title: Sample75.LungProgenitor.203833040026_R08C01

description:
203833040026_R08C01
genomic DNA methylation from tissue=LungProgenitor species=Human

source_name: LungProgenitor

value: LungProgenitor


title: WT_sham1_FB_24

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 FB

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: Fibroblasts

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.

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: Fibroblasts

tag: strain

tag: operation

value: sham

tag: tissue

value: heart

tag: name in supplementary file

tag: molecule subtype

value: Full length

tag: protocol


title: Sample21.EndothelialCell.201004900074_R06C01

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:
201004900074_R06C01
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.

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

organism: Homo sapiens

source_name: EndothelialCell

label_protocol: Standard Illumina Protocol.

growth_protocol: DNA extracted from cells.

extract_protocol: Genomic DNA was extracted.

tag: age

tag: Sex

value: not collected

value: EndothelialCell

tag: condition

value: Clone

tag: populationdoublinglevel

tag: passagenumber


title: Sample19.EndothelialCell.201004900074_R04C01

description:
201004900074_R04C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sample76.KeratinocyteStemCell.203839170033_R02C01

description:
203839170033_R02C01
genomic DNA methylation from tissue=KeratinocyteStemCell species=Human

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

source_name: KeratinocyteStemCell

value: Male

value: KeratinocyteStemCell


title: Sp44_K_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

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

value: male

tag: stimulation

value: Control

tag: time point


title: WT_sham1_FB_22

description: WT sham1 FB


title: Sample74.BasalCell.203833040026_R07C01

description:
203833040026_R07C01
genomic DNA methylation from tissue=BasalCell species=Human

source_name: BasalCell

value: BasalCell


title: Sample27.EndothelialCell.201004900074_R06C02

description:
201004900074_R06C02
genomic DNA methylation from tissue=EndothelialCell species=Human


title: WT_sham1_FB_23

description: WT sham1 FB


title: Sample18.EndothelialCell.201004900074_R03C01

description:
201004900074_R03C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: WT_sham1_FB_28

description: WT sham1 FB


title: Sample73.BasalCell.203833040026_R06C01

description:
203833040026_R06C01
genomic DNA methylation from tissue=BasalCell species=Human


title: Sp44_K_3h


title: Sample17.EndothelialCell.201004900074_R02C01

description:
201004900074_R02C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sample22.EndothelialCell.201004900074_R01C02

description:
201004900074_R01C02
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sample72.LungProgenitor.203833040026_R05C01

description:
203833040026_R05C01
genomic DNA methylation from tissue=LungProgenitor species=Human


title: Sample71.AnteriorForegutEndoderm.203833040026_R04C01

description:
203833040026_R04C01
genomic DNA methylation from tissue=AnteriorForegutEndoderm species=Human

source_name: AnteriorForegutEndoderm

value: AnteriorForegutEndoderm


title: Sample16.EndothelialCell.201004900074_R01C01

description:
201004900074_R01C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sp44_Nm_3h

value: N. meningitidis


title: WT_sham1_FB_18

description: WT sham1 FB


title: Sample15.Fibroblast.201004900137_R01C02

description:
201004900137_R01C02
genomic DNA methylation from tissue=Fibroblast species=Human

source_name: Fibroblast

value: Fibroblast


title: Sample20.EndothelialCell.201004900074_R05C01

description:
201004900074_R05C01
genomic DNA methylation from tissue=EndothelialCell species=Human


title: Sample69.iPSC.203833040026_R02C01

description:
203833040026_R02C01
genomic DNA methylation from tissue=iPSC species=Human

source_name: iPSC

value: iPSC


title: Sample14.Fibroblast.201004900137_R06C01

description:
201004900137_R06C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: Female


title: Sp43_Sa_3h

value: S. aureus


title: WT_sham1_FB_17

description: WT sham1 FB

value: Fibroblasts

value: sham


title: WT_sham1_FB_19

description: WT sham1 FB

value: heart

value: Full length


title: Sample68.iPSC.203833040026_R01C01

description:
203833040026_R01C01
genomic DNA methylation from tissue=iPSC species=Human


title: Sp43_Sa_6h


title: Sample67.LungProgenitor.203833040106_R08C01

description:
203833040106_R08C01
genomic DNA methylation from tissue=LungProgenitor species=Human

value: LungProgenitor


title: Sample66.BasalCell.203833040106_R07C01

description:
203833040106_R07C01
genomic DNA methylation from tissue=BasalCell species=Human


title: Sample13.Keratinocyte.201004900137_R05C01

description:
201004900137_R05C01
genomic DNA methylation from tissue=Keratinocyte species=Human

source_name: Keratinocyte

value: Keratinocyte


title: Sample12.Fibroblast.201004900137_R04C01

description:
201004900137_R04C01
genomic DNA methylation from tissue=Fibroblast species=Human

value: Male


title: Sp43_Nm_3h


title: WT_sham1_FB_21

description: WT sham1 FB


title: Sp43_Nm_6h


title: WT_sham1_FB_14

description: WT sham1 FB


title: Sp43_K_6h


title: WT_sham1_FB_20

description: WT sham1 FB


title: Sp44_Af_3h

value: A. fumigatus


title: WT_sham1_FB_15

description: WT sham1 FB


title: Sample11.Fibroblast.201004900137_R02C01

description:
201004900137_R02C01
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample70.iPSC.203833040026_R03C01

description:
203833040026_R03C01
genomic DNA methylation from tissue=iPSC species=Human


title: Sp44_Af_6h

value: male


title: Sample64.LungProgenitor.203833040106_R05C01

description:
203833040106_R05C01
genomic DNA methylation from tissue=LungProgenitor species=Human


title: Sample9.Fibroblast.201004900138_R04C02

description:
201004900138_R04C02
genomic DNA methylation from tissue=Fibroblast species=Human


title: WT_sham1_FB_13

description: WT sham1 FB


title: WT_sham1_FB_12

description: WT sham1 FB


title: Sample10.Keratinocyte.201004900137_R01C01

description:
201004900137_R01C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sp42_Sa_6h


title: WT_sham1_FB_11

description: WT sham1 FB


title: Sp43_Af_3h


title: Sample62.iPSC.203833040106_R03C01

description:
203833040106_R03C01
genomic DNA methylation from tissue=iPSC species=Human


title: Sample8.Keratinocyte.201004900138_R03C02

description:
201004900138_R03C02
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sample63.AnteriorForegutEndoderm.203833040106_R04C01

description:
203833040106_R04C01
genomic DNA methylation from tissue=AnteriorForegutEndoderm species=Human


title: WT_sham1_FB_16

description: WT sham1 FB


title: Sp43_Af_6h


title: Sample7.Keratinocyte.201004900138_R02C02

description:
201004900138_R02C02
genomic DNA methylation from tissue=Keratinocyte species=Human


title: WT_sham1_FB_10

description: WT sham1 FB


title: Sample61.iPSC.203833040106_R02C01

description:
203833040106_R02C01
genomic DNA methylation from tissue=iPSC species=Human


title: Sample6.Fibroblast.201004900138_R01C02

description:
201004900138_R01C02
genomic DNA methylation from tissue=Fibroblast species=Human


title: Sample65.BasalCell.203833040106_R06C01

description:
203833040106_R06C01
genomic DNA methylation from tissue=BasalCell species=Human


title: Sp42_Sa_3h


title: WT_sham1_FB_9

description: WT sham1 FB


title: Sp42_Nm_6h


title: Sp43_K_3h

value: Control


title: Sample59.BasalCellCarcinoma.203833040019_R08C01

description:
203833040019_R08C01
genomic DNA methylation from tissue=BasalCellCarcinoma species=Human

source_name: BasalCellCarcinoma

value: BasalCellCarcinoma


title: Sample60.iPSC.203833040106_R01C01

description:
203833040106_R01C01
genomic DNA methylation from tissue=iPSC species=Human


title: Sample58.Skin.203833040019_R07C01

description:
203833040019_R07C01
genomic DNA methylation from tissue=Skin species=Human

source_name: Skin

value: Skin


title: WT_sham1_FB_8_bulk

description: WT sham1 FB


title: Sample5.Keratinocyte.201004900138_R05C01

description:
201004900138_R05C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sp42_Nm_3h

value: N. meningitidis


title: Sample57.BasalCellCarcinoma.203839170026_R08C01

description:
203839170026_R08C01
genomic DNA methylation from tissue=BasalCellCarcinoma species=Human


title: WT_sham1_FB_7

description: WT sham1 FB


title: Sample4.Keratinocyte.201004900138_R04C01

description:
201004900138_R04C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sample2.Keratinocyte.201004900138_R02C01

description:
201004900138_R02C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sample3.EndothelialCell.201004900138_R03C01

description:
201004900138_R03C01
genomic DNA methylation from tissue=EndothelialCell species=Human

value: EndothelialCell


title: Sp42_K_6h


title: WT_sham1_FB_5

description: WT sham1 FB


title: WT_sham1_FB_6

description: WT sham1 FB


title: Sample55.BasalCellCarcinoma.203839170022_R08C01

description:
203839170022_R08C01
genomic DNA methylation from tissue=BasalCellCarcinoma species=Human


title: Sp42_K_3h


title: Sample1.Keratinocyte.201004900138_R01C01

description:
201004900138_R01C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sp42_Af_6h


title: Sample54.Skin.203839170022_R07C01

description:
203839170022_R07C01
genomic DNA methylation from tissue=Skin species=Human


title: WT_sham1_FB_3

description: WT sham1 FB


title: WT_sham1_FB_2

description: WT sham1 FB


title: Sample53.BasalCellCarcinoma.203836210057_R08C01

description:
203836210057_R08C01
genomic DNA methylation from tissue=BasalCellCarcinoma species=Human


title: Sp41_Sa_6h


title: Sp41_Sa_3h


title: WT_sham1_FB_1

description: WT sham1 FB


title: NCM SS2 TAC2_140

description: NCM SS2 TAC2

source_name: Non-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 12-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).
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 25 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: Non-cardiomyocytes

value: TAC (W2)


title: Sp41_Nm_6h


title: Sample56.Skin.203839170026_R07C01

description:
203839170026_R07C01
genomic DNA methylation from tissue=Skin species=Human


title: Sample51.Keratinocyte.203836210073_R04C01

description:
203836210073_R04C01
genomic DNA methylation from tissue=Keratinocyte species=Human

value: CCCP


title: Sp41_Nm_3h


title: Sample50.Keratinocyte.203836210073_R03C01

description:
203836210073_R03C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sample49.Keratinocyte.203836210073_R02C01

description:
203836210073_R02C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sp41_K_6h


title: WT_sham1_FB_4

description: WT sham1 FB

value: Fibroblasts


title: Sp41_K_3h


title: W2442-2

type: RNA

city: Nanjing

first: Pengfei

last: Shao

address: 300 Guangzhou Road

country: China

institute: The First Affiliated Hospital of Nanjing Medical University

description: Gene expression from data A498 cells infected with shMCM8

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip primeview human PathArrayTM.

scan_protocol: Affymetrix human GeneChip PrimeView and the outcomes were scanned by Affymetrix Scanner 3000.

data_processing:
The statistical significance of raw data was completed by a Welch t-test with Benjamini-Hochberg FDR.
|Fold Change| ≥ 1.3 and FDR < 0.05 as significant.

label: 3’ IVT Biotin Label

source_name: A498 cells infected with shMCM8

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells were cultured in MEM (Gibco) medium with 10% FBS (Gibco) , placing in a 37°C incubator containing 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: A498 cells in logarithmic growth phase were infected by adding 20 μL 1×108 TU/mL shCtrl or shMCM8 lentivirus, culturing in 1640 medium with 10% FBS in a 6-well dish with 2×105 cells per well.

