GRCh38.89
Supplementary_files_format_and_content: tab delimited text file with unnormalised read counts
Supplementary_files_format_and_content: tab delimited text file with MRN normalised read counts

organism: Homo sapiens

source_name: monocytes

growth_protocol: CD14+ monocytes were isolated from EDTA-anticoagulated blood after Ficoll-Paque density gradient centrifugation by magnetic-activated cell sorting using human CD14 MicroBeads and the autoMACS Pro Separator system according to the manufacturer’s instructions (Miltenyi Biotec). CD14+ monocytes were resuspended in RPMI1640 with L-glutamine supplemented with 20 % heat-inactivated FBS and cultured at a density of 2.5 x 106 cells/ml. After overnight resting, monocyte viability was determined by trypan blue staining (≥85 %) prior to stimulation.

extract_protocol:
After stimulation, the cells were separated from the supernatant by centrifugation. Total RNA was purified using the AllPrep96 DNA/RNA Kit from Qiagen according to the manufacturer’s instructions.
RNA-sequencing used the QuantSeq-3’-mRNA library preparation kit (Lexogen, Vienna, Austria). Next generation sequencing (NGS) libraries were sequenced at the end of the 3' poly-A tail using a HiSeq 2500 platform (Illumina, San Diego, USA).

treatment_protocol: Monocytes were stimulated with inactivated A. fumigatus germ tubes (multiplicity of infection [MOI] =0.5), S. aureus (MOI =5), N. meningitidis (MOI =1) or media as unstimulated control for 3h or 6h

