title: shJmjd1a plus WT, Day 2, Rep 3


title: LOX-IMVI_shCtrl_1

status: Public on Apr 29 2025

type: SRA

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v24.0.1 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCh38 genome.
Default settings: Reference type = Genome annotated with genes and transcripts; Reference sequence = Homo sapiens (GRCh38); Gene track = Homo sapiens (GRCh38.109)  (Gene); mRNA track = Homo sapiens (GRCh38.109)  (RNA); Use spike-in controls = no; Mismatch cost = 2; Insertion cost = 3; Deletion cost = 3; Length fraction = 0,8; Similarity fraction = 0,8; Global alignment = No; Strand specific = Reverse; Library type = Bulk; Maximum number of hits for a read = 10; Count paired reads as two = No; Ignore broken pairs = Yes; Expression value = TPM
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files including raw counts, TPM and RPKM. Expression values in manuscript=TPM

molecule: total RNA

organism: Homo sapiens

source_name: LOX-IMVI

growth_protocol: LOX-IMVI cells were maintained in RPMI-1640 medium supplemented with 10% FCS and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen, Cat. 79306), followed by DNase I digestion to remove contaminating DNA. 1.2 µg of total RNA was used for the construction of sequencing libraries.
Total RNA was isolated using Qiazol. Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Total RNA (RIN>8) was sent to Novogene (Cambridge, UK) for library preparation and sequencing (PE150) on a NovaSeq 6000 (Illumina).

tag: cell line

value: LOX-IMVI

tag: cell type

value: melanoma cells

tag: genotype

value: Ctrl


title: shJmjd1a plus LacZ, Day 2, Rep 2

city: Maebashi

first: Tetsuro

last: Komatsu

address: 3-39-15 Showa-machi

country: Japan

institute: Gunma University

data_processing:
FASTQ files were pre-processed using fastp with the default setting (Galaxy Version 0.23.2+galaxy0).
Reads were aligned to the mm9 mouse genome using HISAT2 with the default setting (Galaxy Version 2.2.1+galaxy1).
Read counting was performed using featureCounts with the default setting (Galaxy Version 2.0.3+galaxy2, paired-end and count them as 1 single fragment).
Assembly: mm9
Supplementary files format and content: txt, raw read counts

molecule: polyA RNA

organism: Mus musculus

source_name: 3T3-L1 preadipocyte cell line

growth_protocol: Cells were maintained in DMEM-HG (high glucose), 10% CS until reaching confluent. 2 days before differentiation induction, the medium was replaced with fresh DMEM-HG, 10% CS. On day of differentiation induction (Day 0), the medium was replaced with DMEM-HG, 10% FBS supplemented with 1.67 uM insulin, 1 uM dexamethasone, and 115 ug/mL of IBMX.

extract_protocol:
Total RNA was purified from cells using RNeasy Lipid Tissue Mini Kit (QIAGEN, 74804).
Library construction was done using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra RNA Library Prep Kit for Illumina (E7530).

treatment_protocol: Knockdown and exogenous expression were carried out using the pMXs-based retroviral vector system.

value: 3T3-L1 preadipocyte cell line


title: MPM tumor, surgically resected (P.002.T2.1)

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

data_processing:
Sequenced reads were aligned using RSEM along with Bowtie2 against the human genome (version: GRCh38)
DESeq2 was used to normalize the reads and obtain the differentially expressed genes
Assembly: GRCh38
Supplementary files format and content: Lognormalized counts in text format (We used only 72 but decided submit all the samples)

source_name: Malignant pleural mesothelioma tumor

extract_protocol:
DNAseI treated total RNA was extracted from tumor samples using the ZymoResearch DirectZol miniprep kit with tissue homogenization
Lexogen Quantseq

treatment_protocol: Tumor samples were collected throughout surgical resection of tumors

tag: tissue

value: Malignant pleural mesothelioma tumor

tag: time (from_surgery_start_in_minutes)


title: NoMet_ethyl4hydroxybenzoate_111988_1_0.001uM_TC00003594_E10

city: RTP

first: Monique

last: Hazemi

state: NC

address: 109 T.W. Alexander Dr

institute: US EPA

description:
Library name: TC00003594_E10
TC00003594_E10

data_processing:
Read alignment: Each FASTQ file was aligned to the probe sequences in the hWTv2 assay using HISAT2 v2.1.0 with spliced alignment disabled.
Probe counts: Aligned reads in SAM format were processed with SAMtools v1.9 to compute the number of uniquely aligned reads for each probe. Probe counts and associated meta-data for each well were stored for analysis using MongoDB v3.6.14.
Assembly: hWTv2
Supplementary files format and content: aime_prepilot_count_data.csv.gz: A table of probe counts in CSV format, with rows corresponding to TempO-seq probe IDs (see httr_aime_prepilot-probe_manifest.csv file for probe ID mapping information) and columns corresponding to sample IDs.
Supplementary files format and content: httr_aime_prepilot-probe_manifest.csv: For each probe ID listed in the table of probe counts (aime_prepilot_count_data.csv.gz), a corresponding mapping of probe sequence, Entrez ID, and gene symbol are listed.

growth_protocol: Experiments were peformed in VM7Luc4E2 cells, a sub-clone of MCF-7 breast adenocarcinoma cells that stably expresses and estrogen receptor trans-activation reporter construct. Prior to experimentation, VM7Luc4E2 cultures were maintained in growth medium (Minimum Essential Medium alpha (MEMa) supplemented with 10% fetal bovine serum (FBS) and 1X Gibco Anti-Anti antibiotics). Four days prior to seeding in assay plates, cultures were switched to estrogen-stripping medium (Dulbecco’s Modified Eagle Medium (DMEM) (low glucose, with pyruvate, no phenol red) supplemented with 5% charcoal/dextran-treated FBS and 4 mM L-Glutamine). Estrogen stripping was performed by refreshing the estrogen-stripping media daily for four days. For chemical testing experiments, VM7Luc4E2 cells were passaged, resuspended in assay medium (DMEM (low glucose, with pyruvate, no phenol red) supplemented with 1% charcoal/dextran-treated FBS, 4 mM L-Glutamine and 10 mM HEPES), and plated in 384-well plates in a volume of 30 µL per well and an initial seeding density of 7,500 cells / well. Cells were allowed a 24 hour recovery period prior to treatment with AIME conditioned medium.  Cells were lysed for TempO-Seq analysis 24 hours after treatment with AIME conditioned medium.

extract_protocol:
At 24 hours after treatment with condition media, assay plates were removed from the incubator, assay wells were washed twice with 1X phosphate-buffered saline and the final PBS wash was aspirated from each well leaving a residual volume of 10 µL.  Cells were subsequently lysed by adding 10 µL of 2X BioSpyder Enhanced Lysis buffer.  Assay plates were then sealed, agitated for 30 seconds on the stage of a MultiFlo FX washer / dispenser and then placed in a hybridization oven at 37°C for 10 minutes. Plates were then immediately transferred to a -80°C freezer for storage. Plates were subsequently shipped frozen to BioSpyder Technologies (Carlsbad, CA) for analysis with the human whole transcriptome TempO-Seq assay.  The TempO-Seq assay was conducted directly on cell lysates with no RNA extraction step.
Plates containing cell lysates were shipped to BioSpyder, Inc. frozen (on dry ice) using overnight priority shipping. Cell lysates were then analyzed by BioSpyder using the unattenuated TempO-Seq human whole transcriptome version 2 (hWTv2) assay, which includes 22,537 probes covering 19,703 genes. 2 µL of each lysate was hybridized with 2 µL of detector oligos from the hWTv2 assay using the following thermal cycler protocol: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, terminating with 45°C incubation for 16-24 h. Excess oligos were then removed via nuclease digestion (90 min at 37°C), and hybridized detector oligos were ligated (1 h at 37°C) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured, and 10 µL of each ligation product were transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification with well coordinate-specific “barcoded” primer pairs containing universal adaptors for sequencing. Samples were pooled into sequencing libraries, distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA). The TempO-seq libraries were sequenced to a target read depth of 3.0x106 mapped reads per sample.

treatment_protocol: The experiments were carried out using the alginate immobilization of metabolic enzymes (AIME) technology. DMSO solubilized chemicals (120 nL) were dispensed into 384-well microplates. Locations of treatments were randomized by well coordinate on the 384-well plate. After chemical dispensing, 60 µL of assay medium charged with phase 1 and phase 2 metabolic co-factors (NADPH (1:11.4), uridine S’-diphosphoglucuronic acid trisodium salt (UDPGA; 0.5 mM), glutathione (GSH; 1 mM), and adenosine 3-phosphate 5-phosphosulfate lithium salt hydrate (PAPS; 2 µM)) was dispensed into each well and plates were shaken at 500 RPM for 7 minutes on an orbital shaker. AIME peg lids with hydrogels containing either hepatic rat S9 (AIME+ condition) or deionized water (AIME- condition) were inserted into the plates and incubated for 2 hours to create conditioned media. Then, 30 µL of conditioned media was transferred to assay plates containing VM7Luc4E2 cells and 30 µL of assay medium.  The final concentration of DMSO in all treatment wells was 0.1%. Assy plates were then incubated for 24 hours in a cell culture incubator (37°C and 5% CO2).

tag: treatment

value: 24h exposure of 0.001 uM of Ethylparaben

tag: media

value: VM7Luc4E2 Assay Medium

tag: chemical name

value: Ethylparaben

tag: chemical sample_id

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: sample qc_issue

value: OK


title: MPM tumor, surgically resected (P.006-RP.T2.1)


title: NoMet_ethyl4hydroxybenzoate_111988_5_11uM_TC00003594_E09

description:
Library name: TC00003594_E09
TC00003594_E09

value: 24h exposure of 11 uM of Ethylparaben

value: 11 uM


title: shJmjd1a plus LacZ, Day 2, Rep 1


title: shJmjd1a plus Mut, Day 2, Rep 3


title: shJmjd1a, Day 2, Rep 3


title: MPM tumor, surgically resected (P.002.T2.2)


title: Giprfl/fl mGIPR-Ab/P1, Liver, biol rep5

city: Thousand Oaks

first: Murielle

middle: M

last: Véniant

state: CA

address: 1 Amgen Center Dr

institute: Amgen

description:
Library name: 20388
Colname in FPKM_Liver_GIPR.txt: 20388

data_processing:
Following sample demultiplexing, sequencing reads were aligned to the Mouse B39 reference genome using the Omicsoft OSA alignment software (Qiagen). The gene annotation model was a hybrid model adopted from the Omicsoft (Qiagen) and GenCode (v28) gene models.
Aligned reads were quantified at the gene level using an expectation maximization method (RSEM) and gene counts were combined across samples into a sample-by-gene count matrix.
Assembly: Mouse B39
Supplementary files format and content: FPKM (Fragments Per Kilobase of transcript per Million mapped reads)

source_name: Liver

extract_protocol:
Liver and inguinal white adipose tissue (WAT) collected from DIO GiprSyn-/- and Glp1rWnt1-/- mouse studies with mGIPR-Ab/P1 peptide-antibody conjugate treatment were processed and analyzed using bulk RNA-sequencing. For the extraction of total RNA, tissue samples were pulverized using GenoGrinder (Cole-Parmer), then homogenized in Tri Reagent (Molecular Research Center, Cincinnati, OH, USA or Ambion by Life Technologies) using a MagNa Lyser or TissueLyser II system (Qiagen, Germantown, MD, USA).  mRNA was then chloroform extracted and precipitated using isopropanol and washed with 75% ethanol or precipitated using the RNeasy Plus 96 Kit (Qiagen). RNA was reconstituted with DEPC-treated water.
Sequencing libraries were constructed from RNA samples using the TruSeq Stranded mRNA Library Prep kit (Illumina) and IDT for Illumina-TruSeq RNA UD Indexes. Libraries were pooled and sequenced on a NovaSeq X sequencing system (Illumina).