tag: cell line

value: renal cell carcinoma

tag: treatment

value: infected with shMCM8


title: Sp42_Af_3h


title: NCM SS2 TAC2_138

description: NCM SS2 TAC2

value: heart

value: Full length


title: NCM SS2 TAC2_136

description: NCM SS2 TAC2


title: Sp41_Af_6h


title: NCM SS2 TAC2_137

description: NCM SS2 TAC2


title: Sample48.Keratinocyte.203836210073_R01C01

description:
203836210073_R01C01
genomic DNA methylation from tissue=Keratinocyte species=Human

value: Keratinocyte


title: W2442-1


title: W2441-3

description: Gene expression from data A498 cells infected with shCtrl

source_name: A498 cells infected with shCtrl

value: infected with shCtrl


title: Sample52.Skin.203836210057_R07C01

description:
203836210057_R07C01
genomic DNA methylation from tissue=Skin species=Human

value: Male


title: W2441-2


title: W2442-3


title: Sample46.Skin.203833040110_R07C01

description:
203833040110_R07C01
genomic DNA methylation from tissue=Skin species=Human

value: Female


title: Mucoepidermoid Carcinomas sample 8B

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

description: Tumor sample Cy3-labeled mixed with reference sample Cy5-labeled

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: The array images were acquired with a microarray scanner using the Scan Control (version 8.1) software program (Agilent Technologies, CA, USA).  Images were quantified using Agilent Feature Extraction Software version v.10.1.1.1 (Agilent Technologies, CA, USA).

data_processing: Data matrix was generated and normalized by intensity-dependent global normalization (LOWESS) with Feature Extraction v11.0.1.1 software (Agilent)

source_name: Mucoepidermoid Carcinomas sample

label_protocol: Mucoepidermoid Carcinomas and normal-adjacent salivary gland samples (300ng) were differentially labeled using Low Input Quick Amp Labeling (Agilent) (Agilent Technologies, Santa Clara, CA, USA)

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

value: Mucoepidermoid Carcinomas sample

source_name: Human Universal Reference Total RNA, Clontech, Mountain View, California, EUA

value: Universal Reference


title: Sp41_Af_3h

value: male

value: A. fumigatus


title: Sample47.BasalCellCarcinoma.203833040110_R08C01

description:
203833040110_R08C01
genomic DNA methylation from tissue=BasalCellCarcinoma species=Human

value: BasalCellCarcinoma


title: NCM SS2 TAC2_135

description: NCM SS2 TAC2

value: Non-cardiomyocytes


title: NCM SS2 TAC2_139

description: NCM SS2 TAC2

value: TAC (W2)


title: Sample45.Keratinocyte.203833040110_R04C01

description:
203833040110_R04C01
genomic DNA methylation from tissue=Keratinocyte species=Human

value: Bezafibrate


title: Sp40_Sa_6h

value: S. aureus


title: Sp40_Sa_3h


title: NCM SS2 TAC2_134

description: NCM SS2 TAC2


title: NCM SS2 TAC2_133

description: NCM SS2 TAC2


title: W2441-1

value: renal cell carcinoma


title: Sample44.Keratinocyte.203833040110_R03C01

description:
203833040110_R03C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: NCM SS2 TAC2_132

description: NCM SS2 TAC2


title: Sample43.Keratinocyte.203833040110_R02C01

description:
203833040110_R02C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sp40_Nm_6h

value: N. meningitidis


title: Mucoepidermoid Carcinomas sample 22


title: Sp40_Nm_3h


title: Mucoepidermoid Carcinomas sample 7B


title: Mucoepidermoid Carcinomas sample 23


title: Sample42.Keratinocyte.203833040110_R01C01

description:
203833040110_R01C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: NCM SS2 TAC2_129

description: NCM SS2 TAC2

value: heart


title: Mucoepidermoid Carcinomas sample 21


title: Mucoepidermoid Carcinomas sample 10


title: Sp40_K_3h

value: Control


title: Sample39.BasalCellCarcinoma.203833040016_R08C01

description:
203833040016_R08C01
genomic DNA methylation from tissue=BasalCellCarcinoma species=Human


title: NCM SS2 TAC2_128

description: NCM SS2 TAC2

value: Full length


title: Sp40_Af_6h


title: Sp40_K_6h


title: Sample41.BasalCellCarcinoma.203833030031_R07C01

description:
203833030031_R07C01
genomic DNA methylation from tissue=BasalCellCarcinoma species=Human

value: not collected


title: Sp39_Sa_6h


title: Sp40_Af_3h


title: NCM SS2 TAC2_130

description: NCM SS2 TAC2


title: Sample38.Skin.203833040016_R07C01

description:
203833040016_R07C01
genomic DNA methylation from tissue=Skin species=Human

value: Male

value: Skin


title: NCM SS2 TAC2_127

description: NCM SS2 TAC2


title: Mucoepidermoid Carcinomas sample 1B

value: Mucoepidermoid Carcinomas sample


title: NCM SS2 TAC2_131

description: NCM SS2 TAC2


title: Sample37.BasalCellCarcinoma.203833030102_R07C01

description:
203833030102_R07C01
genomic DNA methylation from tissue=BasalCellCarcinoma species=Human


title: Sample36.Skin.203833030102_R06C01

description:
203833030102_R06C01
genomic DNA methylation from tissue=Skin species=Human


title: Mucoepidermoid Carcinomas sample 11B

value: Universal Reference


title: Mucoepidermoid Carcinomas sample 7


title: Mucoepidermoid Carcinomas sample 32


title: Sp39_Nm_6h

value: male


title: NCM SS2 TAC2_126

description: NCM SS2 TAC2


title: Mucoepidermoid Carcinomas sample 4


title: Mucoepidermoid Carcinomas sample 20


title: Sp39_Nm_3h


title: Sp39_Sa_3h


title: Mucoepidermoid Carcinomas sample 15


title: NCM SS2 TAC2_122

description: NCM SS2 TAC2


title: Sample33.Keratinocyte.203833030102_R02C01

description:
203833030102_R02C01
genomic DNA methylation from tissue=Keratinocyte species=Human

value: Keratinocyte

value: NR


title: Sample32.Keratinocyte.203833030102_R01C01

description:
203833030102_R01C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sp39_Af_6h

value: A. fumigatus


title: Sp39_K_6h


title: Sample40.Skin.203833030031_R06C01

description:
203833030031_R06C01
genomic DNA methylation from tissue=Skin species=Human


title: Mucoepidermoid Carcinomas sample 19


title: Sp39_K_3h


title: Sample34.Keratinocyte.203833030102_R03C01

description:
203833030102_R03C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sample35.Keratinocyte.203833030102_R04C01

description:
203833030102_R04C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sample31.BasalCellCarcinoma.203833030100_R08C01

description:
203833030100_R08C01
genomic DNA methylation from tissue=BasalCellCarcinoma species=Human

value: BasalCellCarcinoma


title: NCM SS2 TAC2_125

description: NCM SS2 TAC2

value: Non-cardiomyocytes

value: TAC (W2)


title: NCM SS2 TAC2_121

description: NCM SS2 TAC2


title: Mucoepidermoid Carcinomas sample 8

description: Tumor sample Cy3-labeled mixed with reference sample Cy5-labeled


title: Mucoepidermoid Carcinomas sample 17


title: Mucoepidermoid Carcinomas sample 3


title: NCM SS2 TAC2_124

description: NCM SS2 TAC2


title: NCM SS2 TAC2_120

description: NCM SS2 TAC2


title: NCM SS2 TAC2_123

description: NCM SS2 TAC2


title: NCM SS2 TAC2_118

description: NCM SS2 TAC2


title: Sample30.Skin.203833030100_R07C01

description:
203833030100_R07C01
genomic DNA methylation from tissue=Skin species=Human


title: NCM SS2 TAC2_119

description: NCM SS2 TAC2


title: Sp39_Af_3h


title: Sp38_Sa_3h

value: S. aureus


title: NCM SS2 TAC2_117

description: NCM SS2 TAC2


title: Sp38_Nm_6h

value: N. meningitidis


title: Sample28.Keratinocyte.203833030100_R04C01

description:
203833030100_R04C01
genomic DNA methylation from tissue=Keratinocyte species=Human

value: NAD


title: Sp38_Sa_6h


title: Mucoepidermoid Carcinomas sample 12B


title: Sample27.Keratinocyte.203833030100_R03C01

description:
203833030100_R03C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sample29.Keratinocyte.203833030100_R05C01

description:
203833030100_R05C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: NCM SS2 TAC2_116

description: NCM SS2 TAC2

value: heart


title: Sp38_Nm_3h


title: Mucoepidermoid Carcinomas sample 5B


title: NCM SS2 TAC2_115

description: NCM SS2 TAC2

value: Full length


title: Sample26.Keratinocyte.203833030100_R02C01

description:
203833030100_R02C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sp38_K_6h

value: Control


title: Sample25.Keratinocyte.203833030100_R01C01

description:
203833030100_R01C01
genomic DNA methylation from tissue=Keratinocyte species=Human

value: Male


title: Mucoepidermoid Carcinomas sample 25


title: NCM SS2 TAC2_114

description: NCM SS2 TAC2


title: Sp38_K_3h


title: Mucoepidermoid Carcinomas sample 9B


title: NCM SS2 TAC2_113

description: NCM SS2 TAC2


title: Sp38_Af_6h


title: Sample23.Skin.203833030058_R06C01

description:
203833030058_R06C01
genomic DNA methylation from tissue=Skin species=Human

value: Skin


title: Sp38_Af_3h


title: Sample22.Keratinocyte.203833030058_R04C01

description:
203833030058_R04C01
genomic DNA methylation from tissue=Keratinocyte species=Human

value: Metformin


title: NCM SS2 TAC2_111

description: NCM SS2 TAC2


title: Mucoepidermoid Carcinomas sample 24

value: Mucoepidermoid Carcinomas sample

value: Universal Reference


title: Mucoepidermoid Carcinomas sample 18


title: Sp37_Sa_6h

value: male


title: Mucoepidermoid Carcinomas sample 16


title: Mucoepidermoid Carcinomas sample 3B


title: Sample21.Keratinocyte.203833030058_R03C01

description:
203833030058_R03C01
genomic DNA methylation from tissue=Keratinocyte species=Human

value: Keratinocyte


title: Sp37_Sa_3h


title: NCM SS2 TAC2_110

description: NCM SS2 TAC2


title: Sample20.Keratinocyte.203833030058_R02C01

description:
203833030058_R02C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: NCM SS2 TAC2_109

description: NCM SS2 TAC2


title: Mucoepidermoid Carcinomas sample 11


title: Mucoepidermoid Carcinomas sample 9


title: Sp37_Nm_6h


title: Sample19.Keratinocyte.203833030058_R01C01

description:
203833030058_R01C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: NCM SS2 TAC2_108

description: NCM SS2 TAC2


title: NCM SS2 TAC2_107

description: NCM SS2 TAC2


title: Sample24.BasalCellCarcinoma.203833030058_R07C01

description:
203833030058_R07C01
genomic DNA methylation from tissue=BasalCellCarcinoma species=Human


title: NCM SS2 TAC2_112

description: NCM SS2 TAC2


title: Sp37_Nm_3h


title: Mucoepidermoid Carcinomas sample 13


title: Mucoepidermoid Carcinomas sample 14


title: Sample18.BasalCellCarcinoma.203833040035_R07C01

description:
203833040035_R07C01
genomic DNA methylation from tissue=BasalCellCarcinoma species=Human


title: Sp37_K_6h


title: NCM SS2 TAC2_106

description: NCM SS2 TAC2


title: Sp37_K_3h


title: Sample17.Skin.203833040035_R06C01

description:
203833040035_R06C01
genomic DNA methylation from tissue=Skin species=Human


title: Sample16.Keratinocyte.203833040035_R04C01

description:
203833040035_R04C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: NCM SS2 TAC2_105

description: NCM SS2 TAC2


title: Mucoepidermoid Carcinomas sample 12


title: Sp37_Af_6h

value: A. fumigatus


title: Mucoepidermoid Carcinomas sample 2


title: Sample15.Keratinocyte.203833040035_R03C01

description:
203833040035_R03C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: NCM SS2 TAC2_104

description: NCM SS2 TAC2


title: Sp37_Af_3h


title: Mucoepidermoid Carcinomas sample 1

description: Tumor sample Cy3-labeled mixed with reference sample Cy5-labeled


title: NCM SS2 TAC2_103

description: NCM SS2 TAC2


title: Sp36_Sa_6h


title: Sample14.Keratinocyte.203833040035_R02C01

description:
203833040035_R02C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Sample13.Keratinocyte.203833040035_R01C01