tag: Sex

value: male

tag: stimulation

value: A. fumigatus

tag: time point


title: Sp193_Af_3h


title: WT_sham2_CM_35

description: WT sham1 CM


title: WT_sham2_CM_34

description: WT sham1 CM


title: Sp192_Sa_6h

value: S. aureus


title: WT_sham2_CM_33

description: WT sham1 CM


title: Sp192_Sa_3h


title: Sp192_Nm_3h

value: N. meningitidis


title: WT_sham2_CM_32

description: WT sham1 CM


title: Sp192_K_6h

value: Control


title: WT_sham2_CM_31

description: WT sham1 CM


title: WT_sham2_CM_30

description: WT sham1 CM


title: Sp192_Nm_6h


title: Sp192_K_3h


title: Sp194_K_6h


title: Sp192_Af_6h


title: WT_sham2_CM_29

description: WT sham1 CM


title: WT_sham2_CM_28

description: WT sham1 CM


title: Sp192_Af_3h


title: WT_sham2_CM_27

description: WT sham1 CM


title: Sp191_Sa_6h


title: Sp191_Sa_3h


title: WT_sham2_CM_43

description: WT sham1 CM


title: WT_sham2_CM_24

description: WT sham1 CM


title: Sp191_Nm_3h


title: WT_sham2_CM_23

description: WT sham1 CM


title: WT_sham2_CM_21

description: WT sham1 CM


title: Sp191_K_6h


title: WT_sham2_CM_22

description: WT sham1 CM


title: Sp191_K_3h


title: Sp191_Af_6h


title: WT_sham2_CM_20

description: WT sham1 CM


title: WT_sham2_CM_19

description: WT sham1 CM


title: Sp191_Af_3h


title: Sp190_Sa_6h


title: WT_sham2_CM_18

description: WT sham1 CM


title: Sp190_Sa_3h


title: WT_sham2_CM_17

description: WT sham1 CM


title: Sp190_Nm_6h


title: Sp190_Nm_3h


title: WT_sham2_CM_16

description: WT sham1 CM


title: WT_sham2_CM_15

description: WT sham1 CM


title: Sp190_K_6h


title: Sp190_K_3h


title: WT_sham2_CM_13

description: WT sham1 CM


title: WT_sham2_CM_14

description: WT sham1 CM


title: Sp190_Af_6h


title: WT_sham2_CM_12

description: WT sham1 CM


title: Sp189_Sa_6h


title: Sp189_Sa_3h


title: Sp190_Af_3h


title: WT_sham2_CM_11

description: WT sham1 CM


title: WT_sham2_CM_9

description: WT sham1 CM


title: WT_sham2_CM_8

description: WT sham1 CM


title: WT_sham2_CM_10

description: WT sham1 CM


title: WT_sham2_CM_7

description: WT sham1 CM


title: Sp191_Nm_6h


title: Sp189_K_6h


title: WT_sham2_CM_26

description: WT sham1 CM


title: WT_sham2_CM_6

description: WT sham1 CM


title: WT_sham2_CM_25

description: WT sham1 CM


title: Sp189_K_3h


title: WT_sham2_CM_5

description: WT sham1 CM


title: Sp189_Af_6h


title: Sp189_Af_3h


title: Sp188_Sa_6h


title: WT_sham2_CM_2

description: WT sham1 CM


title: WT_sham2_CM_4

description: WT sham1 CM


title: Sp188_Sa_3h


title: Sp188_Nm_3h


title: WT_sham2_CM_1_bulk

description: WT sham1 CM


title: Sp188_Af_6h


title: WT_sham2_CM_3

description: WT sham1 CM


title: Sp188_K_3h


title: Sp187_Sa_6h


title: WT_sham1_CM_88

description: WT sham1 CM


title: WT_sham1_CM_89

description: WT sham1 CM


title: Sp189_Nm_6h


title: Sp188_Af_3h


title: Sp187_K_6h


title: Sp189_Nm_3h


title: Sp187_Af_6h


title: Sp188_K_6h


title: WT_sham1_CM_86

description: WT sham1 CM


title: WT_sham1_CM_81

description: WT sham1 CM


title: Sp187_Sa_3h


title: WT_sham1_CM_80

description: WT sham1 CM


title: WT_sham1_CM_91

description: WT sham1 CM


title: Sp188_Nm_6h


title: WT_sham1_CM_87

description: WT sham1 CM


title: WT_sham1_CM_78

description: WT sham1 CM


title: WT_sham1_CM_90

description: WT sham1 CM


title: Sp187_Af_3h


title: Sp187_Nm_3h


title: WT_sham1_CM_84

description: WT sham1 CM


title: WT_sham1_CM_77

description: WT sham1 CM


title: Sp186_Sa_6h


title: WT_sham1_CM_82

description: WT sham1 CM


title: WT_sham1_CM_83

description: WT sham1 CM


title: WT_sham1_CM_85

description: WT sham1 CM


title: WT_sham1_CM_79

description: WT sham1 CM


title: Sp187_Nm_6h


title: WT_sham1_CM_70

description: WT sham1 CM


title: WT_sham1_CM_71

description: WT sham1 CM


title: Sp186_Af_3h


title: WT_sham1_CM_74

description: WT sham1 CM


title: Sp186_Nm_3h


title: WT_sham1_CM_73

description: WT sham1 CM


title: WT_sham1_CM_76

description: WT sham1 CM


title: Sp185_Sa_3h


title: Sp186_Sa_3h


title: WT_sham1_CM_66

description: WT sham1 CM


title: Sp186_Af_6h


title: Sp186_K_3h


title: Sp185_Nm_3h


title: Sp187_K_3h


title: WT_sham1_CM_69

description: WT sham1 CM


title: Sp185_Sa_6h


title: WT_sham1_CM_65

description: WT sham1 CM


title: WT_sham1_CM_64

description: WT sham1 CM


title: Sp185_Af_6h


title: WT_sham1_CM_68

description: WT sham1 CM


title: Sp185_Af_3h


title: WT_sham1_CM_63

description: WT sham1 CM


title: WT_sham1_CM_75

description: WT sham1 CM


title: Sp186_Nm_6h


title: Sp185_Nm_6h


title: Sp186_K_6h


title: WT_sham1_CM_62

description: WT sham1 CM


title: Sp185_K_3h


title: WT_sham1_CM_61

description: WT sham1 CM


title: WT_sham1_CM_72

description: WT sham1 CM


title: Sp185_K_6h


title: Sp184_Sa_3h


title: Sp184_Nm_3h


title: WT_sham1_CM_60

description: WT sham1 CM


title: WT_sham1_CM_67

description: WT sham1 CM


title: Sp184_K_6h


title: WT_sham1_CM_58

description: WT sham1 CM


title: WT_sham1_CM_57

description: WT sham1 CM


title: Sp184_K_3h


title: WT_sham1_CM_59

description: WT sham1 CM


title: Sp183_Sa_6h


title: WT_sham1_CM_53

description: WT sham1 CM


title: Sp184_Af_3h


title: Sp183_Nm_6h


title: WT_sham1_CM_56

description: WT sham1 CM


title: Sp183_Sa_3h


title: WT_sham1_CM_54

description: WT sham1 CM


title: WT_sham1_CM_55

description: WT sham1 CM


title: Sp183_Nm_3h


title: WT_sham1_CM_52

description: WT sham1 CM


title: Sp184_Nm_6h


title: WT_sham1_CM_51

description: WT sham1 CM


title: WT_sham1_CM_50

description: WT sham1 CM


title: Sp183_K_6h


title: Sp183_K_3h


title: Sp182_Sa_6h


title: WT_sham1_CM_47

description: WT sham1 CM


title: Sp183_Af_3h


title: WT_sham1_CM_49

description: WT sham1 CM


title: Sp183_Af_6h


title: Sp184_Af_6h


title: WT_sham1_CM_46

description: WT sham1 CM


title: Sp182_Sa_3h


title: Sp182_Nm_6h


title: WT_sham1_CM_44

description: WT sham1 CM


title: WT_sham1_CM_43

description: WT sham1 CM


title: Sp182_K_3h


title: Sp182_Nm_3h


title: WT_sham1_CM_42

description: WT sham1 CM


title: WT_sham1_CM_45

description: WT sham1 CM


title: Sp182_Af_3h


title: Sp182_K_6h


title: Sp182_Af_6h


title: Sp181_Sa_3h


title: WT_sham1_CM_41

description: WT sham1 CM


title: Sp181_Sa_6h


title: WT_sham1_CM_39

description: WT sham1 CM


title: WT_sham1_CM_40

description: WT sham1 CM


title: Sp181_Nm_6h


title: WT_sham1_CM_36

description: WT sham1 CM


title: WT_sham1_CM_38

description: WT sham1 CM


title: WT_sham1_CM_48

description: WT sham1 CM


title: Sp181_Nm_3h


title: Sp181_K_6h


title: Sp181_K_3h


title: WT_sham1_CM_34

description: WT sham1 CM


title: WT_sham1_CM_37

description: WT sham1 CM


title: WT_sham1_CM_31

description: WT sham1 CM


title: WT_sham1_CM_33

description: WT sham1 CM


title: WT_sham1_CM_35

description: WT sham1 CM


title: Sp181_Af_6h


title: WT_sham1_CM_32

description: WT sham1 CM


title: Sp181_Af_3h


title: Sp180_Sa_6h


title: Sp180_Sa_3h


title: WT_sham1_CM_30

description: WT sham1 CM


title: WT_sham1_CM_29

description: WT sham1 CM


title: Sp81_Af_3h


title: WT_sham1_CM_28

description: WT sham1 CM


title: WT_sham1_CM_27

description: WT sham1 CM


title: Sp80_Sa_6h


title: WT_sham1_CM_26

description: WT sham1 CM


title: Sp80_Sa_3h


title: WT_sham1_CM_25

description: WT sham1 CM


title: Sp80_K_6h


title: Sp80_Nm_3h


title: Sp80_K_3h


title: WT_sham1_CM_24

description: WT sham1 CM


title: Sp79_Sa_6h


title: WT_sham1_CM_21

description: WT sham1 CM


title: WT_sham1_CM_23

description: WT sham1 CM


title: WT_sham1_CM_20

description: WT sham1 CM


title: Sp80_Af_6h


title: Sp79_Nm_6h


title: Sp79_K_6h


title: WT_sham1_CM_22

description: WT sham1 CM


title: Sp79_Af_6h


title: WT_sham1_CM_16

description: WT sham1 CM


title: Sp79_K_3h


title: WT_sham1_CM_19

description: WT sham1 CM


title: Sp79_Af_3h


title: WT_sham1_CM_15

description: WT sham1 CM


title: Sp78_Sa_6h


title: WT_sham1_CM_14

description: WT sham1 CM


title: WT_sham1_CM_12

description: WT sham1 CM


title: WT_sham1_CM_13

description: WT sham1 CM


title: Sp80_Nm_6h


title: WT_sham1_CM_10

description: WT sham1 CM


title: Sp78_K_3h


title: WT_sham1_CM_11

description: WT sham1 CM


title: Sp78_Af_6h


title: Sp78_K_6h


title: WT_sham1_CM_18

description: WT sham1 CM


title: WT_sham1_CM_8

description: WT sham1 CM


title: Sp77_Sa_6h


title: Sp78_Nm_6h


title: Sp78_Af_3h


title: Sp77_Sa_3h


title: Sp77_Nm_6h


title: Sp78_Sa_3h


title: WT_sham1_CM_7

description: WT sham1 CM


title: WT_sham1_CM_2

description: WT sham1 CM


title: WT_sham1_CM_17

description: WT sham1 CM


title: Sp77_K_3h


title: WT_sham1_CM_6

description: WT sham1 CM


title: Sp78_Nm_3h


title: KO_TAC2_FB_45

description: Htra3KO TAC2 FB

source_name: Fibroblasts

extract_protocol:
For the isolation and collection of non-cardiomyocytes, hearts were minced and enzymatically dissociated using 2 mg/mL type 2 collagenase (Worthington), 1 mg/mL dispase (Roche), and 20 U/mL DNAse I (Roche), with 5 cycles of digestion for a total 40 min at 37 °C. After using a 40-μm cell strainer (Greiner) to remove the cardiomyocytes, cells were stained with Zombie Green Fixable Viability Kit (BioLegend) and live cells were collected by fluorescence-activated cell sorting (FACS) using a FACSJazz cell sorter (BD Biosciences). To isolate cardiac fibroblasts, cells were stained with APC conjugated anti-mouse CD140a (PDGFR-α) antibody (#135907, BioLegend), FITC conjugated anti-mouse CD31 Antibody (#102512, BioLegend), and Zombie Green, after which PDGFR-α positive live cells were collected by FACS.
Single-cell cDNA libraries were generated using the Smart-seq2 protocol. For the cDNA libraries constructed by Smart-seq2, the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Actb for non-cardiomyocytes) 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: Actb mRNA forward: CAACTGGGACGACATGGAGA; and Actb mRNA reverse: GCATACAGGGACAGCACAGC. A Ct value of 32 was set as the threshold.

treatment_protocol: TAC surgery was performed in mice randomly selected from among those weighing 20–23 g at the age of 9–11 weeks. After the mice were anaesthetized with 2% isoflurane via inhalation, the aorta was approached via minimal sternal incision and a 7-0 ligature was placed around the vessel using a 26-gauge needle to ensure consistent occlusion. The surgeon was not informed about the genotypes of the mice. Mice that died within 1 week after the operation were excluded from the analysis. Transthoracic echocardiography was performed on conscious mice, using a Vevo 2100 imaging system (Visualsonics, Inc.). To minimize variation in the data, cardiac function was assessed only when the heart rate was 600–700 beats per minute. M-mode echocardiographic images were obtained from a longitudinal view to measure the size and function of the left ventricle.

value: Fibroblasts

value: TAC (W2)


title: KO_TAC2_FB_44

description: Htra3KO TAC2 FB


title: WT_sham1_CM_5

description: WT sham1 CM


title: WT_sham1_CM_4

description: WT sham1 CM


title: Sp77_Nm_3h


title: Sp76_Sa_6h


title: Sp76_Sa_3h


title: WT_sham1_CM_3

description: WT sham1 CM


title: Sp76_Nm_6h


title: KO_TAC2_FB_40

description: Htra3KO TAC2 FB


title: Sp77_Af_6h


title: KO_TAC2_FB_38

description: Htra3KO TAC2 FB


title: Sp76_Af_6h


title: Sp77_K_6h


title: KO_TAC2_FB_35

description: Htra3KO TAC2 FB


title: WT_sham1_CM_9

description: WT sham1 CM


title: Sp75_Sa_6h


title: Sp75_Sa_3h


title: Sp75_Nm_3h


title: Sp76_K_6h


title: Sp77_Af_3h


title: KO_TAC2_FB_43

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_34

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_36

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_37

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_41

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_33

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_42

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_39

description: Htra3KO TAC2 FB


title: WT_sham1_CM_1_bulk

description: WT sham1 CM


title: Sp76_Nm_3h


title: KO_TAC2_FB_31

description: Htra3KO TAC2 FB


title: Sp75_Af_6h


title: Sp75_K_6h


title: Sp76_Af_3h


title: Sp76_K_3h


title: KO_TAC2_FB_30

description: Htra3KO TAC2 FB


title: Sp75_Af_3h


title: KO_TAC2_FB_29

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_26

description: Htra3KO TAC2 FB


title: Sp74_Nm_6h


title: KO_TAC2_FB_28

description: Htra3KO TAC2 FB


title: Sp74_Sa_3h


title: KO_TAC2_FB_27

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_32

description: Htra3KO TAC2 FB


title: Sp75_K_3h


title: Sp74_Sa_6h


title: Sp74_K_3h


title: KO_TAC2_FB_22

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_21

description: Htra3KO TAC2 FB


title: Sp73_Sa_6h


title: Sp74_K_6h


title: KO_TAC2_FB_25

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_23

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_20

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_17

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_19

description: Htra3KO TAC2 FB


title: Sp74_Af_6h


title: Sp74_Nm_3h


title: KO_TAC2_FB_24

description: Htra3KO TAC2 FB


title: Sp73_Af_6h


title: Sp73_Nm_6h


title: KO_TAC2_FB_14

description: Htra3KO TAC2 FB


title: Sp73_Nm_3h


title: KO_TAC2_FB_16

description: Htra3KO TAC2 FB


title: Sp74_Af_3h


title: Sp73_Af_3h


title: Sp72_Nm_6h


title: Sp73_K_6h


title: Sp73_K_3h


title: KO_TAC2_FB_18

description: Htra3KO TAC2 FB


title: Sp73_Sa_3h


title: Sp71_Sa_3h


title: KO_TAC2_FB_13

description: Htra3KO TAC2 FB


title: Sp71_Nm_6h


title: KO_TAC2_FB_10

description: Htra3KO TAC2 FB


title: Sp72_Nm_3h


title: KO_TAC2_FB_5

description: Htra3KO TAC2 FB


title: Sp72_K_6h


title: Sp71_Nm_3h


title: KO_TAC2_FB_12

description: Htra3KO TAC2 FB


title: Sp72_Af_6h


title: KO_TAC2_FB_6

description: Htra3KO TAC2 FB


title: Sp71_K_6h


title: Sp72_Af_3h


title: KO_TAC2_FB_15

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_3

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_7

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_8

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_11

description: Htra3KO TAC2 FB


title: Sp71_Af_6h


title: KO_TAC2_FB_9

description: Htra3KO TAC2 FB


title: Sp71_Sa_6h


title: KO_TAC1_FB_11

description: Htra3KO TAC1 FB

growth_protocol: C57BL/6N mice were purchased from CLEA Japan, Inc. Female and male mice were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 18-h light/dark cycle with ad libitum access to food and water. All experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines of the University of Tokyo for animal experiments.

extract_protocol:
For the isolation and collection of non-cardiomyocytes, hearts were minced and enzymatically dissociated using 2 mg/mL type 2 collagenase (Worthington), 1 mg/mL dispase (Roche), and 20 U/mL DNAse I (Roche), with 5 cycles of digestion for a total 40 min at 37 °C. After using a 40-μm cell strainer (Greiner) to remove the cardiomyocytes, cells were stained with Zombie Green Fixable Viability Kit (BioLegend) and live cells were collected by fluorescence-activated cell sorting (FACS) using a FACSJazz cell sorter (BD Biosciences). To isolate cardiac fibroblasts, cells were stained with APC conjugated anti-mouse CD140a (PDGFR-α) antibody (#135907, BioLegend), FITC conjugated anti-mouse CD31 Antibody (#102511, BioLegend), and Zombie Green, after which PDGFR-α positive live cells were collected by FACS.
Single-cell cDNA libraries were generated using the Smart-seq2 protocol. For the cDNA libraries constructed by Smart-seq2, the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Actb for non-cardiomyocytes) 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: Actb mRNA forward: CAACTGGGACGACATGGAGA; and Actb mRNA reverse: GCATACAGGGACAGCACAGC. A Ct value of 31 was set as the threshold.