value: Liver

value: Giprfl/fl


title: Giprfl/fl mGIPR-Ab/P1, Inguinal White Adipose, biol rep5

description:
Library name: 20390
Colname in FPKM_ING_GIPR.txt: 20390

source_name: Inguinal White Adipose

value: Inguinal White Adipose


title: GiprSyn-/- Vehicle, Inguinal White Adipose, biol rep5

description:
Library name: 20391
Colname in FPKM_ING_GIPR.txt: 20391

value: GiprSyn-/-

value: Vehicle


title: shJmjd1a, Day 2, Rep 2


title: Giprfl/fl Vehicle, Liver, biol rep5

description:
Library name: 20387
Colname in FPKM_Liver_GIPR.txt: 20387


title: MPM tumor, surgically resected, rep for validation, unknown timepoint (P.002RP.TNA.1)


title: NoMet_daidzein_D7802_4_3.73uM_TC00003594_D11

description:
Library name: TC00003594_D11
TC00003594_D11

value: 24h exposure of 3.73 uM of Daidzein

value: Daidzein


title: shJmjd1a, Day 2, Rep 1


title: NoMet_daidzein_D7802_8_100uM_TC00003594_D10

description:
Library name: TC00003594_D10
TC00003594_D10

value: 24h exposure of 100 uM of Daidzein


title: Giprfl/fl mGIPR-Ab/P1, Liver, biol rep4

description:
Library name: 20386
Colname in FPKM_Liver_GIPR.txt: 20386


title: MPM tumor, surgically resected (P.006.T2.1)


title: shEmpty, Day 2, Rep 3


title: NoMet_transstilbene_139939_8_100uM_TC00003594_D09

description:
Library name: TC00003594_D09
TC00003594_D09

value: 24h exposure of 100 uM of trans-Stilbene

value: trans-Stilbene


title: Giprfl/fl Vehicle, Inguinal White Adipose, biol rep5

description:
Library name: 20054
Colname in FPKM_ING_GIPR.txt: 20054


title: GiprSyn-/- Vehicle, Inguinal White Adipose, biol rep4

description:
Library name: 20050
Colname in FPKM_ING_GIPR.txt: 20050


title: NoMet_daidzein_D7802_1_0.001uM_TC00003594_C12

description:
Library name: TC00003594_C12
TC00003594_C12

value: 24h exposure of 0.001 uM of Daidzein


title: MPM tumor, surgically resected (P.005.TNA.1)

value: Malignant pleural mesothelioma tumor


title: shEmpty, Day 2, Rep 2

value: 3T3-L1 preadipocyte cell line


title: MPM tumor, surgically resected (P.038.T2.1)


title: NoMet_ethyl4hydroxybenzoate_111988_2_0.093uM_TC00003594_C11

description:
Library name: TC00003594_C11
TC00003594_C11

value: 24h exposure of 0.093 uM of Ethylparaben

value: VM7Luc4E2 Assay Medium

value: Ethylparaben


title: NoMet_transstilbene_139939_3_0.865uM_TC00003594_D12

description:
Library name: TC00003594_D12
TC00003594_D12

value: 24h exposure of 0.865 uM of trans-Stilbene

value: OK


title: MPM tumor, surgically resected (P.029.T2.2)


title: Giprfl/fl Vehicle, Inguinal White Adipose, biol rep4

description:
Library name: 20048
Colname in FPKM_ING_GIPR.txt: 20048

value: Giprfl/fl


title: NoMet_ethyl4hydroxybenzoate_111988_8_100uM_TC00003594_C10

description:
Library name: TC00003594_C10
TC00003594_C10

value: 24h exposure of 100 uM of Ethylparaben


title: MPM tumor, surgically resected (P.005.T2.1)


title: GiprSyn-/- Vehicle, Inguinal White Adipose, biol rep3

description:
Library name: 20047
Colname in FPKM_ING_GIPR.txt: 20047

value: Inguinal White Adipose

value: GiprSyn-/-


title: brain,scRNAseq,bAVM2

city: Beijing

first: Xing-jun

last: Chen

address: Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District

country: China

institute: Chinese Institute for Brain Research, Beijing(CIBR)

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The expression level of detected genes was estimated by DESeq2.A volcano plot was generated by ggplot2 in R, with a cutoff of p-value less than 0.01 and the absolute value of log2 (Foldchange) more than 4, measured by DESeq2.
Volcano plot, Scatter plotting and heatmaps were generated using R packages (ggplot2; pheatmap) implemented in R studio.
For gene set enrichment analysis (GSEA)76, we generated a KEGG_2019_Mouse geneset based on a database file from Enrichr online library(https://amp.pharm.mssm.edu/Enrichr/)77. Genes were pre-ranked through the metrics algorithm (log fold change × -log10(p-value[not adjusted p-val]) according to the statistical result of DESeq2. Pre-ranked (.rnk) file and custom geneset were used as input for GSEA v4.0.3(https://www.gsea-msigdb.org/gsea/index.jsp). The number of permutations was set at 1000 and enrichment statistics were set at “weighted”. For the general significance threshold, false discovery rate (FDR) q-val < 0.25 and |NES| > 1.5 were considered as significant enrichment.
Assembly: Hisat2 GRCm38
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz

molecule: nuclear RNA

source_name: brain

extract_protocol:
mouse brain of our bAVM model were harvested
Single-cell RNA-Seq libraries were prepared using SeekOne® MM Single Cell 3’ library preparation kit (SeekGene, Cat# SO01V3.1)

value: brain

tag: strain

value: endothelial cells

tag: age

value: Braf-CAfl/fl

value: inject with AAV-miniBEND


title: brain,scRNAseq,Ctrl


title: NoMet_transstilbene_139939_4_3.73uM_TC00003594_C09

description:
Library name: TC00003594_C09
TC00003594_C09

tag: cell line

value: 24h exposure of 3.73 uM of trans-Stilbene

value: trans-Stilbene


title: brain,scRNAseq,bAVM1

tag: cell type


title: NoMet_DMSO_0_0uM_TC00003594_B12

description:
Library name: TC00003594_B12
TC00003594_B12

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: Giprfl/fl mGIPR-Ab/P1, Inguinal White Adipose, biol rep3

description:
Library name: 20046
Colname in FPKM_ING_GIPR.txt: 20046

tag: genotype


title: E13.5_PGC_TRIM28KO_Female_3

city: Los Angeles

first: Jonathan

last: DiRusso

state: California

address: 615 Charles E. Young Drive

department: Molecular, Cell and Developmental Biology

institute: University of California Los Angeles

data_processing:
Reads were aligned with STAR v2.7.10a with settings --outFilterMultimapNmax 1000, --outSAMmultNmax 1, --outFilterMismatchNmax 3, and  --alignIntronMax 1. Feature count files were generated using Subread v2.0.2 featureCounts function.
Assembly: GRCm39 (mm39), ENSEMBL v109
Supplementary files format and content: Featurecount files from Subread v2.0.2 featureCounts function options -p -B -P -C -T 20 -t gene -g gene_id

source_name: PGC

extract_protocol:
PGCs from dissected embryonic gonads (E12.5, E13.5, E14.5) and dissected embryo trunks (E10.5, E11.5) were dissociated in 0.05% Trypsin in 5% CO2/37C for 5 minutes. Digestions was quenched using 10% FBS in DMEM High Glucose media and cells were pelleted at 1200 rpm x 5 minutes. Resulting pellet was resuspended in 10% FBS, High Glucose DMEM + DNAse and treated for 5 minutes at 5%CO2/37C and pelleted by centrifugation at 1,200 RPM for 5 minutes. PGCs were then suspended in DPBS + 1% BSA and GFP+, 7AAD- cells were collected in Qiagen Buffer RLT.
RNA was isolated with Qiagen RNEasy kit according to manufacturers instructions. cDNA conversion was performed using Tecan Genomics Ovation RNA-seq System V2. Resulting cDNA was sonicated using a Covaris S2 sonicator and the resulting fragmented cDNA isolated using Quiagen MinElute columns according to the manufacturer's instructions. Isolated cDNA was repaired and barcoded using Tecan Genomics Encore Rapid Library barcoding according to the manufacturers instructions. Samples were quantified using KAPA quanitifcation according to the manufacturer's instructions. Libraries were sequenced using a NovaSeq 6000.

tag: tissue

value: PGC

tag: embryonic day

tag: Sex

value: Female

value: TRIM28 KO


title: GiprSyn-/- Vehicle, Inguinal White Adipose, biol rep2

description:
Library name: 20044
Colname in FPKM_ING_GIPR.txt: 20044

tag: treatment

value: Vehicle


title: NoMet_DMSO_0_0uM_TC00003594_B11

description:
Library name: TC00003594_B11
TC00003594_B11

tag: media

value: VM7Luc4E2 Assay Medium

tag: chemical name

value: OK


title: E13.5_PGC_TRIM28KO_Female_2


title: MPM tumor, surgically resected (P.029.T2.1)

value: Malignant pleural mesothelioma tumor

tag: time (from_surgery_start_in_minutes)


title: shEmpty, Day 2, Rep 1

value: 3T3-L1 preadipocyte cell line


title: MPM tumor, surgically resected (P.026.T2.1)


title: Giprfl/fl mGIPR-Ab/P1, Inguinal White Adipose, biol rep4

description:
Library name: 20049
Colname in FPKM_ING_GIPR.txt: 20049

value: Inguinal White Adipose

value: Giprfl/fl


title: Giprfl/fl mGIPR-Ab/P1, Inguinal White Adipose, biol rep2

description:
Library name: 20042
Colname in FPKM_ING_GIPR.txt: 20042


title: NoMet_daidzein_D7802_2_0.093uM_TC00003594_B10

description:
Library name: TC00003594_B10
TC00003594_B10

value: 24h exposure of 0.093 uM of Daidzein

value: Daidzein

tag: chemical sample_id

tag: chemical concentration

tag: dose level


title: Giprfl/fl Vehicle, Inguinal White Adipose, biol rep3

description:
Library name: 20041
Colname in FPKM_ING_GIPR.txt: 20041


title: E13.5_PGC_TRIM28KO_Female_1


title: NoMet_bestradiol_E2758_1_0.0001uM_TC00003594_B09

description:
Library name: TC00003594_B09
TC00003594_B09

value: 24h exposure of 1e-04 uM of 17beta-Estradiol

tag: exposure time

tag: assay plate

tag: assay plate_well


title: MPM tumor, surgically resected, rep for validation (P.004.TNA.1)


title: NoMet_ethyl4hydroxybenzoate_111988_7_53.5uM_TC00003594_A12

description:
Library name: TC00003594_A12
TC00003594_A12

value: 24h exposure of 53.5 uM of Ethylparaben

value: Ethylparaben

tag: sample qc_issue


title: MPM tumor, surgically resected (P.004.T2.1)


title: E13.5_PGC_Control_Female_3

value: Control


title: Giprfl/fl mGIPR-Ab/P1, Inguinal White Adipose, biol rep1

description:
Library name: 20040
Colname in FPKM_ING_GIPR.txt: 20040


title: Giprfl/fl Vehicle, Inguinal White Adipose, biol rep2

description:
Library name: 20038
Colname in FPKM_ING_GIPR.txt: 20038


title: E13.5_PGC_Control_Female_2


title: NoMet_transstilbene_139939_7_53.5uM_TC00003594_A11

description:
Library name: TC00003594_A11
TC00003594_A11

tag: cell line

value: 24h exposure of 53.5 uM of trans-Stilbene

value: trans-Stilbene


title: MPM tumor, surgically resected (P.041.T2.1)


title: E13.5_PGC_Control_Female_1

value: PGC

value: Female


title: NoMet_DMSO_0_0uM_TC00003594_A10

description:
Library name: TC00003594_A10
TC00003594_A10

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: GiprSyn-/- Vehicle, Inguinal White Adipose, biol rep1

description:
Library name: 20037
Colname in FPKM_ING_GIPR.txt: 20037

value: GiprSyn-/-

value: Vehicle


title: MPM tumor, surgically resected, rep for validation, unknown timepoint (P.006RP.TNA.1)

value: Malignant pleural mesothelioma tumor


title: E13.5_PGC_TRIM28KO_Male_4

value: Male

value: TRIM28 KO


title: Giprfl/fl Vehicle, Inguinal White Adipose, biol rep1

description:
Library name: 20035
Colname in FPKM_ING_GIPR.txt: 20035

value: Inguinal White Adipose

value: Giprfl/fl


title: NoMet_transstilbene_139939_5_11uM_TC00003594_A09

description:
Library name: TC00003594_A09
TC00003594_A09

value: 24h exposure of 11 uM of trans-Stilbene

value: VM7Luc4E2 Assay Medium

value: 11 uM

value: OK


title: MPM tumor, surgically resected (P.027.T1.2)


title: E13.5_PGC_TRIM28KO_Male_3


title: Giprfl/fl Vehicle, Liver, biol rep4

description:
Library name: 20034
Colname in FPKM_Liver_GIPR.txt: 20034

value: Liver


title: Met_daidzein_D7802_7_53.5uM_TC00003591_H12

description:
Library name: TC00003591_H12
TC00003591_H12

value: 24h exposure of 53.5 uM of Daidzein

value: Daidzein


title: Met_DMSO_0_0uM_TC00003591_H11

description:
Library name: TC00003591_H11
TC00003591_H11

value: 0.5% DMSO vehicle control


title: GiprSyn-/- Vehicle, Liver, biol rep5

description:
Library name: 20033
Colname in FPKM_Liver_GIPR.txt: 20033


title: E13.5_PGC_TRIM28KO_Male_1

value: PGC


title: Met_daidzein_D7802_4_3.73uM_TC00003591_H10

description:
Library name: TC00003591_H10
TC00003591_H10

value: 24h exposure of 3.73 uM of Daidzein


title: MPM tumor, surgically resected (P.037.T1.1)


title: MPM tumor, surgically resected (P.026.T2.2)


title: E13.5_PGC_TRIM28KO_Male_2


title: MPM tumor, surgically resected (P.034.T1.1)


title: MPM tumor, surgically resected (P.029.T1.1)


title: Giprfl/fl mGIPR-Ab/P1, Liver, biol rep2

description:
Library name: 20029
Colname in FPKM_Liver_GIPR.txt: 20029


title: MPM tumor, surgically resected (P.033.T1.2)


title: GiprSyn-/- Vehicle, Liver, biol rep4

description:
Library name: 20030
Colname in FPKM_Liver_GIPR.txt: 20030

value: GiprSyn-/-


title: Met_ethyl4hydroxybenzoate_111988_4_3.73uM_TC00003591_H09

description:
Library name: TC00003591_H09
TC00003591_H09

value: 24h exposure of 3.73 uM of Ethylparaben

value: Ethylparaben


title: E13.5_PGC_Control_Male_2

value: Male

value: Control


title: Met_daidzein_D7802_5_11uM_TC00003591_G12

description:
Library name: TC00003591_G12
TC00003591_G12

value: 24h exposure of 11 uM of Daidzein


title: MPM tumor, surgically resected (P.027.T1.1)

value: Malignant pleural mesothelioma tumor


title: E13.5_PGC_Control_Male_3


title: E13.5_PGC_Control_Male_1


title: MPM tumor, surgically resected (P.032.T1.2)


