title: 03S034.03B9203_013

description:
03B9203_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 05S007.05B9104_010

status: Public on Dec 08 2020

type: SRA

city: New Haven

first: Jen-hwa

last: Chu

state: CT

department: Pulmonary, Critical Care and Sleep Medicine

country: USA

institute: Yale University School of Medicine

description:
05B9104_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

library_source: transcriptomic

data_processing:
Basecalls using Torrent Suite Software Version 5.0.5
mRNA-seq reads were aligned to hg19 using a two stage mapping strategy. In the first stage, tophat version 2.0.12 was used with annotation and the --b2-very-sensitive option. In the second stage, bowtie 2.0.5 was used with local alignment and the --very-sensitive option.
Data were filtered using principal component analysis to remove outleirs.
Genome_build: hg19
Supplementary_files_format_and_content: text files that contain the  Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were generated using cufflinks 2.2.0

molecule: total RNA

organism: Homo sapiens

source_name: Stage II-III, untreated_BAL

extract_protocol:
Total RNA was extracted from BALF\ and PBMC samples using Qiazol following Qiagen’s miRNeasy protocol (Qiagen 217004) and using QiaCube
cDNA libraries were made from 1ug of total RNA that had RNA Integrity Number (RINe) over 6.5 upon Poly-A selection using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Ambion 61021) and fragmentation using the AB Library Builder™ System (Life Technologies 4463592) with the Ion Total RNA-Seq Kit for AB Library Builder™ System (Life Technologies 4482416).

tag: phenotype group

value: Stage II-III, untreated

tag: scadding

value: II

tag: tissue

value: bronchoalveolar lavage


title: WT paracardial fat, biological rep4

type: RNA

city: Columbus

first: Federica

last: Accornero

state: Ohio

address: 473 W 12th Ave

department: Physiology and Cell Biology

institute: The Ohio State University

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained according to manufacturer's instructions in the manual target preparation for GeneChip Whole Transcript (WT) Expression Arrays for the GeneChipWT Pico Reagent Kit (Applied Biosystems).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

data_processing: The data were normalized by RMA method with Affymetrix Expression Console software. Linear model and moderated t-test was used for testing differentially expressed genes by using SAS and R packages.

label: biotin

organism: Mus musculus

source_name: WT C57, paracardial fat

label_protocol: Fragmented cDNA was labeled by terminal deoxynucleotidyl transferase (TdT) using a DNA Labeling Reagent that is covalently linked to biotin (GeneChip Pico Reagent Kit, Applied Biosystems) according to manufacturer instructions by Ohio State Genomics Shared Resource-Comprehensive Cancer Center core facility.

extract_protocol:
tissue isolated directly from animals and placed in lysis buffer for homogenization.
RNA was isolated from the pCF and iVF depot of wild type using the Norgen Fatty Tissue RNA Purification Kit (Norgen Biotek Corp) according to the manufacturer's instructions.

value: paracardial fat depot

tag: strain

tag: gender

value: male


title: 06S025.06B9133_008

description:
06B9133_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 04S041.04B9250_015

description:
04B9250_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 09S012.09B9161_003

description:
09B9161_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 08S055.08B9156_002

description:
08B9156_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G164_3_S3_L003

city: Syracuse

first: Vladimir

middle: A

last: Kuznetsov

state: NY

address: 750 E Adams St

department: Urology / Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

data_processing:
Illumina’s bcl2fastq program was used for conversion of base calls to FASTQ files with default settings
STAR was used to align sequences to the GRCm38/mm10 mouse genome with default settings
STAR was also used for quantification of reads per gene using -quantMode
Raw counts between tumors and days for each genotype were summed
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Processed table with summed gene counts for each replicate

source_name: breast tumor

growth_protocol: PyMT males were bred to homozygous Abi1 females to generate PyMT;Abi1 (fl/wt) males, which were then backcrossed to homozygous Abi1 females. The resulting progeny were used to establish PyMT animals with heterozygous or homozygous Abi1 floxed, with and without MMTV-cre expression

extract_protocol:
Tissue was homogenized in QIAzol reagent with a Qiagen TissueRuptor, and RNA was extracted using QIAzol/choloroform phase separation followed by purification with Qiagen RNeasy Mini Columns
Illumina TruSeq Stranded Total RNA Kit with RiboZer Gold H/M/R

tag: date

tag: lane

tag: abi1 genotype (all mice are pyvt+)

value: fl/wt

tag: cre


title: WT paracardial fat, biological rep3


title: 03S052.03B9216_012

description:
03B9216_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s68

city: Amsterdam

first: Joe

last: Butler

address: Meibergdreef 9

department: Infectious diseases

country: Netherlands

institute: Amsterdam UMC

data_processing:
Reads were trimmed using Trimmomatic version 0.36.
Read alignment done by bowtie2 version 2.3.4.3
Count data were generated by means of the FeatureCounts method.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: monocytes

growth_protocol: Isolation of PBMCs was performed by density-gradient centrifugation with Ficoll-Paque PLUS. CD14+ monocytes were subsequently purified using MACS CD14 microbeads for positive selection. Monocytes were plated in 48-wells tissue culture treated plates for adherent monocytes or 48-wells plates with cell-repellent surface for non-adherent monocytes (both 5x105 cells/well).

extract_protocol:
Total RNA was isolated using the Nucleospin RNA Isolation kit. RNA quality was assessed by bioanalysis (Agilent); samples with RNA integrity number > 7 were included for RNA sequencing.
Libraries were prepared from 100-200 ng total RNA using KAPA RNA Hyperprep with RiboErase (Roche) kits.

treatment_protocol: Monocytes were plated in 48-wells tissue culture treated plates for adherent monocytes or 48-wells plates with cell-repellent surface for non-adherent monocytes (both 5x105 cells/well). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (no glutamine; 31870074; Gibco; Thermo Fisher, Waltham, MA) supplemented with 10 μg/ml gentamicin (Gibco), 1 mM sodium pyruvate (Gibco), 2 mM glutamax (Gibco), 20 mM HEPES (Gibco) and 10% fetal bovine serum (FBS; HyClone; GE Healthcare) or glucose free RPMI (no glucose; with glutamine; 11879020; Gibco) supplemented with gentamicin, sodium pyruvate, HEPES and FBS. After one hour of incubation, monocytes were stimulated for 24 hours with 10 ng/ml ultrapure LPS (from Escherichia coli 0111:B4; InvivoGen, Toulouse, France)

tag: donorid

tag: adhcond

value: adherent

tag: lpscond

value: LPS

tag: glucond

value: glucose


title: 03S015.03B9067_005

description:
03B9067_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G164_3_S3_L002


title: WT paracardial fat, biological rep1


title: WT paracardial fat, biological rep2


title: 03S056.03B9219_008

description:
03B9219_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 06S013.06B9128_013

description:
06B9128_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: III


title: 04S006.04B9088_016

description:
04B9088_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 02S018.02B9057_003

description:
02B9057_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G144_8_S2_L003


title: Breast tumor, 190617_G164_3_S3_L004


title: s65


title: 05S041.05B9348_002

description:
05B9348_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G164_3_S3_L001


title: s64


title: s63


title: 06S011.06B9125_013

description:
06B9125_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s67


title: Breast tumor, 190617_G144_8_S2_L002


title: Breast tumor, 190617_G164_6_S4_L001


title: s66


title: s61


title: 03S048.03B9212_011

description:
03B9212_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 09S025.09B9428_010

description:
09B9428_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s60


title: s62


title: Breast tumor, 190617_G144_8_S2_L004


title: 03S099.03B9443_002

description:
03B9443_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G144_6_S1_L004


title: 06S034.06B9138_002

description:
06B9138_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Replicate 4 H53 wildtype with 2mM H2O2

city: Baltimore

first: Diego

middle: Rivera

last: Gelsinger

state: MD

address: 910 Light Street, Apartment 2

department: Biology

institute: The Johns Hopkins Univeristy

data_processing:
We used a read count-based differential expression analysis to identify putative targets of SHOxi that were differentially expressed during oxidative stress and in ΔSHOxi. The program featureCounts was used to rapidly count reads that map to the NCBI H. volcanii annotation. featureCounts was run with strand-specific options on, paired-end mode on or off, multi-mapping off. The read counts were then used in the R differential expression software package DESeq2 (ref). Briefly, read counts were converted into a data matrix and normalized by sequencing depth and geometric mean. Differential expression was calculated by finding the difference in read counts between the SHOxi knockout oxidative stress state to the normalized read counts from the wild-type oxidative stress normalized read counts. The differentially expressed mRNAs were filtered based on the statistical parameter of False Discovery Rate (FDR) under 5%. In addition, only mRNAs with converse differential expression levels (FDR < 5%) in our previous wild type no challenge/oxi stress differential expression comparison (Gelsinger & DiRuggiero, 2018b) were labeled as specific putative targets of SHOxi. Alll libraries deposited here were used as well as WT no challenge and WT oxidative stress mRNA-seq libraries previously deposited on GEO: GSE103893. Read counts from previous libraries are noted in GEO_submission_raw_readcounts.txt with (GSE103893).
Genome_build: ASM2568v1 GCF_000025685.1
Supplementary_files_format_and_content: .xlsx, .txt

organism: Haloferax volcanii DS2

source_name: Cellular culture

growth_protocol: H. volcanii auxotrophic strain H53 (Δpyre2, ΔtrpA) and H98 (Δpyre2, ΔthyH) were used for all experiments. Culturing in liquid and solid media was done in rich medium (Hv-YPC) or selection medium (Hv-Cab), at 42°C and with shaking at 220 rpm (Amerix Gyromax 737) (Dyall-Smith, 2009). Uracil, tryptophan, thymidine, and hypoxanthine were added to a final concentration of 50 µg/mL, each.