title: KO_TAC2_FB_2

description: Htra3KO TAC2 FB


title: KO_TAC2_FB_1

description: Htra3KO TAC2 FB


title: Sp70_Sa_6h


title: Sp71_K_3h


title: Sp71_Af_3h


title: Sp70_Sa_3h


title: KO_TAC1_FB_10

description: Htra3KO TAC1 FB


title: KO_TAC1_FB_8

description: Htra3KO TAC1 FB


title: KO_TAC1_FB_9

description: Htra3KO TAC1 FB


title: Sp70_Nm_6h


title: KO_TAC1_FB_6

description: Htra3KO TAC1 FB


title: KO_TAC2_FB_4

description: Htra3KO TAC2 FB


title: Sp70_Nm_3h


title: KO_TAC1_FB_7

description: Htra3KO TAC1 FB


title: Sp70_K_3h


title: Sp70_K_6h


title: KO_TAC1_FB_5

description: Htra3KO TAC1 FB


title: KO_TAC1_FB_4

description: Htra3KO TAC1 FB


title: Sp70_Af_6h


title: KO_sham2_FB_19

description: Htra3KO sham2 FB

growth_protocol: C57BL/6N mice were purchased from CLEA Japan, Inc. Female and male mice were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 17-h light/dark cycle with ad libitum access to food and water. All experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines of the University of Tokyo for animal experiments.

extract_protocol:
For the isolation and collection of non-cardiomyocytes, hearts were minced and enzymatically dissociated using 2 mg/mL type 2 collagenase (Worthington), 1 mg/mL dispase (Roche), and 20 U/mL DNAse I (Roche), with 5 cycles of digestion for a total 40 min at 37 °C. After using a 40-μm cell strainer (Greiner) to remove the cardiomyocytes, cells were stained with Zombie Green Fixable Viability Kit (BioLegend) and live cells were collected by fluorescence-activated cell sorting (FACS) using a FACSJazz cell sorter (BD Biosciences). To isolate cardiac fibroblasts, cells were stained with APC conjugated anti-mouse CD140a (PDGFR-α) antibody (#135907, BioLegend), FITC conjugated anti-mouse CD31 Antibody (#102510, BioLegend), and Zombie Green, after which PDGFR-α positive live cells were collected by FACS.
Single-cell cDNA libraries were generated using the Smart-seq2 protocol. For the cDNA libraries constructed by Smart-seq2, the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Actb for non-cardiomyocytes) 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: Actb mRNA forward: CAACTGGGACGACATGGAGA; and Actb mRNA reverse: GCATACAGGGACAGCACAGC. A Ct value of 30 was set as the threshold.


title: Sp69_Nm_3h


title: KO_sham2_FB_18

description: Htra3KO sham2 FB


title: Sp69_K_6h


title: Sp69_Sa_3h


title: KO_sham2_FB_16

description: Htra3KO sham2 FB


title: Sp70_Af_3h


title: Sp69_Nm_6h


title: KO_TAC1_FB_3

description: Htra3KO TAC1 FB


title: KO_TAC1_FB_1

description: Htra3KO TAC1 FB


title: Sp69_Af_3h


title: KO_sham2_FB_17

description: Htra3KO sham2 FB


title: Sp69_Sa_6h


title: Sp68_Nm_6h


title: Sp69_Af_6h


title: KO_TAC1_FB_2

description: Htra3KO TAC1 FB


title: Sp69_K_3h


title: KO_sham2_FB_14

description: Htra3KO sham2 FB


title: Sp68_Sa_3h


title: Sp68_Sa_6h


title: KO_sham2_FB_15

description: Htra3KO sham2 FB


title: KO_sham2_FB_11

description: Htra3KO sham2 FB


title: KO_sham2_FB_12

description: Htra3KO sham2 FB


title: Sp68_K_3h


title: Sp68_K_6h


title: Sp68_Nm_3h


title: KO_sham2_FB_9

description: Htra3KO sham2 FB


title: KO_sham2_FB_10

description: Htra3KO sham2 FB


title: Sp68_Af_3h


title: Sp68_Af_6h


title: Sp67_K_6h


title: KO_sham2_FB_5

description: Htra3KO sham2 FB


title: Sp67_Nm_3h


title: KO_sham2_FB_6

description: Htra3KO sham2 FB


title: KO_sham2_FB_4

description: Htra3KO sham2 FB


title: KO_sham2_FB_13

description: Htra3KO sham2 FB


title: KO_sham2_FB_1

description: Htra3KO sham2 FB


title: Sp66_Nm_6h


title: KO_sham2_FB_7

description: Htra3KO sham2 FB


title: Sp66_Sa_3h


title: Sp67_Af_6h


title: KO_sham2_FB_8

description: Htra3KO sham2 FB


title: KO_sham2_FB_2

description: Htra3KO sham2 FB


title: KO_sham2_FB_3

description: Htra3KO sham2 FB


title: Sp66_K_6h


title: Sp66_Nm_3h


title: KO_sham1_FB_32

description: Htra3KO sham1 FB

growth_protocol: C57BL/6N mice were purchased from CLEA Japan, Inc. Female and male mice were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 16-h light/dark cycle with ad libitum access to food and water. All experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines of the University of Tokyo for animal experiments.

extract_protocol:
For the isolation and collection of non-cardiomyocytes, hearts were minced and enzymatically dissociated using 2 mg/mL type 2 collagenase (Worthington), 1 mg/mL dispase (Roche), and 20 U/mL DNAse I (Roche), with 5 cycles of digestion for a total 40 min at 37 °C. After using a 40-μm cell strainer (Greiner) to remove the cardiomyocytes, cells were stained with Zombie Green Fixable Viability Kit (BioLegend) and live cells were collected by fluorescence-activated cell sorting (FACS) using a FACSJazz cell sorter (BD Biosciences). To isolate cardiac fibroblasts, cells were stained with APC conjugated anti-mouse CD140a (PDGFR-α) antibody (#135907, BioLegend), FITC conjugated anti-mouse CD31 Antibody (#102509, BioLegend), and Zombie Green, after which PDGFR-α positive live cells were collected by FACS.
Single-cell cDNA libraries were generated using the Smart-seq2 protocol. For the cDNA libraries constructed by Smart-seq2, the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Actb for non-cardiomyocytes) 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: Actb mRNA forward: CAACTGGGACGACATGGAGA; and Actb mRNA reverse: GCATACAGGGACAGCACAGC. A Ct value of 29 was set as the threshold.


title: KO_sham1_FB_37

description: Htra3KO sham1 FB


title: KO_sham1_FB_34

description: Htra3KO sham1 FB


title: KO_sham1_FB_35

description: Htra3KO sham1 FB


title: Sp66_Af_6h


title: KO_sham1_FB_36

description: Htra3KO sham1 FB


title: KO_sham1_FB_33

description: Htra3KO sham1 FB


title: Sp65_Sa_6h


title: Sp67_K_3h


title: KO_sham1_FB_30

description: Htra3KO sham1 FB


title: Sp67_Af_3h


title: Sp65_Nm_3h


title: KO_sham1_FB_28

description: Htra3KO sham1 FB


title: Sp66_K_3h


title: Sp65_K_3h


title: Sp65_K_6h


title: Sp66_Af_3h


title: KO_sham1_FB_27

description: Htra3KO sham1 FB


title: KO_sham1_FB_25

description: Htra3KO sham1 FB


title: KO_sham1_FB_31

description: Htra3KO sham1 FB


title: Sp65_Af_6h


title: KO_sham1_FB_24

description: Htra3KO sham1 FB


title: Mucoepidermoid Carcinomas sample 18

type: RNA

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

hyb_protocol: Hybridization was performed in hybridization chambers (Agilent Technologies) for 20 hours at 55°C and then washed as recommended.

scan_protocol: Image capture was performed on the Agilent Technologies Scanner (Agilent Technologies), using Scan Control Software 9.X

data_processing: Data extraction and normalization were performed using Software Feature Extraction v.12.0.0.7 (Agilent Technologies). Using default parameters, the background was subtracted and spatially detrended. Data files were analyzed using GeneSpring GX12.6 software (Agilent Technologies).

source_name: Mucoepidermoid Carcinomas sample

label_protocol: The Agilent microRNA Spike-In Kit (Agilent Technologies) was used to control the labeling process and hybridization efficiency. In summary, RNA samples (100ng) were dephosphorylated by incubation with calf intestinal phosphatase at 37°C for 30 minutes and incubated in 100% DMSO at 100°C for 7 minutes. T4 ligase was used for labeling with pCp-Cy3 at 16°C for 2 hours.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions

value: MEC


title: Mucoepidermoid Carcinomas sample 16


title: Mucoepidermoid Carcinomas sample 25


title: Mucoepidermoid Carcinomas sample 14


title: Mucoepidermoid Carcinomas sample 12


title: Sp65_Nm_6h


title: Mucoepidermoid Carcinomas sample 24


title: KO_sham1_FB_29

description: Htra3KO sham1 FB


title: Mucoepidermoid Carcinomas sample 13


title: KO_sham1_FB_23

description: Htra3KO sham1 FB


title: Mucoepidermoid Carcinomas sample 11


title: Sp64_Sa_3h


title: Mucoepidermoid Carcinomas sample 9


title: KO_sham1_FB_22

description: Htra3KO sham1 FB


title: Sp65_Af_3h


title: Mucoepidermoid Carcinomas sample 2


title: KO_sham1_FB_26

description: Htra3KO sham1 FB


title: Sp64_Sa_6h


title: Sp64_Nm_6h


title: Sp64_Nm_3h


title: Mucoepidermoid Carcinomas sample 32


title: Mucoepidermoid Carcinomas sample 6


title: KO_sham1_FB_20

description: Htra3KO sham1 FB


title: KO_sham1_FB_21

description: Htra3KO sham1 FB


title: Sp64_K_6h


title: KO_sham1_FB_19

description: Htra3KO sham1 FB


title: Mucoepidermoid Carcinomas sample 17


title: KO_sham1_FB_18

description: Htra3KO sham1 FB


title: Sp64_Af_6h


title: Mucoepidermoid Carcinomas sample 8


title: Mucoepidermoid Carcinomas sample 19


title: Mucoepidermoid Carcinomas sample 15


title: Mucoepidermoid Carcinomas sample 21


title: KO_sham1_FB_17

description: Htra3KO sham1 FB


title: Mucoepidermoid Carcinomas sample 26


title: Sp64_Af_3h


title: Mucoepidermoid Carcinomas sample 3


title: Mucoepidermoid Carcinomas sample 5


title: Mucoepidermoid Carcinomas sample 23


title: Sp64_K_3h


title: Mucoepidermoid Carcinomas sample 20


title: Mucoepidermoid Carcinomas sample 1


title: Mucoepidermoid Carcinomas sample 7


title: Sp63_Sa_6h


title: Mucoepidermoid Carcinomas sample 4


title: KO_sham1_FB_16

description: Htra3KO sham1 FB


title: KO_sham1_FB_15

description: Htra3KO sham1 FB


title: Sp63_Sa_3h


title: Normal adjacent salivary gland 30

source_name: Normal adjacent salivary gland

value: normal salivary gland


title: Sp63_Nm_3h


title: Normal adjacent salivary gland 33


title: Sp63_K_6h


title: KO_sham1_FB_13

description: Htra3KO sham1 FB


title: Normal adjacent salivary gland 28


title: KO_sham1_FB_12

description: Htra3KO sham1 FB


title: Normal adjacent salivary gland 27


title: KO_sham1_FB_11

description: Htra3KO sham1 FB


title: MDSCs-oe57Rik

city: Tianjin

first: Ya

last: Wang

address: Weijin South Road, Nankai District

country: China

institute: Nankai University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: Myeloid-derived suppressor cell