title: Met_DMSO_0_0uM_TC00003591_G11

description:
Library name: TC00003591_G11
TC00003591_G11

value: DMSO

value: 0 uM


title: E12.5_PGC_TRIM28KO_Female_4

value: Female

value: TRIM28 KO


title: Giprfl/fl Vehicle, Liver, biol rep3

description:
Library name: 20028
Colname in FPKM_Liver_GIPR.txt: 20028

value: Liver

value: Giprfl/fl

value: Vehicle


title: Met_ethyl4hydroxybenzoate_111988_3_0.865uM_TC00003591_G10

description:
Library name: TC00003591_G10
TC00003591_G10

value: 24h exposure of 0.865 uM of Ethylparaben

value: VM7Luc4E2 Assay Medium

value: OK


title: MPM tumor, surgically resected (P.035.T1.1)


title: MPM tumor, surgically resected, rep for validation (P.003.TNA.1)


title: Met_DMSO_0_0uM_TC00003591_G09

description:
Library name: TC00003591_G09
TC00003591_G09

value: 0.5% DMSO vehicle control


title: Giprfl/fl mGIPR-Ab/P1, Liver, biol rep3

description:
Library name: 20032
Colname in FPKM_Liver_GIPR.txt: 20032


title: MPM tumor, surgically resected (P.034.T1.2)


title: E12.5_PGC_TRIM28KO_Female_2

value: PGC


title: Met_ethyl4hydroxybenzoate_111988_2_0.093uM_TC00003591_F12

description:
Library name: TC00003591_F12
TC00003591_F12

value: 24h exposure of 0.093 uM of Ethylparaben

value: Ethylparaben


title: Giprfl/fl Vehicle, Liver, biol rep2

description:
Library name: 20019
Colname in FPKM_Liver_GIPR.txt: 20019


title: MPM tumor, surgically resected (P.006-RP.T1.1)


title: Met_transstilbene_139939_5_11uM_TC00003591_F11

description:
Library name: TC00003591_F11
TC00003591_F11

value: 24h exposure of 11 uM of trans-Stilbene

value: trans-Stilbene

value: 11 uM


title: E12.5_PGC_Control_Female_4

value: Control


title: MPM tumor, surgically resected (P.028.T1.1)

value: Malignant pleural mesothelioma tumor


title: E12.5_PGC_Control_Female_3

value: Female


title: E12.5_PGC_TRIM28KO_Female_1

value: TRIM28 KO


title: Met_transstilbene_139939_3_0.865uM_TC00003591_F10

description:
Library name: TC00003591_F10
TC00003591_F10

value: 24h exposure of 0.865 uM of trans-Stilbene


title: Giprfl/fl Vehicle, Liver, biol rep1

description:
Library name: 20016
Colname in FPKM_Liver_GIPR.txt: 20016

value: Liver

value: Giprfl/fl


title: Met_daidzein_D7802_1_0.001uM_TC00003591_F09

description:
Library name: TC00003591_F09
TC00003591_F09

value: 24h exposure of 0.001 uM of Daidzein

value: Daidzein


title: MPM tumor, surgically resected (P.040.T1.1)


title: MPM tumor, surgically resected (P.039.T1.2)


title: GiprSyn-/- Vehicle, Liver, biol rep1

description:
Library name: 20018
Colname in FPKM_Liver_GIPR.txt: 20018

value: GiprSyn-/-

value: Vehicle


title: Glp1rfl/fl mGIPR-Ab/P1, Inguinal White Adipose, biol rep5

description:
Library name: 19971
Colname in FPKM_ING_GLP1R.txt: 19971

value: Inguinal White Adipose


title: MPM tumor, surgically resected (P.038.T1.1)


title: Met_daidzein_D7802_6_26.1uM_TC00003591_E12

description:
Library name: TC00003591_E12
TC00003591_E12

value: 24h exposure of 26.1 uM of Daidzein

value: VM7Luc4E2 Assay Medium

value: OK


title: E12.5_PGC_TRIM28KO_Female_3

value: PGC


title: E12.5_PGC_Control_Female_2


title: GiprSyn-/- Vehicle, Liver, biol rep3

description:
Library name: 20027
Colname in FPKM_Liver_GIPR.txt: 20027


title: E12.5_PGC_Control_Female_1


title: Met_transstilbene_139939_1_0.001uM_TC00003591_E11

description:
Library name: TC00003591_E11
TC00003591_E11

value: 24h exposure of 0.001 uM of trans-Stilbene

value: trans-Stilbene


title: E12.5_PGC_TRIM28KO_Male_3

value: Male


title: MPM tumor, surgically resected (P.001.T1.1)

value: Malignant pleural mesothelioma tumor


title: Met_bestradiol_E2758_1_0.0001uM_TC00003591_E10

description:
Library name: TC00003591_E10
TC00003591_E10

value: 24h exposure of 1e-04 uM of 17beta-Estradiol


title: GiprSyn-/- Vehicle, Liver, biol rep2

description:
Library name: 20024
Colname in FPKM_Liver_GIPR.txt: 20024


title: MPM tumor, surgically resected (P.033.T1.1)


title: Glp1rfl/fl mGIPR-Ab/P1, Inguinal White Adipose, biol rep3

description:
Library name: 19969
Colname in FPKM_ING_GLP1R.txt: 19969


title: E12.5_PGC_TRIM28KO_Male_2

value: TRIM28 KO


title: MPM tumor, surgically resected (P.031.T1.2)


title: Glp1rfl/fl mGIPR-Ab/P1, Inguinal White Adipose, biol rep2

description:
Library name: 19968
Colname in FPKM_ING_GLP1R.txt: 19968


title: E12.5_PGC_Control_Male_4

value: Control


title: Met_daidzein_D7802_2_0.093uM_TC00003591_D12

description:
Library name: TC00003591_D12
TC00003591_D12

value: 24h exposure of 0.093 uM of Daidzein


title: Glp1rWnt1-/- Vehicle, Inguinal White Adipose, biol rep5

description:
Library name: 19966
Colname in FPKM_ING_GLP1R.txt: 19966


title: MPM tumor, surgically resected (P.037.T1.2)


title: Glp1rfl/fl mGIPR-Ab/P1, Inguinal White Adipose, biol rep1

description:
Library name: 19967
Colname in FPKM_ING_GLP1R.txt: 19967


title: Met_ethyl4hydroxybenzoate_111988_8_100uM_TC00003591_D11

description:
Library name: TC00003591_D11
TC00003591_D11

value: 24h exposure of 100 uM of Ethylparaben

value: Ethylparaben


title: MPM tumor, surgically resected (P.024.T1.1)


title: E12.5_PGC_Control_Male_3


title: Met_ethyl4hydroxybenzoate_111988_1_0.001uM_TC00003591_D10

description:
Library name: TC00003591_D10
TC00003591_D10

value: 24h exposure of 0.001 uM of Ethylparaben


title: Glp1rfl/fl mGIPR-Ab/P1, Inguinal White Adipose, biol rep4

description:
Library name: 19970
Colname in FPKM_ING_GLP1R.txt: 19970


title: Glp1rWnt1-/- Vehicle, Inguinal White Adipose, biol rep4

description:
Library name: 19965
Colname in FPKM_ING_GLP1R.txt: 19965

value: Vehicle


title: MPM tumor, surgically resected (P.035.T1.2)


title: Glp1rWnt1-/- Vehicle, Inguinal White Adipose, biol rep3

description:
Library name: 19964
Colname in FPKM_ING_GLP1R.txt: 19964

value: Inguinal White Adipose


title: MPM tumor, surgically resected (P.030.T1.1)


title: E12.5_PGC_Control_Male_1


title: Met_ethyl4hydroxybenzoate_111988_6_26.1uM_TC00003591_C12

description:
Library name: TC00003591_C12
TC00003591_C12

value: 24h exposure of 26.1 uM of Ethylparaben


title: Glp1rWnt1-/- Vehicle, Inguinal White Adipose, biol rep2

description:
Library name: 19963
Colname in FPKM_ING_GLP1R.txt: 19963


title: Glp1rWnt1-/- Vehicle, Inguinal White Adipose, biol rep1

description:
Library name: 19962
Colname in FPKM_ING_GLP1R.txt: 19962


title: E12.5_PGC_TRIM28KO_Male_1


title: Met_transstilbene_139939_6_26.1uM_TC00003591_C11

description:
Library name: TC00003591_C11
TC00003591_C11

value: 24h exposure of 26.1 uM of trans-Stilbene

value: VM7Luc4E2 Assay Medium


title: Met_transstilbene_139939_7_53.5uM_TC00003591_E09

description:
Library name: TC00003591_E09
TC00003591_E09

value: 24h exposure of 53.5 uM of trans-Stilbene

value: OK


title: Giprfl/fl mGIPR-Ab/P1, Liver, biol rep1

description:
Library name: 20026
Colname in FPKM_Liver_GIPR.txt: 20026

value: Liver

value: Giprfl/fl


title: E11.5_PGC_TRIM28KO_Female_2

value: PGC

value: Female


title: MPM tumor, surgically resected (P.032.T1.1)

value: Malignant pleural mesothelioma tumor


title: MPM tumor, surgically resected (P.039.T1.1)


title: E12.5_PGC_Control_Male_2

value: Male

value: Control


title: Met_transstilbene_139939_4_3.73uM_TC00003591_C09

description:
Library name: TC00003591_C09
TC00003591_C09

value: 24h exposure of 3.73 uM of trans-Stilbene

value: trans-Stilbene


title: Glp1rfl/fl Vehicle, Inguinal White Adipose, biol rep4

description:
Library name: 19960
Colname in FPKM_ING_GLP1R.txt: 19960


title: Met_bestradiol_E2758_1_0.0001uM_TC00003591_D09

description:
Library name: TC00003591_D09
TC00003591_D09

value: 24h exposure of 1e-04 uM of 17beta-Estradiol


title: MPM tumor, surgically resected (P.030.T1.2)


title: E11.5_PGC_TRIM28KO_Female_1

value: TRIM28 KO


title: Glp1rfl/fl Vehicle, Inguinal White Adipose, biol rep5

description:
Library name: 19961
Colname in FPKM_ING_GLP1R.txt: 19961

value: Inguinal White Adipose

value: Vehicle


title: Glp1rfl/fl Vehicle, Inguinal White Adipose, biol rep3

description:
Library name: 19959
Colname in FPKM_ING_GLP1R.txt: 19959


title: E11.5_PGC_Control_Female_3


title: Met_bestradiol_E2758_1_0.0001uM_TC00003591_B12

description:
Library name: TC00003591_B12
TC00003591_B12


title: Glp1rfl/fl Vehicle, Inguinal White Adipose, biol rep2

description:
Library name: 19958
Colname in FPKM_ING_GLP1R.txt: 19958


title: E11.5_PGC_TRIM28KO_Female_3


title: MPM tumor, surgically resected (P.026.T1.1)


title: MPM tumor, surgically resected (P.003.T1.1)


title: E11.5_PGC_Control_Female_1


title: Met_DMSO_0_0uM_TC00003591_B11

description:
Library name: TC00003591_B11
TC00003591_B11

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: Glp1rfl/fl Vehicle, Inguinal White Adipose, biol rep1

description:
Library name: 19957
Colname in FPKM_ING_GLP1R.txt: 19957


title: E11.5_PGC_Control_Female_2


title: MPM tumor, surgically resected (P.041.T1.2)


title: E11.5_PGC_TRIM28KO_Male_4


title: Glp1rfl/fl mGIPR-Ab/P1, Liver, biol rep5

description:
Library name: 19951
Colname in FPKM_Liver_GLP1R.txt: 19951


title: MPM tumor, surgically resected, rep for validation (P.001.TNA.1)


title: Met_DMSO_0_0uM_TC00003591_B09

description:
Library name: TC00003591_B09
TC00003591_B09

value: VM7Luc4E2 Assay Medium

value: OK


title: Met_transstilbene_139939_8_100uM_TC00003591_C10

description:
Library name: TC00003591_C10
TC00003591_C10

value: 24h exposure of 100 uM of trans-Stilbene


title: Glp1rfl/fl mGIPR-Ab/P1, Liver, biol rep4

description:
Library name: 19950
Colname in FPKM_Liver_GLP1R.txt: 19950

value: Liver


title: MPM tumor, surgically resected (P.041.T1.1)


title: E11.5_PGC_TRIM28KO_Male_3

value: PGC


title: Met_transstilbene_139939_2_0.093uM_TC00003591_A12

description:
Library name: TC00003591_A12
TC00003591_A12

value: 24h exposure of 0.093 uM of trans-Stilbene


title: MPM tumor, surgically resected (P.031.T1.1)

value: Malignant pleural mesothelioma tumor


title: Glp1rfl/fl mGIPR-Ab/P1, Liver, biol rep3

description:
Library name: 19949
Colname in FPKM_Liver_GLP1R.txt: 19949


title: E11.5_PGC_TRIM28KO_Male_2

value: Male


title: Met_daidzein_D7802_3_0.865uM_TC00003591_A11

description:
Library name: TC00003591_A11
TC00003591_A11

value: 24h exposure of 0.865 uM of Daidzein

value: Daidzein


title: MPM tumor, surgically resected (P.006.T1.1)


title: E11.5_PGC_TRIM28KO_Male_1


title: Glp1rfl/fl mGIPR-Ab/P1, Liver, biol rep2

description:
Library name: 19948
Colname in FPKM_Liver_GLP1R.txt: 19948


title: MPM tumor, surgically resected, rep for validation (P.008.TNA.1)


title: Met_daidzein_D7802_8_100uM_TC00003591_A10

description:
Library name: TC00003591_A10
TC00003591_A10

value: 24h exposure of 100 uM of Daidzein


title: E11.5_PGC_Control_Male_4

value: Control


title: Glp1rfl/fl mGIPR-Ab/P1, Liver, biol rep1

description:
Library name: 19947
Colname in FPKM_Liver_GLP1R.txt: 19947


title: E11.5_PGC_Control_Male_3


title: MPM tumor, surgically resected (P.009.T0.2)


title: Met_ethyl4hydroxybenzoate_111988_7_53.5uM_TC00003591_B10

description:
Library name: TC00003591_B10
TC00003591_B10

value: 24h exposure of 53.5 uM of Ethylparaben

value: Ethylparaben


title: NoMet_ethyl4hydroxybenzoate_111988_3_0.865uM_TC00003588_H12

description:
Library name: TC00003588_H12
TC00003588_H12

value: 24h exposure of 0.865 uM of Ethylparaben


title: MPM tumor, surgically resected (P.003.T0.1)


title: E11.5_PGC_Control_Male_2


title: Met_ethyl4hydroxybenzoate_111988_5_11uM_TC00003591_A09

description:
Library name: TC00003591_A09
TC00003591_A09

value: 24h exposure of 11 uM of Ethylparaben

value: 11 uM


title: Glp1rWnt1-/- Vehicle, Liver, biol rep5

description:
Library name: 19946
Colname in FPKM_Liver_GLP1R.txt: 19946

value: Vehicle


title: Glp1rWnt1-/- Vehicle, Liver, biol rep4

description:
Library name: 19945
Colname in FPKM_Liver_GLP1R.txt: 19945


title: MPM tumor, surgically resected (P.002.T0.1)


title: E11.5_PGC_Control_Male_1


title: Glp1rWnt1-/- Vehicle, Liver, biol rep3

description:
Library name: 19944
Colname in FPKM_Liver_GLP1R.txt: 19944


title: MPM tumor, surgically resected (P.033.T0.1)


title: E125_PGC_Male_ChIP_Input_2

library_source: genomic

data_processing:
Alignment was performed with STAR/2.7.10a, samples deduplicated using SAMtools.
Assembly: GRCm39 (mm39) ENSEMBL v109
Supplementary files format and content: BigWig files produced using DeepTools bamcoverage.