description:
203833040035_R01C01
genomic DNA methylation from tissue=Keratinocyte species=Human


title: Mucoepidermoid Carcinomas sample 6


title: NCM SS2 TAC2_102

description: NCM SS2 TAC2


title: Sp36_Sa_3h


title: NCM SS2 TAC2_101

description: NCM SS2 TAC2


title: Sp36_Nm_6h


title: Sample12.Paired BCC.203774260074_R08C01

description:
203774260074_R08C01
genomic DNA methylation from tissue=Paired BCC species=Human

source_name: Paired BCC

value: Paired BCC


title: NCM SS2 TAC2_100

description: NCM SS2 TAC2

value: Non-cardiomyocytes


title: Normal adjacent salivary gland 33

source_name: normal adjacent salivary gland

value: Normal adjacent salivary gland


title: Mucoepidermoid Carcinomas sample 5


title: Sp36_Nm_3h


title: Normal adjacent salivary gland 29


title: NCM SS2 TAC2_99

description: NCM SS2 TAC2

value: TAC (W2)


title: Sp36_K_6h


title: Sp36_K_3h


title: NCM SS2 TAC2_97

description: NCM SS2 TAC2


title: Sample8.Paired BCC.203786210061_R08C01

description:
203786210061_R08C01
genomic DNA methylation from tissue=Paired BCC species=Human


title: NCM SS2 TAC2_98

description: NCM SS2 TAC2


title: S200_2

city: Singapore

first: Jessica

middle: R

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University

description: 200 Hz basolateral amygdala (BLA) stimulation (100 pulses at 100 Hz) + STET

data_processing:
Raw sequencing reads were processed on the Gekko high-performance computing system (Nanyang Technological University) using Trimmomatic (v0.39) (Bolger et al. 2014) to trim Illumina adapters and remove low-quality or short-length reads (quality score < 15 or length < 30), STAR (v2.7.1a) (Dobin et al. 2013) to align reads, and HTseq (v0.11.2) (Anders et al. 2015) to quantify aligned reads.
Differential expression (DE) analyses were conducted in R 4.0.2 (R Core Team, 2020) using limma-voom (Law et al. 2014; Ritchie et al. 2015; Law et al. 2016). Counts were first filtered to remove low-count genes (Chen et al. 2016), retaining n = 19,528 genes, and then normalized using the trimmed mean of M-values method (Robinson and Oshlack 2010). Counts were then converted to log-transformed counts per million mapped reads and precision weights were calculated using voom to account for the mean–variance dependency in RNAseq count data.
To assess DE, linear models were fitted for contrasts between all pairs of conditions and empirical Bayes moderated t-statistics were computed. To reduce variability between samples due to technical factors, limma’s weighted surrogate variable analysis function with weighting by standard deviation was used to construct surrogate variables representing 2 factors of residual variability in gene expression, which were incorporated into the design matrix for DE analysis and used to generate normalized expression values. Using this method, we found that genes associated with known common contaminants of hippocampal RNA samples such as choroid plexus (Stankiewicz et al., 2015) were removed from the list of DE genes, whereas known primary response genes (PRGs) were retained.
DE genes were identified using a false discovery rate (FDR) threshold of 0.1. Expression of PRGs (Saha et al. 2011; Tyssowski et al. 2018) was visualized in a heatmap of log2 fold changes (LFCs) compared with basal stimulation. Genes were sorted by maximum LFC and genes with FDR < 0.1 or P-value < 0.01 in the stimulation conditions compared with the control condition were indicated.
Genome_build: Gencode M24
Supplementary_files_format_and_content: Raw count matrix for every gene and sample

molecule: polyA RNA

source_name: vCA1 acute slices

extract_protocol:
The horizontal brain slices were collected and flash_x0002_frozen with liquid nitrogen 30 min after stimulation. A 1 mm2 area (length × width) of vCA1 where the electrodes were located was microdissected from the frozen slices on ice and homogenised immediately in TRIzol (Invitrogen) reagent, then stored at −20 ◦C prior to extraction.  Six slices were pooled for each sample. Total RNA was extracted with chloroform and column purified with the PicoPure RNA isolation kit (Arcturus) according to the user manuals.
Directional poly(A) mRNA libraries were prepared for RNAseq by NovogeneAIT Genomics (Singapore) and 45 M 150 bp paired-end reads per sample were generated by sequenc_x0002_ing on the Illumina Novaseq 6000 platform.

treatment_protocol:
slice preparation protocol: Acute horizontal brain slices were prepared using method described previously (von Bohlen und Halbach and Albrecht 2002). The mice were decapitated after CO2 anesthesia and the brain was quickly removed into cold (4 ◦C) artificial cerebrospinal fluid (aCSF) saturated with carbogen (95% O2 and 5% CO2, flow rate: 16 L/h). 400 µm slices containing the amygdala, hippocampus, and part of the associated cortical regions were obtained using a Leica vibratome. The slices were placed onto an interface chamber (Scientific System Design) maintained at 32 ◦C and perfused with carbogenated aCSF at a rate of 1 mL/min. The slices were incubated for at least 3 h before starting the experiments to achieve a metabolic stability (Sajikumar et al. 2005; Shetty et al. 2015). Per mouse, 4 slices were obtained, with one slice allocated to each of the 4 experimental groups.
Monopolar, lacquer-coated, stainless steel electrodes (5 MΩ, AM Systems) were used in all field electrophysiological experiments. The electrodes were positioned in the horizontal slices: in the hippocampal area vCA1, 2 stimulating electrodes, S1 and S2, were placed on the stratum radiatum layer to evoke field excitatory postsynaptic potential (fEPSP) at Schaffer collateral/commissural fibers-CA1 synapses. An extra stimulating electrode (S3) was added in the vCA1 region whenever necessary. A recording electrode was placed on the apical dendritic layer. Meanwhile, 1 stimulating electrode (priming electrode) and 1 recording electrode were placed in the BLA region to stimulate the neurons. The recorded signals were amplified by a differential amplifier (Model 1700, AM Systems) and digitized with a CED 1401 analogue-to-digital converter (Cambridge Electronic Design). A stable baseline of 30 min was recorded before the induction of LTP. See description for stimulation protocols.

value: vCA1 acute slices

tag: genotype

value: Wild-type

value: 5-7 weeks

tag: sample composition

value: 6 slices pooled from individual subjects


title: S200_3

tag: strain


title: Sp36_Af_6h


title: Normal adjacent salivary gland 27


title: Sample7.Skin.203786210061_R07C01

description:
203786210061_R07C01
genomic DNA methylation from tissue=Skin species=Human

tag: cell type


title: NCM SS2 TAC2_96

description: NCM SS2 TAC2

tag: operation

tag: tissue

value: heart

value: Full length


title: S200_1

value: Male


title: Normal adjacent salivary gland 28


title: S100_3

description: 100 Hz basolateral amygdala (BLA) stimulation (100 pulses at 100 Hz) + STET


title: NCM SS2 TAC2_95

description: NCM SS2 TAC2

tag: name in supplementary file

tag: molecule subtype


title: Normal adjacent salivary gland 30


title: Sp36_Af_3h


title: Sp35_Sa_6h

value: S. aureus


title: Sample6.Paired BCC.203786210086_R08C01

description:
203786210086_R08C01
genomic DNA methylation from tissue=Paired BCC species=Human

tag: age


title: Sample5.Skin.203786210086_R07C01

description:
203786210086_R07C01
genomic DNA methylation from tissue=Skin species=Human

tag: Sex

value: Skin


title: S100_2


title: NCM SS2 TAC2_94

description: NCM SS2 TAC2

tag: protocol


title: Sample11.Skin.203774260074_R07C01

description:
203774260074_R07C01
genomic DNA methylation from tissue=Skin species=Human

tag: condition

tag: populationdoublinglevel


title: Sp35_Sa_3h

tag: stimulation


title: Sample4.Paired BCC.203786210060_R08C01

description:
203786210060_R08C01
genomic DNA methylation from tissue=Paired BCC species=Human

value: Female

tag: passagenumber


title: NCM SS2 TAC2_93

description: NCM SS2 TAC2


title: Sample10.Paired BCC.203774260138_R08C01

description:
203774260138_R08C01
genomic DNA methylation from tissue=Paired BCC species=Human


title: S100_1


title: Sample9.Skin.203774260138_R07C01

description:
203774260138_R07C01
genomic DNA methylation from tissue=Skin species=Human


title: NCM SS2 TAC2_92

description: NCM SS2 TAC2


title: Sample3.Skin.203786210060_R07C01

description:
203786210060_R07C01
genomic DNA methylation from tissue=Skin species=Human


title: LTP3

description: strong tetanization (STET) protocol to induce late-LTP (3 stimulus trains of 100 pulses at 100 Hz)


title: Sample2.Paired BCC.203786210088_R08C01

description:
203786210088_R08C01
genomic DNA methylation from tissue=Paired BCC species=Human


title: LTP2


title: Sp35_K_6h

value: male

value: Control

tag: time point


title: NCM SS2 TAC2_91

description: NCM SS2 TAC2


title: Sp35_Nm_3h

value: N. meningitidis


title: Sample1.Skin.203786210088_R07C01

description:
203786210088_R07C01
genomic DNA methylation from tissue=Skin species=Human


title: NCM SS2 TAC2_90

description: NCM SS2 TAC2


title: Ctrl3

description: slices positioned with electrodes but only basal stimulation provided


title: LTP1


title: NCM SS2 TAC2_89

description: NCM SS2 TAC2


title: Sp35_K_3h


title: Ctrl2


title: Ctrl1


title: NCM SS2 TAC2_87

description: NCM SS2 TAC2


title: Sp35_Af_6h

value: A. fumigatus


title: Sp35_Af_3h


title: W 34/70 minimal medium rep 3

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
For each strain a reference genome was created by combining chromosomes from S. cerevisiae and S. eubayanus and adjusting for SNVs detected through WGS of the lab strains (88k and 126k for CBS1538 and W 34/70, respectively)
Paired-end reads were mapped through STAR with parameters --outMultimapperOrder Random and --outSAMmultNmax 1
STAR results were filtered for high-quality mappings using samtools view with the parameter -q 255
Reads were aggregated using featureCounts with the parameters -B and -P
Differentially expression analysis was carried out with DESeq2 through iDEP9.1 (http://bioinformatics.sdstate.edu/idep/)
Genome_build: Saccharomyces cerevisiae S288C R64-2-1_20150113 and Saccharomyces eubayanus strain FM1318 (04-NOV-2015) with SNV modifications based on whole-genome sequencing of CBS1538 and W 34/70
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Saccharomyces pastorianus

source_name: lager yeast

growth_protocol: For the samples labelled "Minimal Medium", cells were grown in 2% YPDM overnight, washed with sterile water and inoculated at a cell density of 1x106 cells/mL into 60 mL of minimal medium (0.17% Yeast Nitrogen Base w/o amino acids and ammonium salts supplemented with 1% of dextrose and 1% of maltose, and 0.5% (NH4)2SO4 as a nitrogen source. The cultures were grown at 20ºC, in triplicate, and cells were harvested in the exponential phase. For fermentation samples (Day 2 and Day4) , cells were propagated in 200 mL of 4% YPDM at 25ºC for two days and were pitched into wort at a cell density of 1.5x107/mL. Fermentations (10mL)  were carried out in 10% wort containing 1mM ZnSO4 in triplicate at 13ºC without shaking. 10mL aliquots of the starting fermentation culture were added to 15mL glass tubes, each fitted with a water trap airlock attached to a bung.