growth_protocol: Monocyte cells were obtained from peripheral blood and transfected with lnc57Rik siRNA, negative control siRNA or pcDNA3.1-lnc57Rik, and pcDNA3.1 control using Lipofectamine 3000 (Invitrogen) or HiPerFect transfection reagent (siRNA transfection; Qiagen) according to the manufacturer's instructions, then cultured in RPMI-1640 medium supplemented with GM-CSF for 4 days

extract_protocol:
RNA was extracted using TRIzol (Life Technologies). Contaminating DNAs were removed using RNeasy spin columns (Qiagen). The quality of isolated RNA samples was evaluated with an Agilent Bioanalyzer 2100 (Agilent technologies) and the purified RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Infinigen Biotech).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with lnc57Rik siRNA, negative control siRNA or pcDNA3.1-lnc57Rik, and pcDNA3.1 control using Lipofectamine 3000 (Invitrogen) or HiPerFect transfection reagent (siRNA transfection; Qiagen) according to the manufacturer's instructions

value: Myeloid-derived suppressor cell

value: peripheral blood

tag: genotype


title: MDSCs-siNC

value: negative control siRNA


title: MDSCs-si57Rik

value: lnc57Rik siRNA


title: Sp63_K_3h


title: MDSCs-lncGM1082 ko

growth_protocol: Bone marrow cells were obtained from the femurs of C57BL/6 or lnc57Rik KO mice and cultured in RPMI-1640 medium supplemented with GM-CSF plus IL6 for 4 days

value: Bone marrow


title: Sample317.Fibroblast.202897370020_R08C01

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

description:
202897370020_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium HumanMethylation850 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
Noob normalization as implemented in the minfi R package M. Aryee et al. 2014. PMID: 24478339
datBetaNormalized.csv: Comma-separated text file includes Noob normalized beta values.

molecule: genomic DNA

source_name: Fibroblast

label_protocol: Standard Illumina Protocol.

growth_protocol: DNA extracted from cells.

extract_protocol: Genomic DNA was extracted.

tag: age

value: Male

value: Fibroblast

tag: condition

value: Radiation

tag: populationdoublinglevel

tag: passagenumber


title: MDSCs-oeNC

value: pcDNA3.1 control


title: KO_sham1_FB_9

description: Htra3KO sham1 FB

value: sham

value: heart

value: Full length


title: Sp63_Af_3h

value: male

value: A. fumigatus


title: MDSCs-lnc57Rik ko


title: KO_sham1_FB_14

description: Htra3KO sham1 FB

value: Fibroblasts


title: KO_sham1_FB_10

description: Htra3KO sham1 FB


title: Sample316.Fibroblast.202897370020_R07C01

description:
202897370020_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp62_Sa_6h

value: S. aureus


title: Sample315.Fibroblast.202897370020_R06C01

description:
202897370020_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: KO_sham1_FB_8

description: Htra3KO sham1 FB


title: Sample314.Fibroblast.202897370020_R05C01

description:
202897370020_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Normal adjacent salivary gland 29

value: normal salivary gland


title: Sp62_Sa_3h


title: Sample313.Fibroblast.202897370020_R04C01

description:
202897370020_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: KO_sham1_FB_7

description: Htra3KO sham1 FB


title: Sample312.Fibroblast.202897370020_R03C01

description:
202897370020_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample311.Fibroblast.202897370020_R02C01

description:
202897370020_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp62_Nm_6h

value: N. meningitidis


title: Sample310.Fibroblast.202897370020_R01C01

description:
202897370020_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: KO_sham1_FB_6

description: Htra3KO sham1 FB


title: Sp63_Af_6h


title: Sp62_Nm_3h


title: Sample309.Fibroblast.202897270061_R08C01

description:
202897270061_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: KO_sham1_FB_5

description: Htra3KO sham1 FB


title: Sp62_K_6h

value: Control


title: MDSCs-NC

value: Myeloid-derived suppressor cell

value: wild type


title: Sample305.Fibroblast.202897270061_R04C01

description:
202897270061_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample308.Fibroblast.202897270061_R07C01

description:
202897270061_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: KO_sham1_FB_4

description: Htra3KO sham1 FB


title: Sample307.Fibroblast.202897270061_R06C01

description:
202897270061_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample304.Fibroblast.202897270061_R03C01

description:
202897270061_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp62_K_3h


title: Sample306.Fibroblast.202897270061_R05C01

description:
202897270061_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp62_Af_6h


title: Sample302.Fibroblast.202897270061_R01C01

description:
202897270061_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: KO_sham1_FB_3

description: Htra3KO sham1 FB


title: KO_sham1_FB_2

description: Htra3KO sham1 FB


title: Sample301.Fibroblast.202884930029_R08C01

description:
202884930029_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp62_Af_3h


title: Sample303.Fibroblast.202897270061_R02C01

description:
202897270061_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: KO_sham1_FB_1

description: Htra3KO sham1 FB


title: Sample299.Fibroblast.202884930029_R06C01

description:
202884930029_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample296.Fibroblast.202884930029_R03C01

description:
202884930029_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample300.Fibroblast.202884930029_R07C01

description:
202884930029_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp61_K_6h


title: Sample294.Fibroblast.202884930029_R01C01

description:
202884930029_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp61_Nm_6h


title: Sample298.Fibroblast.202884930029_R05C01

description:
202884930029_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp61_K_3h


title: Sample297.Fibroblast.202884930029_R04C01

description:
202884930029_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample292.Fibroblast.202900540056_R07C01

description:
202900540056_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_38

description: WT TAC1 FB

growth_protocol: C57BL/6N mice were purchased from CLEA Japan, Inc. Female and male mice were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 15-h light/dark cycle with ad libitum access to food and water. All experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines of the University of Tokyo for animal experiments.

extract_protocol:
For the isolation and collection of non-cardiomyocytes, hearts were minced and enzymatically dissociated using 2 mg/mL type 2 collagenase (Worthington), 1 mg/mL dispase (Roche), and 20 U/mL DNAse I (Roche), with 5 cycles of digestion for a total 40 min at 37 °C. After using a 40-μm cell strainer (Greiner) to remove the cardiomyocytes, cells were stained with Zombie Green Fixable Viability Kit (BioLegend) and live cells were collected by fluorescence-activated cell sorting (FACS) using a FACSJazz cell sorter (BD Biosciences). To isolate cardiac fibroblasts, cells were stained with APC conjugated anti-mouse CD140a (PDGFR-α) antibody (#135907, BioLegend), FITC conjugated anti-mouse CD31 Antibody (#102508, BioLegend), and Zombie Green, after which PDGFR-α positive live cells were collected by FACS.
Single-cell cDNA libraries were generated using the Smart-seq2 protocol. For the cDNA libraries constructed by Smart-seq2, the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Actb for non-cardiomyocytes) 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: Actb mRNA forward: CAACTGGGACGACATGGAGA; and Actb mRNA reverse: GCATACAGGGACAGCACAGC. A Ct value of 28 was set as the threshold.

value: TAC (W2)


title: WT_TAC1_FB_37

description: WT TAC1 FB


title: WT_TAC1_FB_39

description: WT TAC1 FB


title: Sample293.Fibroblast.202900540056_R08C01

description:
202900540056_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: Male


title: WT_TAC1_FB_35

description: WT TAC1 FB


title: Sample289.Fibroblast.202900540056_R04C01

description:
202900540056_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: Fibroblast


title: Sample295.Fibroblast.202884930029_R02C01

description:
202884930029_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: Radiation


title: Sample291.Fibroblast.202900540056_R06C01

description:
202900540056_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_34

description: WT TAC1 FB


title: Sp60_Sa_6h


title: WT_TAC1_FB_40

description: WT TAC1 FB


title: Sample288.Fibroblast.202900540056_R03C01

description:
202900540056_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample286.Fibroblast.202900540056_R01C01

description:
202900540056_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp60_Nm_6h


title: Sp61_Af_3h


title: WT_TAC1_FB_36

description: WT TAC1 FB


title: Sample285.Fibroblast.202900540099_R08C01

description:
202900540099_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample287.Fibroblast.202900540056_R02C01

description:
202900540056_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample290.Fibroblast.202900540056_R05C01

description:
202900540056_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample283.Fibroblast.202900540099_R06C01

description:
202900540099_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample284.Fibroblast.202900540099_R07C01

description:
202900540099_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample282.Fibroblast.202900540099_R05C01

description:
202900540099_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample280.Fibroblast.202900540099_R03C01

description:
202900540099_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp60_Af_6h


title: Sp61_Sa_6h


title: Sp59_Sa_6h


title: Sample277.Fibroblast.202900540130_R08C01

description:
202900540130_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_30

description: WT TAC1 FB


title: Sp59_Sa_3h


title: Sample281.Fibroblast.202900540099_R04C01

description:
202900540099_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp60_K_6h


title: WT_TAC1_FB_32

description: WT TAC1 FB


title: WT_TAC1_FB_33

description: WT TAC1 FB


title: Sample276.Fibroblast.202900540130_R07C01

description:
202900540130_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp61_Af_6h


title: Sample279.Fibroblast.202900540099_R02C01

description:
202900540099_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_28

description: WT TAC1 FB


title: Sp59_Nm_6h


title: Sample278.Fibroblast.202900540099_R01C01

description:
202900540099_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_29

description: WT TAC1 FB


title: Sp59_Nm_3h


title: Sample275.Fibroblast.202900540130_R06C01

description:
202900540130_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample273.Fibroblast.202900540130_R04C01