molecule: genomic DNA

source_name: PCG

extract_protocol:
Gonads from time-mated CD1 mice were dissected at E12.5. Following dissection, gonads were seperated from the mesonephrous and digested with 0.05% trypsin. Digestion was stopped with 10% FBS + High Glucose DMEM with 1x DNAse. Cells were resuspended in 10% FBS + Hgih Glucose DMEM and passed through a 70 um strainer to make a single-cell suspension. The resulting pellet was resuspended in 1X DPBS + 0.1% BSA + 0.5% EDTA. Suspension was incubated with antiobodies against SSEA1 (ovarian and testicular PGCs) and CD31 (ovarian PGCs only) at 4C for 30 minutes (ovarian PGCs) or 20 minutes (testicular PGCs). Cells were pelleted by centrifugation and resuspended then loaded onto an MS column on a MiniMACS magnet. After incuibation 1 mL of 0.1% BSA, 0.5% EDTA and 1x DPBS was loaded onto the column and cells released using the supplied plunger.
After isolation cells were washed in 1x DPBS and resuspended in 1% paraformaldehyde at room temperature for 10 minutes. Fixation was stopped with 0.14M Glycine in DPBS and incubated rotating at room temperature for 10 minutes. Cells were pelleted by centrifugation, supernatant removed and flash frozen in liquid nitrogen. After thaw, cells were resuspended in 10 mM Tris-HCl, 0.25% Triton-X, 10 mM EDTA, 0.5 mM EGTA and Roche cOmplete and incubated at room temperature for 15 minutes. Cells were pelleted by centrifugation at 4000 RPM for 5 minutes. Pellets were resuspended in 10 mM Tris-HCl, 200 mM NaCl, 10 mM EDTA, 0.5 mM EGTA, and Roche cOmplete for 10 minutes rotating at 4C. Cells were pelleted by centrifugation at 4000 RPM for 5 minutes. Resulting pellet was resuspended in 10 mM Tris-HCl, 10 mM EDTA, 0.5 mM EGTA, Roche cOmplete. Resuspended cells were sonictaed using a Covaris S2 with the following program: Intensity = 5, Cycles/burst = 200, duty cycle = 5% with a 30" on/30" off cycle for an effective sonication time of 4 minutes. Sonicated lysate was centrifuged at 14000 rpm for 10 minutes at 4C. 10% of clarified lysate was held for input. Samples were pre-cleared with Protein A Dynabeads. Beads were removed at antibody added to sample to incubate, rotating, overnight at 4C. Protein A dynabeads were then added to the sample and left to incubate for 2 hours at 4C. Dynabeads were seperated via magenetic separation. Washed Dynabeads were then resuspended in 50 mM Tris-HCl, 1 mM EDTA, 1% SDS for elution on a thermoshaker at 65C, shaking at 1400 rpm for 10 minutes. Dynabeads were seperated and the elution was performed again on sperated beads. Input and eluted chromatin from above were then incubated overnight at 65C. Samples were treated with RNAse A for 30 minutes at 37C and then proteinase K at 56C for 2 hours. DNA was eluted using a MinElute column. Library was prepared using Tecan Genomics UltaLow System V2 according to manufacturer's instructions.

value: PCG

tag: chip antibody

value: Input

tag: replicate


title: NoMet_daidzein_D7802_3_0.865uM_TC00003588_H10

description:
Library name: TC00003588_H10
TC00003588_H10

value: VM7Luc4E2 Assay Medium

value: OK


title: NoMet_bestradiol_E2758_1_0.0001uM_TC00003588_H09

description:
Library name: TC00003588_H09
TC00003588_H09

value: 24h exposure of 1e-04 uM of 17beta-Estradiol


title: Glp1rWnt1-/- Vehicle, Liver, biol rep2

description:
Library name: 19943
Colname in FPKM_Liver_GLP1R.txt: 19943

tag: tissue

value: Liver

tag: genotype


title: E125_PGC_Male_ChIP_Input_1

tag: embryonic day

tag: Sex

value: Male


title: MPM tumor, surgically resected (P.002-RP.T0.1)

value: Malignant pleural mesothelioma tumor


title: Glp1rWnt1-/- Vehicle, Liver, biol rep1

description:
Library name: 19942
Colname in FPKM_Liver_GLP1R.txt: 19942

tag: treatment


title: NoMet_ethyl4hydroxybenzoate_111988_6_26.1uM_TC00003588_G12

description:
Library name: TC00003588_G12
TC00003588_G12

value: 24h exposure of 26.1 uM of Ethylparaben

tag: media

tag: chemical name


title: MPM tumor, surgically resected (P.012.T0.1)

tag: time (from_surgery_start_in_minutes)


title: E125_PGC_Male_ChIP_TRIM28_2


title: NoMet_bestradiol_E2758_1_0.0001uM_TC00003588_G11

description:
Library name: TC00003588_G11
TC00003588_G11

tag: chemical sample_id

tag: chemical concentration


title: MPM tumor, surgically resected (P.012.T0.2)


title: Glp1rfl/fl Vehicle, Liver, biol rep4

description:
Library name: 19940
Colname in FPKM_Liver_GLP1R.txt: 19940


title: E125_PGC_Male_ChIP_TRIM28_1


title: Glp1rfl/fl Vehicle, Liver, biol rep3

description:
Library name: 19939
Colname in FPKM_Liver_GLP1R.txt: 19939


title: NoMet_daidzein_D7802_6_26.1uM_TC00003588_G10

description:
Library name: TC00003588_G10
TC00003588_G10

value: 24h exposure of 26.1 uM of Daidzein

value: Daidzein

tag: dose level

tag: exposure time


title: E125_PGC_Female_ChIP_Input_2

value: Female


title: NoMet_daidzein_D7802_5_11uM_TC00003588_H11

description:
Library name: TC00003588_H11
TC00003588_H11

value: 24h exposure of 11 uM of Daidzein

tag: assay plate

tag: assay plate_well


title: MPM tumor, surgically resected (P.030.T0.1)


title: Glp1rfl/fl Vehicle, Liver, biol rep2

description:
Library name: 19938
Colname in FPKM_Liver_GLP1R.txt: 19938


title: NoMet_daidzein_D7802_7_53.5uM_TC00003588_G09

description:
Library name: TC00003588_G09
TC00003588_G09

tag: cell line

value: 24h exposure of 53.5 uM of Daidzein

tag: sample qc_issue


title: E125_PGC_Female_ChIP_Input_1

tag: chip antibody

tag: replicate


title: NoMet_DMSO_0_0uM_TC00003588_F12

description:
Library name: TC00003588_F12
TC00003588_F12

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: MPM tumor, surgically resected (P.008.T0.1)

tag: tissue


title: Glp1rfl/fl Vehicle, Liver, biol rep1

description:
Library name: 19937
Colname in FPKM_Liver_GLP1R.txt: 19937

tag: genotype

value: Vehicle


title: NoMet_transstilbene_139939_6_26.1uM_TC00003588_F11

description:
Library name: TC00003588_F11
TC00003588_F11

value: 24h exposure of 26.1 uM of trans-Stilbene

value: trans-Stilbene


title: E125_PGC_Female_ChIP_TRIM28_2

value: PCG

tag: embryonic day

tag: Sex


title: MPM tumor, surgically resected (P.034.T0.1)


title: NoMet_ethyl4hydroxybenzoate_111988_4_3.73uM_TC00003588_F10

description:
Library name: TC00003588_F10
TC00003588_F10

tag: treatment

value: 24h exposure of 3.73 uM of Ethylparaben

tag: media

value: VM7Luc4E2 Assay Medium

value: Ethylparaben

value: OK


title: E125_PGC_Female_ChIP_TRIM28_1


title: E14.5_PGC_Female_TRIM28_ATAC_3

data_processing:
Adapter trimming performed with TrimGalore v0.6.10. Alignment was performed with STAR 2.7.9a. PCR duplicates were removed using Picard Tools MarkDuplicates v2.25.0.
Bigwig files of merged replicates. Generated using DeepTools v3.5.1.
Assembly: GRCm39 (ENSEMBL) v109
Supplementary files format and content: BigWig

extract_protocol:
PGCs from dissected embryonic gonads (E12.5, E13.5, E14.5) and dissected embryo trunks (E10.5, E11.5) were dissociated in 0.05% Trypsin in 5% CO2/37C for 5 minutes. Digestions was quenched using 10% FBS in DMEM High Glucose media and cells were pelleted at 1200 rpm x 5 minutes. Resulting pellet was resuspended in 10% FBS, High Glucose DMEM + DNAse and treated for 5 minutes at 5%CO2/37C and pelleted by centrifugation at 1,200 RPM for 5 minutes. PGCs were then suspended in DPBS + 1% BSA and GFP+, 7AAD- cells were collected in DPBS + 1% BSA. .
Libraries were prepared according to the protocols published in Corces et al., Nature Methods 2017 (DOI: https://doi.org/10.1038/nmeth.4396) Briefly: Samples were spun down at 750 r.c.f at 4C for 10 minutes, resuspended in buffer RSB and spun again at 750 r.c.f at 4C for 10 minutes. After last centrifugation, buffer RSB was removed and Tn5 Enzyme mix added. Samples were treated at 37C for 30 minutes, shaking at 1000 rpm. Reaction was immediately quenched on ice with ice-cold PBS. DNA was purified using NEB Monarch DNA Purification kit according to the manufacturer's instructions. Purified DNA was used as a template and Nexteera indexing adapters added to the reaction with NEB Next High fidelity PCR mix. Samples were run for 5 cycles, split and run for an additional 4 and 8 cycles. Resulting libraries were purified using Agencourt XP beads and quantified using the Quibit HS DNA quantification kit according to manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq 6000 (E14.5) or Illumina NovaSeq X Plus (E10.5).

value: PGC

value: Male


title: MPM tumor, surgically resected (P.004.T0.1)

value: Malignant pleural mesothelioma tumor

tag: time (from_surgery_start_in_minutes)


title: Glp1rfl/fl Vehicle, Liver, biol rep5

description:
Library name: 19941
Colname in FPKM_Liver_GLP1R.txt: 19941

value: Liver


title: E14.5, KO (Wt1Cre;Sox9fl/fl;R26mG)

city: Charleston

first: Allison

last: Trouten

state: SC

address: 173 Ashley Ave Room BSB 642

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

description:
Library name: 110
10x Genomics

data_processing:
Fastq files were aligned to the mm10 reference transcriptome using the count function in the Cell Ranger software (v7.1, 10x Genomics, Pleasanton, CA, USA). Quality control was performed using a pipeline including exclusion of cells containing high mitochondrial read fraction, low detection of unique genes / number of UMIs per cell, and doublet filtering. Dimensional reduction and unsupervised clustering were performed RunUMAP and FindClusters functions in Seurat. Differential expression analyses were carried out in Seurat.
Assembly: mm10
Supplementary files format and content: h5 gene matrix file

source_name: majority of the left and right atrial appendage

extract_protocol:
Hearts were dissected, pooled by genotype, and dissociated in 200ug/mL Liberase TM (Sigma-Aldrich) dissolved in Hibernate E minus calcium media (Transnetyx) for 30 minutes at 37°C
Single-cell suspensions loaded onto a 10X Genomics Next GEM Chip and emulsified with 3’ Single Cell Next GEM beads using a ChromiumTM Controller (10X Genomics). All embryos were dissected, digested, and barcoded on the same day to minimize variation. From barcoded cDNAs, gene expression libraries were constructed using ChromiumTM Single Cell 3ʹ Library Kits (10X Genomics) at the Translational Science Laboratory (Medical University of South Carolina). Next-generation sequencing was performed on each sample using an Illumina NovaSeq S4 flow cell at the VANTAGE facility (Vanderbilt University Medical Center)

tag: cell type

value: mixed

tag: batch

value: N = 3 pooled


title: E14.5, het (Wt1cre;Sox9fl/+;R26mG)

description:
Library name: 109
10x Genomics

value: majority of the left and right atrial appendage


title: MPM tumor, surgically resected (P.002-RP.T0.2)


title: NoMet_DMSO_0_0uM_TC00003588_F09

description:
Library name: TC00003588_F09
TC00003588_F09

value: 0.5% DMSO vehicle control

tag: chemical name

value: DMSO

tag: chemical sample_id

tag: chemical concentration

tag: dose level


title: E14.5, control (Wt1cre;Sox9+/+;R26mG)

description:
Library name: 108
10x Genomics


title: E14.5_PGC_Female_TRIM28_ATAC_2


title: MPM tumor, surgically resected (P.005.T0.1)


title: shJmjd1a plus Mut, Day 2, Rep 3

description: Library name: MH210_9_shJmjd1a_Mut

data_processing:
All fastq files were first subjected to pre-processing with fastp (Galaxy Version 0.24.0+galaxy3).
Reads were aligned to the mm9 mouse genome using Bowtie 2 (Galaxy Version 2.5.3+galaxy1).
Removal of multi-mapped (<40 MAPQ), duplicated, and mitochondrial reads were carried out using samtools sort (Galaxy Version 2.0.5), fixmate (Version 1.20), view (Version 1.20), and markdup (Galaxy Version 1.20+galaxy2).
For visualization on IGV (Integrative Genomics Viewer, version 2.8.7), aligned reads (BAM files) were converted to bigWig files using the bamCoverage function of deepTools (normalized as CPM (Counts Per Million), Galaxy Version 3.5.4+galaxy0).
Assembly: mm9
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed essentially as described in the original protocol (Kaya-Okur et al. 2019 Nat Commun), using anti-H3K9me2 antibody (CMA317/6D11, Hayashi-Tanaka et al. 2011 Nucleic Acids Res).
After CUT&Tag reactions, column-purified DNA samples were PCR-amplified with indexed primers using NEBNext HiFi (New England Biolabs), followed by size selection with AMPure XP Beads (BECKMAN COULTER).