extract_protocol:
RNA extraction was carried out following the protocol previously described (57) but with some modifications. Cells were resuspended in 400 µL of buffer containing 50 mM of NaOAc, pH 5.2, 10 mM EDTA pH 8.0 and 40 mL of 10% SDS, 400 µL of Phenol-Chloroform-Isoamyl alcohol (PCA; 25:24:10), pH 4.2, and 100 mL of acid washed glass beads were added. The tubes were placed in a heat block at 65ºC for 10 min and vortexed intermittently. The samples were placed on ice for 5 min. After centrifugation, the supernatant was re-extracted with PCA, pH 4.2 and then once with chloroform. Nucleic acids in the supernatant were precipitated, washed twice with 70% ethanol and then resuspended in 100 µL RNase-free H2O. The RNA concentration was measured using a Nanodrop spectrophotometer and RNA integrity was checked by Agilent 2100  Bioanalyzer as per manufacturer’s instructions.
Paired-end (150bp)  Illlumina

value: Weihenstephan 34/70

value: minimal medium


title: NCM SS2 TAC2_88

description: NCM SS2 TAC2

value: Non-cardiomyocytes

value: TAC (W2)


title: W 34/70 minimal medium rep 1


title: Sp34_Sa_6h

source_name: monocytes


title: NCM SS2 TAC2_86

description: NCM SS2 TAC2


title: Sp35_Nm_6h


title: ADAR1-KO_FLAG-ZBP1[IFNb-72h]: Z22 (bio rep 2)

city: Oxford

first: Aleksandr

last: Fedorov

address: John Radcliffe Hospital/Headley Way

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

description:
EditingIndex.tsv.gz
ADAR1-KO_FLAG-ZBP1_IFNb-72h_Z22_2.bw

data_processing:
Data preprocessing was performed using the nf-core RNA-seq pipeline (v3.3), which includes trimming adapters and low-quality bases(Trimgalore), alignment to the reference(STAR), pseudo-alignment and expression quantification(Salmon).
Coverage tracks were created using bamCoverage (v3.5.1) with CPM normalization.
Alu editing index(AEI) was estimated for ADAR1-KO and ADAR1-WT cells(with FLAG-ZBP1) using RNAEditingIndexer.
Genes with transcripts enriched in ADAR1-KO_ZBP1-KO RIP(IgG/Z22) were identified using DESeq2(v1.30.1). Matched total RNA-seq from an adjacent GEO SubSeries was used as a control. DESeq2 parameters: alpha = 0.01, lfcThreshold = 1 altHypothesis = 'greater', apeglm for LFC shrinkage.
Genome_build: GRCm38
Supplementary_files_format_and_content: transcripts.quant.sf.tar.gz is a tar archive that contains Salmon transcript level abundance estimates, as well as mapping between Ensembl genes and provided transcript ids.
Supplementary_files_format_and_content: .csv.gz files contain the results of DE analysis with DESeq2(Z22/IgG enriched genes)
Supplementary_files_format_and_content: bigWig(.bw) files contain CPM-normalized coverage tracks
Supplementary_files_format_and_content: .tsv.gz file is compressed output from RNAEditingIndexer (AEI)

source_name: Mouse embryonic fibroblasts

growth_protocol: Immortalized MEFs were maintained in DMEM supplemented with 10% FBS, 1 mM sodium pyruvate, 1x GlutaMAX, and 1% penicillin/streptomycin. Cells were maintained at 37℃ and 5% CO2.

extract_protocol:
Cells were subjected to RIP using Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore) following the manufacturer’s instructions.
Libraries were constructed with the Illumina Stranded Total RNA kit with hybridization-based rRNA depletion. Unstranded RIP used NEBnext ultra II RNA Library Prep Kit for Illumina.

treatment_protocol: MEFs were treated with IFNβ for 24, 48 or 72 hours.

value: Immortalized Zbp1-/-; Adar1-/- stably reconstituted with FLAG-ZBP1

tag: antibody

tag: ifnb

tag: stranding

value: unstranded

tag: rrna depletion

value: no


title: Sp34_Sa_3h


title: W 34/70 Day4 rep 2

tag: strain

value: day 4


title: W 34/70 Day4 rep 3


title: ADAR1-KO_FLAG-ZBP1[IFNb-72h]: Z22 (bio rep 1)

description:
EditingIndex.tsv.gz
ADAR1-KO_FLAG-ZBP1_IFNb-72h_Z22_1.bw

tag: genotype


title: Sp34_Nm_6h


title: NCM SS2 TAC2_84

description: NCM SS2 TAC2

tag: cell type

tag: operation

tag: tissue

value: heart

value: Full length


title: ADAR1-KO_FLAG-ZBP1[IFNb-0h]: Z22 (bio rep 2)

description:
EditingIndex.tsv.gz
ADAR1-KO_FLAG-ZBP1_IFNb-0h_Z22_2.bw


title: W 34/70 Day4 rep 1


title: NCM SS2 TAC2_83

description: NCM SS2 TAC2

tag: name in supplementary file

tag: molecule subtype


title: ADAR1-KO_FLAG-ZBP1[IFNb-0h]: Z22 (bio rep 1)

description:
EditingIndex.tsv.gz
ADAR1-KO_FLAG-ZBP1_IFNb-0h_Z22_1.bw


title: Sp34_Nm_3h

tag: Sex


title: FLAG-ZBP1[IFNb-72h]: Z22 (bio rep 2)

description:
EditingIndex.tsv.gz
FLAG-ZBP1_IFNb-72h_Z22_2.bw

value: Immortalized Zbp1-/- stably reconstituted with FLAG-ZBP1


title: NCM SS2 TAC2_82

description: NCM SS2 TAC2

tag: protocol


title: W 34/70 Day2 rep 2

tag: condition

value: day 2


title: W 34/70 minimal medium rep 2


title: Sp34_K_3h

tag: stimulation


title: W 34/70 Day2 rep 1


title: NCM SS2 TAC2_81

description: NCM SS2 TAC2


title: FLAG-ZBP1[IFNb-0h]: Z22 (bio rep 2)

description:
EditingIndex.tsv.gz
FLAG-ZBP1_IFNb-0h_Z22_2.bw


title: Sp34_Af_6h


title: Sp34_K_6h


title: NCM SS2 TAC2_80

description: NCM SS2 TAC2


title: CBS1538 minimal medium rep 3


title: Sp34_Af_3h


title: FLAG-ZBP1[IFNb-0h]: Z22 (bio rep 1)

description:
EditingIndex.tsv.gz
FLAG-ZBP1_IFNb-0h_Z22_1.bw


title: NCM SS2 TAC2_79

description: NCM SS2 TAC2


title: NCM SS2 TAC2_85

description: NCM SS2 TAC2


title: CBS1538 minimal medium rep 2


title: Sp33_Sa_6h

value: S. aureus


title: NCM SS2 TAC2_78

description: NCM SS2 TAC2


title: ADAR1-KO_ZBP1-KO[IFNb-48h]: Z22 (bio rep 2, tech rep 2)

description:
transcripts.quant.sf.tar.gz
ADAR1-KO_ZBP1-KO_IFNb-48h_Z22_2.bw

value: Immortalized Zbp1-/-; Adar1-/- stably reconstituted with empty vector

value: antisense

value: yes


title: Sp33_Sa_3h

value: male


title: CBS1538 minimal medium rep 1


title: W 34/70 Day2 rep 3

value: Weihenstephan 34/70


title: ADAR1-KO_ZBP1-KO[IFNb-48h]: Z22 (bio rep 2, tech rep 1)


title: CBS1538 Day4 rep 3


title: ADAR1-KO_ZBP1-KO[IFNb-48h]: Z22 (bio rep 1, tech rep 2)

description:
transcripts.quant.sf.tar.gz
ADAR1-KO_ZBP1-KO_IFNb-48h_Z22_1.bw


title: NCM SS2 TAC2_76

description: NCM SS2 TAC2


title: Sp33_Nm_6h

value: N. meningitidis


title: ADAR1-KO_ZBP1-KO[IFNb-48h]: Z22 (bio rep 1, tech rep 1)


title: Sp33_K_3h

value: Control


title: NCM SS2 TAC2_74

description: NCM SS2 TAC2

value: Non-cardiomyocytes

value: TAC (W2)


title: ADAR1-KO_ZBP1-KO[IFNb-48h]: IgG (bio rep 2, tech rep 2)

description:
transcripts.quant.sf.tar.gz
ADAR1-KO_ZBP1-KO_IFNb-48h_IgG_2.bw

value: IgG


title: ADAR1-KO_ZBP1-KO[IFNb-48h]: IgG (bio rep 2, tech rep 1)


title: FLAG-ZBP1[IFNb-72h]: Z22 (bio rep 1)

description:
EditingIndex.tsv.gz
FLAG-ZBP1_IFNb-72h_Z22_1.bw

value: unstranded

value: no


title: CBS1538 Day4 rep 1

value: day 4


title: Sp33_Af_3h

value: A. fumigatus


title: NCM SS2 TAC2_75

description: NCM SS2 TAC2

value: heart

value: Full length


title: ADAR1-KO_ZBP1-KO[IFNb-24h]: Z22 (bio rep 2, tech rep 2)

description:
transcripts.quant.sf.tar.gz
ADAR1-KO_ZBP1-KO_IFNb-24h_Z22_2.bw


title: ELK3KD-231 +ELK3, rep1

city: Seongnam-si

first: Joo Dong

last: Park

state: Gyeonggi-do

address: 335, Pangyo-ro

department: Biomedical Science

country: South Korea

institute: CHA University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

growth_protocol: The human breast cancer cell line MDA-MB 231 were obtained from the American Type Culture Collection (ATCC, Manassas , VA, USA) and were cultured in Dulbecco’s modified Eagle’s medium (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (Gibco) and 5% penicillin-streptomycin (Gibco).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol:
Stable knockdown of ELK3 in MDA-MB231 was established by using retroviruses expressing shRNA targeting ELK3 (catalog no. RHS4531-EG2004)
ELK3KD-231 were transfected with pLenti-cMyc-DDK or pLenti-cMyc-DDK-ELK3 (1ug) using Lipofectamine 2000

tag: disease state

value: Triple negative breast cancer (TNBC)

tag: cell line

tag: cell line source

value: American Type Culture Collection (ATCC)

value: ELK3 knockdown

tag: transfection

value: 48hrs after plenti-cMyc-DDK-ELK3 transfection


title: ELK3KD-231 +CV, rep2

value: 48hrs after plenti-cMyc-DDK transfection


title: CBS1538 Day2 rep 2

value: day 2


title: Sp32_Nm_6h

value: male

value: N. meningitidis

tag: time point


title: Sp33_Nm_3h


title: NCM SS2 TAC2_73

description: NCM SS2 TAC2

value: Non-cardiomyocytes


title: Sp32_Sa_3h

value: S. aureus


title: 231-C, rep2

treatment_protocol:
Control cell lines were established by infecting MDA-MB231 cells with a retrovirus generated from control retroviral plasmid
ELK3KD-231 were transfected with pLenti-cMyc-DDK or pLenti-cMyc-DDK-ELK3 (1ug) using Lipofectamine 2000

value: control


title: Sp32_Sa_6h


title: NCM SS2 TAC2_77

description: NCM SS2 TAC2

value: TAC (W2)


title: ADAR1-KO_ZBP1-KO[IFNb-24h]: Z22 (bio rep 2, tech rep 1)

value: Immortalized Zbp1-/-; Adar1-/- stably reconstituted with empty vector

tag: antibody

tag: ifnb

tag: stranding

value: antisense

tag: rrna depletion

value: yes


title: ADAR1-KO_ZBP1-KO[IFNb-24h]: Z22 (bio rep 1, tech rep 1)

description:
transcripts.quant.sf.tar.gz
ADAR1-KO_ZBP1-KO_IFNb-24h_Z22_1.bw

tag: strain

tag: genotype


title: CBS1538 Day2 rep 3


title: ADAR1-KO_ZBP1-KO[IFNb-24h]: IgG (bio rep 2, tech rep 2)

description:
transcripts.quant.sf.tar.gz
ADAR1-KO_ZBP1-KO_IFNb-24h_IgG_2.bw

value: IgG


title: CBS1538 Day4 rep 2

value: day 4


title: ADAR1-KO_ZBP1-KO[IFNb-48h]: IgG (bio rep 1, tech rep 2)

description:
transcripts.quant.sf.tar.gz
ADAR1-KO_ZBP1-KO_IFNb-48h_IgG_1.bw


title: Sp32_K_6h

value: Control


title: 231-C, rep1

value: Triple negative breast cancer (TNBC)

value: American Type Culture Collection (ATCC)


title: ELK3KD-231 +ELK3, rep2

value: ELK3 knockdown

value: 48hrs after plenti-cMyc-DDK-ELK3 transfection


title: CBS1538 Day2 rep 1

value: day 2


title: Sp32_Nm_3h

value: male


title: Sp33_K_6h


title: ADAR1-KO_ZBP1-KO[IFNb-48h]: IgG (bio rep 1, tech rep 1)


title: ADAR1-KO_ZBP1-KO[IFNb-24h]: IgG (bio rep 2, tech rep 1)


title: Sp33_Af_6h

value: A. fumigatus


title: Sp32_Af_6h


title: Sp32_Af_3h


title: ELK3KD-231 +CV, rep1

value: 48hrs after plenti-cMyc-DDK transfection


title: ELK3KD-231 +Flag-ELK3_Input

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
The reads were trimmed and aligned using Bowtie2 (Langmead and Salzberg, 2012).
We used MACS (Model-based Analysis of ChIP-Seq) to identify peaks from the alignment file.
Genome_build: hg19

growth_protocol: The human breast cancer cell line MDA-MB231 were obtained from the American Type Culture Collection (ATCC, Manassas , VA, USA).  Stable knockdown of ELK3 in MDA-MB231 was established by using retroviruses expressing shRNA targeting ELK3, and these cells were cultured in Dulbecco’s modified Eagle’s medium (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (Gibco) and 5% penicillin-streptomycin (Gibco).