description:
202900540130_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_27

description: WT TAC1 FB


title: WT_TAC1_FB_31

description: WT TAC1 FB


title: Sample270.Fibroblast.202900540130_R01C01

description:
202900540130_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_26

description: WT TAC1 FB


title: Sample271.Fibroblast.202900540130_R02C01

description:
202900540130_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp59_K_6h


title: Sp59_K_3h


title: WT_TAC1_FB_25

description: WT TAC1 FB


title: Sample268.Fibroblast.202148010165_R04C01

description:
202148010165_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample267.Fibroblast.202148010165_R03C01

description:
202148010165_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample265.Fibroblast.202148010165_R01C01

description:
202148010165_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample266.Fibroblast.202148010165_R02C01

description:
202148010165_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample274.Fibroblast.202900540130_R05C01

description:
202900540130_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp59_Af_3h


title: Sample263.EmbryonicStemCell.203450830029_R07C01

description:
203450830029_R07C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human

source_name: EmbryonicStemCell

value: EmbryonicStemCell


title: WT_TAC1_FB_24

description: WT TAC1 FB


title: Sp59_Af_6h


title: Sp58_Sa_6h


title: Sample262.EmbryonicStemCell.203450830029_R06C01

description:
203450830029_R06C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human


title: Sample261.EndothelialCell.203450830029_R05C01

description:
203450830029_R05C01
genomic DNA methylation from tissue=EndothelialCell species=Human

source_name: EndothelialCell

value: EndothelialCell


title: Sp58_Nm_6h


title: Sample264.EmbryonicStemCell.203450830029_R08C01

description:
203450830029_R08C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human


title: WT_TAC1_FB_22

description: WT TAC1 FB

value: heart


title: WT_TAC1_FB_21

description: WT TAC1 FB

value: Full length


title: Sample260.EndothelialCell.203450830029_R04C01

description:
203450830029_R04C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sample272.Fibroblast.202900540130_R03C01

description:
202900540130_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample259.EndothelialCell.203450830029_R03C01

description:
203450830029_R03C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Normal adjacent salivary gland 34


title: Sp58_Nm_3h

value: male


title: WT_TAC1_FB_20

description: WT TAC1 FB


title: Sample258.EndothelialCell.203450830029_R02C01

description:
203450830029_R02C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sample269.Fibroblast.202148010165_R05C01

description:
202148010165_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample257.EndothelialCell.203450830029_R01C01

description:
203450830029_R01C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sp58_K_6h


title: WT_TAC1_FB_19

description: WT TAC1 FB


title: Sample256.EmbryonicStemCell.203450830037_R08C01

description:
203450830037_R08C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human


title: Sp58_K_3h


title: Sample255.EmbryonicStemCell.203450830037_R07C01

description:
203450830037_R07C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human


title: WT_TAC1_FB_23

description: WT TAC1 FB


title: Sample254.EmbryonicStemCell.203450830037_R06C01

description:
203450830037_R06C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human


title: WT_TAC1_FB_18

description: WT TAC1 FB


title: Sp58_Af_6h

value: A. fumigatus


title: WT_TAC1_FB_17

description: WT TAC1 FB

value: Fibroblasts


title: Sample253.EndothelialCell.203450830037_R05C01

description:
203450830037_R05C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sample252.EndothelialCell.203450830037_R04C01

description:
203450830037_R04C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sample251.EndothelialCell.203450830037_R03C01

description:
203450830037_R03C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: WT_TAC1_FB_16

description: WT TAC1 FB


title: Sp58_Af_3h


title: Sample249.EndothelialCell.203450830037_R01C01

description:
203450830037_R01C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sample248.Fibroblast.203440280053_R08C01

description:
203440280053_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: RAS


title: WT_TAC1_FB_15

description: WT TAC1 FB


title: Sample250.EndothelialCell.203450830037_R02C01

description:
203450830037_R02C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sp57_Sa_6h

value: S. aureus


title: WT_TAC1_FB_14

description: WT TAC1 FB


title: Sp57_Sa_3h


title: Sample246.Fibroblast.203440280053_R06C01

description:
203440280053_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: Replication


title: Sample245.Fibroblast.203440280053_R05C01

description:
203440280053_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp57_Nm_6h

value: N. meningitidis


title: Sp57_Nm_3h


title: Sample244.Fibroblast.203440280053_R04C01

description:
203440280053_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_12

description: WT TAC1 FB


title: WT_TAC1_FB_13

description: WT TAC1 FB


title: Sample242.Fibroblast.203440280053_R02C01

description:
203440280053_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp57_K_6h

value: Control


title: Sample241.Fibroblast.203440280053_R01C01

description:
203440280053_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample240.Fibroblast.203440060036_R08C01

description:
203440060036_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_10

description: WT TAC1 FB


title: Sample239.Fibroblast.203440060036_R07C01

description:
203440060036_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: X-ray


title: Sp57_K_3h


title: Sample238.Fibroblast.203440060036_R06C01

description:
203440060036_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp57_Af_6h


title: Sample236.Fibroblast.203440060036_R04C01

description:
203440060036_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample237.Fibroblast.203440060036_R05C01

description:
203440060036_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample235.Fibroblast.203440060036_R03C01

description:
203440060036_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_9

description: WT TAC1 FB

value: TAC (W2)


title: Sample234.Fibroblast.203440060036_R02C01

description:
203440060036_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: Male


title: Sp57_Af_3h


title: WT_TAC1_FB_8

description: WT TAC1 FB


title: Sample233.Fibroblast.203440060036_R01C01

description:
203440060036_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: Fibroblast


title: Sample232.Fibroblast.203440060022_R08C01

description:
203440060022_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp56_Sa_6h


title: Sample247.Fibroblast.203440280053_R07C01

description:
203440280053_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp56_Sa_3h


title: WT_TAC1_FB_7

description: WT TAC1 FB


title: Sample231.Fibroblast.203440060022_R07C01

description:
203440060022_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample230.Fibroblast.203440060022_R06C01

description:
203440060022_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample243.Fibroblast.203440280053_R03C01

description:
203440280053_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_5

description: WT TAC1 FB


title: Sample229.Fibroblast.203440060022_R05C01

description:
203440060022_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp56_Nm_3h


title: Sp56_Nm_6h


title: WT_TAC1_FB_6

description: WT TAC1 FB


title: Sample228.Fibroblast.203440060022_R04C01

description:
203440060022_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample227.Fibroblast.203440060022_R03C01

description:
203440060022_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample226.Fibroblast.203440060022_R02C01

description:
203440060022_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_11

description: WT TAC1 FB


title: Sample224.Fibroblast.203440280067_R08C01

description:
203440280067_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp56_K_6h


title: Sample223.Fibroblast.203440280067_R07C01

description:
203440280067_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp56_K_3h


title: Sample225.Fibroblast.203440060022_R01C01

description:
203440060022_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample222.Fibroblast.203440280067_R06C01

description:
203440280067_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_3

description: WT TAC1 FB


title: WT_TAC1_FB_4

description: WT TAC1 FB


title: Sp56_Af_6h


title: Sp56_Af_3h


title: Sample218.Fibroblast.203440280067_R02C01

description:
203440280067_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_2

description: WT TAC1 FB


title: Sample217.Fibroblast.203440280067_R01C01

description:
203440280067_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_TAC1_FB_1

description: WT TAC1 FB


title: Sample219.Fibroblast.203440280067_R03C01

description:
203440280067_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample221.Fibroblast.203440280067_R05C01

description:
203440280067_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample220.Fibroblast.203440280067_R04C01

description:
203440280067_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp55_Sa_6h


title: Sample216.Fibroblast.203440280051_R08C01

description:
203440280051_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_32

description: WT sham2 FB

growth_protocol: C57BL/6N mice were purchased from CLEA Japan, Inc. Female and male mice were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 14-h light/dark cycle with ad libitum access to food and water. All experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines of the University of Tokyo for animal experiments.

extract_protocol:
For the isolation and collection of non-cardiomyocytes, hearts were minced and enzymatically dissociated using 2 mg/mL type 2 collagenase (Worthington), 1 mg/mL dispase (Roche), and 20 U/mL DNAse I (Roche), with 5 cycles of digestion for a total 40 min at 37 °C. After using a 40-μm cell strainer (Greiner) to remove the cardiomyocytes, cells were stained with Zombie Green Fixable Viability Kit (BioLegend) and live cells were collected by fluorescence-activated cell sorting (FACS) using a FACSJazz cell sorter (BD Biosciences). To isolate cardiac fibroblasts, cells were stained with APC conjugated anti-mouse CD140a (PDGFR-α) antibody (#135907, BioLegend), FITC conjugated anti-mouse CD31 Antibody (#102507, BioLegend), and Zombie Green, after which PDGFR-α positive live cells were collected by FACS.
Single-cell cDNA libraries were generated using the Smart-seq2 protocol. For the cDNA libraries constructed by Smart-seq2, the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Actb for non-cardiomyocytes) 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: Actb mRNA forward: CAACTGGGACGACATGGAGA; and Actb mRNA reverse: GCATACAGGGACAGCACAGC. A Ct value of 27 was set as the threshold.