tag: cell line

value: preadipocyte cell line

value: shJmjd1a plus Mut


title: E14.5_PGC_Female_TRIM28_ATAC_1


title: MPM tumor, surgically resected (P.024.T0.1)


title: MPM tumor, surgically resected (P.028.T0.1)


title: NoMet_transstilbene_139939_1_0.001uM_TC00003588_E11

description:
Library name: TC00003588_E11
TC00003588_E11

value: 24h exposure of 0.001 uM of trans-Stilbene

value: trans-Stilbene

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: sample qc_issue


title: E14.5_PGC_Female_Control_ATAC_4

tag: tissue

value: Female

tag: genotype

value: Control


title: NoMet_ethyl4hydroxybenzoate_111988_1_0.001uM_TC00003588_E10

description:
Library name: TC00003588_E10
TC00003588_E10

value: 24h exposure of 0.001 uM of Ethylparaben

value: VM7Luc4E2 Assay Medium

value: Ethylparaben


title: shJmjd1a plus WT, Day 2, Rep 3

description: Library name: MH210_8_shJmjd1a_WT

value: shJmjd1a plus WT


title: E14.5_PGC_Female_Control_ATAC_3

value: PGC

tag: embryonic day

tag: Sex


title: MPM tumor, surgically resected (P.027.T0.1)

value: Malignant pleural mesothelioma tumor


title: NoMet_ethyl4hydroxybenzoate_111988_5_11uM_TC00003588_E09

description:
Library name: TC00003588_E09
TC00003588_E09

tag: treatment

value: 24h exposure of 11 uM of Ethylparaben

tag: media

value: 11 uM

value: OK


title: MPM tumor, surgically resected (P.001.T0.1)

tag: time (from_surgery_start_in_minutes)


title: E14.5_PGC_Female_Control_ATAC_2


title: NoMet_transstilbene_139939_3_0.865uM_TC00003588_D12

description:
Library name: TC00003588_D12
TC00003588_D12

value: 24h exposure of 0.865 uM of trans-Stilbene


title: shJmjd1a plus Mut, Day 2, Rep 2

description: Library name: MH210_6_shJmjd1a_Mut

tag: cell type


title: shJmjd1a plus WT, Day 2, Rep 2

description: Library name: MH210_5_shJmjd1a_WT


title: MPM tumor, surgically resected (P.013.T0.2)


title: NoMet_daidzein_D7802_4_3.73uM_TC00003588_D11

description:
Library name: TC00003588_D11
TC00003588_D11

value: 24h exposure of 3.73 uM of Daidzein

tag: chemical name

value: Daidzein


title: MPM tumor, surgically resected (P.013.T0.1)


title: E14.5_PGC_Male_TRIM28_ATAC_3

value: Male


title: NoMet_daidzein_D7802_8_100uM_TC00003588_D10

description:
Library name: TC00003588_D10
TC00003588_D10

value: 24h exposure of 100 uM of Daidzein

tag: chemical sample_id


title: NoMet_transstilbene_139939_2_0.093uM_TC00003588_E12

description:
Library name: TC00003588_E12
TC00003588_E12

value: 24h exposure of 0.093 uM of trans-Stilbene

value: trans-Stilbene

tag: chemical concentration


title: shJmjd1a plus LacZ, Day 2, Rep 2

description: Library name: MH210_4_shJmjd1a_LacZ

value: preadipocyte cell line

value: shJmjd1a plus LacZ


title: MPM tumor, surgically resected (P.020.T0.3)


title: E14.5_PGC_Male_TRIM28_ATAC_2


title: NoMet_transstilbene_139939_8_100uM_TC00003588_D09

description:
Library name: TC00003588_D09
TC00003588_D09

value: 24h exposure of 100 uM of trans-Stilbene

value: VM7Luc4E2 Assay Medium

tag: dose level


title: shJmjd1a plus WT, Day 2, Rep 1

description: Library name: MH210_2_shJmjd1a_WT

tag: cell line

value: shJmjd1a plus WT


title: shJmjd1a plus Mut, Day 2, Rep 1

description: Library name: MH210_3_shJmjd1a_Mut

value: shJmjd1a plus Mut


title: shJmjd1a plus LacZ, Day 2, Rep 3

description: Library name: MH210_7_shJmjd1a_LacZ


title: NoMet_daidzein_D7802_1_0.001uM_TC00003588_C12

description:
Library name: TC00003588_C12
TC00003588_C12

value: 24h exposure of 0.001 uM of Daidzein

tag: exposure time


title: E14.5_PGC_Male_Control_ATAC_4

value: PGC

value: Control


title: shJmjd1a plus LacZ, Day 2, Rep 1

description: Library name: MH210_1_shJmjd1a_LacZ


title: NoMet_ethyl4hydroxybenzoate_111988_2_0.093uM_TC00003588_C11

description:
Library name: TC00003588_C11
TC00003588_C11

value: 24h exposure of 0.093 uM of Ethylparaben

value: Ethylparaben

tag: assay plate

value: OK


title: MPM tumor, surgically resected (P.011.T0.1)

value: Malignant pleural mesothelioma tumor


title: E14.5_PGC_Male_TRIM28_ATAC_1

value: Male


title: E14.5_PGC_Male_Control_ATAC_3


title: TS92_128_replicate_3

city: Wurzburg

first: Wilma

last: Ziebuhr

address: Josef-Schneider-Strasse 2

department: Institute of Molecular Infection Biology

institute: University of Wurzburg

description:
Raw_count_table.csv
DESeq2_comparison_TS92_128_vs_TS92_0_table.csv
DESeq2_comparison_TS92_128_vs_TS92_32_table.csv

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) v2.1 (parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment processed reads to M. sciuri TS92 reference genome using segemehl v0.2.0 with READemption (Förstner et al., 2014) v0.4.5 (parameters: align -l 12 -a 95)
Calculation of raw read counts via READemption (parameters: gene_quanti -o 10 --features "CDS,rRNA,tmRNA,tRNA" -a)
Differential expression analysis via DESeq2 v1.24.0 with fold-change shrinkage applied by setting the parameter betaPrior to TRUE
Assembly: PRJNA1074542; SAMN39864404
Supplementary files format and content: Character (TAB) separated value file containing raw read counts (Raw_count_table.csv)
Supplementary files format and content: Character (TAB) separated value file containing normalized reads counts for all libraries and DESeq2 results for the respective comparison (DESeq2_comparison_X_vs_Y_table.csv)

organism: Mammaliicoccus sciuri

source_name: bacterial cell

growth_protocol: Cells were grown in Muller-Hinton broth and incubated at 37 °C and 200 rpm shaking

extract_protocol:
Total RNA was extracted using hot phenol extraction method
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). cDNA libraries suitable for sequencing were prepared from 1000 ng of total RNA after DNase I treatment (Thermo Fisher). RNAs were treated for rRNA depletion with RiboPOOLs (siTOOLs), except one sample (WT), were fragmented using Mg2+ ions 2 min 45 sec (NEBNext Magnesium RNA fragmentation module) and were treated with T4 PNK for phosphorylation/dephosphorylation and RppH for decapping followed by NEBNext® Multiplex Small RNA Library Prep (New England Biolabs). The number of the PCR cycles was determined at 14 by qPCR and the elongation time was set to 15 sec. Libraries were quantified by QubitTM dsDNA HS Assay Kit 3.0 Fluorometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent Technologies) before pooling. Sequencing of pooled libraries, spiked with 5% PhiX control library, was performed at ~11-15 M reads/sample in single-end mode with 75 nt read length on the NextSeq 500 platform (Illumina).

treatment_protocol: Bacterial culture stayed untreated or was supplemented with 32 µg/ml or 128 µg/mL daptomycin and incubated for 30 minutes before total RNA extraction

tag: strain

value: bacterial cell

value: wt

value: 128 µg/mL daptomycin

tag: biological replicate

value: replicate 3


title: MPM tumor, surgically resected (P.040.T0.1)

tag: tissue


title: NoMet_ethyl4hydroxybenzoate_111988_8_100uM_TC00003588_C10

description:
Library name: TC00003588_C10
TC00003588_C10

value: 24h exposure of 100 uM of Ethylparaben

tag: assay plate_well

tag: sample qc_issue


title: E14.5_PGC_Female_Control_ATAC_1

tag: embryonic day

tag: Sex

value: Female

tag: genotype


title: MPM tumor, surgically resected (P.011.T0.2)

tag: time (from_surgery_start_in_minutes)


title: E14.5_PGC_Male_Control_ATAC_2


title: NoMet_transstilbene_139939_4_3.73uM_TC00003588_C09

description:
Library name: TC00003588_C09
TC00003588_C09

tag: treatment

value: 24h exposure of 3.73 uM of trans-Stilbene

tag: media

value: VM7Luc4E2 Assay Medium

value: trans-Stilbene


title: TS92_128_replicate_2

tag: cell type

value: replicate 2


title: TS92_128_replicate_1

value: replicate 1


title: E14.5_PGC_Male_Control_ATAC_1

value: PGC

value: Control


title: MPM tumor, surgically resected (P.032.T0.1)


title: NoMet_DMSO_0_0uM_TC00003588_B12

description:
Library name: TC00003588_B12
TC00003588_B12

value: 0.5% DMSO vehicle control

tag: chemical name

value: DMSO

tag: chemical sample_id

tag: chemical concentration

value: 0 uM


title: Mouse colonic organoid, Bmal1, CUT&Tag

first: Ye-guang

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

data_processing:
Qualified libraries were sequenced with Illumina Novaseq 6000 platform.
CUT&Tag reads were aligned to the reference genome GRCm38 using the hisat2 software, and only uniquely and non-duplicate mapped reads were used to perform the downstream analysis.
The reads coverage and depth were calculated by samtools software.
The BAM files were subjected to peak calling analysis using MACS2 to identify regions in the genome exhibiting significant enrichment of reads.
The identified peaks were further subjected to gene annotation analysis and visualization using the Chipseeker package and IGV software.
Assembly: mm10
Supplementary files format and content: control_Bmal1_sorted_peaks.narrowPeak

source_name: colonic

extract_protocol:
For CUT&Tag-seq, the libraries were prepared using a CUT&Tag 4.0 High-Sensitivity Kit according to the manufacturer’s instructions.
Colonic organoids were fixed in 1% formaldehyde and lysed with lysis buffer, followed by digestion with micrococcal nuclease.
We used a BMAL1 antibody (CST; 14020S) and goat anti-rabbit IgG secondary antibody.