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA Miniprep kit with the following modifications: H. volcanii liquid culture is slimy and viscous thus to increase cellular lysis a 23 G needle and syringe were used to break down the cell pellet after addition of RNA lysis buffer to the frozen pellets to insure complete cell lysis. Total RNA was then extracted following the standard kit protocol. Total RNA was DNase I (NEB) treated (37 °C for 2 hours) as previously described (Gelsinger et al. 2018).
Total RNA was then rRNA-depleted using the Ribo-zero Bacteria kit (Illumina). Strand-specific libraries were prepared using the SMART-seq Ultralow RNA input kit (Takara), insert sizes checked with the Bioanalyzer RNA pico kit (Agilent), and either paired-end sequenced (2 x 150 bp) or single-end sequenced (100 bp) on the Illumina HiSeq 2500 platform at the Johns Hopkins University Genetic Resources Core Facility (GRCF).

treatment_protocol: H. volcanii liquid cultures were exposed to H2O2 as previously described (Gelsinger & DiRuggiero, 2018b). In brief, cultures were grown in 160 mL of Hv-YPC or Hv-Cab under optimal conditions to an OD of 0.4 (mid exponential phase). 2 mM H2O2 was directly added to the cultures followed by an hour incubation at 42 °C with shaking at 220 rpm. Cultures were then rapidly cooled down, centrifuged at 5,000 x g for 5 minutes and the pellets resuspended in 18% sea water. The cell suspensions were then transferred to a 1 mL tube and centrifuged at 6,000 x g for 3 minutes, the pellets were flash frozen and stored at -80 °C until ready for RNA extraction.

tag: strain/background

value: auxotrophic strain H53 (<delta>pyre2, <delta>trpA)

tag: genotype/variatiion

value: wild type

tag: treatment

value: 2mM H2O2


title: Replicate 5 H53 wildtype with 2mM H2O2


title: s59


title: 06S002.06B9122_011

description:
06B9122_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 04S036.04B9243_001

description:
04B9243_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G144_6_S1_L003


title: s58


title: Replicate 3 H53 wildtype with 2mM H2O2 [re-analysis]


title: 06S001.06B9120_009

description:
06B9120_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s57


title: Breast tumor, 190617_G144_6_S1_L002


title: 04S005.04B9089_006

description:
04B9089_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S058.03B9324_006

description:
03B9324_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Breast tumor, 190617_G144_8_S2_L001


title: Breast tumor, 190617_G144_6_S1_L001


title: s56


title: Replicate 1 H53 wildtype with 2mM H2O2 [re-analysis]


title: Replicate 4 H53 wildtype with no challenge


title: Overexpression YAP Rep 3

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

description:
OE YAP-3
OE_analysys.xlsx

data_processing:
Reads mapping and transcripts expression quantification with Rsem/STAR (default parameters) on the RefSeq transcripts annotation (mm10 retrieved from the UCSC genome browser).
edgeR was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: The .txt files contain the output of genes abundance quantification obtained using RSEM. The two .xls files contain the results of the differential expression analysis carried out using edgeR. Each xlsx file contains a CPM tab with the Counts Per Million expression levels for all expressed genes and a Deregulated tab with the genes deregulated at FDR <= 0.05 and their associated logFC.

source_name: ESCs

extract_protocol:
Total RNAs from three independent experiments were extracted by TriSure (Bioline) and subjected to high-throughput sequencing with Illumina Genome Analyzer platform (Illumina).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

tag: cell type

value: embryonic stem cells

tag: developmental stage

value: pluripotent

value: Transient transfection with plasmid encoding mYAP


title: s55


title: Replicate 3 H53 wildtype with no challenge [re-analysis]


title: s54


title: Overexpression YAP Rep 1

description:
OE YAP-1
OE_analysys.xlsx


title: 03S025.03B9077_001

description:
03B9077_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

tag: phenotype group

tag: scadding


title: Replicate 2 H53 wildtype with no challenge [re-analysis]

tag: strain


title: 02S027.02B9263_005

description:
02B9263_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

tag: tissue


title: s53


title: 02S013.02B9056_009

description:
02B9056_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Overexpression Control Rep 3

description:
OE CTR-3
OE_analysys.xlsx

value: Transient transfection with plasmid encoding GFP


title: Replicate 1 H53 wildtype with no challenge [re-analysis]


title: 03S100.03B9450_001

description:
03B9450_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

source_name: Stage II-III, treated_BAL

value: Stage II-III, treated


title: Overexpression Control Rep 2

description:
OE CTR-2
OE_analysys.xlsx


title: s52

value: control


title: Replicate 3 H98 SHOxi knockout (ΔSHOxi) with 2mM H2O2

value: H98 (<delta>pyre2, <delta>thyH)

value: SHOxi knockout


title: s51


title: Replicate 2 H53 wildtype with 2mM H2O2 [re-analysis]


title: 03S024.03B9073_003

description:
03B9073_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: II

value: bronchoalveolar lavage


title: 09S005.09B9176_006

description:
09B9176_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s50


title: Overexpression Control Rep 1

description:
OE CTR-1
OE_analysys.xlsx


title: Knock Down YAP Rep 3

description:
KD YAP-3
KD_analysys.xlsx

value: Transient transfection with siRNAs targeting mYAP


title: Overexpression YAP Rep 2

description:
OE YAP-2
OE_analysys.xlsx


title: 03S016.03B9068_009

description:
03B9068_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Replicate 2 H98 SHOxi knockout (ΔSHOxi) with 2mM H2O2


title: s49


title: Replicate 4 H53 SHOxi knockout (ΔSHOxi) with 2mM H2O2


title: Replicate 1 H98 SHOxi knockout (ΔSHOxi) with 2mM H2O2


title: Knock Down YAP Rep 1

description:
KD YAP-1
KD_analysys.xlsx


title: Knock Down YAP Rep 2

description:
KD YAP-2
KD_analysys.xlsx


title: 05S016.05B9115_006

description:
05B9115_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Replicate 3 H53 SHOxi knockout (ΔSHOxi) with 2mM H2O2


title: Knock Down Control Rep 3

description:
KD CTR-3
KD_analysys.xlsx

value: Transient transfection with siRNAs scrambled


title: 03S097.03B9442_004

description:
03B9442_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s48

value: adherent


title: Knock Down Control Rep 2

description:
KD CTR-2
KD_analysys.xlsx


title: s47

value: glucose


title: s46


title: s45


title: 01S007.01B9024_005

description:
01B9024_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Replicate 2 H53 SHOxi knockout (ΔSHOxi) with 2mM H2O2

value: auxotrophic strain H53 (<delta>pyre2, <delta>trpA)


title: Replicate 1 H53 SHOxi knockout (ΔSHOxi) with 2mM H2O2


title: Knock Down Control Rep 1

description:
KD CTR-1
KD_analysys.xlsx


title: mESCs - INPUT rep2

library_source: genomic

data_processing:
Seq were mapped with Bowtie for Illumina from Galaxy platform
ChIP-seq reads were aligned to the mm9 genome assembly
peaks were called using MACS
Genome_build: mm9
Supplementary_files_format_and_content: MACS peak files

molecule: genomic DNA

source_name: E14Tg2a mESCs

extract_protocol:
Lysates were clarified from sonicated nuclei and YAP-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

value: pluripotent cells

tag: chip antibody


title: 04S065.04B9460_015

description:
04B9460_IonXpressRNA_015
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s44


title: s43


title: 05S006.05B9103_006

description:
05B9103_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: III


title: mESCs - INPUT rep1

value: embryonic stem cells


title: 04S052.04B9407_002

description:
04B9407_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: mESCs - IP a-YAP rep2

value: rabbit polyclonal anti-Yap (NB110-58358 Novus Biological)


title: 03S036.03B9205_007

description:
03B9205_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s41


title: s42


title: mESCs - IP a-YAP rep1


title: s40


title: 03S018.03B9069_016

description:
03B9069_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 04S053.04B9416_004

description:
04B9416_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s39


title: Knock Down YAP T4 Rep 1 (BS-Seq)

description: KD YAP-1 T4

data_processing:
Reads have been quality trimmed using trim galore with parameters --paired --trim1 --phred33 -j 4
Mapping on in silico bisulphitated mm9 genome have been carried out using Bismark/Bowtie2 with parameter -p 12 -X 1000
Methylated positions have been called using the processBismarkAln of methylKit
Differentially methylated regions (DMRs) have been calles using the tileMethylCounts and calculateDiffMeth of functions of methylKit with window size 250bp and step size 125bp.
Genome_build: mm9 (bisulphitated in silico using Bismark)
Supplementary_files_format_and_content: Differential Methylated Regions analysis (tabular file). DMR_analysis.xlsx contains the DMRs between CTRL0/YAP0, CTRL4/YAP4, CTRL0/CTRL4, and YAP0/YAPT4 with the associated qvalue and % of diff.

source_name: embryonic stem cells

extract_protocol:
Genomic DNA from two independent experiment was extracted and purified by QIAamp DNA Kit (QIAGEN) according to the manufacturer’s instructions.
Illumina SureSelectXT Methyl-Seq Target Enrichment System

tag: cell differentiation

value: 4 days differentiated toward neuroectoderm

value: ES-derived neuronal precursor


title: s38


title: Knock Down YAP T4 Rep 2 (BS-Seq)

description: KD YAP-2 T4


title: s37


title: s36

value: LPS


title: Knock Down YAP T0 Rep 1 (BS-Seq)

description: KD YAP-1 T0

value: Undifferentiated

value: pluripotent


title: 04S014.04B9083_013

description:
04B9083_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: Stage II-III, treated


title: Knock Down Control T4 Rep 2 (BS-Seq)

description: KD CTR-2 T4


title: s35


title: 05S003.05B9102_009

description:
05B9102_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: II


title: 04S002.04B9090_014

description:
04B9090_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: bronchoalveolar lavage


title: 02S019.02B9050_005

description:
02B9050_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Knock Down Control T4 Rep 1 (BS-Seq)

description: KD CTR-1 T4


title: s34


title: Knock Down Control T0 Rep 2 (BS-Seq)

description: KD CTR-2 T0


title: 04S027.04B9094_002

description:
04B9094_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s33


title: 01S017.01B9034_013

description:
01B9034_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Knock Down Control T0 Rep 1 (BS-Seq)

description: KD CTR-1 T0


title: 01S021.01B9039_012

description:
01B9039_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: scRNA-seq_P8_3Sham

city: New York

first: Zhaoning

last: Wang

state: New York

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

institute: Columbia University

description: P8+3 dps

data_processing:
The Cell Ranger Single-Cell Software Suit (10xGenomics) was used to perform sample demultiplexing, barcode processing and single-cell 3′ gene counting.
The cDNA reads were aligned to the mm10/GRCm38 mRNA reference genome to generated gene-barcode matrix.
R package Seurat was used for downstream quality filtering and data analysis. Potential cell doublets, red blood cells, and low quality cells were removed from the data.
Data were normalized and scaled, taken number of genes (nGene) and unique molecular/ identifiers (nUMI) into consideration.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated value (tsv) files and matrix (mtx) files for filtered gene barcode matrices generated from CellRanger primary analysis from raw sequencing data.

source_name: Single cells isolated from ventricle tissue below left anterior descending artery ligation plane

growth_protocol: Animals were housed in a 12 h light/dark cycle in a temperature-controlled room in the Animal Research Center of UT Southwestern, with ad libitum access to water and food.

extract_protocol:
Mice were euthanized at 1d or 3d post surgery. Ventricle tissues below LAD ligation plane from MI hearts, and ventricle tissues from similar region of sham hearts, were collected and digested into single cell suspension.
Single cells digested from the tissue were subjected to single cell RNA-sequencing using 10xGenomics platform. Library preparation was performed using Single Cell 3’ Reagent Kits v2 (10xGenomics) according to the manufacturer’s protocol.