value: sham


title: WT_sham2_FB_33

description: WT sham2 FB


title: Sp55_Sa_3h


title: WT_sham2_FB_31

description: WT sham2 FB


title: Sample213.Fibroblast.203440280051_R05C01

description:
203440280051_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample214.Fibroblast.203440280051_R06C01

description:
203440280051_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_30

description: WT sham2 FB


title: Sp55_Nm_3h


title: Sample211.Fibroblast.203440280051_R03C01

description:
203440280051_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample212.Fibroblast.203440280051_R04C01

description:
203440280051_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample208.Fibroblast.203441400054_R08C01

description:
203441400054_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp55_K_3h


title: Sample209.Fibroblast.203440280051_R01C01

description:
203440280051_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp55_K_6h


title: Sample203.Fibroblast.203441400054_R03C01

description:
203441400054_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_28

description: WT sham2 FB


title: WT_sham2_FB_26

description: WT sham2 FB


title: Sample206.Fibroblast.203441400054_R06C01

description:
203441400054_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp55_Af_6h


title: WT_sham2_FB_27

description: WT sham2 FB


title: Sp54_Sa_6h


title: Sample204.Fibroblast.203441400054_R04C01

description:
203441400054_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_24

description: WT sham2 FB


title: Sample201.Fibroblast.203441400054_R01C01

description:
203441400054_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp55_Nm_6h


title: Sample215.Fibroblast.203440280051_R07C01

description:
203440280051_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp54_Nm_6h


title: Sp54_Nm_3h


title: WT_sham2_FB_23

description: WT sham2 FB


title: Sample198.Fibroblast.203440280004_R06C01

description:
203440280004_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample199.Fibroblast.203440280004_R07C01

description:
203440280004_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample197.Fibroblast.203440280004_R05C01

description:
203440280004_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample210.Fibroblast.203440280051_R02C01

description:
203440280051_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample196.Fibroblast.203440280004_R04C01

description:
203440280004_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample202.Fibroblast.203441400054_R02C01

description:
203441400054_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_25

description: WT sham2 FB


title: Sample195.Fibroblast.203440280004_R03C01

description:
203440280004_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_29

description: WT sham2 FB


title: Sample207.Fibroblast.203441400054_R07C01

description:
203441400054_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample194.Fibroblast.203440280004_R02C01

description:
203440280004_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp55_Af_3h


title: Sample205.Fibroblast.203441400054_R05C01

description:
203441400054_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample193.Fibroblast.203440280004_R01C01

description:
203440280004_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp54_K_3h


title: Sp54_Af_6h


title: Sample191.Fibroblast.203440060050_R07C01

description:
203440060050_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample190.Fibroblast.203440060050_R06C01

description:
203440060050_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample200.Fibroblast.203440280004_R08C01

description:
203440280004_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_19

description: WT sham2 FB


title: Sp54_Af_3h


title: Sample189.Fibroblast.203440060050_R05C01

description:
203440060050_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_18

description: WT sham2 FB


title: Sample187.Fibroblast.203440060050_R03C01

description:
203440060050_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample188.Fibroblast.203440060050_R04C01

description:
203440060050_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_17

description: WT sham2 FB


title: Sp53_Sa_6h


title: WT_sham2_FB_22

description: WT sham2 FB


title: Sp53_Sa_3h


title: Sample184.Fibroblast.203447100082_R08C01

description:
203447100082_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_16

description: WT sham2 FB


title: Sample185.Fibroblast.203440060050_R01C01

description:
203440060050_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample183.Fibroblast.203447100082_R07C01

description:
203447100082_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp53_Nm_6h


title: Sp54_K_6h


title: WT_sham2_FB_21

description: WT sham2 FB


title: Sample180.Fibroblast.203447100082_R04C01

description:
203447100082_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample182.Fibroblast.203447100082_R06C01

description:
203447100082_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp53_Nm_3h


title: Sample181.Fibroblast.203447100082_R05C01

description:
203447100082_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample177.Fibroblast.203447100082_R01C01

description:
203447100082_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_13

description: WT sham2 FB


title: WT_sham2_FB_14

description: WT sham2 FB


title: WT_sham2_FB_20

description: WT sham2 FB


title: Sp53_K_3h


title: Sample179.Fibroblast.203447100082_R03C01

description:
203447100082_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_15

description: WT sham2 FB


title: Sample178.Fibroblast.203447100082_R02C01

description:
203447100082_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_12

description: WT sham2 FB


title: Sample186.Fibroblast.203440060050_R02C01

description:
203440060050_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample192.Fibroblast.203440060050_R08C01

description:
203440060050_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_11

description: WT sham2 FB


title: Sp53_K_6h


title: Sample174.Fibroblast.203447100084_R06C01

description:
203447100084_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample176.Fibroblast.203447100084_R08C01

description:
203447100084_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp53_Af_6h


title: Sample173.Fibroblast.203447100084_R05C01

description:
203447100084_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample175.Fibroblast.203447100084_R07C01

description:
203447100084_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp53_Af_3h


title: Sample172.Fibroblast.203447100084_R04C01

description:
203447100084_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_10

description: WT sham2 FB


title: Sp52_Sa_6h


title: Sp52_Sa_3h


title: Sample170.Fibroblast.203447100084_R02C01

description:
203447100084_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_9

description: WT sham2 FB


title: WT_sham2_FB_7

description: WT sham2 FB


title: Sample167.Fibroblast.203447100081_R07C01

description:
203447100081_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample165.Fibroblast.203447100081_R05C01

description:
203447100081_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample168.Fibroblast.203447100081_R08C01

description:
203447100081_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_6

description: WT sham2 FB


title: Sample164.Fibroblast.203447100081_R04C01

description:
203447100081_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_5

description: WT sham2 FB


title: Sample162.Fibroblast.203447100081_R02C01

description:
203447100081_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp52_Nm_3h


title: WT_sham2_FB_4

description: WT sham2 FB


title: Sample160.Fibroblast.203447100010_R08C01

description:
203447100010_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample163.Fibroblast.203447100081_R03C01

description:
203447100081_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample161.Fibroblast.203447100081_R01C01

description:
203447100081_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp52_Nm_6h


title: Sample159.Fibroblast.203447100010_R07C01

description:
203447100010_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample158.Fibroblast.203447100010_R06C01

description:
203447100010_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_3_bulk

description: WT sham2 FB


title: Sample157.Fibroblast.203447100010_R05C01

description:
203447100010_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp52_K_6h


title: Sample171.Fibroblast.203447100084_R03C01

description:
203447100084_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp52_Af_3h


title: Sp52_Af_6h


title: WT_sham2_FB_2

description: WT sham2 FB


title: Sample156.Fibroblast.203447100010_R04C01

description:
203447100010_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample155.Fibroblast.203447100010_R03C01

description:
203447100010_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample169.Fibroblast.203447100084_R01C01

description:
203447100084_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sp51_Sa_6h


title: WT_sham2_FB_8

description: WT sham2 FB


title: Sample166.Fibroblast.203447100081_R06C01

description:
203447100081_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample154.Fibroblast.203447100010_R02C01

description:
203447100010_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample153.Fibroblast.203447100010_R01C01

description:
203447100010_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham2_FB_1

description: WT sham2 FB


title: WT_sham1_FB_81

description: WT sham1 FB

growth_protocol: C57BL/6N mice were purchased from CLEA Japan, Inc. Female and male mice were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 13-h light/dark cycle with ad libitum access to food and water. All experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines of the University of Tokyo for animal experiments.

extract_protocol:
For the isolation and collection of non-cardiomyocytes, hearts were minced and enzymatically dissociated using 2 mg/mL type 2 collagenase (Worthington), 1 mg/mL dispase (Roche), and 20 U/mL DNAse I (Roche), with 5 cycles of digestion for a total 40 min at 37 °C. After using a 40-μm cell strainer (Greiner) to remove the cardiomyocytes, cells were stained with Zombie Green Fixable Viability Kit (BioLegend) and live cells were collected by fluorescence-activated cell sorting (FACS) using a FACSJazz cell sorter (BD Biosciences). To isolate cardiac fibroblasts, cells were stained with APC conjugated anti-mouse CD140a (PDGFR-α) antibody (#135907, BioLegend), FITC conjugated anti-mouse CD31 Antibody (#102506, BioLegend), and Zombie Green, after which PDGFR-α positive live cells were collected by FACS.
Single-cell cDNA libraries were generated using the Smart-seq2 protocol. For the cDNA libraries constructed by Smart-seq2, the efﬁciency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Actb for non-cardiomyocytes) 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: Actb mRNA forward: CAACTGGGACGACATGGAGA; and Actb mRNA reverse: GCATACAGGGACAGCACAGC. A Ct value of 26 was set as the threshold.


title: Sp51_Sa_3h


title: Sample152.Neural progenitors_neurons.205379740119_R08C01

description:
205379740119_R08C01
genomic DNA methylation from tissue=Neural progenitors_neurons species=Human

source_name: Neural progenitors_neurons

value: Female

value: Neural progenitors_neurons


title: Sp52_K_3h


title: Sample151.Neural progenitors_neurons.205379740119_R07C01

description:
205379740119_R07C01
genomic DNA methylation from tissue=Neural progenitors_neurons species=Human


title: Sp51_Nm_6h


title: Sample150.Neural progenitors.205379740119_R06C01

description:
205379740119_R06C01
genomic DNA methylation from tissue=Neural progenitors species=Human

source_name: Neural progenitors

value: Neural progenitors


title: WT_sham1_FB_80

description: WT sham1 FB

value: heart

value: Full length


title: Sample149.Neural progenitors.205379740119_R05C01

description:
205379740119_R05C01
genomic DNA methylation from tissue=Neural progenitors species=Human


title: Sp51_Nm_3h

value: male


title: Sample146.EmbryonicStemCell.205379740119_R02C01

description:
205379740119_R02C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human

value: EmbryonicStemCell


title: Sample148.EmbryonicStemCell.205379740119_R04C01

description:
205379740119_R04C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human


title: Sp51_K_3h


title: WT_sham1_FB_79

description: WT sham1 FB

value: Fibroblasts


title: Sp51_K_6h


title: WT_sham1_FB_78

description: WT sham1 FB


title: Sample145.EmbryonicStemCell.205379740119_R01C01

description:
205379740119_R01C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human


title: WT_sham1_FB_77

description: WT sham1 FB


title: Sp51_Af_6h

value: A. fumigatus


title: Sample147.EmbryonicStemCell.205379740119_R03C01

description:
205379740119_R03C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human


title: Sample142.Neural progenitors.205379740101_R06C01

description:
205379740101_R06C01
genomic DNA methylation from tissue=Neural progenitors species=Human


title: Sample144.Mostly neurons.205379740101_R08C01

description:
205379740101_R08C01
genomic DNA methylation from tissue=Mostly neurons species=Human

source_name: Mostly neurons

value: Mostly neurons


title: Sample143.Neural progenitors_neurons.205379740101_R07C01

description:
205379740101_R07C01
genomic DNA methylation from tissue=Neural progenitors_neurons species=Human


title: WT_sham1_FB_76

description: WT sham1 FB


title: Sp51_Af_3h


title: Sample141.Neural progenitors.205379740101_R05C01

description:
205379740101_R05C01
genomic DNA methylation from tissue=Neural progenitors species=Human


title: WT_sham1_FB_75

description: WT sham1 FB


title: Sample139.EmbryonicStemCell.205379740101_R03C01

description:
205379740101_R03C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human


title: Sp50_Sa_6h

value: S. aureus


title: Sample138.EmbryonicStemCell.205379740101_R02C01

description:
205379740101_R02C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human