value: colonic

tag: cell line

value: colonic organoid

value: Mouse colonic organoid


title: MPM tumor, surgically resected, rep for validation (P.008.TNA.2)

value: Malignant pleural mesothelioma tumor


title: TS92_32_replicate_3

description:
Raw_count_table.csv
DESeq2_comparison_TS92_32_vs_TS92_0_table.csv
DESeq2_comparison_TS92_128_vs_TS92_32_table.csv

value: bacterial cell

value: wt

value: 32 µg/mL daptomycin

value: replicate 3


title: NoMet_DMSO_0_0uM_TC00003588_B11

description:
Library name: TC00003588_B11
TC00003588_B11

value: VM7Luc4E2 Assay Medium

tag: dose level

tag: exposure time

tag: assay plate

value: OK


title: MPM tumor, surgically resected (P.006.T0.1)

tag: tissue


title: Mouse colonic organoid, control, CUT&Tag

value: control


title: NoMet_daidzein_D7802_2_0.093uM_TC00003588_B10

description:
Library name: TC00003588_B10
TC00003588_B10

value: 24h exposure of 0.093 uM of Daidzein

value: Daidzein

tag: assay plate_well


title: TS92_32_replicate_1

tag: strain

tag: biological replicate

value: replicate 1


title: brian, snRNAseq, PID15_Ctrl

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The expression level of detected genes was estimated by DESeq2.A volcano plot was generated by ggplot2 in R, with a cutoff of p-value less than 0.01 and the absolute value of log2 (Foldchange) more than 4, measured by DESeq2.
Volcano plot, Scatter plotting and heatmaps were generated using R packages (ggplot2; pheatmap) implemented in R studio.
For gene set enrichment analysis (GSEA)76, we generated a KEGG_2019_Mouse geneset based on a database file from Enrichr online library(https://amp.pharm.mssm.edu/Enrichr/)77. Genes were pre-ranked through the metrics algorithm (log fold change × -log10(p-value[not adjusted p-val]) according to the statistical result of DESeq2. Pre-ranked (.rnk) file and custom geneset were used as input for GSEA v4.0.3(https://www.gsea-msigdb.org/gsea/index.jsp). The number of permutations was set at 1000 and enrichment statistics were set at “weighted”. For the general significance threshold, false discovery rate (FDR) q-val < 0.25 and |NES| > 1.5 were considered as significant enrichment.
Assembly: Hisat2 GRCm38
Supplementary files format and content: PD27_LJ_a1_filtered_feature_bc_matrix.tar.gz
Supplementary files format and content: PD27_LJ_c1_filtered_feature_bc_matrix.tar.gz
Supplementary files format and content: PID15_LJ_a2_filtered_feature_bc_matrix.tar.gz
Supplementary files format and content: PID15_LJ_c2_filtered_feature_bc_matrix.tar.gz

source_name: brian

value: brian

value: endothelial cells

tag: group

value: Ctrl

value: Braf-CAfl/fl

tag: agent

value: inject with AAV-miniBEND


title: MPM tumor, surgically resected (P.020.T0.2)

tag: time (from_surgery_start_in_minutes)


title: MPM tumor, surgically resected (P.031.T0.1)


title: brian, snRNAseq, PID15_bAVM

value: bAVM

tag: genotype


title: TS92_0_replicate_3

description:
Raw_count_table.csv
DESeq2_comparison_TS92_128_vs_TS92_0_table.csv
DESeq2_comparison_TS92_32_vs_TS92_0_table.csv

tag: treatment

value: untreated


title: NoMet_ethyl4hydroxybenzoate_111988_7_53.5uM_TC00003588_A12

description:
Library name: TC00003588_A12
TC00003588_A12

value: 24h exposure of 53.5 uM of Ethylparaben

tag: media

value: Ethylparaben

tag: sample qc_issue


title: NoMet_bestradiol_E2758_1_0.0001uM_TC00003588_B09

description:
Library name: TC00003588_B09
TC00003588_B09

value: 24h exposure of 1e-04 uM of 17beta-Estradiol

tag: chemical name

tag: chemical sample_id


title: MPM tumor, surgically resected (P.008.T0.2)

value: Malignant pleural mesothelioma tumor


title: MPM tumor, surgically resected (P.020.T0.1)


title: TS92_0_replicate_2

tag: cell type

value: bacterial cell

value: wt

value: replicate 2


title: MPM tumor, surgically resected (P.019.T0.1)


title: NoMet_transstilbene_139939_7_53.5uM_TC00003588_A11

description:
Library name: TC00003588_A11
TC00003588_A11

tag: cell line

value: 24h exposure of 53.5 uM of trans-Stilbene

value: VM7Luc4E2 Assay Medium

value: trans-Stilbene

tag: chemical concentration

tag: dose level

value: OK


title: MPM tumor, surgically resected (P.019.T0.2)

tag: tissue


title: brian, snRNAseq, PID27_Ctrl

value: brian

value: endothelial cells


title: TS92_0_replicate_1

value: replicate 1


title: brian, snRNAseq, PID27_bAVM

value: Braf-CAfl/fl

value: inject with AAV-miniBEND


title: NoMet_transstilbene_139939_5_11uM_TC00003588_A09

description:
Library name: TC00003588_A09
TC00003588_A09

value: 24h exposure of 11 uM of trans-Stilbene

value: 11 uM

tag: exposure time

tag: assay plate

tag: assay plate_well


title: MPM tumor, surgically resected (P.009.T0.1)


title: Rice_Nanopore_004_dRNAseq

city: Guangzhou

first: Yingyuan

last: Xie

state: GuangDong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
raw signals were basecalled using dorado (v0.7.2) with default parameters and converted into fastq format
Reads that passed the quality threshold (7) and had a length greater than 25bp were then aligned to the reference genome using Minimap2 (v2.22-r1101)
f5c (v1.4) eventalign module was used to align raw signals to 5mer bases with the parameter settings "--scale-events --samples --signal-index".
sam2tsv was used to extract bases quality and alignment results for each read from bam files
In-house python scripts were used to extract and organize current features and base quality features for each 39 motif within each read.
These features were then used as inputs for SingleMod for training or prediction.
Assembly: hg38 (HEK293T_Nanopore_004_dRNAseq), IRGSP-1.0 (Rice_Nanopore_004_dRNAseq)
Supplementary files format and content: tab-delimited text file, methylation rate of all As in 39 motifs predicted by SingleMod

organism: Oryza sativa

source_name: root

extract_protocol:
After extracting total RNA from the samples using TRIzol (Thermo Fisher Scientifific, 15596026), mRNA was isolated via a Dynabeads mRNA Purifification Kit (Thermo Fisher Scientifific, 61006) with genomic DNA removal using TuRBO DNase kit (Thermo Fisher, AM2238).
Nanopore direct RNA sequencing was conducted following instructions provided by Oxford Nanopore Technologies (Oxford, UK) using DRS kits (SQK-RNA004) and PromethION flowcells (FLO-PRO004).

value: root


title: mESC_GLORI_rep2

data_processing:
Raw reads were preprocessed using cutadapt (v4.1), seqkit (v0.8.1) rmdup module and fastp (v0.21.0) for adaptor trimming, deduplication and quality control as well as UMI trimming, respectively.
Then, the clean data were processed using the RNA-m5C pipeline developed by Huang T et al., 2022, with some modifications described.
All A sites with signal greater than 0.9 (representing the ratio of reads with no more than 3 non-converted A to all reads) and coverage greater than 15 after discarding non-converted reads were retained for methylation rate calculation
mm10
Assembly: mm10, TAIR10, Creinhardtii_281_v5.0
Supplementary files format and content: tab-delimited text file, quantification of m6A in all As with coverage >= 15.
Supplementary files format and content: tab-delimited text file, methylation rate of all As in DRACN motifs predicted by SingleMod

source_name: embryonic stem cells

extract_protocol:
After extracting total RNA from the samples using TRIzol (Thermo Fisher Scientifific, 15596026), mRNA was isolated via a Dynabeads mRNA Purifification Kit (Thermo Fisher Scientifific, 61006) with genomic DNA removal using TuRBO DNase kit (Thermo Fisher, AM2238).
GLORI experiments were conducted following instructions provided in Cong Liu et al., 202214, with an adjusted incubation temperature in deamination step of 25 ℃.

value: embryonic stem cells


title: NoMet_DMSO_0_0uM_TC00003588_A10

description:
Library name: TC00003588_A10
TC00003588_A10

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: Rice_Nanopore_dRNAseq

data_processing:
raw signals were basecalled using Guppy (v6.3.7) with default parameters and converted into fastq format
Reads that passed the quality threshold (7) and had a length greater than 25bp were then aligned to the reference genome using Minimap2 (v2.22-r1101)
Nanopolish (v0.13.2) eventalign module was used to align raw signals to 5mer bases with the parameter settings "--scale-events --samples --signal-index".
sam2tsv was used to extract bases quality and alignment results for each read from bam files
In-house python scripts were used to extract and organize current features and base quality features for each 39 motif within each read.
These features were then used as inputs for SingleMod for training or prediction.
Assembly: IRGSP-1.0
Supplementary files format and content: tab-delimited text file, methylation rate of all As in 39 motifs predicted by SingleMod

extract_protocol:
After extracting total RNA from the samples using TRIzol (Thermo Fisher Scientifific, 15596026), mRNA was isolated via a Dynabeads mRNA Purifification Kit (Thermo Fisher Scientifific, 61006) with genomic DNA removal using TuRBO DNase kit (Thermo Fisher, AM2238).
Nanopore direct RNA sequencing was conducted following instructions provided by Oxford Nanopore Technologies (Oxford, UK) using DRS kits (SQK-RNA002) and PromethION flowcells (FLO-PRO002, R9.4.1 pore).


title: TS92_32_replicate_2

tag: strain

value: bacterial cell

value: wt

value: 32 µg/mL daptomycin

tag: biological replicate

value: replicate 2


title: mESC_GLORI_rep1

data_processing:
Raw reads were preprocessed using cutadapt (v4.1), seqkit (v0.8.1) rmdup module and fastp (v0.21.0) for adaptor trimming, deduplication and quality control as well as UMI trimming, respectively.
Then, the clean data were processed using the RNA-m5C pipeline developed by Huang T et al., 2022, with some modifications described.
All A sites with signal greater than 0.9 (representing the ratio of reads with no more than 3 non-converted A to all reads) and coverage greater than 15 after discarding non-converted reads were retained for methylation rate calculation
Assembly: mm10, TAIR10, Creinhardtii_281_v5.0
Supplementary files format and content: tab-delimited text file, quantification of m6A in all As with coverage >= 15.
Supplementary files format and content: tab-delimited text file, methylation rate of all As in DRACN motifs predicted by SingleMod


title: Olympic champion 56

status: Public on Apr 28 2025

type: genomic

city: Budapest

first: Zsolt

last: Radák

address: Alkotás Street 44, building L3

country: Hungary

institute: Research Center for Molecular Exercise Science, Hungarian University of Sports Science

description:
MethylationEPIC (850 k)
OLYMP.2.EPIC.A

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing:
The raw methylation signal intensities were retrieved using the function read.metharray.exp of the minfi v1.40.0 R package, followed by linear dye bias correction and noob background correction to account for technical variation in background fluorescence signal. Specifically, the value was calculated from the intensity of the methylated and unmethylated sites, as the ratio of fluorescent signals.
*processed value definition: Average Beta

label: Cy3 and Cy5

source_name: Blood

label_protocol: standard protocol

extract_protocol: standard protocol

value: Blood

tag: project batch

tag: gender

value: male

tag: olympic champion

value: yes

tag: sport

value: kayak-canoe

tag: date of sampling

tag: age (days)