treatment_protocol: Neonatal P1 or P8 mice were subjected to myocardial infarction, induced by permanent ligation of LAD coronary artery, or sham surgery.

value: ventricle

tag: surgery performed at developmental age

tag: sample collected at post-surgical day

tag: surgery type

value: Sham


title: s32

tag: donorid

tag: adhcond


title: Knock Down YAP T0 Rep 2 (BS-Seq)

description: KD YAP-2 T0

value: Transient transfection with siRNAs targeting mYAP


title: scRNA-seq_P8_3MI

description: P8+3 dpi

value: MI


title: 06S026.06B9134_010

description:
06B9134_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 03S101.03B9444_012

description:
03B9444_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 08S007.08B9143_008

description:
08B9143_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s28

value: adherent

tag: lpscond

tag: glucond


title: s30


title: scRNA-seq_P8_1MI

description: P8+1 dpi


title: 01S018.01B9032_008

description:
01B9032_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: scRNA-seq_P1_3Sham

description: P1+3 dps


title: 01S013.01B9029_005

description:
01B9029_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s27


title: scRNA-seq_P1_1Sham

description: P1+1 dps


title: s26

value: glucose


title: scRNA-seq_P1_3MI

description: P1+3 dpi


title: s25


title: s24


title: s31


title: 06S009.06B9123_014

description:
06B9123_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: III


title: scATAC-seq_P8_3Sham

description: P8+3 dps

data_processing:
The Cell Ranger ATAC software suit (10xGenomics) was used to perform sample demultiplexing, barcode processing and read counting
The open chromatin reads were aligned to the mm10/GRCm38 reference genome to generated region-barcode matrix.
R packages Seurat and Signac was used for downstream quality filtering and data analysis. Potential cell doublets, and low quality cells were removed from the data.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated value (tsv) files, hdf5 (h5) matrix, bed files ,and matrix (mtx) files for peak barcode matrices and mapped genomic fragments generated from CellRanger ATAC primary analysis of the raw sequencing data.

extract_protocol:
Mice were euthanized at 3d post surgery. Ventricle tissues below LAD ligation plane from MI hearts, and ventricle tissues from similar region of sham hearts, were collected for nuclei extraction.
Single nucleus suspension was subjected to Tn5 transposition and single cell ATAC-sequencing using 10xGenomics platform. Library preparation was performed using NextGEM Single Cell ATAC Library & Gel Bead Kit v1.1 (10xGenomics) according to the manufacturer’s protocol. Please note we performed two runs of sequencing (Run1 and Run2) for higher sequencing depth.


title: 01S025.01B9280_016

description:
01B9280_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s29


title: scATAC-seq_P8_3MI

description: P8+3 dpi


title: 05S005.05B9105_003

description:
05B9105_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s22


title: 03S040.03B9209_004

description:
03B9209_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: scRNA-seq_P8_1Sham

description: P8+1 dps


title: scATAC-seq_P1_3Sham

description: P1+3 dps


title: s21


title: 01S009.01B9026_006RUN265

description:
01B9026_IonXpressRNA_006RUN265
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: scATAC-seq_P1_3MI

description: P1+3 dpi


title: s20


title: 03S037.03B9207_003

description:
03B9207_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 01S002.01B9021_011

description:
01B9021_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 04S046.04B9256_007

description:
04B9256_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

source_name: Non-acute, Stage I, untreated_BAL

value: Non-acute, Stage I, untreated

value: I


title: scRNA-seq_P1_1MI

description: P1+1 dpi


title: 01S001.01B9022_001

description:
01B9022_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s19


title: s18

value: control


title: ALKBH5_WT_H3K9me3_ChIP_rep2

city: Shanghai

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

country: China

institute: Fudan university

data_processing:
Raw reads were aligned to the mm10 genome using Bowtie2 (v 2.2.5).
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: mm10
Supplementary_files_format_and_content: Genome coverage bigwig files

source_name: Embryonic stem cells

growth_protocol: E14Tg2a murine embryonic stem cells (mES) were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% fetal bovine serum (FBSGibco #16000-044), 1% MEM non-essential amino acid (Gibco #11140), 55 mM β-Mercaptoethanol (Gibco#21985-023), 100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1000 units/mL LIF (Millipore #ESG1107,) and MEK inhibitor PD0325901 (1μM) and GSK3β inhibitor CH99021 (3μM) at 37℃ with 5% CO2. For EB differentiation, embryoid bodies (EBs) were allowed to form in the absence of LIF by hanging drops containing ~1,000 mES cells/drop on petri dish lids for 2days, and then collected and transferred to standard mES culture (without LIF and MEK and GSK3β inhibitor) in non-coated petri dishes 5days.

extract_protocol:
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

value: Embryonic stem cells

tag: genotype

value: ALKBH5 WT

tag: antibody

value: H3K9me3 (Active motif, #39161)


title: ALKBH5_KO_H3K9me3_ChIP_rep2

tag: cell type

value: ALKBH5 KO

tag: treatment


title: ALKBH5_KO_H3K9me3_ChIP_rep1


title: RNA_mm9_vkChe_3

city: Rome

first: Maurizio

last: Fanciulli

address: via Chianesi

institute: IRCCS National Institute of Cancer Regina Elena

data_processing:
RNA-seq basic analysis was carried out with RAP (D'Antonio et al., 2015), a cloud Tuxedo-suite (Trapnell et al., 2009) based pipeline.
Raw reads we extracted using HTseq (Anders et al., 2015)  for NCBI’s RefSeq gene annotation and our custom spike-in annotation.
Gene-based differential expression was carried out using spike-in raw reads count as scaling factors with DEseq2 (Love et al., 2014)
Genome_build: mm9
Supplementary_files_format_and_content: deseq2 output

extract_protocol:
cd138 positive cell from spleen of VK*Che-1 and Control mice were extracted by TRizol (ThermoFisher/Life Tech) and purified by Qiagen Mini Elute.
Library construction using Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, CA).

treatment_protocol: transgenic mice for Che1/AATF overxpression (VK*Che-1)

tag: genotype/variation

value: VK-Che (overexpression)

tag: spike in used


title: RNA_mm9_vkChe_1


title: 08S079.08B9302_011

description:
08B9302_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

tag: phenotype group

tag: scadding


title: ALKBH5_WT_H3K9me3_ChIP_rep1


title: 08S076.08B9309_008

description:
08B9309_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

tag: tissue


title: RNA_mm9_Control3


title: s17


title: RNA_mm9_Control2


title: 04S024.04B9091_016

description:
04B9091_IonXpressRNA_016
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s15


title: 01S027.01B9282_002

description:
01B9282_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: YTHDC1_W428A_total_RNA_rep2

data_processing:
Raw reads were aligned to the mm10 genome using TopHat (v2.1.1) with parameter “--max-multihits 1”.
PCR duplicates were removed using samtools (v1.7) rmdup.
Strand specific reads were separated by samtools (v1.7) view with specific flags 99, 147, 83, 163.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: mm10
Supplementary_files_format_and_content: Genome coverage bigwig files

growth_protocol: E14Tg2a murine embryonic stem cells (mES) were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% fetal bovine serum (FBSGibco #16000-044), 1% MEM non-essential amino acid (Gibco #11140), 55 mM β-Mercaptoethanol (Gibco#21985-023), 100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1000 units/mL LIF (Millipore #ESG1107,) and MEK inhibitor PD0325901 (1μM) and GSK3β inhibitor CH99021 (3μM) at 37℃ with 5% CO2.

extract_protocol:
Total RNAs were isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instruction.
Strand specific total RNA library preparation was performed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420S).

value: YTHDC1 W428A


title: s23

value: LPS


title: RNA_mm9_Control1


title: YTHDC1_KO_total_RNA_rep2

value: YTHDC1 KO


title: 01S042.01B9297_003

description:
01B9297_IonXpressRNA_003
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: bronchoalveolar lavage


title: YTHDC1_W428A_total_RNA_rep1


title: YTHDC1_KO_total_RNA_rep1


title: s14


title: RNA_mm9_vkChe_2


title: 02S005.02B9047_008

description:
02B9047_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s13


title: ATAC_MM_mm10_VK-Che_22

data_processing:
aligned to the reference genome using bowtie 2.3.4.2
The generated sequence alignments were converted into binary files (BAM), then sorted and indexed using the SAMtools. V1.7
ATAC-seq peaks were generated using MACS v2.2.5 with parameters ‘--nomodel --shift -100 --extsize 200 -B --SPMR --call-summits -q 0.01’.
Peaks in  bedGraph format (.bdg) were converted in bigWig (.bw) format using bedGraphToBigWig tool
All peaks matching blacklisted regions were discarded from further processing.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig and bed

extract_protocol:
positive cd138 plasma cell from bone marrow extracted by protocol as described in Nat Methods. 2013;10(12):1213-1218. (Buenrostro JD., et al;)
Library construction as described in Nat Methods. 2013;10(12):1213-1218. (Buenrostro JD:, et al;)

treatment_protocol: transgenic mice overexpressing Che-1/AATF  (VK*Che-1) or WT


title: s12


title: YTHDC1_WT_total_RNA_rep2

value: YTHDC1 WT


title: 05S011.05B9110_005

description:
05B9110_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 08S069.08B9317_002

description:
08B9317_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: ATAC_MM_mm10_VK-Che20


title: 06S032.06B9221_009

description:
06B9221_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s16


title: s10


title: SETDB1_KO_chromRNA_Input_rep2

value: SETDB1 KO


title: ATAC_MM_mm10_WT4

value: WT


title: ATAC_MM_mm10_VK-Che_19


title: SETDB1_KO_chromRNA_Input_rep1


title: 01S019.01B9033_014

description:
01B9033_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: s9


title: SETDB1_KO_chromRNA_m6A_rep2


title: ATAC_MM_mm10_WT3


title: s8

value: glucose


title: ATAC_MM_mm10_WT2


title: SETDB1_KO_chromRNA_m6A_rep1


title: 06S030.06B9137_008

description:
06B9137_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 06S020.06B9132_002

description:
06B9132_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: ATAC_MM_mm10_VK-Che_27


title: ATAC_MM_mm10_WT1


title: s6

value: adherent


title: 06S027.06B9135_001

description:
06B9135_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: Non-acute, Stage I, untreated


title: METTL3_KO_chromRNA_Input_rep2

value: METTL3 KO


title: YTHDC1_WT_total_RNA_rep1


title: s7

value: control


title: METTL3_KO_chromRNA_Input_rep1

value: Embryonic stem cells


title: s11


title: B10-II

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Base-calling was performed using Illumina Casava v1.8.2
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using Rsubread::align.
Genewise counts were obtained using featureCounts with Rsubread's inbuilt mm10 annotation.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text giving Entrez Gene IDs, gene length (number of bases in union of all exons) and the number of read-pairs assigned to that read.