title: Sample140.EmbryonicStemCell.205379740101_R04C01

description:
205379740101_R04C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human


title: Sample136.HCAEC.205022250065_R08C01

description:
205022250065_R08C01
genomic DNA methylation from tissue=HCAEC species=Human

source_name: HCAEC

value: HCAEC

value: Clone


title: Sample137.EmbryonicStemCell.205379740101_R01C01

description:
205379740101_R01C01
genomic DNA methylation from tissue=EmbryonicStemCell species=Human


title: Sp50_Sa_3h


title: Sample135.HCAEC.205022250065_R07C01

description:
205022250065_R07C01
genomic DNA methylation from tissue=HCAEC species=Human


title: WT_sham1_FB_72

description: WT sham1 FB


title: Sp50_Nm_3h

value: N. meningitidis


title: WT_sham1_FB_73

description: WT sham1 FB


title: WT_sham1_FB_71

description: WT sham1 FB


title: Sample131.HCAEC.205022250065_R03C01

description:
205022250065_R03C01
genomic DNA methylation from tissue=HCAEC species=Human

value: Male


title: Sample133.HCAEC.205022250065_R05C01

description:
205022250065_R05C01
genomic DNA methylation from tissue=HCAEC species=Human


title: Sample130.HCAEC.205022250065_R02C01

description:
205022250065_R02C01
genomic DNA methylation from tissue=HCAEC species=Human


title: Sample132.HCAEC.205022250065_R04C01

description:
205022250065_R04C01
genomic DNA methylation from tissue=HCAEC species=Human


title: Sp50_K_3h

value: Control


title: WT_sham1_FB_70

description: WT sham1 FB

value: sham


title: Sample128.HUVEC.205038930106_R07C01

description:
205038930106_R07C01
genomic DNA methylation from tissue=HUVEC species=Human

source_name: HUVEC

value: HUVEC

value: Rapamycin


title: WT_sham1_FB_69

description: WT sham1 FB


title: Sample129.HUVEC.205038930106_R08C01

description:
205038930106_R08C01
genomic DNA methylation from tissue=HUVEC species=Human


title: Sp50_K_6h


title: Sp50_Af_6h


title: WT_sham1_FB_68

description: WT sham1 FB


title: Sp50_Af_3h


title: Sample125.HUVEC.205038930106_R04C01

description:
205038930106_R04C01
genomic DNA methylation from tissue=HUVEC species=Human


title: Sample126.HUVEC.205038930106_R05C01

description:
205038930106_R05C01
genomic DNA methylation from tissue=HUVEC species=Human


title: WT_sham1_FB_74

description: WT sham1 FB


title: Sp49_Sa_6h


title: WT_sham1_FB_67

description: WT sham1 FB


title: Sample123.HUVEC.205038930106_R02C01

description:
205038930106_R02C01
genomic DNA methylation from tissue=HUVEC species=Human


title: Sample134.HCAEC.205022250065_R06C01

description:
205022250065_R06C01
genomic DNA methylation from tissue=HCAEC species=Human


title: Sp50_Nm_6h


title: Sample122.HUVEC.205038930106_R01C01

description:
205038930106_R01C01
genomic DNA methylation from tissue=HUVEC species=Human


title: WT_sham1_FB_66

description: WT sham1 FB


title: WT_sham1_FB_65

description: WT sham1 FB


title: Sample121.HUVEC.205038930078_R08C01

description:
205038930078_R08C01
genomic DNA methylation from tissue=HUVEC species=Human


title: Sp49_Sa_3h


title: Sample120.HUVEC.205038930078_R07C01

description:
205038930078_R07C01
genomic DNA methylation from tissue=HUVEC species=Human


title: Sp49_Nm_3h


title: Sample127.HUVEC.205038930106_R06C01

description:
205038930106_R06C01
genomic DNA methylation from tissue=HUVEC species=Human


title: WT_sham1_FB_63

description: WT sham1 FB


title: Sp49_K_3h


title: Sample114.HUVEC.205038930078_R01C01

description:
205038930078_R01C01
genomic DNA methylation from tissue=HUVEC species=Human


title: WT_sham1_FB_64

description: WT sham1 FB


title: Sp49_Nm_6h


title: WT_sham1_FB_62

description: WT sham1 FB


title: Sample117.HUVEC.205038930078_R04C01

description:
205038930078_R04C01
genomic DNA methylation from tissue=HUVEC species=Human


title: Sp49_Af_6h


title: Sample115.HUVEC.205038930078_R02C01

description:
205038930078_R02C01
genomic DNA methylation from tissue=HUVEC species=Human


title: Sample112.Fibroblast.205035150153_R07C01

description:
205035150153_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: Fibroblast

value: Chronic Radiation


title: Sample118.HUVEC.205038930078_R05C01

description:
205038930078_R05C01
genomic DNA methylation from tissue=HUVEC species=Human


title: WT_sham1_FB_60

description: WT sham1 FB

value: heart

value: Full length


title: WT_sham1_FB_59

description: WT sham1 FB


title: Sample111.Fibroblast.205035150153_R06C01

description:
205035150153_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham1_FB_61

description: WT sham1 FB


title: Tumor 2_H89

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

country: France

institute: UMR INSERM 1231

description: In TPM.csv: Sample 5

data_processing:
pseudo alignment and quantification using kallisto
differential analysis using DESeq2 R library
Genome_build: GRCm38
Supplementary_files_format_and_content: TPM.csv

source_name: CT26 solid tumors

extract_protocol:
CT26 solid tumors were removed at day 14, flash frozen on liquid nitrogen and RNA was harvested using Trizol reagent. BGIseq500 sequencing system was used.
Sequencing, data quality, and reds repartition were performed by BGIseq500 platform (BGI-Shenzhen, China)

treatment_protocol: CT26-bearing mice (500 000 CT26 cells in s.c) were treated or not (Nacl, i.p.) with H89 (10 mg/kg, i.p.) twice a week

tag: cell line

value: CT26 murine colorectal carcinoma cell line

value: Balb/c

tag: treatment

tag: tumor stage

value: 14 days after CT26 injection

value: CT26 solid tumors


title: Tumor 3_H89

description: In TPM.csv: Sample 6

tag: strain


title: Sp49_K_6h

value: male


title: Sample116.HUVEC.205038930078_R03C01

description:
205038930078_R03C01
genomic DNA methylation from tissue=HUVEC species=Human

tag: cell type


title: Sample113.Fibroblast.205035150153_R08C01

description:
205035150153_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample124.HUVEC.205038930106_R03C01

description:
205038930106_R03C01
genomic DNA methylation from tissue=HUVEC species=Human


title: Sample110.Fibroblast.205035150153_R05C01

description:
205035150153_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham1_FB_58

description: WT sham1 FB

value: Fibroblasts

tag: operation

tag: tissue


title: Sample119.HUVEC.205038930078_R06C01

description:
205038930078_R06C01
genomic DNA methylation from tissue=HUVEC species=Human


title: Tumor 1_H89

description: In TPM.csv: Sample 4


title: Sp49_Af_3h

value: A. fumigatus


title: Sample109.Fibroblast.205035150153_R04C01

description:
205035150153_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Tumor 3_NaCl

description: In TPM.csv: Sample 3

value: control


title: Sp48_Nm_6h

value: N. meningitidis


title: Tumor 2_NaCl

description: In TPM.csv: Sample 2


title: Sample108.Fibroblast.205035150153_R03C01

description:
205035150153_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: Male


title: WT_sham1_FB_57

description: WT sham1 FB

value: sham

tag: name in supplementary file

tag: molecule subtype


title: WT_sham1_FB_56

description: WT sham1 FB

tag: protocol


title: WT_sham1_FB_55

description: WT sham1 FB


title: Sample107.Fibroblast.205035150153_R02C01

description:
205035150153_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human

tag: Sex


title: Sample106.Fibroblast.205035150153_R01C01

description:
205035150153_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham1_FB_54

description: WT sham1 FB


title: Sp48_K_6h

tag: stimulation

value: Control

tag: time point


title: Sample104.Keratinocyte.205035150053_R07C01

description:
205035150053_R07C01
genomic DNA methylation from tissue=Keratinocyte species=Human

source_name: Keratinocyte

tag: age

value: Keratinocyte


title: Sp48_K_3h


title: Sample105.Keratinocyte.205035150053_R08C01

description:
205035150053_R08C01
genomic DNA methylation from tissue=Keratinocyte species=Human

tag: condition


title: WT_sham1_FB_53

description: WT sham1 FB


title: 4MOSC1-LIGHT-rep3

city: Wuhan

first: Hao

last: Li

address: 237 Luoyu Road

department: Shool and Hospital of Stomatology

institute: Wuhan University

data_processing:
BGISEQ-500 sequencer
Clean reads were mapped to the reference genome using HISAT/Bowtie2 tools.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Tumor

growth_protocol: Mice were housed under specific pathogen-free (SPF) conditions (temperature ~22 °C, humidity ~50%) with a 12/12 h dark/light cycle

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
DNase I was used to digest double-stranded and single-stranded DNAin total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to carry out end repair. The cDNA fragments with adapters were amplyfied by PCR, and the products were purified byAmpure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products above were heated denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGI-Shenzhen, China)
DNBSEQ Transcriptome

treatment_protocol: To establish mouse HNSCC model, 4MOSC1-con cells or 4MOSC1-LIGHT (overexpression of LIGHT) cells were orthotopically injected into the tongue of each C57BL/6 mouse.