title: Olympic champion 58

description:
MethylationEPIC (850 k)
OLYMP.4.EPIC.A

value: wrestling


title: Olympic champion 55

description:
MethylationEPIC (850 k)
OLYMP.11.EPIC.A

value: gymnastics


title: Olympic champion 59

description:
MethylationEPIC (850 k)
OLYMP.7.EPIC.A

value: female


title: Olympic champion 57

description:
MethylationEPIC (850 k)
OLYMP.3.EPIC.A

value: fencing


title: Olympic champion 54

description:
MethylationEPIC (850 k)
OLYMP.1.EPIC.A


title: Olympic champion 52

description:
MethylationEPIC (850 k)
OLY.8.EPIC.A

value: swimming


title: Olympic champion 53

description:
MethylationEPIC (850 k)
OLY.9.EPIC.A


title: Olympic champion 49

description:
MethylationEPIC (850 k)
OLY.6.EPIC.A


title: Olympic champion 47

description:
MethylationEPIC (850 k)
OLY.58.EPIC.A

value: water polo


title: Olympic champion 43

description:
MethylationEPIC (850 k)
OLY.53.EPIC.A


title: Olympic champion 51

description:
MethylationEPIC (850 k)
OLY.61.EPIC.A


title: Olympic champion 45

description:
MethylationEPIC (850 k)
OLY.56.EPIC.A


title: Olympic champion 48

description:
MethylationEPIC (850 k)
OLY.59.EPIC.A


title: Olympic champion 50

description:
MethylationEPIC (850 k)
OLY.60.EPIC.A


title: Olympic champion 46

description:
MethylationEPIC (850 k)
OLY.57.EPIC.A


title: Olympic champion 41

description:
MethylationEPIC (850 k)
OLY.51.EPIC.A


title: Olympic champion 42

description:
MethylationEPIC (850 k)
OLY.52.EPIC.A


title: Olympic champion 38

description:
MethylationEPIC (850 k)
OLY.49.EPIC.A


title: Olympic champion 40

description:
MethylationEPIC (850 k)
OLY.50.EPIC.A


title: Olympic champion 39

description:
MethylationEPIC (850 k)
OLY.5.EPIC.A

value: fives


title: Olympic champion 36

description:
MethylationEPIC (850 k)
OLY.47.EPIC.A


title: Olympic champion 37

description:
MethylationEPIC (850 k)
OLY.48.EPIC.A


title: Olympic champion 33

description:
MethylationEPIC (850 k)
OLY.44.EPIC.A


title: Olympic champion 32

description:
MethylationEPIC (850 k)
OLY.43.EPIC.A


title: Olympic champion 31

description:
MethylationEPIC (850 k)
OLY.42.EPIC.A


title: Olympic champion 34

description:
MethylationEPIC (850 k)
OLY.45.EPIC.A


title: Olympic champion 35

description:
MethylationEPIC (850 k)
OLY.46.EPIC.A


title: Olympic champion 30

description:
MethylationEPIC (850 k)
OLY.41.EPIC.A


title: Olympic champion 29

description:
MethylationEPIC (850 k)
OLY.40.EPIC.A


title: Olympic champion 26

description:
MethylationEPIC (850 k)
OLY.37.EPIC.A


title: Olympic champion 25

description:
MethylationEPIC (850 k)
OLY.36.EPIC.A


title: Olympic champion 24

description:
MethylationEPIC (850 k)
OLY.35.EPIC.A


title: Olympic champion 23

description:
MethylationEPIC (850 k)
OLY.34.EPIC.A


title: Olympic champion 22

description:
MethylationEPIC (850 k)
OLY.33.EPIC.A


title: Olympic champion 44

description:
MethylationEPIC (850 k)
OLY.54.EPIC.A


title: Olympic champion 20

description:
MethylationEPIC (850 k)
OLY.31.EPIC.A


title: Olympic champion 14

description:
MethylationEPIC (850 k)
OLY.25.EPIC.A


title: Olympic champion 21

description:
MethylationEPIC (850 k)
OLY.32.EPIC.A


title: Olympic champion 17

description:
MethylationEPIC (850 k)
OLY.28.EPIC.A


title: Olympic champion 19

description:
MethylationEPIC (850 k)
OLY.30.EPIC.A


title: Olympic champion 18

description:
MethylationEPIC (850 k)
OLY.29.EPIC.A


title: Olympic champion 13

description:
MethylationEPIC (850 k)
OLY.24.EPIC.A


title: Olympic champion 12

description:
MethylationEPIC (850 k)
OLY.23.EPIC.A


title: Olympic champion 8

description:
MethylationEPIC (850 k)
OLY.18.EPIC.A

value: short track speed skating


title: Olympic champion 11

description:
MethylationEPIC (850 k)
OLY.21.EPIC.A


title: Olympic champion 9

description:
MethylationEPIC (850 k)
OLY.19.EPIC.A


title: Olympic champion 7

description:
MethylationEPIC (850 k)
OLY.17.EPIC.A


title: Olympic champion 6

description:
MethylationEPIC (850 k)
OLY.16.EPIC.A


title: Olympic champion 5

description:
MethylationEPIC (850 k)
OLY.15.EPIC.A


title: Olympic champion 10

description:
MethylationEPIC (850 k)
OLY.20.EPIC.A


title: Olympic champion 4

description:
MethylationEPIC (850 k)
OLY.14.EPIC.A


title: Olympic champion 3

description:
MethylationEPIC (850 k)
OLY.13.EPIC.A

value: football


title: Olympic champion 28

description:
MethylationEPIC (850 k)
OLY.39.EPIC.A


title: Olympic champion 1

description:
MethylationEPIC (850 k)
OLY.10.EPIC.A


title: Olympic champion 27

description:
MethylationEPIC (850 k)
OLY.38.EPIC.A


title: Control participant 295

description:
MethylationEPIC (850 k)
X258

value: no

value: controll

tag: vo2 max est.

value: low

tag: gripmax[kg]

tag: gripmax[kg/bm]

tag: jumpmax[cm]

tag: jumpmax[cm/bh]

tag: bmi

tag: cognition

tag: ldl

tag: hdl

tag: ch

tag: tg


title: Olympic champion 2

description:
MethylationEPIC (850 k)
OLY.12.EPIC.A

tag: tissue

tag: project batch


title: Control participant 294

description:
MethylationEPIC (850 k)
X254

tag: gender

tag: olympic champion


title: Control participant 293

description:
MethylationEPIC (850 k)
X251

tag: sport

tag: date of sampling


title: Control participant 292

description:
MethylationEPIC (850 k)
X231

tag: age (days)

tag: vo2 max est.

tag: irisin


title: Control participant 291

description:
MethylationEPIC (850 k)
X220

tag: gripmax[kg]

tag: gripmax[kg/bm]

tag: jumpmax[cm]


title: Olympic champion 16

description:
MethylationEPIC (850 k)
OLY.27.EPIC.A


title: Olympic champion 15

description:
MethylationEPIC (850 k)
OLY.26.EPIC.A


title: Control participant 290

description:
MethylationEPIC (850 k)
X210

tag: jumpmax[cm/bh]

tag: cognition


title: Control participant 288

description:
MethylationEPIC (850 k)
X97

tag: bmi

tag: ldl

tag: hdl


title: Control participant 289

description:
MethylationEPIC (850 k)
X203

tag: tissue


title: Control participant 287

description:
MethylationEPIC (850 k)
X61

tag: project batch

tag: ch

tag: tg


title: Control participant 284

description:
MethylationEPIC (850 k)
X48

tag: gender

tag: olympic champion

tag: sport


title: Control participant 285

description:
MethylationEPIC (850 k)
X53

tag: date of sampling

tag: age (days)

tag: vo2 max est.


title: Control participant 283

description:
MethylationEPIC (850 k)
X47

tag: gripmax[kg]

tag: gripmax[kg/bm]


title: Control participant 282

description:
MethylationEPIC (850 k)
X46

tag: jumpmax[cm]

tag: jumpmax[cm/bh]


title: Control participant 286

description:
MethylationEPIC (850 k)
X54

tag: bmi

tag: cognition


title: Control participant 281

description:
MethylationEPIC (850 k)
X42

tag: ldl

tag: hdl


title: Control participant 280

description:
MethylationEPIC (850 k)
X41

tag: tissue

tag: project batch


title: Control participant 279

description:
MethylationEPIC (850 k)
X37

tag: ch

tag: tg


title: Control participant 278

description:
MethylationEPIC (850 k)
X35

tag: gender

tag: olympic champion


title: Control participant 274

description:
MethylationEPIC (850 k)
X22

tag: sport

tag: date of sampling


title: Control participant 277

description:
MethylationEPIC (850 k)
X34

tag: age (days)

tag: vo2 max est.


title: Control participant 270

description:
MethylationEPIC (850 k)
X12

tag: gripmax[kg]

tag: gripmax[kg/bm]


title: Control participant 276

description:
MethylationEPIC (850 k)
X31

tag: jumpmax[cm]

tag: jumpmax[cm/bh]


title: Control participant 268

description:
MethylationEPIC (850 k)
X10

tag: bmi

tag: cognition


title: Control participant 296

description:
MethylationEPIC (850 k)
X284

tag: ldl

tag: hdl


title: Control participant 267

description:
MethylationEPIC (850 k)
X9

tag: tissue

tag: project batch


title: Control participant 269

description:
MethylationEPIC (850 k)
X11

tag: ch

tag: tg


title: Control participant 265

description:
MethylationEPIC (850 k)
X7

tag: gender

tag: olympic champion


title: Control participant 272

description:
MethylationEPIC (850 k)
X18

tag: sport

tag: date of sampling


title: Control participant 264

description:
MethylationEPIC (850 k)
X4

tag: age (days)

tag: vo2 max est.


title: Control participant 266

description:
MethylationEPIC (850 k)
X8

tag: gripmax[kg]

tag: gripmax[kg/bm]


title: Control participant 263

description:
MethylationEPIC (850 k)
X204088030153_R03C01

tag: jumpmax[cm]

tag: jumpmax[cm/bh]

tag: irisin


title: Control participant 262

description:
MethylationEPIC (850 k)
X204086170008_R06C01

tag: bmi

tag: cognition

tag: ldl


title: Control participant 259

description:
MethylationEPIC (850 k)
X204088030020_R06C01

tag: tissue

tag: project batch

tag: hdl


title: Control participant 261

description:
MethylationEPIC (850 k)
X204088010124_R01C01

tag: gender

tag: ch

tag: tg


title: Control participant 258

description:
MethylationEPIC (850 k)
X204071680079_R02C01

tag: olympic champion

tag: sport

tag: date of sampling


title: Control participant 260

description:
MethylationEPIC (850 k)
X204088030022_R02C01

tag: age (days)

tag: vo2 max est.

tag: gripmax[kg]


title: Control participant 257

description:
MethylationEPIC (850 k)
X204088030148_R04C01

tag: gripmax[kg/bm]

tag: jumpmax[cm]

tag: jumpmax[cm/bh]


title: Control participant 253

description:
MethylationEPIC (850 k)
X204088020057_R08C01

tag: bmi

tag: cognition

tag: irisin


title: Control participant 275

description:
MethylationEPIC (850 k)
X30

tag: tissue

tag: project batch

tag: ldl


title: Control participant 273

description:
MethylationEPIC (850 k)
X21

tag: gender

tag: hdl

tag: ch


title: Control participant 252

description:
MethylationEPIC (850 k)
X204088030080_R06C01

tag: olympic champion

tag: sport

tag: tg


title: Control participant 250

description:
MethylationEPIC (850 k)
X204088030009_R05C01

tag: date of sampling

tag: age (days)

tag: vo2 max est.


title: Control participant 249

description:
MethylationEPIC (850 k)
X204088030009_R01C01

tag: gripmax[kg]

tag: gripmax[kg/bm]

tag: jumpmax[cm]


title: Control participant 248

description:
MethylationEPIC (850 k)
X204088030143_R03C01

tag: jumpmax[cm/bh]

tag: bmi

tag: cognition


title: Control participant 251

description:
MethylationEPIC (850 k)
X204088030022_R05C01

tag: tissue

tag: project batch

tag: irisin


title: Control participant 271

description:
MethylationEPIC (850 k)
X15

tag: gender

tag: ldl

tag: hdl


title: Control participant 246

description:
MethylationEPIC (850 k)
X204088030153_R01C01

tag: olympic champion

tag: sport

tag: ch


title: Control participant 247

description:
MethylationEPIC (850 k)
X204088030095_R03C01

tag: date of sampling

tag: age (days)

tag: tg


title: Control participant 245

description:
MethylationEPIC (850 k)
X204088010150_R08C01

tag: vo2 max est.

tag: gripmax[kg]

tag: gripmax[kg/bm]


title: Control participant 244

description:
MethylationEPIC (850 k)
X204088010153_R06C01

tag: jumpmax[cm]

tag: jumpmax[cm/bh]

tag: bmi


title: Control participant 243

description:
MethylationEPIC (850 k)
X204088030022_R01C01

tag: tissue

tag: project batch

tag: cognition


title: Control participant 241

description:
MethylationEPIC (850 k)
X204073580111_R03C01

tag: gender

tag: ldl


title: Control participant 242

description:
MethylationEPIC (850 k)
X204088030095_R04C01

tag: olympic champion

tag: hdl


title: Control participant 240

description:
MethylationEPIC (850 k)
X204086170008_R05C01

tag: sport

tag: ch


title: Control participant 239

description:
MethylationEPIC (850 k)
X204088030124_R08C01

tag: date of sampling

tag: age (days)

tag: irisin


title: Control participant 237

description:
MethylationEPIC (850 k)
X204086170046_R06C01

tag: vo2 max est.

tag: gripmax[kg]

tag: tg


title: Control participant 238

description:
MethylationEPIC (850 k)
X204088030065_R02C01

tag: gripmax[kg/bm]

tag: jumpmax[cm]

tag: jumpmax[cm/bh]


title: Control participant 236

description:
MethylationEPIC (850 k)
X204088030152_R05C01

tag: tissue

tag: project batch

tag: bmi


title: Control participant 256

description:
MethylationEPIC (850 k)
X204088030080_R04C01

tag: gender

tag: cognition

tag: ldl


title: Control participant 235

description:
MethylationEPIC (850 k)
X204088010153_R08C01

tag: olympic champion

tag: sport

tag: hdl


title: Control participant 255

description:
MethylationEPIC (850 k)
X204074220153_R07C01

tag: date of sampling

tag: age (days)

tag: ch


title: Control participant 234

description:
MethylationEPIC (850 k)
X204088030022_R07C01

tag: vo2 max est.

tag: gripmax[kg]

tag: irisin


title: Control participant 254

description:
MethylationEPIC (850 k)
X204086170008_R01C01

tag: gripmax[kg/bm]

tag: jumpmax[cm]

tag: tg


title: Control participant 233

description:
MethylationEPIC (850 k)
X204074220153_R05C01

tag: tissue

tag: project batch

tag: jumpmax[cm/bh]


title: Control participant 232

description:
MethylationEPIC (850 k)
X204088020020_R06C01

tag: gender

tag: bmi

tag: cognition


title: Control participant 230

description:
MethylationEPIC (850 k)
X204088030138_R07C01

tag: olympic champion

tag: sport

tag: ldl


title: Control participant 228

description:
MethylationEPIC (850 k)
X204088030148_R02C01

tag: date of sampling

tag: age (days)

tag: hdl


title: Control participant 227

description:
MethylationEPIC (850 k)
X204088010124_R06C01

tag: vo2 max est.

tag: gripmax[kg]

tag: ch


title: Control participant 231

description:
MethylationEPIC (850 k)
X204086170046_R08C01

tag: gripmax[kg/bm]

tag: jumpmax[cm]


title: Control participant 229

description:
MethylationEPIC (850 k)
X204088030086_R05C01

tag: tissue

tag: irisin

tag: tg


title: Control participant 226

description:
MethylationEPIC (850 k)
X204088020057_R05C01

tag: project batch

tag: gender

tag: jumpmax[cm/bh]


title: Control participant 224

description:
MethylationEPIC (850 k)
X204086170008_R08C01

tag: olympic champion

tag: bmi

tag: cognition


title: Control participant 223

description:
MethylationEPIC (850 k)
X204088030100_R08C01

tag: sport

tag: date of sampling

tag: ldl


title: Control participant 221

description:
MethylationEPIC (850 k)
X204071680079_R06C01

tag: age (days)

tag: vo2 max est.

tag: hdl


title: Control participant 218

description:
MethylationEPIC (850 k)
X204088030094_R01C01

tag: gripmax[kg]

tag: gripmax[kg/bm]

tag: ch


title: Control participant 220

description:
MethylationEPIC (850 k)
X204086170008_R02C01

tag: tissue

tag: jumpmax[cm]

tag: irisin


title: Control participant 217

description:
MethylationEPIC (850 k)
X204088030052_R02C01

tag: project batch

tag: gender

tag: tg


title: Control participant 216

description:
MethylationEPIC (850 k)
X204088030080_R07C01

tag: olympic champion

tag: jumpmax[cm/bh]

tag: bmi


title: Control participant 215

description:
MethylationEPIC (850 k)
X204088030100_R06C01

tag: sport

tag: date of sampling

tag: cognition


title: Control participant 212

description:
MethylationEPIC (850 k)
X204088030143_R06C01

tag: age (days)

tag: vo2 max est.