extract_protocol:
ELK3KD-231 cells were transfected with pLenti-cMyc-Flag-ELK3. After 48hrs, cells were fixed in 1% paraformaldehyde solution to cross-link proteins and genomic DNA. Glycine was added to quench the formaldehyde. After washing, cells were lysed using cell lysis buffer. lysates were sonicated to fragment genomic DNA and then centrifuged. The supernatants were mixed with protein A/G magnetic beads and incubated with anti-Flag antibody. After washing, proteinase K and SDS were added to separate the DNA-protein complexes. Immunoprecipitated genomic DNA was purified using the phenol/chloroform extraction method.
The construction of library was performed using NEBNext®UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer’s instructions.

treatment_protocol:
Stable knockdown of ELK3 in MDA-MB231 was established by using retroviruses expressing shRNA targeting ELK3 (catalog no. RHS4531-EG2004)
ELK3KD-231 were transfected with pLenti-cMyc-DDK-ELK3 (1ug) using Lipofectamine 2000

value: 48hrs after plenti-cMyc-Flag-ELK3 transfection

tag: chip-seq antibody

tag: fraction

value: Input genomic DNA


title: ELK3KD-231 +Flag-ELK3_anti-Flag

value: anti-Flag

value: Immunoprecipitated DNA using anti-Flag


title: ADAR1-KO_ZBP1-KO[IFNb-24h]: IgG (bio rep 1, tech rep 2)

description:
transcripts.quant.sf.tar.gz
ADAR1-KO_ZBP1-KO_IFNb-24h_IgG_1.bw

value: Immortalized Zbp1-/-; Adar1-/- stably reconstituted with empty vector

value: antisense


title: Sp32_K_3h

tag: Sex


title: Sp31_Sa_6h

value: S. aureus


title: Sp31_Sa_3h


title: ADAR1-KO_ZBP1-KO[IFNb-0h]: Z22 (bio rep 2, tech rep 1)

description:
transcripts.quant.sf.tar.gz
ADAR1-KO_ZBP1-KO_IFNb-0h_Z22_2.bw

value: yes


title: ADAR1-KO_ZBP1-KO[IFNb-24h]: Z22 (bio rep 1, tech rep 2)


title: ADAR1-KO_ZBP1-KO[IFNb-24h]: IgG (bio rep 1, tech rep 1)

value: IgG


title: Sp31_Nm_3h

value: N. meningitidis


title: ADAR1-KO_ZBP1-KO[IFNb-0h]: Z22 (bio rep 1, tech rep 2)

description:
transcripts.quant.sf.tar.gz
ADAR1-KO_ZBP1-KO_IFNb-0h_Z22_1.bw


title: ADAR1-KO_ZBP1-KO[IFNb-0h]: Z22 (bio rep 2, tech rep 2)


title: Sp31_Af_6h


title: ADAR1-KO_ZBP1-KO[IFNb-0h]: IgG (bio rep 2, tech rep 1)

description:
transcripts.quant.sf.tar.gz
ADAR1-KO_ZBP1-KO_IFNb-0h_IgG_2.bw


title: ADAR1-KO_ZBP1-KO[IFNb-0h]: IgG (bio rep 2, tech rep 2)


title: Sp31_K_6h

value: Control


title: ADAR1-KO_ZBP1-KO[IFNb-0h]: IgG (bio rep 1, tech rep 2)

description:
transcripts.quant.sf.tar.gz
ADAR1-KO_ZBP1-KO_IFNb-0h_IgG_1.bw


title: Sp31_Af_3h


title: ADAR1-KO_ZBP1-KO[IFNb-0h]: IgG (bio rep 1, tech rep 1)


title: Sp31_K_3h


title: ADAR1-KO_ZBP1-KO_IFNb-48h(bio rep 4, tech rep 2)

description:
ADAR1-KO_ZBP1-KO_IFNb-48h_4.bw
transcripts.quant.sf.tar.gz

data_processing:
Data preprocessing was performed using the nf-core RNA-seq pipeline (v3.3), which includes trimming adapters and low-quality bases(Trimgalore), alignment to the reference(STAR), pseudo-alignment and expression quantification(Salmon).
One replica was excluded from the analysis [IFNb-0h (bio rep 1)] due to failed rRNA depletion.
IFNb stimulated genes were identified using DESeq2(v1.30.1). Parameters: alpha = 0.01, lfcThreshold = 0.585, altHypothesis = 'greater', apeglm for LFC shrinkage.
Coverage tracks were created using bamCoverage (v3.5.1) with CPM normalization.
Genome_build: GRCm38
Supplementary_files_format_and_content: transcripts.quant.sf.tar.gz is a tar archive that contains Salmon transcript level abundance estimates for each sample, as well as mapping between Ensembl genes and provided transcript ids.
Supplementary_files_format_and_content: .csv.gz files contain the results of DE analysis with DESeq2(IFNb stimulated genes)
Supplementary_files_format_and_content: bigWig(.bw) files contain CPM-normalized coverage tracks

extract_protocol:
Cells were lysed in RIP lysis buffer. Total RNA recovered by phenol:chloroform:isoamyl alcohol purification.
Libraries were constructed with the Illumina Stranded Total RNA kit with hybridization-based rRNA depletion.

treatment_protocol: MEFs were treated with IFNβ for 24 or 48 hours.


title: Sp30_Sa_3h


title: Sp30_Nm_6h


title: Sp30_Nm_3h


title: ccRCC tumor  ffpe_c_10

city: Paris

first: Maxime

last: Meylan

state: Paris

address: 15 rue de l'école de Médecine

country: France

institute: UMRS 1138 - Centre de Recherche des Cordeliers

data_processing:
Raw fatsqs were processed with SpaceRranger
Genome_build: hg38
Supplementary_files_format_and_content: matrices, images and json files

source_name: fresh ccRCC human tumor

extract_protocol:
RNA extraction with the 10X Visium protocol
Libraries preparation with illumina Truseq kit

value: renal cell cancer

tag: tissue

value: ccRCC tumor


title: ADAR1-KO_ZBP1-KO_IFNb-48h(bio rep 3, tech rep 1)

description:
ADAR1-KO_ZBP1-KO_IFNb-48h_3.bw
transcripts.quant.sf.tar.gz


title: ADAR1-KO_ZBP1-KO_IFNb-48h(bio rep 4, tech rep 1)


title: ADAR1-KO_ZBP1-KO_IFNb-48h(bio rep 3, tech rep 2)


title: ADAR1-KO_ZBP1-KO_IFNb-48h(bio rep 2, tech rep 1)

description:
ADAR1-KO_ZBP1-KO_IFNb-48h_2.bw
transcripts.quant.sf.tar.gz


title: ADAR1-KO_ZBP1-KO_IFNb-48h(bio rep 1, tech rep 2)

description:
ADAR1-KO_ZBP1-KO_IFNb-48h_1.bw
transcripts.quant.sf.tar.gz


title: Sp30_Af_3h


title: ADAR1-KO_ZBP1-KO[IFNb-0h]: Z22 (bio rep 1, tech rep 1)


title: Sp30_K_3h


title: ADAR1-KO_ZBP1-KO_IFNb-48h(bio rep 2, tech rep 2)


title: ADAR1-KO_ZBP1-KO_IFNb-48h(bio rep 1, tech rep 1)


title: Sp31_Nm_6h


title: Sp29_Sa_3h


title: Sp29_Nm_6h


title: ADAR1-KO_ZBP1-KO_IFNb-24h(bio rep 4, tech rep 2)

description:
ADAR1-KO_ZBP1-KO_IFNb-24h_4.bw
transcripts.quant.sf.tar.gz


title: ADAR1-KO_ZBP1-KO_IFNb-24h(bio rep 4, tech rep 1)


title: Sp29_Nm_3h


title: Sp29_Sa_6h


title: sub15_SL6

city: Rehovot

first: Saar

last: Ezagouri

address: Rehovot

country: Israel

institute: Weizmann Institute of Science

data_processing:
Illumina bcl2fastq software used for basecalling.
fastq files from both runs were concatenated sample-wise for subsequent analysis. The rest of analysis was done through the UTAP pipline.
Reads were trimmed using cutadapt
Reads were mapped to genome (/shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index) using STAR (default parameters)
The pipeline quantifies the genes annotated in RefSeq (that have expanded with 1000 bases toward 5’ edge and 100 bases toward 3’ bases)
Counting was done using htseq-count (union mode)
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files containing the raw counts for each gene and sample

source_name: Whole blood

extract_protocol:
RNA from the samples collected on the PAXgene tubes was isolated according to the manufacturer protocol (PAXgene Blood RNA kit #762174, PreAnalytiX, Qiagen, Hombrechtikon, Swizerland). Briefly, PAXgene tubes were thawed at 20°C for 2 h 30 min. Then, RNA was isolated, eluted in water (ultrapure DEPC-treated water #750024, Thermo Fisher Scientific), flash-frozen in liquid nitrogen and stored at -80°C.  RNA quality check. RNA concentration (OD260) and purity (OD260/280 and OD260/230) was measured using NanoDrop ND100 spectrophotometer (Thermo Fisher Scientific).
cDNA was generated from 1ul of mRNA of each sample. cDNA quantity in each sample was evaluated by qPCR for Actin B gene, and then equivalent amounts of mRNA of each sample were taken for RNAseq library construction. Library construction was performed in a 96-well plate format. First, to open secondary RNA structures and allow annealing of the RT primer, the samples were incubated at 72˚C for 3 min and immediately transferred to 4˚C. Then, RT reaction mix (10 mM DTT, 4 mM dNTP, 2.5 U/µl Superscript III RT enzyme in 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2) was added into each well of the 96-well plate and the reaction was mixed. The 96-well plate was then spun down and moved into a cycler (Eppendorf) for the following incubation: 2 min at 42˚C, 50 min at 50˚C, 5 min at 85˚C. Indexed samples with equivalent amount of cDNA were pooled.  The pooled cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20µl reaction, incubating for 2.5 h at 16˚C. The product was purified with 1.4x volumes of SPRI beads, eluted in 8 µl and in-vitro transcribed (with the beads) at 37˚C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37˚C and the amplified RNA (aRNA) purified with 1.2x volumes of SPRI beads. Library preparation for high-throughput sequencing: The aRNA was chemically fragmented into short molecules (median size ~200 nucleotides) by incubating 3 min at 70˚C in Zn2+ RNA fragmentation solution (Ambion) and purified with two volumes of SPRI beads. The aRNA (5 µl) was preincubated 3 min at 70˚C with 1 µl of 100 µM ligation adapter; then, 14 µl of a mix containing 9.5% DMSO, 1 mM ATP, 20% PEG8000 and 1 U/µl T4 ligase in 50 mM Tris HCl pH7.5, 10 mM MgCl2 and 1mM DTT was added. The reaction was incubated at 22˚C for 2 h. The ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent; reaction mix contains Affinity Script RT buffer, 10 mM DTT, 4 mM dNTP, 2.5 U/µl RT enzyme) and a primer complementary to the ligated adapter. The reaction was incubated for 2 min at 42˚C, 45 min at 50˚C and 5 min at 85˚C.  The cDNA was purified with 1.5x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 µM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kapa Biosystems). The forward primer contains the Illumina P5-Read1 sequences and the reverse primer contains the P7-Read2 sequences. The amplified pooled library was purified with 0.7x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent). MARS-Seq libraries were sequenced using an Illumina NovaSeq 6000.
The prepared libraries were sequenced on NovaSeq 6000 (Illumina), using the NovaSeq 6000 SP Reagent Kit v1.5 (100cycles) (Illumina). The entire library was run twice, in order to increase depth.