molecule: polyA RNA

source_name: activated B cell

growth_protocol: B lymphocytes were cultured in RPMI 1640 with 2mM GlutaMAX, 50 μM β-mercaptoethanol and 10% heat-inactivated fetal calf serum

extract_protocol:
Total RNA was extracted using NucleoSpin RNA Plus (Macherey-Nagel) from sorted naïve/activated/differentiated B cell populations
mRNA reverse transcription cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: Naïve B cells were negatively isolated (Miltenyi, 130-090-862), CTV labelled and stimulated with 25μg/ml LPS (Salmonella typhosa origin, Sigma)

tag: strain

value: 10 hours after LPS treatment


title: 01S020.01B9036_010

description:
01B9036_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: I


title: s5


title: B10-I


title: B3-II

value: 3 hours after LPS treatment


title: s4


title: METTL3_KO_chromRNA_m6A_rep2


title: 04S034.04B9242_008

description:
04B9242_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 08S012.08B9149_005

description:
08B9149_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: METTL3_KO_chromRNA_m6A_rep1


title: s3


title: B3-I


title: Parental_chromRNA_Input_rep2

value: Parental


title: 04S047.04B9412_005

description:
04B9412_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: B33-II

value: 33 hours after LPS treatment


title: 06S039.06B9229_001

description:
06B9229_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Parental_chromRNA_Input_rep1


title: s1


title: B33-I


title: Parental_chromRNA_m6A_rep2


title: 06S017.06B9129_013

description:
06B9129_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: PB-II

source_name: plasmablast

value: 4 days after LPS treatment


title: 03S039.03B9206_009

description:
03B9206_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Parental_chromRNA_m6A_rep1


title: MUC8814: 30298559_NCT

city: Neuherberg

first: Martin

last: Selmansberger

state: Bavaria

address: Ingolstaedter Landstrasse 1

department: Department of Radiation Cytogenetics

country: Germany

institute: Helmholtz Zentrum Muenchen

data_processing:
trimming of adapter sequences using BBDUK k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
alignment of sequences using STAR against GRCm38.94 --runThreadN 8 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
counting of reads at gene level using Rsubread featureCounts function in strand-specific-mode and  Mus_musculus.GRCm38.94.gtf
DESeq2 differential expression analysis (variance-sabilazed-counts, vsd)
Genome_build: GRCm38
Supplementary_files_format_and_content: Counts-Matrix txt-File, generated by featureCounts in strand-specific-mode, Genes (ENSMUSG-Ids) in rows, Samples in colums (identical order as in Sample-Information (MUC8788 - MUC8814)

source_name: thyroid tissue mouse

extract_protocol:
Qiagen miRNeasy Micro Kit
QuantSeq Lexogen 3´Library Prep Kit

treatment_protocol: laser-capture-microdissectied tissue

tag: Sex

value: m

tag: group

value: NCT

value: thyroid


title: PB-I


title: MUC8813: 30298547_PL

value: PL


title: 03S009.03B9062_012

description:
03B9062_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: bronchoalveolar lavage


title: Ab-II


title: IAPEz_ChIRP_rep2

extract_protocol:
E14 ES cells were crosslinked with 3% formaldehyde for 30 min at room temperature. Crosslinking was then quenched with 0.125 M glycine for 5 min. Chromatin was then solubilized by sonicating in lysis buffer (50 mM Tris 7.0, 10 mM EDTA, 1% SDS, 0.5 mM DTT, and RNase Inhibitors). Chromatin is diluted in two times volume of hybridization buffer (750mM NaCl, 1% SDS, 50 mM Tris 7.0, 1 mM EDTA, 15% Formamide, 0.5 mM DTT, and RNase Inhibitors). 10 pmol probes were added to 3 ml of diluted chromatin, which was mixed by end-to-end rotation at 37 °C for 6 hr. Streptavidin beads were washed three times in nuclear lysis buffer and added into the reaction, which was mixed for another 45 min at 37 °C. Beads were captured by magnets (Invitrogen) and washed five times with wash buffer (2x SSC, 0.5% SDS, add DTT and PMSF fresh). chromatin was reverse crosslinked at 65 °C overnight. After 1 hour of RNase A (1unit/μl) at 37 °C and Proteinase K (1unit/μl) digestion at 55 °C, DNA samples were then purified using PCR extraction kit (QIAGEN #28006). The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).
ChIRP-Seq

value: parental

tag: probe

value: IAPEz-int DNA


title: 02S028.02B9271_001

description:
02B9271_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

extract_protocol:
Total RNA was extracted from BALF\ and PBMC samples using Qiazol following Qiagen’s miRNeasy protocol (Qiagen 217004) and using QiaCube
cDNA libraries were made from 1ug of total RNA that had RNA Integrity Number (RINe) over 6.5 upon Poly-A selection using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Ambion 61021) and fragmentation using the AB Library Builder™ System (Life Technologies 4463592) with the Ion Total RNA-Seq Kit for AB Library Builder™ System (Life Technologies 4482416).

value: Non-acute, Stage I, untreated


title: Ab-I


title: MUC8810: 30291040_NCT

value: f


title: MUC8812: 30298547_NT

value: NT


title: rescue_Mut_H33_ChIP_rep2

treatment_protocol: For knockdown, mES cells were seeded in a 6-well plate, and transfected with RNAiMAX (Invitrogen, 13778-150) according to the manual. Cells were harvested after three days.

value: Embryonic stem cells

value: METTL3 KO + Mut METTL3


title: Naive-II

source_name: Naïve B cell


title: 02S015.02B9055_006

description:
02B9055_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: I


title: MUC8809: 30291035_NCT


title: rescue_WT_H33_ChIP_rep2

value: METTL3 KO + WT METTL3


title: s2

tag: donorid

value: control

value: glucose


title: METTL3_KO_H33_ChIP_rep2

value: METTL3 KO


title: Naive-I


title: 01S034.01B9285_013

description:
01B9285_IonXpressRNA_013
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: Multi-organ


title: MUC8808: 30291061_NT

value: m


title: 02S061.02B9266_008

description:
02B9266_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: Parental_H33_ChIP_rep2


title: B cell activation 33 hours Pre-S 2

data_processing:
Reads pairs from each sample were aligned to the mouse genome and counted into 50 kB bin pairs using the R package diffHic v1.9.1.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The .mtx files are space-delimited text files in Matrix Market Exchange format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format file GenomicRegions.bed.gz. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.

source_name: Activated B cells

extract_protocol:
Cells were fixed with formaldehyde as described by Rao et al (Cell 2014; PMID: 25497547)
In situ Hi-C was performed as described by Rao et al (Cell 2014; PMID: 25497547).

value: C57BL/6 FUCCI (Sakaue-Sawano et al, 2008, PMID:18267078)

tag: activation time after lps stimulation

value: 33 hours (pre S-phase)


title: 03S066.03B9332_014

description:
03B9332_IonXpressRNA_014
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

data_processing:
Basecalls using Torrent Suite Software Version 5.0.5
mRNA-seq reads were aligned to hg19 using a two stage mapping strategy. In the first stage, tophat version 2.0.12 was used with annotation and the --b2-very-sensitive option. In the second stage, bowtie 2.0.5 was used with local alignment and the --very-sensitive option.
Data were filtered using principal component analysis to remove outleirs.
Genome_build: hg19
Supplementary_files_format_and_content: text files that contain the  Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were generated using cufflinks 2.2.0

value: II

value: bronchoalveolar lavage


title: MUC8807: 30291061_PL

value: PL

value: thyroid


title: IAPEz_ChIRP_Input_rep2

value: parental


title: MUC8806: 30291017_PL

value: f


title: B cell activation 33 hours Pre-S 1


title: MUC8811: 30291105_NCT

value: NCT


title: 05S049.05B9351_002

description:
05B9351_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: rescue_Mut_YTHDC1_ChIP_rep2

value: Embryonic stem cells

value: METTL3 KO + Mut METTL3


title: rescue_WT_YTHDC1_ChIP_rep2

value: METTL3 KO + WT METTL3


title: B cell activation 33 hours 2

value: 33 hours (imminent division)


title: MUC8805: 30291017_NT

value: NT


title: METTL3_KO_YTHDC1_ChIP_rep2

value: METTL3 KO


title: 03S065.03B9331_005

description:
03B9331_IonXpressRNA_005
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: Multi-organ


title: B cell activation 10 hours 2

value: 10 hours


title: MUC8804: 30291015_NT


title: MUC8803: 30291015_PL


title: 03S032.03B9201_011

description:
03B9201_IonXpressRNA_011
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: I


title: B cell activation 10 hours 1


title: MUC8802: 30280559_PL


title: siVIRILIZER_METTL3_ChIP_rep1

value: Parental

value: siVIRILIZER

value: METTL3 (Bethyl, #A301-567A)


title: 05S008.05B9111_010

description:
05B9111_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: III

value: bronchoalveolar lavage


title: MUC8801: 30280559_NT

value: thyroid


title: 06S029.06B9136_009

description:
06B9136_IonXpressRNA_009
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: II


title: B cell activation 3 hours 1

value: 3 hours


title: siZC3H13_METTL3_ChIP_rep2

value: Embryonic stem cells


title: B cell activation 3 hours 2


title: MUC8800: 30280522_NCT

value: f

value: NCT


title: siZC3H13_METTL3_ChIP_rep1


title: MUC8799: 30280511_NT


title: LncMyoD Control Rep 1

city: Hong Kong

first: Tom

last: Cheung

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

description: cultured satellite cells treated with control siRNA

data_processing:
Illumina bcl2fastq v2.19 with default parameters was used for basecalling to generate demultiplexed FASTQ files.
To improve mappability of reads, low quality bases were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters ‘SLIDINGWINDOW:10:20 MINLEN:30’.
Trimmed reads were mapped to mm10 using HISAT2 v2.1.0 (Kim et al., 2015) with default parameters. Unmapped reads and read alignments with a mapping quality below 10 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 516 -q 10 -b’.
After read mapping, StringTie v1.3.3 (Pertea et al., 2015) was used with the default parameters and the Gencode vM19 gene annotation GTF file to estimate the expression of annotated transcripts.
Ballgown v2.2.0 (Frazee et al., 2015) was used to calculate gene expression FPKM values and output the gene expression table.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated value table of genes with their corresponding FPKM values as output by Ballgown

source_name: Skeletal muscle

growth_protocol: Satellite cells were isolated from mouse hindlimb and cultured in F10 supplemented with 10% HS and P/S

extract_protocol:
Medium was removed, and total RNA was isolated using NucleoSpin RNA XS (Macherey-Nagel).
cDNA was generated following the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) protocol. The RNA-Seq libraries were sheared with a Covaris S220 and generated using Ovation Ultralow DR Multiplex System 9-16 (NuGEN Technologies). The libraries were sequenced using Illumina NextSeq 500 (2 x 150).