tag: ldl


title: Control participant 211

description:
MethylationEPIC (850 k)
X204088020020_R05C01

tag: gripmax[kg]

tag: gripmax[kg/bm]

tag: hdl


title: Control participant 210

description:
MethylationEPIC (850 k)
X204071680141_R08C01

tag: tissue

tag: jumpmax[cm]

tag: ch


title: Control participant 209

description:
MethylationEPIC (850 k)
X204088030009_R02C01

tag: project batch

tag: gender

tag: irisin


title: Control participant 208

description:
MethylationEPIC (850 k)
X204088020016_R03C01

tag: olympic champion

tag: jumpmax[cm/bh]

tag: tg


title: Control participant 207

description:
MethylationEPIC (850 k)
X204088010150_R02C01

tag: sport

tag: date of sampling

tag: bmi


title: Control participant 205

description:
MethylationEPIC (850 k)
X204088010050_R02C01

tag: age (days)

tag: vo2 max est.

tag: cognition


title: Control participant 206

description:
MethylationEPIC (850 k)
X204071680091_R03C01

tag: gripmax[kg]

tag: gripmax[kg/bm]

tag: ldl


title: Control participant 204

description:
MethylationEPIC (850 k)
X204088010050_R04C01

tag: tissue

tag: hdl


title: Control participant 202

description:
MethylationEPIC (850 k)
X204088030143_R02C01

tag: project batch

tag: jumpmax[cm]

tag: ch


title: Control participant 225

description:
MethylationEPIC (850 k)
X204074220153_R02C01

tag: gender

tag: olympic champion

tag: irisin


title: Control participant 203

description:
MethylationEPIC (850 k)
X204086170062_R08C01

tag: sport

tag: jumpmax[cm/bh]

tag: tg


title: Control participant 199

description:
MethylationEPIC (850 k)
X204088020016_R08C01

tag: date of sampling

tag: age (days)

tag: bmi


title: Control participant 198

description:
MethylationEPIC (850 k)
X204088010050_R05C01

tag: vo2 max est.

tag: gripmax[kg]

tag: cognition


title: Control participant 197

description:
MethylationEPIC (850 k)
X204088030124_R01C01

tag: tissue

tag: gripmax[kg/bm]

tag: ldl


title: Control participant 195

description:
MethylationEPIC (850 k)
X204088030080_R05C01

tag: project batch

tag: jumpmax[cm]

tag: hdl


title: Control participant 194

description:
MethylationEPIC (850 k)
X204088010153_R07C01

tag: gender

tag: olympic champion

tag: ch


title: Control participant 200

description:
MethylationEPIC (850 k)
X204071680079_R05C01

tag: sport

tag: jumpmax[cm/bh]


title: Control participant 222

description:
MethylationEPIC (850 k)
X204088030143_R04C01

tag: date of sampling

tag: tg


title: Control participant 219

description:
MethylationEPIC (850 k)
X204088030100_R04C01

tag: age (days)

tag: bmi


title: Control participant 193

description:
MethylationEPIC (850 k)
X204088030138_R04C01

tag: vo2 max est.

tag: gripmax[kg]

tag: irisin


title: Control participant 191

description:
MethylationEPIC (850 k)
X204073580111_R06C01

tag: tissue

tag: gripmax[kg/bm]

tag: cognition


title: Control participant 192

description:
MethylationEPIC (850 k)
X204088010153_R03C01

tag: project batch

tag: jumpmax[cm]

tag: ldl


title: Control participant 214

description:
MethylationEPIC (850 k)
X204088030153_R08C01

tag: gender

tag: olympic champion

tag: hdl


title: Control participant 189

description:
MethylationEPIC (850 k)
X204088010050_R08C01

tag: sport

tag: jumpmax[cm/bh]

tag: ch


title: Control participant 213

description:
MethylationEPIC (850 k)
X204088020020_R02C01

tag: date of sampling

tag: age (days)

tag: tg


title: Control participant 188

description:
MethylationEPIC (850 k)
X204074220153_R04C01

tag: vo2 max est.

tag: gripmax[kg]

tag: bmi


title: Control participant 187

description:
MethylationEPIC (850 k)
X204088030143_R01C01

tag: tissue

tag: gripmax[kg/bm]

tag: irisin


title: Control participant 186

description:
MethylationEPIC (850 k)
X204088030153_R06C01

tag: project batch

tag: jumpmax[cm]

tag: cognition


title: Control participant 185

description:
MethylationEPIC (850 k)
X204071680141_R03C01

tag: gender

tag: olympic champion

tag: ldl


title: Control participant 184

description:
MethylationEPIC (850 k)
X204088030095_R08C01

tag: sport

tag: jumpmax[cm/bh]

tag: hdl


title: Control participant 183

description:
MethylationEPIC (850 k)
X204088030052_R06C01

tag: date of sampling

tag: age (days)

tag: ch


title: Control participant 182

description:
MethylationEPIC (850 k)
X204088010153_R02C01

tag: vo2 max est.

tag: gripmax[kg]

tag: tg


title: Control participant 201

description:
MethylationEPIC (850 k)
X204088030094_R04C01

tag: tissue

tag: gripmax[kg/bm]

tag: bmi


title: Control participant 180

description:
MethylationEPIC (850 k)
X204088030152_R04C01

tag: project batch

tag: jumpmax[cm]

tag: irisin


title: Control participant 179

description:
MethylationEPIC (850 k)
X204088010153_R05C01

tag: gender

tag: olympic champion

tag: cognition


title: Control participant 178

description:
MethylationEPIC (850 k)
X204088010150_R07C01

tag: sport

tag: jumpmax[cm/bh]

tag: ldl


title: Control participant 196

description:
MethylationEPIC (850 k)
X204088030148_R05C01

tag: date of sampling

tag: age (days)

tag: hdl


title: Control participant 177

description:
MethylationEPIC (850 k)
X204088020057_R02C01

tag: vo2 max est.

tag: gripmax[kg]

tag: ch


title: Control participant 176

description:
MethylationEPIC (850 k)
X204073570112_R08C01

tag: tissue

tag: gripmax[kg/bm]

tag: tg


title: Control participant 173

description:
MethylationEPIC (850 k)
X204088030094_R08C01

tag: project batch

tag: jumpmax[cm]

tag: bmi


title: Control participant 172

description:
MethylationEPIC (850 k)
X204088030153_R02C01

tag: gender

tag: olympic champion


title: Control participant 175

description:
MethylationEPIC (850 k)
X204088030065_R05C01

tag: sport

tag: cognition

tag: irisin


title: Control participant 168

description:
MethylationEPIC (850 k)
X204088020016_R01C01

tag: date of sampling

tag: jumpmax[cm/bh]

tag: ldl


title: Control participant 190

description:
MethylationEPIC (850 k)
X204088020016_R05C01

tag: age (days)

tag: vo2 max est.

tag: hdl


title: Control participant 171

description:
MethylationEPIC (850 k)
X204088020033_R07C01

tag: tissue

tag: gripmax[kg]

tag: ch


title: Control participant 164

description:
MethylationEPIC (850 k)
X204088030095_R02C01

tag: project batch

tag: gripmax[kg/bm]

tag: tg


title: Control participant 174

description:
MethylationEPIC (850 k)
X204088030152_R07C01

tag: gender

tag: jumpmax[cm]

tag: bmi


title: Control participant 162

description:
MethylationEPIC (850 k)
X204088020057_R06C01

tag: olympic champion

tag: sport

tag: cognition


title: Control participant 166

description:
MethylationEPIC (850 k)
X204088010153_R04C01

tag: date of sampling

tag: jumpmax[cm/bh]

tag: irisin


title: Control participant 163

description:
MethylationEPIC (850 k)
X204088010050_R01C01

tag: age (days)

tag: vo2 max est.

tag: ldl


title: Control participant 167

description:
MethylationEPIC (850 k)
X204088010150_R01C01

tag: tissue

tag: gripmax[kg]

tag: hdl


title: Control participant 165

description:
MethylationEPIC (850 k)
X204088030009_R07C01

tag: project batch

tag: gripmax[kg/bm]

tag: ch


title: Control participant 161

description:
MethylationEPIC (850 k)
X204086170032_R05C01

tag: gender

tag: jumpmax[cm]


title: Control participant 160

description:
MethylationEPIC (850 k)
X204073580111_R05C01

tag: olympic champion

tag: bmi


title: Control participant 169

description:
MethylationEPIC (850 k)
X204071680141_R01C01

tag: sport

tag: cognition

tag: tg


title: Control participant 159

description:
MethylationEPIC (850 k)
X204088030095_R07C01

tag: date of sampling

tag: jumpmax[cm/bh]


title: Control participant 158

description:
MethylationEPIC (850 k)
X204088030148_R06C01

tag: age (days)

tag: vo2 max est.


title: Control participant 156

description:
MethylationEPIC (850 k)
X204073570112_R03C01

tag: tissue

tag: ldl


title: Control participant 181

description:
MethylationEPIC (850 k)
X204088030052_R04C01

tag: gripmax[kg]

tag: hdl


title: Control participant 157

description:
MethylationEPIC (850 k)
X204088030065_R01C01

tag: project batch

tag: gripmax[kg/bm]


title: Control participant 155

description:
MethylationEPIC (850 k)
X204071680141_R02C01

tag: gender

tag: ch


title: Control participant 154

description:
MethylationEPIC (850 k)
X204088030148_R08C01

tag: olympic champion

tag: jumpmax[cm]


title: Control participant 153

description:
MethylationEPIC (850 k)
X204088030152_R03C01

tag: sport

tag: bmi

tag: irisin


title: Control participant 152

description:
MethylationEPIC (850 k)
X204074220153_R01C01

tag: date of sampling

tag: cognition

tag: tg


title: Control participant 170

description:
MethylationEPIC (850 k)
X204086170046_R04C01

tag: age (days)

tag: vo2 max est.

tag: jumpmax[cm/bh]


title: Control participant 150

description:
MethylationEPIC (850 k)
X204086170046_R02C01

tag: tissue

tag: gripmax[kg]

tag: ldl


title: Control participant 149

description:
MethylationEPIC (850 k)
X204088030052_R08C01

tag: project batch

tag: gripmax[kg/bm]

tag: hdl


title: Control participant 148

description:
MethylationEPIC (850 k)
X204071680079_R04C01

tag: gender

tag: olympic champion

tag: ch


title: Control participant 147

description:
MethylationEPIC (850 k)
X204088030143_R05C01

tag: sport

tag: jumpmax[cm]

tag: bmi


title: Control participant 143

description:
MethylationEPIC (850 k)
X204088020020_R01C01

tag: date of sampling

tag: cognition


title: Control participant 145

description:
MethylationEPIC (850 k)
X204071680079_R07C01

tag: age (days)

tag: tg


title: Control participant 142

description:
MethylationEPIC (850 k)
X204088020057_R01C01

tag: vo2 max est.

tag: jumpmax[cm/bh]


title: Control participant 144

description:
MethylationEPIC (850 k)
X204088030020_R01C01

tag: tissue

tag: gripmax[kg]

tag: irisin


title: Control participant 141

description:
MethylationEPIC (850 k)
X204088030124_R02C01

tag: project batch

tag: gripmax[kg/bm]

tag: ldl


title: Control participant 139

description:
MethylationEPIC (850 k)
X204088030065_R08C01

tag: gender

tag: olympic champion

tag: hdl


title: Control participant 140

description:
MethylationEPIC (850 k)
X204088020057_R04C01

tag: sport

tag: jumpmax[cm]

tag: ch


title: Control participant 138

description:
MethylationEPIC (850 k)
X204088020016_R06C01

tag: date of sampling

tag: bmi

tag: cognition


title: Control participant 135

description:
MethylationEPIC (850 k)
X204088030020_R05C01

tag: age (days)

tag: vo2 max est.

tag: tg


title: Control participant 137

description:
MethylationEPIC (850 k)
X204086170046_R07C01

tag: tissue

tag: gripmax[kg]

tag: jumpmax[cm/bh]


title: Control participant 134

description:
MethylationEPIC (850 k)
X204086170062_R04C01

tag: project batch

tag: gripmax[kg/bm]


title: Control participant 136

description:
MethylationEPIC (850 k)
X204086170008_R03C01

tag: gender

tag: irisin

tag: ldl


title: Control participant 132

description:
MethylationEPIC (850 k)
X204073570112_R05C01

tag: olympic champion

tag: sport

tag: hdl


title: Control participant 133

description:
MethylationEPIC (850 k)
X204088020057_R07C01

tag: date of sampling

tag: jumpmax[cm]

tag: ch


title: Control participant 130

description:
MethylationEPIC (850 k)
X204088030086_R02C01

tag: age (days)

tag: bmi

tag: cognition


title: Control participant 129

description:
MethylationEPIC (850 k)
X204073570112_R06C01

tag: tissue

tag: vo2 max est.

tag: tg


title: Control participant 126

description:
MethylationEPIC (850 k)
X204088010050_R07C01

tag: project batch

tag: gripmax[kg]

tag: jumpmax[cm/bh]


title: Control participant 128

description:
MethylationEPIC (850 k)
X204088010150_R03C01

tag: gender

tag: gripmax[kg/bm]


title: Control participant 123

description:
MethylationEPIC (850 k)
X204074220153_R08C01

tag: olympic champion

tag: ldl


title: Control participant 124

description:
MethylationEPIC (850 k)
X204088010124_R08C01

tag: sport

tag: hdl


title: Control participant 127

description:
MethylationEPIC (850 k)
X204086170046_R03C01

tag: date of sampling

tag: jumpmax[cm]

tag: irisin