treatment_protocol: At each altitude level (SL, PU and RI) and time around the clock (6:00am, 10:00am, 2:00pm, 6:00pm, 10:00pm and 2:00am), a whole blood sample (2.5 mL) was collected in a dedicated blood RNA tube (PAXgene, PreAnalytiX, Qiagen, Hombrechtikon, Swizerland) from a venipuncture of the arm for each participant (totaling 144 tubes). Blood RNA tubes were immediately frozen and stored at -20°C  after sampling for further analysis.

tag: altitude

value: SL

tag: subject

value: E

tag: time


title: Sp30_Sa_6h

value: male

tag: stimulation


title: ADAR1-KO_ZBP1-KO_IFNb-24h(bio rep 3, tech rep 1)

description:
ADAR1-KO_ZBP1-KO_IFNb-24h_3.bw
transcripts.quant.sf.tar.gz


title: Sp29_K_6h


title: ADAR1-KO_ZBP1-KO_IFNb-24h(bio rep 3, tech rep 2)


title: sub87_SL6

value: H


title: ADAR1-KO_ZBP1-KO_IFNb-24h(bio rep 2, tech rep 2)

description:
ADAR1-KO_ZBP1-KO_IFNb-24h_2.bw
transcripts.quant.sf.tar.gz


title: sub21_SL6

value: A


title: sub75_SL6

value: D


title: Sp30_K_6h


title: Sp30_Af_6h

value: A. fumigatus


title: Sp29_Af_6h


title: Sp29_Af_3h


title: sub96_SL6

value: B


title: sub79_SL6

value: G


title: ADAR1-KO_ZBP1-KO_IFNb-0h(bio rep 4, tech rep 2)

description:
ADAR1-KO_ZBP1-KO_IFNb-0h_4.bw
transcripts.quant.sf.tar.gz

value: Immortalized Zbp1-/-; Adar1-/- stably reconstituted with empty vector

value: antisense


title: Sp29_K_3h


title: ADAR1-KO_ZBP1-KO_IFNb-24h(bio rep 2, tech rep 1)

value: yes


title: Sp28_Sa_3h

value: S. aureus


title: sub78_SL22


title: sub3_SL22

value: C


title: ADAR1-KO_ZBP1-KO_IFNb-24h(bio rep 1, tech rep 1)

description:
ADAR1-KO_ZBP1-KO_IFNb-24h_1.bw
transcripts.quant.sf.tar.gz


title: sub100_SL22


title: sub77_SL6

value: F


title: ADAR1-KO_ZBP1-KO_IFNb-0h(bio rep 3, tech rep 2)

description:
ADAR1-KO_ZBP1-KO_IFNb-0h_3.bw
transcripts.quant.sf.tar.gz


title: ADAR1-KO_ZBP1-KO_IFNb-0h(bio rep 4, tech rep 1)


title: sub73_SL22


title: sub2_SL6


title: Sp28_Nm_6h

value: N. meningitidis


title: ADAR1-KO_ZBP1-KO_IFNb-0h(bio rep 2, tech rep 1)

description:
ADAR1-KO_ZBP1-KO_IFNb-0h_2.bw
transcripts.quant.sf.tar.gz


title: sub24_SL22


title: ADAR1-KO_ZBP1-KO_IFNb-0h(bio rep 2, tech rep 2)


title: Sp28_K_6h

value: Control


title: Sp28_Af_3h


title: Sp28_Nm_3h


title: sub16_SL22

value: SL


title: Sp28_Sa_6h


title: Sp28_Af_6h


title: Sp28_K_3h


title: CBL0137(14h): FLAG (tech rep 2)

description:
CBL0137-14h-FLAG-vs-IgG-fold-enrichment.bw
CBL0137-14h-FLAG-vs-IgG.narrowPeak

data_processing:
Adapters and low-quality base pairs were trimmed using the Trim Galore tool (v0.6.5).
The trimmed reads were aligned to the mm10 mouse reference genome assembly using minimap2 aligner (v2.17).
Duplicate fragments were marked using SAMtools (v1.7).
Libraries were filtered to remove duplicates, reads that failed to form proper pairs, supplementary and secondary alignments.
Peaks were called using MACS2 (v2.2.6) with default parameters, except for fold enrichment threshold(--fe-cutoff 2) and keeping all duplicates for technical replicas(--keep-dup=all).
Fold enrichment tracks were generated by MACS2 as recommended in the documentation.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files(.bw) with fold enrichment estimated by MACS2(v2.2.6).
Supplementary_files_format_and_content: .narrowPeak files with peaks called by MACS2(v2.2.6), FDR<0.05 and fold enrichment > 2.

extract_protocol:
Cells were subjected to ChIP using the EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit (#17-10461, Millipore) following the manufacturer’s instructions.
Library preparation and paired-end 150bp DNA sequencing was performed by Novogene.

treatment_protocol: Immortalized MEFs treated with or without CBL0137 (2µM) for 14 hours

value: Immortalized ZBP1-/- stably reconstituted with FLAG-ZBP1

tag: treatment

value: CBL0137 for 14 hours

value: FLAG


title: sub88_SL22

value: H


title: ADAR1-KO_ZBP1-KO_IFNb-0h(bio rep 1, tech rep 2)

description:
ADAR1-KO_ZBP1-KO_IFNb-0h_1.bw
transcripts.quant.sf.tar.gz


title: Sp27_Sa_6h

value: male


title: sub10_SL22

value: A


title: sub23_SL2


title: Sp27_Sa_3h


title: sub80_SL2

value: E


title: CBL0137(14h): FLAG (tech rep 1)


title: sub92_SL2

value: G


title: CBL0137(0h): FLAG (tech rep 2)

description:
CBL0137-0h-FLAG-vs-IgG-fold-enrichment.bw
CBL0137-0h-FLAG-vs-IgG.narrowPeak

value: untreated


title: Sp27_Nm_6h


title: Sp27_Nm_3h


title: sub62_SL2

value: D


title: Sp27_K_6h


title: sub12_SL2

value: B


title: CBL0137(14h): Z22 (tech rep 2)

description:
CBL0137-14h-Z22-vs-IgG-fold-enrichment.bw
CBL0137-14h-Z22-vs-IgG.narrowPeak


title: CBL0137(14h): Z22 (tech rep 1)


title: Sp27_K_3h


title: ADAR1-KO_ZBP1-KO_IFNb-0h(bio rep 1, tech rep 1)

value: Immortalized Zbp1-/-; Adar1-/- stably reconstituted with empty vector

value: antisense

value: failed


title: sub104_SL2

value: C


title: Sp27_Af_6h

value: A. fumigatus


title: CBL0137(14h): IgG (tech rep 2)

value: IgG


title: ADAR1-KO_ZBP1-KO_IFNb-24h(bio rep 1, tech rep 2)

value: yes


title: sub57_SL2

value: SL

value: F


title: sub94_SL18

value: H


title: Sp27_Af_3h

value: male


title: Sp26_Sa_6h

value: S. aureus


title: CBL0137(0h): IgG (tech rep 2)

value: Immortalized ZBP1-/- stably reconstituted with FLAG-ZBP1


title: sub13_SL18

value: A


title: Sp26_Sa_3h


title: CBL0137(0h): IgG (tech rep 1)

value: untreated


title: sub63_SL18

value: G


title: B108-Placenta (RNA-seq)

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

data_processing:
Trim Galore was used to trim adapters.
STAR was used to align to the reference genome and extract gene counts.
MultiQC was used for quality control.
Genome_build: mm10
Supplementary_files_format_and_content: Gene count matrix

source_name: Placenta

growth_protocol: Fetal brain and placenta were harvested on gestational day 18

extract_protocol:
Tissue was flash frozen and nucleic acids were extracted using the Qiagen TissueLyser and AllPrep DNA/RNA/miRNA kit
KAPA mRNA HyperPrep

treatment_protocol: Pregnant dams were exposed to 1.0 mg/kg/d of a PCB mixture or a vehicle control

value: Control

value: female

tag: embryo

tag: litter

value: Placenta


title: Sp26_Nm_3h

value: N. meningitidis

tag: time point


title: B107-Placenta (RNA-seq)


title: CBL0137(0h): FLAG (tech rep 1)

tag: antibody

value: FLAG


title: Sp26_K_6h


title: sub17_SL18

value: E


title: B105-Placenta (RNA-seq)


title: sub101_SL18


title: Sp26_K_3h


title: B104-Placenta (RNA-seq)


title: sub89_SL2


title: Sp26_Af_6h

value: A. fumigatus


title: sub102_SL18

value: B


title: B103-Placenta (RNA-seq)


title: B102-Placenta (RNA-seq)


title: Sp26_Af_3h


title: Sp25_Sa_6h


title: sub86_SL14

value: SL

value: D


title: A104-Placenta (RNA-seq)

value: PCB


title: Sp25_Sa_3h

value: male


title: CBL0137(14h): IgG (tech rep 1)

value: CBL0137 for 14 hours

value: IgG


title: A103-Placenta (RNA-seq)


title: sub11_SL14


title: sub34_SL14

value: F


title: Sp26_Nm_6h


title: Sp25_Nm_6h


title: A102-Placenta (RNA-seq)


title: sub60_SL18


title: Sp25_Nm_3h


title: A101-Placenta (RNA-seq)


title: sub37_SL14


title: Sp25_K_6h


title: sub22_SL14

value: A


title: E207-Placenta (RNA-seq)


title: sub76_SL14

value: C


title: ADAR1-KO_ZBP1-KO_IFNb-0h(bio rep 3, tech rep 1)

value: Immortalized Zbp1-/-; Adar1-/- stably reconstituted with empty vector

tag: ifnb

tag: stranding

value: antisense

value: yes


title: Sp25_K_3h

value: Control


title: E206-Placenta (RNA-seq)

value: Placenta


title: Sp25_Af_6h


title: sub95_SL18


title: E205-Placenta (RNA-seq)

value: female


title: sub59_SL14


title: Sp25_Af_3h

value: A. fumigatus


title: sub20_SL14

value: H


title: sub33_SL10

value: SL


title: Sp24_Sa_6h

value: S. aureus


title: sub58_SL10


title: B203-Placenta (RNA-seq)


title: Sp24_Sa_3h


title: F203-Placenta (RNA-seq)

value: PCB


title: Sp24_Nm_3h

value: male

value: N. meningitidis


title: sub36_SL10


title: Sp24_Nm_6h


title: F202-Placenta (RNA-seq)


title: sub1_SL10

value: B


title: F201-Placenta (RNA-seq)


title: F207-Placenta (RNA-seq)


title: C207-Placenta (RNA-seq)


title: sub18_SL10

value: E


title: sub38_SL10

value: A


title: Sp24_K_6h


title: Sp24_K_3h


title: C206-Placenta (RNA-seq)


title: sub40_SL10

value: C


title: C205-Placenta (RNA-seq)


title: sub103_SL10

value: G


title: Sp24_Af_6h


title: Sp24_Af_3h


title: Sp23_Sa_6h


title: sub108_RI6

value: RI


title: C204-Placenta (RNA-seq)