treatment_protocol: Cultured satellite cells were treated with siRNA targeting LncMyod for 48h before harvest

value: Muscle stem cells

value: Control


title: MUC8798: 30280511_PL

value: PL


title: B cell activation 33 hours 1

value: 33 hours (imminent division)


title: 09S017.09B9421_012

description:
09B9421_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: Multi-organ


title: siWTAP_METTL3_ChIP_rep2

value: siWTAP


title: 03S047.03B9215_012

description:
03B9215_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: 01S028.01B9281_001

description:
01B9281_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: LncMyoD Knockdown Rep 2

description: cultured satellite cells treated with siRNA targeting LncMyod

value: LncMyod-knockdown


title: LncMyoD Control Rep 2


title: MUC8797: 30280506_PL


title: siVIRILIZER_METTL3_ChIP_rep2

value: Parental

value: siVIRILIZER


title: 01S008.01B9023_012

description:
01B9023_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: I


title: MUC8796: 30280506_NT

value: NT


title: Parental_YTHDC1_ChIP_rep2

value: parental


title: 04S031.04B9252_008

description:
04B9252_IonXpressRNA_008
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: II

value: bronchoalveolar lavage


title: LncMyoD Knockdown Rep 1


title: siCtrl_METTL3_ChIP_rep2

value: Embryonic stem cells

value: siCtrl

value: METTL3 (Bethyl, #A301-567A)


title: siCtrl_METTL3_ChIP_rep1


title: 02S055.02B9043_006

description:
02B9043_IonXpressRNA_006
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: III


title: 09S001.09B9175_001

description:
09B9175_IonXpressRNA_001
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: MUC8794: 30280477_NT

value: m

value: thyroid


title: SETDB1_CKO_METTL3_ChIP_rep2

value: SETDB1 cKO


title: QSC H3K4me3 Rep 2

description:
yqsc_h3k4me3_fold-change_signal.bw
yqsc_h3k4me3_peaks.broadPeak
yqsc_h3k4me3_peaks.narrowPeak

data_processing:
Illumina bcl2fastq v2.19 with default parameters was used for basecalling to generate demultiplexed FASTQ files.
To improve mappability of reads, low quality bases were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters ‘LEADING:3 TRAILING:3 SLIDINGWINDOW:10:10 MINLEN:20’.
Trimmed reads were mapped to mm10 using bowtie2 v2.3.2 (Langmead et al., 2009) with default parameters.
Duplicates reads were marked using the MarkDuplicates module of Picard v2.9.2 with default settings. Unmapped and duplicate reads as well as read alignments with a mapping quality below 10 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 1540 -q 10 -b’.
Reads from sample replicates were pooled together into a single file using samtools v1.3 (Li et al., 2009).
For each individual sample replicate as well as pooled replicates, the predominant fragment length was estimated for use during peak calling using phantompeakqualtools v1.2 (Kharchenko, Tolstorukov & Park, 2008).
Relaxed narrow and broad peak calling to determine enriched regions was performed on individual sample replicates as well as pooled replicates using MACS2 v2.1.1 (Zhang et al., 2008) with treatment and control as input files and parameters ‘-g mm -p 1e-2 --nomodel --shift 0 --extsize {estimated fragment length from last step} -B --SPMR’.
Peaks called in the pooled replicates were kept and considered a consensus peak if they had at least a 50% overlap with peaks called in the individual replicates. This was done using intersect in bedtools v2.26.0 (Quinlan, Hall, 2010).
Fold-change signals were generated with the bdgcmp command in MACS2 v2.1.1 (Zhang et al., 2008) and then converted to BigWig format using the UCSC bedGraphToBigWig v332 tool.
Genome_build: mm10
Supplementary_files_format_and_content: broadPeak files containing consensus peak calls of pooled samples; narrowPeak files containing consensus peak calls of pooled samples; BigWig treatment over control fold change tracks

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Library was constructed using ChIPmentation protocol from Schmidl et al., (2015). Briefly, antibody-bound DNA was tagmented using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) and amplified to construct ChIP-seq library. Library was then sequenced using Illumina Nextseq 500 (2 x 75).

value: Muscle stem cells

tag: chip antibody


title: QSC H3K4me3 Rep 2 Input


title: 02S020.02B9054_010

description:
02B9054_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: Multi-organ


title: SETDB1_CKO_METTL3_ChIP_rep1


title: MUC8793: 30280477_PL

value: PL


title: QSC H3K4me3 Rep 1


title: siWTAP_METTL3_ChIP_rep1

value: Parental

value: siWTAP


title: MUC8792: 30266354_PL

value: f


title: SETDB1_CKO_DC1_ChIP_rep2


title: 08S003.08B9145_002

description:
08B9145_IonXpressRNA_002
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: QSC H3K27me3 Rep 2 Input


title: 06S038.06B9228_012

description:
06B9228_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: I


title: SETDB1_WT_METTL3_ChIP_rep2

value: SETDB1 WT


title: QSC H3K27me3 Rep 2

description:
yqsc_h3k27me3_fold-change_signal.bw
yqsc_h3k27me3_peaks.broadPeak
yqsc_h3k27me3_peaks.narrowPeak


title: MUC8790: 30260027_NCT

value: NCT


title: SETDB1_CKO_DC1_ChIP_rep1


title: 06S035.06B9224_012

description:
06B9224_IonXpressRNA_012
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: bronchoalveolar lavage


title: SETDB1_WT_METTL3_ChIP_rep1

value: Embryonic stem cells


title: MUC8791: 30266354_NT

value: NT


title: 06S033.06B9220_010

description:
06B9220_IonXpressRNA_010
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv


title: MUC8795: 30266844_NCT


title: QSC H3K27me3 Rep 1 Input


title: MUC8788: 30260011_NCT


title: QSC H3K4me3 Rep 1 Input


title: QSC H3K27me3 Rep 1


title: 03S027.03B9075_004

description:
03B9075_IonXpressRNA_004
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

value: IV


title: ASC H3K4me3 Rep 2 Input


title: ASC H3K4me3 Rep 2

description:
yasc_h3k4me3_fold-change_signal.bw
yasc_h3k4me3_peaks.broadPeak
yasc_h3k4me3_peaks.narrowPeak


title: 255,(NPRA+/+)

city: 西安

first: Jun

last: Yu

state: Shaanxi

address: North of Wei 32nd Road, and east of Xitai Road, High-tech Zone

department: Clinical Experimental Center

institute: Xi'an International Medical Center Hospital

data_processing:
Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8) used for basecalling
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to the reference genome using Hisat2 software.
The transcript abundances for each sample were estimated with StringTie, and the FPKM value for gene and transcript level were calculated with R package Ballgown.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file format include FPKM values for each Sample

source_name: Myocardium

extract_protocol:
Myocardium were removed, flash frozen on dry ice, and total RNA was isolated from tissue and cell specimens using Trizol reagent (Invitrogen).1-2 µg total RNA was used to prepare the sequencing library.
(1) Total RNA is enriched by oligo (dT) magnetic beads (rRNA removed); (2) RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific. The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by the absolute quantification qPCR method. To sequence the libraries on the Illumina HiSeq 4000 instrument, the barcoded libraries were mixed, denatured to single-stranded DNA in NaOH, captured on Illumina flow cell, amplified in situ, and subsequently sequenced for 150 cycles for both ends on Illumina HiSeq instrument.

value: Myocardium

value: wild type


title: RBM15_15B_DKO_METTL3_ChIP_rep2

value: RBM15/15B DKO

value: METTL3 (Bethyl, #A301-567A)


title: 243,(NPRA+/+)


title: ASC H3K4me3 Rep 1 Input

value: Muscle stem cells


title: RBM15_15B_DKO_METTL3_ChIP_rep1


title: 242,(NPRA+/+)


title: RBM15_15B_WT_METTL3_ChIP_rep2

value: RBM15/15B WT


title: 230,(NPRA+/+)


title: ASC H3K27me3 Rep 2 Input


title: ASC H3K4me3 Rep 1


title: atfs-1 (et18) - 2, batch2

city: Worcester

first: Julie

last: Zhu

state: MA

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned to the C. elegans genome (WBcel235) using STAR (version 2.5.3a) with the following parameter (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
featureCounts (subread-1.5.2) was used to count the features after the alignment.
Bioconductor packages edgeR (version 3.10.0 ) was used for differential gene expression analysis.
Genome_build: WBcel235 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.6/)
Supplementary_files_format_and_content: featureCounts.txt: Tab-delimited text file includes the raw count values from featureCounts for each sample.

organism: Caenorhabditis elegans

source_name: L4 Worms

growth_protocol: Grew on OP50 20c to L4 stage

extract_protocol:
Chloroform Ethanol extraction
Illimina Index in adapters: TruSeq
MultiPLEX single End

tag: strain/background

value: atfs-1 (et18)

value: Whole body

tag: developmental stage


title: atfs-1 (et18) - 1, batch2


title: MUC8789: 30260026_NCT

value: thyroid


title: SETDB1_WT_DC1_ChIP_rep2

tag: genotype

tag: antibody


title: 228,(NPRA+/+)


title: ASC H3K27me3 Rep 2

description:
yasc_h3k27me3_fold-change_signal.bw
yasc_h3k27me3_peaks.broadPeak
yasc_h3k27me3_peaks.narrowPeak

tag: cell type


title: SETDB1_WT_DC1_ChIP_rep1

tag: treatment


title: 241,(NPRA-/-)

value: NPRA-/-


title: N2-1, batch2

tag: genotype/variation

value: WT


title: ASC H3K27me3 Rep 1 Input


title: METTL14_KO_METTL3_ChIP_rep1

value: METTL14 KO


title: METTL14_KO_METTL3_ChIP_rep2


title: N2-2, batch2


title: 240,(NPRA-/-)


title: ASC H3K27me3 Rep 1


title: 231,(NPRA-/-)


title: METTL14_WT_METTL3_ChIP_rep2

value: METTL14 WT


title: atfs-1 (et18) - 3, batch2


title: N2-3, batch2


title: RBM15_15B_WT_METTL3_ChIP_rep1


title: 227,(NPRA-/-)