tag: disease state

value: mouse HNSCC model

value: Tumor

value: murine oral squamous cell carcinoma

value: injection with 4MOSC1-LIGHT

tag: genotype

value: LIGHT overexpresssion


title: Sp48_Af_6h


title: Sp48_Sa_6h

value: S. aureus


title: Tumor 1_NaCl

description: In TPM.csv: Sample 1

tag: cell line

value: CT26 murine colorectal carcinoma cell line

value: Balb/c

value: 14 days after CT26 injection


title: 4MOSC1-LIGHT-rep1

tag: treatment


title: 4MOSC1-LIGHT-rep2


title: 4MOSC1-con-rep3

value: injection with 4MOSC1-con


title: Sample103.Keratinocyte.205035150053_R06C01

description:
205035150053_R06C01
genomic DNA methylation from tissue=Keratinocyte species=Human

value: Chronic Radiation

tag: populationdoublinglevel

tag: passagenumber


title: WT_sham1_FB_51

description: WT sham1 FB

tag: cell type

value: Fibroblasts

tag: strain

value: heart

value: Full length


title: WT_sham1_FB_52

description: WT sham1 FB

tag: operation

value: sham

tag: tissue


title: Sample102.Keratinocyte.205035150053_R05C01

description:
205035150053_R05C01
genomic DNA methylation from tissue=Keratinocyte species=Human

value: Male


title: Sp48_Af_3h

value: male

value: A. fumigatus


title: Sp47_Sa_6h


title: 4MOSC1-con-rep2

value: mouse HNSCC model

value: Tumor

value: control


title: Sp48_Sa_3h


title: WT_sham1_FB_50

description: WT sham1 FB

tag: name in supplementary file

tag: molecule subtype


title: Sample101.Keratinocyte.205035150053_R03C01

description:
205035150053_R03C01
genomic DNA methylation from tissue=Keratinocyte species=Human

tag: Sex

value: Keratinocyte


title: 4MOSC1-con-rep1

value: murine oral squamous cell carcinoma


title: Sp47_Sa_3h

tag: stimulation

value: S. aureus


title: WT_sham1_FB_49

description: WT sham1 FB

tag: protocol


title: Sp48_Nm_3h

value: N. meningitidis

tag: time point


title: Sample100.Keratinocyte.205035150053_R02C01

description:
205035150053_R02C01
genomic DNA methylation from tissue=Keratinocyte species=Human

tag: age

tag: condition


title: Sp47_Nm_6h


title: untreated Escherichia coli str. O157:H7 str. Sakai- replicate 3

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description: grown to OD600 of 0.6 in MEM-HEPES supplemented with 0.1% glucose and 250 nM Fe(NO3)3

data_processing:
Differentially expressed genes were determined using READemption 1.01 (PMID: 25123900)
Rho scores were derived from RNA-seq data using the pipeline from PMID: 33460557
Genome_build: NC_002695.2
Supplementary_files_format_and_content: Differentially expressed gene in CSV table. Predicted Rho termination sites in TEXT table

organism: Escherichia coli

growth_protocol: Three individual colonies were grown in MEM-HEPES supplemented with 0.1% glucose and 250 nM ferric nitrate

extract_protocol:
RNA was extracted using guanidinium thiocyanate phenol as in (Tollervery & Mattaj 1987)
RNA was depleted with Zymo-seq RiboFree Total RNA kit before library prep for sequencing on the NextSeq paired end flow cell

treatment_protocol: At an OD600 of 0.6, cultures were split into two, with half being treated with 50 μg/mL of bicyclomycin

tag: serotype

value: Sakai

value: untreated (OD600 =0.6)


title: WT_sham1_FB_48

description: WT sham1 FB


title: Sample99.Keratinocyte.205035150053_R01C01

description:
205035150053_R01C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sp47_Nm_3h


title: WT_sham1_FB_47

description: WT sham1 FB


title: Sp47_K_6h

value: Control


title: Sample98.Fibroblast.202148010091_R08C01

description:
202148010091_R08C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: Fibroblast

value: hTERT


title: WT_sham1_FB_46

description: WT sham1 FB

value: Fibroblasts

value: heart

value: Full length


title: Sample97.Fibroblast.202148010091_R07C01

description:
202148010091_R07C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: Male


title: untreated Escherichia coli str. O157:H7 str. Sakai- replicate 1


title: bicyclomycin treated Escherichia coli str. O157:H7 str. Sakai- replicate 3

value: bicylomycin treated (15 minutes) at OD600 = 0.6


title: Sp47_K_3h

value: male


title: Sample96.Fibroblast.202148010091_R06C01

description:
202148010091_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham1_FB_45

description: WT sham1 FB

value: sham


title: bicyclomycin treated Escherichia coli str. O157:H7 str. Sakai- replicate 2


title: Sp47_Af_6h

value: A. fumigatus


title: Sample95.Fibroblast.202148010091_R05C01

description:
202148010091_R05C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham1_FB_44

description: WT sham1 FB


title: bicyclomycin treated Escherichia coli str. O157:H7 str. Sakai- replicate 1


title: Sp47_Af_3h


title: WT_sham1_FB_43

description: WT sham1 FB


title: Sample94.Fibroblast.202148010091_R04C01

description:
202148010091_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham1_FB_42

description: WT sham1 FB


title: Sp46_Sa_6h


title: Sample93.Fibroblast.202148010091_R03C01

description:
202148010091_R03C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham1_FB_41

description: WT sham1 FB


title: Sp46_Sa_3h


title: Sample92.Fibroblast.202148010091_R02C01

description:
202148010091_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: untreated Escherichia coli str. O157:H7 str. Sakai- replicate 2


title: WT_sham1_FB_40

description: WT sham1 FB


title: Sp46_Nm_6h


title: WT_sham1_FB_39

description: WT sham1 FB


title: Sample91.Fibroblast.202148010091_R01C01

description:
202148010091_R01C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample89.KeratinocyteStemCell.203836210107_R07C01

description:
203836210107_R07C01
genomic DNA methylation from tissue=KeratinocyteStemCell species=Human

source_name: KeratinocyteStemCell

value: KeratinocyteStemCell


title: Sp46_K_6h

source_name: monocytes


title: Sample88.KeratinocyteWithoutStemCells.203836210107_R06C01

description:
203836210107_R06C01
genomic DNA methylation from tissue=KeratinocyteWithoutStemCells species=Human

source_name: KeratinocyteWithoutStemCells

value: KeratinocyteWithoutStemCells

value: KeratinocyteNoStemCell


title: WT_sham1_FB_38

description: WT sham1 FB

source_name: Fibroblasts


title: Sp46_K_3h


title: Sample90.KeratinocyteWithoutStemCells.203836210107_R08C01

description:
203836210107_R08C01
genomic DNA methylation from tissue=KeratinocyteWithoutStemCells species=Human


title: Sp46_Af_6h


title: kdm6ako.3

city: St Louis

first: Todd

last: Druley

state: Missouri

address: 660 South Euclid Ave

department: Department of Pediatrics

institute: Washington University In St Louis

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 72 top-level assembly with STAR version 2.4.0b
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount.
Sailfish was used to produce isoform estimated counts.
Genome_build: Ensemble R72
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: human induced pluripotent stem cells

extract_protocol:
Qiagen RNAeasy micro plus
Clontech SMRTr

value: human induced pluripotent stem cells

value: undifferentiated cells, 75% confluency

tag: genotype

value: KDM6A Knock out


title: WT_sham1_FB_36

description: WT sham1 FB


title: WT_sham1_FB_35

description: WT sham1 FB


title: kdm6ako.1


title: Sp45_Sa_6h

value: S. aureus


title: Sp46_Af_3h


title: Sample87.KeratinocyteStemCell.203836210107_R05C01

description:
203836210107_R05C01
genomic DNA methylation from tissue=KeratinocyteStemCell species=Human


title: kdm6ako.2


title: WT_sham1_FB_34

description: WT sham1 FB


title: Sample86.Keratinocyte.203836210107_R04C01

description:
203836210107_R04C01
genomic DNA methylation from tissue=Keratinocyte species=Human

value: Keratinocyte


title: Sp45_Sa_3h


title: Sample85.KeratinocyteWithoutStemCells.203836210107_R03C01

description:
203836210107_R03C01
genomic DNA methylation from tissue=KeratinocyteWithoutStemCells species=Human


title: bjff. 3

value: Wild type


title: WT_sham1_FB_33

description: WT sham1 FB

value: Fibroblasts


title: Sample84.KeratinocyteStemCell.203836210107_R02C01

description:
203836210107_R02C01
genomic DNA methylation from tissue=KeratinocyteStemCell species=Human


title: Sp46_Nm_3h

value: N. meningitidis


title: Sample83.Keratinocyte.203836210107_R01C01

description:
203836210107_R01C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sp45_Nm_6h


title: bjff. 2


title: WT_sham1_FB_37

description: WT sham1 FB

value: heart

value: Full length


title: WT_sham1_FB_32

description: WT sham1 FB


title: Sp45_Nm_3h


title: WT_sham1_FB_31

description: WT sham1 FB


title: Sample82.KeratinocyteWithoutStemCells.203839170033_R08C01

description:
203839170033_R08C01
genomic DNA methylation from tissue=KeratinocyteWithoutStemCells species=Human

value: Male


title: bjff. 1


title: WT_sham1_FB_30

description: WT sham1 FB


title: Sample81.KeratinocyteStemCell.203839170033_R07C01

description:
203839170033_R07C01
genomic DNA methylation from tissue=KeratinocyteStemCell species=Human


title: Sp45_K_3h

value: male

value: Control


title: Sp45_K_6h


title: Sample80.KeratinocyteWithoutStemCells.203839170033_R06C01

description:
203839170033_R06C01
genomic DNA methylation from tissue=KeratinocyteWithoutStemCells species=Human


title: Sp45_Af_6h

value: A. fumigatus


title: WT_sham1_FB_29

description: WT sham1 FB

value: sham


title: Sample79.KeratinocyteStemCell.203839170033_R05C01

description:
203839170033_R05C01
genomic DNA methylation from tissue=KeratinocyteStemCell species=Human

value: KeratinocyteStemCell


title: Sample78.Keratinocyte.203839170033_R04C01

description:
203839170033_R04C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sp45_Af_3h


title: Sample24.EndothelialCell.201004900074_R03C02

description:
201004900074_R03C02
genomic DNA methylation from tissue=EndothelialCell species=Human

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina HumanMethylation450 BeadChip using standard Illumina protocol.

value: not collected

value: EndothelialCell

value: Clone


title: Sample26.EndothelialCell.201004900074_R05C02

description:
201004900074_R05C02
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sample77.KeratinocyteWithoutStemCells.203839170033_R03C01

description:
203839170033_R03C01
genomic DNA methylation from tissue=KeratinocyteWithoutStemCells species=Human

value: KeratinocyteWithoutStemCells

value: KeratinocyteNoStemCell


title: Sample25.EndothelialCell.201004900074_R04C02

description:
201004900074_R04C02
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sample23.EndothelialCell.201004900074_R02C02

description:
201004900074_R02C02
genomic DNA methylation from tissue=EndothelialCell species=Human


title: WT_sham1_FB_27

description: WT sham1 FB


title: WT_sham1_FB_26

description: WT sham1 FB


title: WT_sham1_FB_25

description: WT sham1 FB


title: Sp44_Nm_6h


title: Sp44_Sa_6h

value: S. aureus


title: Sp44_Sa_3h