title: sub114_RI6


title: C203-Placenta (RNA-seq)


title: sub156_RI6


title: Sp23_Sa_3h


title: C202-Placenta (RNA-seq)


title: sub68_RI6

value: D


title: Sp23_Nm_6h


title: C201-Placenta (RNA-seq)


title: Sp23_Nm_3h


title: F108-Placenta (RNA-seq)


title: Sp23_K_6h

value: Control


title: F107-Placenta (RNA-seq)

value: Placenta


title: sub130_RI6


title: F106-Placenta (RNA-seq)


title: Sp23_Af_6h


title: sub138_RI6

value: F


title: Sp23_K_3h


title: Sp23_Af_3h

value: A. fumigatus


title: sub8_RI6

value: H


title: F105-Placenta (RNA-seq)

value: female


title: F104-Placenta (RNA-seq)


title: Sp22_Sa_6h

value: S. aureus


title: F102-Placenta (RNA-seq)

value: PCB


title: Sp22_Nm_6h

value: male


title: F103-Placenta (RNA-seq)


title: sub25_RI22


title: sub31_RI22


title: B204-Placenta (RNA-seq)


title: F208-Placenta (RNA-seq)


title: sub122_RI22


title: Sp22_Nm_3h

value: N. meningitidis


title: sub126_RI22


title: B202-Placenta (RNA-seq)


title: sub132_RI22


title: Sp22_K_3h


title: sub99_RI22


title: D206-Placenta (RNA-seq)


title: Sp22_K_6h


title: sub44_RI22


title: Sp21_Sa_6h


title: B201-Placenta (RNA-seq)


title: sub27_RI6


title: Sp22_Af_6h


title: sub48_RI22


title: D201-Placenta (RNA-seq)


title: Sp22_Sa_3h


title: D203-Placenta (RNA-seq)


title: sub67_RI2


title: sub85_RI2


title: D104-Placenta (RNA-seq)


title: sub51_RI2


title: Sp21_K_6h


title: Sp22_Af_3h


title: Sp21_Nm_3h


title: D103-Placenta (RNA-seq)


title: sub83_RI2


title: Sp21_Nm_6h


title: Sp21_K_3h


title: sub136_RI2


title: D101-Placenta (RNA-seq)


title: Sp21_Af_6h


title: D207-Placenta (RNA-seq)


title: sub121_RI2

value: B


title: sub35_RI2


title: B107-Brain (RNA-seq)

source_name: Brain

value: Brain


title: Sp21_Af_3h


title: sub69_RI2


title: Sp20_Sa_3h


title: Sp21_Sa_3h


title: sub54_RI18


title: sub50_RI18


title: B104-Brain (RNA-seq)


title: Sp20_K_6h


title: B103-Brain (RNA-seq)


title: sub70_RI18


title: D102-Placenta (RNA-seq)


title: sub139_RI18


title: sub147_RI18


title: A104-Brain (RNA-seq)


title: Sp20_Nm_3h


title: Sp20_Af_6h


title: sub109_RI18


title: Sp20_K_3h


title: Sp20_Af_3h


title: sub142_RI18

value: A


title: Sp19_Sa_6h


title: A103-Brain (RNA-seq)


title: B105-Brain (RNA-seq)


title: A102-Brain (RNA-seq)


title: sub65_RI18

value: E


title: Sp19_Sa_3h


title: B108-Brain (RNA-seq)


title: Sp19_Nm_3h


title: Sp19_K_6h


title: sub98_RI14


title: E206-Brain (RNA-seq)


title: Sp19_K_3h


title: sub118_RI14

value: G


title: F208-Brain (RNA-seq)


title: Sp19_Af_3h


title: B102-Brain (RNA-seq)


title: Sp18_Sa_3h


title: sub152_RI14

value: RI

value: C


title: F202-Brain (RNA-seq)


title: Sp18_K_6h

value: Control


title: Sp18_K_3h


title: F201-Brain (RNA-seq)


title: sub149_RI14


title: sub120_RI14

value: D


title: sub119_RI14


title: sub135_RI10


title: sub7_RI14


title: Sp18_Af_6h


title: C207-Brain (RNA-seq)


title: A101-Brain (RNA-seq)


title: sub161_RI10


title: sub134_RI14

value: F


title: E207-Brain (RNA-seq)


title: C206-Brain (RNA-seq)


title: E205-Brain (RNA-seq)


title: Sp18_Af_3h

value: A. fumigatus


title: sub107_RI10


title: Sp17_Nm_3h


title: C205-Brain (RNA-seq)


title: Sp17_K_3h


title: C204-Brain (RNA-seq)


title: sub145_RI10


title: sub162_RI10


title: F203-Brain (RNA-seq)


title: F207-Brain (RNA-seq)


title: C203-Brain (RNA-seq)


title: Sp17_Af_3h


title: Sp18_Nm_3h


title: C202-Brain (RNA-seq)


title: sub158_RI10


title: C201-Brain (RNA-seq)


title: F108-Brain (RNA-seq)


title: sub52_RI10


title: sub129_RI10


title: F107-Brain (RNA-seq)


title: Sp16_Nm_6h


title: Sp16_Nm_3h


title: sub140_PU6

value: PU


title: F106-Brain (RNA-seq)


title: Sp16_Sa_6h


title: sub39_PU6


title: sub84_PU6


title: F105-Brain (RNA-seq)

value: female


title: Sp16_K_6h


title: Sp16_K_3h


title: F104-Brain (RNA-seq)


title: Sp16_Af_6h


title: Sp17_Af_6h


title: sub32_PU6


title: sub47_PU6


title: sub110_PU6


title: Sp16_Af_3h


title: sub74_PU6

value: H


title: B204-Brain (RNA-seq)


title: F102-Brain (RNA-seq)

value: PCB


title: Sp15_Sa_6h

value: male

value: S. aureus


title: Sp15_Sa_3h


title: Sp16_Sa_3h


title: sub45_PU22


title: sub106_PU22


title: Sp15_Nm_6h

value: N. meningitidis


title: D207-Brain (RNA-seq)

value: Brain


title: B202-Brain (RNA-seq)


title: B201-Brain (RNA-seq)


title: Sp15_Nm_3h


title: Sp15_K_3h


title: Sp15_K_6h


title: D203-Brain (RNA-seq)


title: D206-Brain (RNA-seq)


title: sub30_PU22

value: B


title: sub127_PU22


title: F103-Brain (RNA-seq)


title: sub28_PU22


title: D201-Brain (RNA-seq)


title: Sp15_Af_3h


title: Sp15_Af_6h


title: sub124_PU22


title: Sp14_Sa_6h


title: sub153_PU6


title: sub133_PU22

value: A


title: sub42_PU2

value: E


title: D103-Brain (RNA-seq)


title: Sp14_Sa_3h


title: D104-Brain (RNA-seq)


title: Sp14_Nm_6h


title: B203-Brain (RNA-seq)


title: D101-Brain (RNA-seq)


title: sub112_PU2


title: sub6_PU2

value: G


title: B107-Placenta (WGBS)

data_processing:
The CpG_Me pipeline (https://github.com/ben-laufer/CpG_Me) was used to perform all data processing steps.
Trim Galore was used to trim adapters and methylation bias.
FastQ Screen was used to screen for sample contamination.
Bismark was used align to the reference genome, remove PCR duplicates, calculate coverage, extract CpG methylation, and generate genome-wide cytosine reports (CpG count matrices).
Picard Tools was used to calculate insert size metrics.
MultiQC was used for quality control.
Genome_build: mm10
Supplementary_files_format_and_content: Bismark genome-wide cytosine reports (CpG count matrices)

extract_protocol:
Tissue was flash frozen and nucleic acids were extracted using the Qiagen TissueLyser and AllPrep DNA/RNA/miRNA kit
Swift BioSciences Accel-NGS Methyl-Seq DNA Library Kit

value: Placenta


title: Sp14_Nm_3h


title: B104-Placenta (WGBS)

value: Control


title: Sp13_Sa_3h


title: sub66_PU2


title: B105-Placenta (WGBS)


title: Sp14_Af_6h


title: Sp14_Af_3h


title: sub111_PU2


title: sub105_PU2


title: sub82_PU22

value: D


title: sub49_PU2


title: sub117_PU18

value: F


title: B102-Placenta (WGBS)


title: sub81_PU2


title: A103-Placenta (WGBS)


title: A104-Placenta (WGBS)


title: D102-Brain (RNA-seq)


title: Sp13_Nm_3h


title: Sp14_K_3h


title: Sp13_K_6h


title: sub128_PU18


title: sub155_PU18


title: A102-Placenta (WGBS)


title: B103-Placenta (WGBS)


title: Sp13_Af_3h

value: A. fumigatus


title: sub72_PU18

value: PU


title: B108-Placenta (WGBS)

value: female


title: Patient_38_Adenomatous Polyp

city: Kaunas

first: Rokas

last: Lukosevicius

address: Eiveniu str. 4

department: Institute for Digestive Research

country: Lithuania

institute: Lithuanian University of Health Sciences

description: small RNA

data_processing:
Trimming of adapter sequences: cutadapt -b TGGAATTCTCGGGTGCCAAGG -m 18 -q 30 –discard-untrimmed (cutadapt v1.9.dev6)
Filtering of reads mapped to viral genome (RefSeq), human tRNAs, rRNAs, snRNAs and sRNAs (Rfam) : blastn  -word_size=18 (BLASTN v2.2.30)
Quantification of miRNAs: miraligner -sub 1 -trim 3 -add 3 -s hsa -i $reads -db miRBase_v21 -o "isomir_$sample" -freq (SeqBuster)
Supplementary_files_format_and_content: tab-delimited text files include miRNA and iso-miRNA counts for each sample

source_name: colon

extract_protocol:
Standard protocol of miRNeasy Mini Kit (Qiagen).
Standard protocol of TruSeq Small RNA Sample Preparation Kit (Illumina)

value: Adenomatous Polyp

tag: gender

value: Male

tag: age

tag: height

tag: side

value: right

tag: weight (kg)

tag: smoking

value: Current

tag: dysplasia

value: high-grade

tag: paris class


title: A101-Placenta (WGBS)

value: PCB

tag: Sex

value: male

tag: tissue


title: human control CM

description: human control CM

data_processing:
Reads were mapped to the human genome (hg19) with the parameters “-S -m 1 -l 36 -n 2 hg19” using Bowtie (Langmead et al., 2009), as previously described.
RPKM values were calculated with reads mapped to the nuclear genome using DEGseq (Wang et al., 2009).
Single-cell transcriptomes consisting of over 2,000 detected genes were used for subsequent analysis.
Genome_build: hg19
Supplementary_files_format_and_content: csv

source_name: cardiomyocytes

growth_protocol: The procedure for single-cell RNA-seq of cardiomyocytes isolated from patients with heart failure and from control subjects was approved by the ethics committee of the University of Tokyo (Approval No. G-10032). All procedures were conducted according to the Declaration of Helsinki, and written informed consent was obtained from all participants.

extract_protocol:
Immediately after the collection of the heart tissue, rod-shaped live cardiomyocytes were isolated and incubated in lysis buffer.
Single-cell cDNA libraries were generated using the Smart-seq2 protocol (Picelli et al., 2014). The efﬁciency of reverse transcription was assessed by examining the Ct values of a control gene (TNNT2) from qRT-PCR using a CFX96 Real-Time PCR Detection System (Bio-Rad). The distribution of the lengths of cDNA fragments was assessed using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer set was used for qRT-PCR: TNNT2 mRNA forward, AAGTGGGAAG AGGCAGACTGA; TNNT2 mRNA reverse, GTCAATGGCC AGCACCTTC. A Ct value of 25 was set as the threshold.

treatment_protocol: Heart tissue was obtained immediately after death from non-cardiac causes or during left ventricular assist device surgery or heart transplantation.

tag: cell type

value: cardiomyocytes

value: heart

tag: name in supplementary file

tag: molecule subtype

value: Full length

tag: protocol


title: Sp14_K_6h

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).