title: QSC Rep 2

description: freshly isolated satellite cells

data_processing:
Illumina bcl2fastq v2.19 with default parameters was used for basecalling to generate demultiplexed FASTQ files.
Adapters were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters ‘ILLUMINACLIP:NexteraPE-Custom.fa:1:13:6:1:True SLIDINGWINDOW:10:10 MINLEN:15’. For the ILLUMINACLIP setting, a custom Nextera paired end adapter FASTA file was used containing the following four adapter entries in it: PrefixA/1 – CTGTCTCTTATACACATCTCCGAGCCCACGAGAC, PrefixA/2 – CTGTCTCTTATACACATCTGACGCTGCCGACGA, Trans1 – TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, Trans2 – GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG.
Trimmed reads were mapped to mm10 using bowtie2 v2.3.2 (Langmead et al., 2009) with parameters ‘--minins 30 --maxins 2000 --dovetail -k 4 --very-sensitive-local’
Duplicates reads were marked using the MarkDuplicates module of Picard v2.9.2 with default settings.
Next, unmapped reads, duplicate reads, non-primary alignments, reads with their mate unmapped and read alignments with a mapping quality below 30 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 1804 -f 2 -q 30 -b’.
Broad peak calling to determine enriched ATAC regions was performed on individual sample replicates as well as pooled replicates using MACS2 v2.1.1 (Zhang et al., 2008) with parameters ‘--nomodel --shift -100 --extsize 200 –broad’. Peaks in blacklisted regions (ENCODE Project Consortium, 2012) were filtered using the bedtools v2.26.0 (Quinlan, Hall, 2010) intersect command.
To generate Tn5 insertion signal tracks, the BAM file created after the read filtering step for each sample replicate was downsampled to the BAM file with the smallest read count using the DownsampleSam module of Picard v2.9.2. Genome wide insertion count tracks were then generated for individual replicates and pooled replicates using the pyatac ins functionality in NucleoATAC v0.3.4 (Schep et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: broadPeak files with blacklisted peaks removed; BigWig files of Tn5 insertion counts along mm10 after downsampling step

growth_protocol: Satellite cells were isolated from mouse hindlimb and cultured in F10 supplemented with 10% HS and P/S.

extract_protocol:
Medium was removed and cells were lysed using ATAC-seq lysis buffer ( (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630).
Library was constructed based on protocols from Buenrostro et al., (2015). Briefly, lysates were tagmented with Nextera DNA Library Preparation Kit (Illumina) and amplified using NEBNext High-Fidelity 2 x PCR Master Mix (NEB). Library was then sequenced using Illlumina NextSeq 500 (2 x 75).

treatment_protocol: Cultured satellite cells were treated with siRNA targeting LncMyod for 48h before harvest.


title: QSC Rep 1

description: freshly isolated satellite cells


title: 03S059.03B9328_007

description:
03B9328_IonXpressRNA_007
processed data file: SARCOIDOSIS_fpkmdata_BAL_clean_withannot_gradsids_added.tsv

tag: phenotype group

value: Multi-organ

value: bronchoalveolar lavage


title: 217,(NPRA-/-)


title: METTL14_WT_METTL3_ChIP_rep1

value: Embryonic stem cells


title: HEK_saC9_RAG1_espC911D10A_VEGFA_Rep3

city: Stanford

first: Marie

last: Le Bouteiller

state: CA

address: 269 campus drive

department: Radiation Oncology

institute: Stanford University

data_processing:
Library strategy: LAM-HTGTS
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg38 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml)
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in DMEM 10% FBS

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using RAG1 primers described in Frock et al., 2015 Nature Biotechnology (PMC4320661) and Illumina Miseq sequencing

treatment_protocol: Cells were transfected with the aid of PEI and genomic DNA was collected 36 hours after delivery of nuclease

tag: nuclease delivery

value: Transfection; saCas9:RAG1.1 + eSpCas9_1.1D10A:VEGFA

tag: treatment protocol

value: 36 hour culture post transfection

tag: target locus

value: RAG1 (saCas9:RAG1.1 gRNA)

tag: extract_protocol (dna fragmentation/blocking methods)

value: Sonication


title: METTL3_N477A_METTL3_ChIP_rep2

value: METTL3 N477A

value: METTL3 (Bethyl, #A301-567A)


title: HEK_saC9_RAG1_spC9D10A_VEGFA_Rep3

value: Transfection; saCas9:RAG1.1 + SpCas9D10A:VEGFA


title: HEK_saC9_RAG1_espC911_VEGFA_Rep3

value: Transfection; saCas9:RAG1.1 + eSpCas9_1.1:VEGFA


title: LncMyod Knockdown Rep 2

tag: strain

value: Muscle stem cells

value: LndMyod Knockdown


title: HEK_saC9_RAG1_spC9_VEGFA_Rep3

value: Transfection; saCas9:RAG1.1 + SpCas9:VEGFA


title: METTL3_N477A_METTL3_ChIP_rep1


title: OX40-2

city: Beijing

first: Kai

last: Liu

address: No. 95 Yong-an Road

institute: Beijing Friendship Hospital, Capital Medical University

description: DNT converted from OX40 knockout mouse

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: OX40, double-negative regulatory T cells

extract_protocol:
Double-negative regulatory T cells (DNT) were converted from naïve CD4 T by standard protocol which have been reported before [BLOOD, 1 MAY 2007   VOLUME 109, NUMBER 9].Then CD3+TCRαβ+NK-CD4-CD8- DNT were sorted by FACS Aria II, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary lymphocyte

tag: cell subtype

tag: protocol

value: Converted from naïve CD4 T cells


title: LncMyod Knockdown Rep 1

value: LncMyod Knockdown


title: HEK_saC9_RAG1_Rep3

value: WT

value: Transfection; saCas9:RAG1.1


title: OX40-1

description: DNT converted from OX40 knockout mouse

value: Double-negative regulatory T cells (DNT)


title: B6-2

description: DNT converted from wildtype

source_name: B6, double-negative regulatory T cells

value: wt


title: LncMyod Control Rep 2

description: cultured satellite cells treated with control siRNA

value: LncMyod Control


title: HEK_saC9_RAG1_espC911D10A_VEGFA_Rep1

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg38 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml)
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using RAG1 primers described in Frock et al., 2015 Nature Biotechnology (PMC4320661) and Illumina Miseq sequencing
LAM-HTGTS

value: Transfection; saCas9:RAG1.1 + eSpCas9_1.1D10A:VEGFA

value: 36 hour culture post transfection

value: RAG1 (saCas9:RAG1.1 gRNA)


title: METTL3_W475A_METTL3_ChIP_rep2

extract_protocol:
Chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006).
The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer’s guidelines (SWIFT, #21096).

value: Embryonic stem cells

value: METTL3 W475A

value: METTL3 (Bethyl, #A301-567A)


title: HEK_saC9_RAG1_espC911D10A_VEGFA_Rep2

value: Sonication


title: METTL3_W475A_METTL3_ChIP_rep1


title: LncMyod Control Rep 1

value: Muscle stem cells


title: B6-1

description: DNT converted from wildtype


title: HEK_saC9_RAG1_spC9D10A_VEGFA_Rep2

value: Transfection; saCas9:RAG1.1 + SpCas9D10A:VEGFA


title: METTL3_WT_METTL3_ChIP_rep1

value: METTL3 WT


title: HEK_saC9_RAG1_spC9D10A_VEGFA_Rep1


title: ASC Rep 2

description: satellite cells isolated 2.5 days post-injury


title: ASC Rep 1


title: UM171_CD86-FCER1-_3

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the 6pb index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version 26, based on Ensembl version 88
Expression values were also computed using RSEM version 1.2.28 based on Ensembl version 88 transcript annotations
Reported expression values take into account a reverse strand orientation.
Genome_build: GRCh38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

source_name: UM171 expanded CD34+ CB

growth_protocol: CD34+ cells were grown in Stemspan media with Flt3 (100ng/ml), TPO (50ng/ml), SCF (100ng/ml) and kept between 300000 and 500000 cells/ml for 7 days before sorting

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
KAPA RNA HyperPrep PolyA

value: CD34+ cord blood cells

tag: agent


title: DC1_W428A_METTL3_ChIP_rep1

data_processing:
Raw reads were aligned to the mm10 genome using Bowtie2 (v 2.2.5).
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: mm10
Supplementary_files_format_and_content: Genome coverage bigwig files

value: YTHDC1 W428A


title: DC1_W428A_METTL3_ChIP_rep2


title: SHAM7

city: TUCSON

first: Roberta

last: Brinton

state: Arizona

address: 1230 N Cherry Ave, PO Box 210242

department: The Center for Innovation in Brain Science

institute: University of Arizona

description: Female Rats were aged at 6 month, followed with 7 weeks treatment of vehicle

data_processing:
Raw fastq data were aligned to mouse transcriptome by kallisto v0.43
Kallisto counts were imported through Tximport to get unnormalized gene expressions
Normalized counts were extracted from DESeq2
Genome_build: Rat ensembl release 90
Supplementary_files_format_and_content: Normalized counts from DESeq2

organism: Rattus norvegicus

source_name: Female Rats,  6 months, 7 weeks vehicle

extract_protocol:
Frozen hippocampal tissues were directly homogenized in TRIzol® Reagent (Invitrogen, 15596026) using The Bullet Blender® and silicon beads. Chloroform was used to extract RNA from the homogenate at a volume ratio of 1:5 to that of the TRIzol® Reagent. Ethanol was then used to precipitate nucleic acids from the aqueous phase. RNA was further purified using PureLink™ RNA Mini Kit (Invitrogen™, 12183018A) following manufacturer’s instructions. Purelink™ DNase (Invitrogen™, 12185010) was used to eliminate DNA contamination. Purified RNA was eluded in RNase-free, diH2O. RNA concentration and quality were checked by NanoDrop™ One.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: Female

value: SHAM

tag: tissue

value: Hippocampus


title: SHAM5


title: HEK_saC9_RAG1_espC911_VEGFA_Rep2

value: WT

value: Transfection; saCas9:RAG1.1 + eSpCas9_1.1:VEGFA


title: HEK_saC9_RAG1_espC911_VEGFA_Rep1


title: UM171_CD86-FCER1-_2


title: SHAM6


title: SHAM4


title: DC1_W428A_H4K20me3_ChIP_rep2


title: HEK_saC9_RAG1_spC9_VEGFA_Rep2

value: Transfection; saCas9:RAG1.1 + SpCas9:VEGFA


title: UM171_CD86-FCER1-_1


title: DC1_W428A_H4K20me3_ChIP_rep1


title: SHAM3


title: HEK_saC9_RAG1_spC9_VEGFA_Rep1

value: 36 hour culture post transfection


title: DC1_W428A_H3K9me3_ChIP_rep2

value: H3K9me3 (Active motif, #39161)


title: SHAM2


title: METTL3_WT_METTL3_ChIP_rep2

value: Embryonic stem cells


title: UM171_FCER1+CD34+_2


title: UM171_FCER1+CD34+_3


title: DC1_W428A_H3K9me3_ChIP_rep1


title: HEK_saC9_RAG1_Rep2

value: Transfection; saCas9:RAG1.1

value: RAG1 (saCas9:RAG1.1 gRNA)


title: SHAM1


title: UM171_FCER1+CD34+_1


title: HEK_saC9_RAG1_Rep1

value: Sonication


title: DC1_W428A_DC1_ChIP_rep2


title: OVX7

description: Female Rats were aged at 6 month before ovary removal, followed with 7 weeks treatment of vehicle

source_name: Female Rats,  6 months before ovary removal, 7 weeks vehicle

value: OVX


title: UM171_FCER+_3

value: FCER+


title: OVX6


title: DC1_W428A_DC1_ChIP_rep1


title: UM171_FCER+_2


title: DC1_KO_METTL3_ChIP_rep2

value: YTHDC1 KO

value: METTL3 (Bethyl, #A301-567A)


title: DC1_KO_METTL3_ChIP_rep1


title: UM171_FCER+_1

value: CD34+ cord blood cells


title: OVX5

value: Female


title: OVX4


title: UM171_CD86+CD34+_3


title: DC1_KO_H4K20me3_ChIP_rep2


title: UM171_CD86+CD34+_2


title: DC1_KO_H4K20me3_ChIP_rep1


title: UM171_CD86+CD34+_1


title: DC1_KO_H3K9me3_ChIP_rep2


title: DC1_KO_H3K9me3_ChIP_rep1


title: DC1_KO_DC1_ChIP_rep2


title: UM171_CD86+_2


title: OVX_E2_Treatment5

description: Female Rats were aged at 6 month before ovary removal, followed with3 weeks treatment of vehicle and 2 weeks treatment of E2 estrogen

source_name: Female Rats,  6 months before ovary removal, 3 weeks vehicle and 2 weeks E2 estrogen


title: UM171_CD86+_1


title: DC1_KO_DC1_ChIP_rep1


title: SR1_CD86-FCER1-_3

source_name: SR1 expanded CD34+ CB


title: OVX3


title: 384h_5F_rep3

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

department: Faculté de Médecine

country: France

institute: UMR1078 - Université de Bretagne Occidentale

description: 384 hours, 5 mM fructose, Replicate 3

hyb_protocol: The RNA labeling and microarray hybridization was performed according to the manufacturer’s recommendations.

scan_protocol: Beadchips were scanned using Illumina BeadScan image data acquisition software

data_processing: The scanned data was acquired in R using the package illiminaio. The non-normalized summarized bead-level data was then annotated with R package  illuminaHumanv4.db.

source_name: SGBS preadipocyte cells

growth_protocol: SGBS preadipocytes were plated at 2x105 cells in 100 mm dishes, supplemented with 10 ml growth medium, grown to confluence and initiated to differentiate as per. All media used for the growth, differentiation and maintenance of adipocytes contained a basal amount of 5 mM glucose, equivalent to the normal blood glucose concentration. Cells were fully differentiated by 192 hours (by oil red O staining, not shown). Cells for RNA and DNA isolations were collected at 24, 48, 96, 192 and 384 hours post induction (0 hr).

extract_protocol: For RNA isolation, media was completely aspirated from cells and a total of 700 ul of QIAzol lysis reagent was added to the cells, and the lysed cells were scraped, collected in an Eppendorf vial, sheer disrupted by passing through a tuberculin syringe about 6 time, and the lysates flash frozen.

treatment_protocol: Fructose doses were based on reports found in the systemic circulation following exposure to fructose-rich food. At the initiation of differentiation, 2.5, 5 and 10 mM fructose or 5mM of glucose concentrations were added and maintained in the medium until the collection of cells and medium at end points of either 192 hours or until 384 hours of differentiation. differentiation and maintenance of adipocytes contained a basal amount of 5 mM glucose, equivalent to the normal blood glucose concentration. Cells were fully differentiated by 192 hours (by oil red O staining, not shown). Cells for RNA and DNA isolations were collected at 24, 48, 96, 192 and 384 hours post induction (0 hr). Fructose doses were based on reports found in the systemic circulation following exposure to fructose-rich food. At the initiation of differentiation, 2.5, 5 and 10 mM fructose concentrations were added and maintained in the medium until the collection of cells and medium at end points of either 192 hours or until 384 hours of differentiation.

tag: cell line

value: SGBS

tag: time

value: 384 hours

value: 5 mM  fructose


title: 192h_0F_rep1

description: 192 hours, 0 mM fructose, Replicate 1

label_protocol: The RNA labeling and microarray hybridization was performed according to the manufacturer’s recommendations.

value: 192 hours

value: 0 mM  fructose


title: 384h_0F_rep1

description: 384 hours, 0 mM fructose, Replicate 1


title: 0h_0F_rep4

description: 0 hours, 0 mM fructose, Replicate 4

value: 0 hours


title: OVX2

value: Hippocampus


title: 192h_5F_rep3

description: 192 hours, 5 mM fructose, Replicate 3


title: DC1_WT_METTL3_ChIP_rep2

source_name: Embryonic stem cells

value: Embryonic stem cells

tag: genotype

value: YTHDC1 WT

tag: antibody


title: OVX_E2_Treatment2

tag: treatment


title: OVX1


title: DC1_WT_METTL3_ChIP_rep1

tag: cell type


title: SR1_CD86-FCER1-_2


title: 384h_2.5F_rep2

description: 384 hours, 2.5 mM fructose, Replicate 2

value: 2.5 mM  fructose


title: OVX_E2_Treatment1


title: 48h_0F_rep3

description: 48 hours, 0 mM fructose, Replicate 3

value: 48 hours


title: OVX_E2_Treatment7


title: DC1_WT_H4K20me3_ChIP_rep2


title: OVX_E2_Treatment6


title: OVX_E2_Prevention5

description: Female Rats were aged at 6 month before ovary removal, followed with 5 weeks treatment of E2 estrogen

source_name: Female Rats,  6 months before ovary removal, 5 weeks E2 estrogen


title: SR1_CD86-FCER1-_1


title: UM171_CD86+_3


title: SR1_CD86+CD34+_3


title: DC1_WT_H4K20me3_ChIP_rep1


title: OVX_E2_Prevention4


title: SR1_CD86+CD34+_2


title: DC1_WT_H3K9me3_ChIP_rep2

value: H3K9me3 (Active motif, #39161)


title: SR1_CD86+CD34+_1


title: 384h_5G_rep1

description: 384 hours, 5 mM glucose, Replicate 1

value: 5 mM  glucose


title: 192h_10F_rep3_dupl

description: 192 hours, 10 mM fructose, Replicate 3, duplicate

value: 10 mM  fructose


title: OVX_E2_Prevention2


title: 192h_2.5F_rep2

description: 192 hours, 2.5 mM fructose, Replicate 2


title: 96h_0F_rep3

description: 96 hours, 0 mM fructose, Replicate 3

value: 96 hours


title: OVX_E2_Prevention3


title: DC1_WT_H3K9me3_ChIP_rep1


title: DC1_WT_DC1_ChIP_rep2


title: OVX_E2_Prevention1


title: 192h_10F_rep3

description: 192 hours, 10 mM fructose, Replicate 3


title: SR1_CD86+_2

value: CD34+ cord blood cells


title: SR1_CD86+_3


title: DC1_WT_DC1_ChIP_rep1


title: SR1_CD86+_1


title: DMSO_CD86-FCER1-_3

source_name: DMSO expanded CD34+ CB

value: DMSO


title: rescue_WT_H3K9me3_ChIP_rep2

value: METTL3 KO + WT METTL3


title: DMSO_CD86-FCER1-_1


title: METTL3_KO_H3K9me3_ChIP_rep2

value: METTL3 KO


title: rescue_Mut_METTL3_ChIP_rep2

value: METTL3 KO + Mut METTL3

value: METTL3 (Bethyl, #A301-567A)


title: Parental_H3K9me3_ChIP_rep2

value: parental


title: rescue_WT_METTL3_ChIP_rep2


title: DMSO_FCER+_2

value: FCER+


title: 24h_0F_rep3

description: 24 hours, 0 mM fructose, Replicate 2

value: SGBS

value: 24 hours

value: 0 mM  fructose


title: rescue_Mut_H3K9me3_ChIP_rep2

value: Embryonic stem cells


title: 24h_0F_rep1

description: 24 hours, 0 mM fructose, Replicate 1


title: OA.Adipo_2uM_3

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: replicate 3

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol for Affymetrix Clariom S Assay Gene Expression Array

data_processing: The data were normalised using RMA normalisation from R/Bioconductor

source_name: CO2 HLC_Oleic_Acid_200µM_AdipoRon_2µM

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: iPSC derived from a healthy control person were differentiated towards hepatocyte like cells (HLCs) as follows: iPSCs were passaged as single cells onto plates coated with a 3:1 mixture of LN111 and LN521. The next day, the medium was changed to definitive endoderm (DE) medium: 96% RPMI 1640, 2% B27 (without retinoic acid), 1 % Glutamax (Glx), 1% Penicillin/Streptomycin (P/S) (all Gibco), 100 ng/ml Activin A (Peprotech), which was replaced daily. On the first day an additional 2.5 µM Chir 99021 (Stemgent) was included. Afterwards the cells were cultivated for 4 days in hepatic endoderm (HE) medium with daily medium changes: 78% Knockout DMEM, 20% Knockout serum replacement, 0.5% Glx, 1% P/S, 0.01% 2-Mercaptoethanol (all Gibco) and 1% DMSO (Sigma). In the last step, hepatocyte like medium was used for up to 10 days with medium change every other day: 82% Leibovitz 15 medium, 8% fetal calf serum, 8% Tryptose Phosphate Broth, 1 % Glx, 1% P/S (all Gibco) with 1 µM Insulin (Sigma), 10 ng/ml hepatocyte growth factor (HGF) (Peprotech), 25 ng/ml Dexamethasone (DEX) (Sigma).

extract_protocol: The RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and the manufactural protocol. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).