tag: stimulation

tag: time point


title: E205-Placenta (WGBS)

tag: treatment

tag: embryo

tag: litter

value: Placenta


title: sub159_PU18

tag: altitude

tag: subject

value: E

tag: time


title: Patient_36_Adenomatous Polyp

description: small RNA

tag: gender

tag: age

tag: height

tag: side

tag: weight (kg)

tag: smoking

value: Never

value: lps


title: sub141_PU18

value: D


title: F208-Placenta (WGBS)

tag: Sex

tag: tissue


title: F207-Placenta (WGBS)


title: sub125_PU14

value: PU

value: C


title: sub160_PU14


title: Patient_39_Adenomatous Polyp

description: small RNA

value: Adenomatous Polyp

value: Female

value: left

tag: dysplasia

tag: paris class


title: E206-Placenta (WGBS)

value: Control


title: human HF CM

description: human HF CM

tag: cell type

tag: name in supplementary file

tag: molecule subtype

tag: protocol


title: Patient_34_Adenomatous Polyp

description: small RNA

value: Male

value: right

value: Current

value: high-grade


title: sub150_PU14

tag: altitude

value: F


title: sub5_PU18

tag: subject


title: sub144_PU18

value: A

tag: time


title: sub151_PU14

value: G


title: C207-Placenta (WGBS)

tag: treatment

value: PCB

value: female

tag: embryo

tag: litter

value: Placenta


title: Patient_31_Adenomatous Polyp

description: small RNA

tag: gender

tag: age

tag: height

value: Never

value: lp/lps


title: Patient_30_Adenomatous Polyp

description: small RNA

tag: weight (kg)

tag: smoking

value: lp


title: Patient_37_Adenomatous Polyp

description: small RNA

tag: tissue

value: Adenomatous Polyp

tag: dysplasia


title: sub26_PU14

value: PU

value: D


title: sub71_PU14

value: B


title: C206-Placenta (WGBS)

tag: Sex


title: F203-Placenta (WGBS)


title: F202-Placenta (WGBS)

value: male


title: sub46_PU14


title: Patient_27_Adenomatous Polyp

description: small RNA

value: Female

tag: side

value: left

tag: paris class


title: Patient_33_Adenomatous Polyp

description: small RNA

value: high-grade


title: E207-Placenta (WGBS)

value: Control


title: F201-Placenta (WGBS)


title: Patient_32_Adenomatous Polyp

description: small RNA

value: Ex-Smoker


title: C202-Placenta (WGBS)


title: Patient_26_Adenomatous Polyp

description: small RNA

value: rectum


title: Patient_35_Adenomatous Polyp

description: small RNA


title: sub55_PU10

value: H


title: C201-Placenta (WGBS)

value: PCB

value: female


title: sub14_PU14


title: Patient_24_Adenomatous Polyp (C4325)

description: small RNA

value: right

value: Current

value: low-grade

value: lps


title: F108-Placenta (WGBS)

value: Placenta


title: F107-Placenta (WGBS)


title: Patient_23_Adenomatous Polyp

description: small RNA

value: Adenomatous Polyp

value: Male


title: Patient_29_Adenomatous Polyp

description: small RNA

value: lp


title: Patient_22_Adenomatous Polyp

description: small RNA


title: sub43_PU10

value: PU

value: C


title: F105-Placenta (WGBS)


title: Patient_20_CRC_Tissue

description: small RNA

value: CRC tissue

value: Female

tag: Stage

tag: tnm classification


title: Patient_28_Adenomatous Polyp

description: small RNA

value: left

value: Never

value: high-grade


title: Healthy_3_Week_Replicate_2

city: Milwaukee

first: Allison

last: Ebert

state: WI

address: 8701 Watertown Plank Rd

institute: Medical College of Wisconsin

data_processing:
Data was trimmed and quality assessed with FastQC and RSeQC
Reads were aligned to the mouse reference Gencode v32 (based on Ensembl v98) using the STAR aligner and MAPR-Seq workflow v3.0
Differential gene expression was processed through EdgeR utilizing both the pairwise and generalized linear model statistics with the cutoffs set at an FDR <0.05 and log 2 fold change ≥1 or ≤-1.
Genome_build: Gencode v32 (GRCh38.p13)

source_name: iPSC-derived Motor Neuron

growth_protocol: iPSCs were differentiated into spinal motor neurons using the protocol described by Maury et al. (Nature Biotechnology, 2015). Motor neurons were plated onto matrigel-coated 6-well plates on D0. Cells were maintained for 3 weeks (21 days) post-platedown, with feedings of motor neuron maturation media (Maury et al.) occuring every 2 days.

extract_protocol:
Frozen cell pellets were resuspended in Qiagen's RLT Plus +beta-mercaptoethanol solution and extracted according to the All Prep DNA/RNA Mini Kit (Qiagen)
RNA was quantifed by fluorimetric methods (Qubit, Invitrogen) and quality assessed by Fragment Analysis (Agilent).  Library preparation was initiated with 500ng of RNA and completed following manufacturer's recommendations for the TruSeq stranded mRNA kit (Illumina).  Final libraries were quantified by qPCR (Kapa Library Quantification Kit, Kapa Biosystems) and fragment size observed with high sensitivity DNA fragment analysis (Agilent).  Paired end sequencing was completed on the NovaSeq 6000 at 2x100bp reads, targeting >50 million reads per sample.

tag: cell type

value: Motor Neuron

tag: als status

value: Non-affected

value: 21 Days Post-Differentiation


title: Healthy_3_Week_Replicate_1


title: F106-Placenta (WGBS)

tag: treatment

value: PCB

value: male


title: ALS_Affected_3_Week_Replicate_4

value: Affected


title: Patient_18_CRC_Tissue

description: small RNA

value: rectum

value: Ex-Smoker


title: C204-Placenta (WGBS)

value: female

tag: embryo

value: Placenta


title: C203-Placenta (WGBS)

tag: litter


title: ALS_Affected_3_Week_Replicate_3


title: Patient_17_CRC_Tissue

description: small RNA

tag: gender


title: Patient_25_Adenomatous Polyp

description: small RNA

value: Adenomatous Polyp

tag: age

value: right

value: ls


title: sub4_PU10

tag: altitude

value: PU

tag: subject

value: D

tag: time


title: sub56_PU10

value: G


title: Ab89

city: St Louis

first: Todd

last: Druley

state: Missouri

address: 660 South Euclid Ave

department: Department of Pediatrics

institute: Washington University In St Louis

description:
h3k27me3.pooled.fc.signal.bigwig
h3k27me3.epic2.naive_overlap_peaks.txt.gz

data_processing:
Sequencing reads were demultiplexed and processed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline with the “histone” option (https://github.com/ENCODE-DCC/chip-seq-pipeline2, version v1.1.6-10-gd4f6442) (Roadmap Epigenomics et al., 2015), which aligns reads to human genome (hg19) by bowtie2, and generates signal strength relative to the control samples using MACS2
epic2 were used to call peaks for the histone markers.
The stables sets of peaks were determined using the "naive ovelap" strategy as used in the ENCODE-chipseq pipline, i.e.,  peaks were called with the pooled reads, and 2 partions of the pooled psuedoreplicates, separately, using relaxed threshold of p<0.05; stable peaks are subset of the peaks from the pooled reads, which overlap at least 50% with peaks from both pseudoreplicates.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for signal strength, tab-delimited text files for called peaks

source_name: human induced pluripotent stem cells

extract_protocol:
Cells extracted after 70% confluency, sonicated by using COVARIS, Histone -DNA complex extracted by using antibdy.
ChIPmentation protocol bySchimdl et al.,2015
ChIPmentation

value: human induced pluripotent stem cells

tag: genotype

value: KDM6A KO


title: Patient_16_CRC_Tissue

description: small RNA

tag: tissue

value: CRC tissue

value: Male

tag: height

tag: weight (kg)

tag: smoking

value: Never


title: B202-Placenta (WGBS)

value: Control

tag: Sex

value: male


title: AB87

description:
h3k27ac.pooled.fc.signal.bigwig
h3k27ac.epic2.naive_overlap_peaks.txt.gz


title: F102-Placenta (WGBS)

value: PCB


title: sub157_PU10

value: E


title: C205-Placenta (WGBS)

value: female


title: ALS_Affected_3_Week_Replicate_1

value: Motor Neuron

value: Affected

value: 21 Days Post-Differentiation


title: Patient_15_CRC_Tissue

description: small RNA

tag: side

value: right

value: Ex-Smoker

tag: Stage

tag: tnm classification


title: AB79

tag: cell type


title: sub131_PU10

value: PU

value: F


title: D207-Placenta (WGBS)

tag: treatment

tag: embryo

value: Placenta


title: sub115_PU10

value: B


title: Patient_24_Adenomatous Polyp (C4324)

description: small RNA

value: Adenomatous Polyp

tag: gender

tag: dysplasia

value: high-grade

tag: paris class

value: lp


title: sub123_PU10

tag: altitude

tag: subject

value: A


title: Patient_13_CRC_Tissue

description: small RNA

value: CRC tissue

value: Male

tag: age

value: Never


title: RNA-seq G401 p53 C16 rep2

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Peaks were called by MACS2 with a q-value of 1e-15.
Differential binding peaks were identified using DiffBind.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each sample
Supplementary_files_format_and_content: ChIP-seq: one peak file per condition

source_name: G401 cells

growth_protocol: G401 cells were grown in DMEM with 10% FBS and 10 U/ml Penicillin-Streptomycin.TTC549, cells were grown in RPMI with 10% FBS and 10 U/ml Penicillin-Streptomycin. All cells were cultured at 37˚C and 5% CO2.

extract_protocol:
For ChIP-seq experiments, chromatin was extracted from nuclear pellets and frozen until ready for immunoprecipitation with antibodies. Immunoprecipitated DNA was extracted using a PCR purification kit. For RNA-seq, Cells were collected in Trizol and RNA was purified with Direct-Zol RNA Miniprep kit (Zymo) with on-column DNaseI treatment.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA-seq, cells were treated with 0.01% DMSO or 500 nM C16 for 3 days. For ChIP-seq, cells were treated with 0.01% DMSO or 500 nM C16 for 4 hours.

tag: cell line

value: G401 cells

tag: condition

value: p53 shRNA

value: 500 nM C16 for 3 days


title: Patient_21_Adenomatous Polyp

description: small RNA

tag: tissue

value: Female

tag: height

value: rectum

tag: weight (kg)

value: Current


title: D206-Placenta (WGBS)

value: Control

tag: Sex

value: female

tag: litter


title: RNA-seq G401 p53 C16 rep1


title: F104-Placenta (WGBS)

value: PCB

value: Placenta


title: F103-Placenta (WGBS)

value: male


title: D203-Placenta (WGBS)


title: AB39

value: human induced pluripotent stem cells

tag: genotype

value: KDM6A KO


title: Patient_11_CRC_Tissue

description: small RNA

tag: side

value: right

tag: smoking

tag: Stage

tag: tnm classification


title: AB23

tag: cell type

value: igg


title: RNA-seq G401 p53 C16 rep3

tag: treatment


title: AB22

description:
h3k4me3.pooled.fc.signal.bigwig
h3k4me3.epic2.naive_overlap_peaks.txt.gz


title: Patient_9_CRC_Tissue

description: small RNA

value: CRC tissue

tag: gender

value: left


title: B204-Placenta (WGBS)

tag: embryo


title: Patient_19_CRC_Tissue

description: small RNA

value: Male

tag: age


title: B203-Placenta (WGBS)


title: RNA-seq G401 scr C16 rep3

tag: cell line

value: G401 cells

value: scr shRNA


title: ALS_Affected_3_Week_Replicate_2

value: Motor Neuron

tag: als status

value: Affected

value: 21 Days Post-Differentiation


title: B201-Placenta (WGBS)

value: Control

tag: tissue


title: Patient_14_CRC_Tissue

description: small RNA

value: Female

value: Current


title: RNA-seq G401 scr C16 rep1

tag: condition

value: 500 nM C16 for 3 days


title: D101-Placenta (WGBS)

value: female

value: Placenta


title: Patient_6_CRC_Tissue

description: small RNA

tag: height

tag: weight (kg)

value: Never