treatment_protocol: For Oleic Acid (OA) treatment, cells were incubated with 200 µM OA bound to BSA from day 10 on for 9 days. AdipoRon was dissolved in DMSO and added to the cells at a concentration of 2 µM from day 10 on for 9 days

value: CO2 HLC_Oleic_Acid_200µM_AdipoRon_2µM


title: 192h_5G_rep3

description: 192 hours, 5 mM glucose, Replicate 3

value: 192 hours


title: 384h_2.5F_rep1

description: 384 hours, 2.5 mM fructose, Replicate 1

value: 384 hours

value: 2.5 mM  fructose


title: 48h_0F_rep2

description: 48 hours, 0 mM fructose, Replicate 2

value: 48 hours


title: OA.Adipo_2uM_2

description: replicate 2


title: 384h_10F_rep3

description: 384 hours, 10 mM fructose, Replicate 3


title: OA.Adipo_2uM_1

description: replicate 1


title: 384h_5F_rep2

description: 384 hours, 5 mM fructose, Replicate 2


title: DMSO_CD86-FCER1-_2

value: CD34+ cord blood cells


title: 0h_0F_rep6

description: 0 hours, 0 mM fructose, Replicate 6

value: 0 hours


title: DMSO_FCER+_1

value: DMSO


title: OA_1

description: replicate 1

source_name: CO2 HLC_Oleic_Acid_200µM

value: CO2 HLC_Oleic_Acid_200µM


title: OA_2

description: replicate 2


title: METTL3_KO_METTL3_ChIP_rep2

value: METTL3 KO


title: 192h_5F_rep2

description: 192 hours, 5 mM fructose, Replicate 2


title: 192h_2.5F_rep1

description: 192 hours, 2.5 mM fructose, Replicate 1


title: DMSO_FCER+_3


title: 0h_0F_rep3

description: 0 hours, 0 mM fructose, Replicate 3


title: DMSO_CD86+CD34+_3


title: Parental_METTL3_ChIP_rep2

value: METTL3 (Bethyl, #A301-567A)


title: 192h_0F_rep3

description: 192 hours, 0 mM fructose, Replicate 3


title: DMSO_CD86+CD34+_2


title: Adipo_2uM_2

description: replicate 2

source_name: CO2 HLC_AdipoRon_2µM

value: CO2 HLC_AdipoRon_2µM


title: rescue_Mut_H4K20me3_ChIP

value: METTL3 KO + Mut METTL3


title: Jc_HiC_72h_S2

city: Ithaca

first: Karin

middle: Revka Loek

last: van der Burg

address: 215 Tower Road, Corson Hall

department: EEB

institute: Cornell University

data_processing:
raw reads were processed using Juicer v 1.5
Genome_build: jc.gen.v1
Supplementary_files_format_and_content: merged_nodups files were created using juicer

organism: Junonia coenia

source_name: whole wing tissue

growth_protocol: Caterpillars and pupae were raised at ~27C

extract_protocol:
Crosslinked DNA was extracted and processed according to Lewis et al., 2019
Libraries were prepared according to NEB instructions accompanying the NEBNext Ultra DNA Library Prep Kit

tag: developmental stage

value: 72 hours after pupation

tag: wing

value: hindwing


title: DMSO_CD86+CD34+_1


title: rescue_WT_H4K20me3_ChIP

value: METTL3 KO + WT METTL3


title: Jc_HiC_72h_S1


title: DMSO_CD86+_3


title: METTL3_KO_H4K20me3_ChIP

value: Embryonic stem cells


title: Jc_HiC_5th

value: 5th instar

value: forewing


title: Parental_H4K20me3_ChIP

value: parental


title: ATACseq_Red_d6_S3

data_processing:
Alignment to Junonia coenia genome using bowtie 2.
Data were filtered to include only uniquely mapping reads with a quality score greater than 20
Peak calls were performed with F-seq
Genome_build: jc.gen.v1
Supplementary_files_format_and_content: RPM normalized files were produced using deeptools

extract_protocol:
Nuclei from whole wing tissue were treated with hyperactive Tn5 as described in the ATAC-seq protocol
Libraries were prepared as described in the ATAC-seq protocol

value: 6 days after pupation


title: 384h_0F_rep3

description: 192 hours, 0 mM fructose, Replicate 3

value: SGBS

value: 384 hours

value: 0 mM  fructose


title: Adipo_2uM_1

description: replicate 1


title: 192h_ 5F_rep1

description: 192 hours, 5 mM fructose, Replicate 1

value: 192 hours

value: 5 mM  fructose


title: ATACseq_Red_d6_S2


title: ctrl_1

description: replicate 1

source_name: CO2 HLC

value: CO2 HLC


title: METTL3_KO_TRIM28_ChIP_rep1

value: METTL3 KO


title: ctrl_2

description: replicate 2


title: Parental_TRIM28_ChIP_rep1


title: 48h _0F_rep1

description: 48 hours, 0 mM fructose, Replicate 1

value: 48 hours


title: 384h _5F_rep1

description: 384 hours, 5 mM fructose, Replicate 1


title: Individual #14, EtOH, rep3

city: Olsztyn

first: Carsten

last: Carlberg

address: ul. Trylińskiego 18

department: Food Research

country: Poland

institute: Polish Academy of Sciences

data_processing:
Quality control using "afterQC"
Read alignment using "kallisto"
Differential gene expression using "EdgeR"
Genome_build: hg38
Supplementary_files_format_and_content: relative abundance in Excel table

source_name: PBMCs

growth_protocol: RPMI 1640 medium supplemented with 10% charcoal-depleted fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and were at 37 °C in a humidified 95% air/5% CO2 incubator.

extract_protocol:
extraction of total RNA using High Pure RNA Isolation kit (Roche)
rRNA-deplete cDNA library following NEB protocols

treatment_protocol: treatment for 24 h with either 10 nM 1,25(OH)2D3 (Sigma-Aldrich) or solvent (0.1% EtOH)

value: peripheral blood mononuclear cells

value: 0.1percent ethanol

tag: time point


title: ATACseq_Red_d6_S1

value: hindwing


title: Individual #14, EtOH, rep2


title: ATACseq_Red_72h_S3

value: 72 hours after pupation


title: 0h_0F_rep5

description: 0 hours, 0 mM fructose, Replicate 5

value: 0 hours


title: 384h _5G_rep3

description: 384 hours, 5 mM glucose, Replicate 3

value: 5 mM  glucose


title: Parental_SETDB1_ChIP_rep2

value: Embryonic stem cells

value: SETDB1 (Proteintech, #11231-1-AP)


title: METTL3_KO_SETDB1_ChIP_rep2


title: ATACseq_Red_72h_S2


title: DMSO_CD86+_1

value: CD34+ cord blood cells

value: DMSO


title: Individual #14, EtOH, rep1


title: rescue_Mut_YTHDC1_ChIP

value: METTL3 KO + Mut METTL3


title: ATACseq_Red_72h_S1


title: 384h_10F_rep2

description: 384 hours, 10 mM fructose, Replicate 2

value: SGBS

value: 384 hours

value: 10 mM  fructose


title: 96h_0F_rep2

description: 96 hours, 0 mM fructose, Replicate 2

value: 96 hours

value: 0 mM  fructose


title: ATACseq_Red_pp_S3

value: pre pupa


title: rescue_WT_YTHDC1_ChIP

value: METTL3 KO + WT METTL3


title: Individual #14, 125D, rep2

value: peripheral blood mononuclear cells


title: METTL3_KO_YTHDC1_ChIP

value: METTL3 KO


title: Individual #14, 125D, rep1


title: DMSO_CD86+_2


title: 384h_5G_rep2

description: 384 hours, 5 mM glucose, Replicate 2


title: ATACseq_Red_pp_S2

value: hindwing


title: 192h_5G_rep2

description: 192 hours, 5 mM glucose, Replicate 2

value: 192 hours


title: 192h_10F_rep2

description: 192 hours, 10 mM fructose, Replicate 2


title: Parental_YTHDC1_ChIP

value: parental


title: Individual #13, EtOH, rep2

value: 0.1percent ethanol


title: ATACseq_Red_5th_S3

value: 5th instar


title: RRBS_A5

city: Tsukuba

first: Keiko

last: Nohara

address: 16-2 Onogawa

department: Center for Health and Environmental Risk Research

country: Japan

institute: National Institute for Environmental Studies

data_processing:
Bisulfite-treated sequencing reads were aligned by a paired-end alignment method for a unique  best hit to the mouse reference genome (NCBI/mm10) using the Bismark program
Adapter trimming and quality control was performed using Trim Galore  (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The aligned data were used  for analyzing DNA methylation profiles using a methylKit package on R
The aligned data were used for analyzing DNA methylation profiles using a methylKit package on R
DMCs were extracted using methylKit for the cytosines in CpG sites with ≥10 reads in coverage and ≥10% methylation differences between control groups and arsenite groups using the logistic regression method. DMRs were detected for regions containing ≥3 CpG sites and at least one DMC and with ≥10% absolute mean CpG methylation difference by using an eDMR package on R
DMRs were annotated by using HOMER(http://homer.ucsd.edu/homer/, v4.10).
Genome_build: mm10

source_name: Sperm

extract_protocol:
Sperm was lysed in lysis buffer (7.3 mM Tris-HCl (pH 7.5), 7.3 mM NaCl, 18.2 mM EDTA, 1.8% SDS, 1.8% 2-ME, 1.4 mg/ml proteinase K) and DNA was extracted with a phenol-chloroform mixture, precipitated with ethanol, dried and dissolved in 10 mM Tris (pH7.4).
RRBS libraries were prepared as previously described (Matsushita et al.,BMC cancer 18: 317, 2018; Okamura et al. Cancer Sci 110:2629, 2019) with some modifications. Briefly, 100 ng of genomic DNA was sonicated for one second by a Focused-ultrasonicator (Covaris) before restriction enzyme reaction.

value: sperm

tag: dam treatment group

value: arsenic


title: Individual #14, 125D, rep3


title: Individual #13, EtOH, rep1


title: RRBS_A4


title: ATACseq_Red_5th_S1


title: Individual #13, 125D, rep3


title: RRBS_A3


title: Individual #13, 125D, rep2


title: RRBS_A2


title: RNAseq_Red_d6_S3

data_processing:
Alignment to junonia coenia genome using tophat.
Read counts overlapping genes were calculated with bedtools
Differential expression analysis was performed using DESeq2
Genome_build: jc.gen.v1
Supplementary_files_format_and_content: normalized bigwig files were produced using ucsc script

extract_protocol:
RNA was isolated from whole wing tissue and poly-A selected using NEB poly-A selection beads
Libraries were prepared using the NEB RNA library prep kit

value: 6 days after pupation


title: ATACseq_Red_pp_S1


title: RRBS_A1


title: Individual #13, EtOH, rep3


title: 384h_0F_rep2

description: 384 hours, 0 mM fructose, Replicate 2

value: SGBS


title: Individual #13, 125D, rep1


title: 192h_5G_rep1

description: 192 hours, 5 mM glucose, Replicate 1

value: 5 mM  glucose


title: RNAseq_Red_d6_S2