title: 5-WT Cdfast

first: Artemii

institute: Inserm

description: eWAT from WT fasted CD-fed mice

source_name: FOXP3-CRE adult male mice


title: 1-WT Cdfast

status: Public on Dec 31 2025

type: RNA

city: Lille

last: Nikitin

address: 1,  Rue du Professeur Calmette

country: France

description: eWAT from WT fasted CD-fed mice

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on MoGene-2_0-st Chip. GeneChips were washed and stained in the Affymetrix Fluidics.

scan_protocol: Affymetrix GeneChip Scanner 7G and Affymetrix GeneChip Command Console software (AGCC).

data_processing: RMA and Quantile Normalization with median polish using Partek. The data obtained are log2-transformed.

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: RNA were processed using Affymetrix GeneChip® WT PLUS Reagent Kit.

growth_protocol: Mice were housed in a temperature-controlled room (22–24°C) with a 12h dark-light cycle. Animal studies were performed in compliance with European Community specifications regarding the use of laboratory animals and approved by the Nord-Pas de Calais Ethical Committee for animal use.

extract_protocol: total RNA extracted with the trizol protocol, clean up with the Nucleospin RNA XS column Macherey Nagel according to the manufacture's instuctions

treatment_protocol: Mice were fed chow diet or HFD

tag: genotype

value: WT

tag: treatment

value: Cdfast


title: 9184 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

type: genomic

city: Maywood

first: Alexandra

middle: L

last: Nowak

state: IL

country: USA

institute: Loyola University Chicago

hyb_protocol: Bisufate converted DNA was amplifiled, fragented, and hybridized to human Infinium EPIC Methylation BeadChip per Illumina protocol

scan_protocol: EPIC Methylation BeadChip scanning performed using the Illumina iScan System.

data_processing: “mediation” R package, v.4.5,1

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: Extraction was performed from DNA Paxgene tubes using a chemical precipitatin method.

tag: race/sex

value: Black/Female

tag: disease state (preterm = <37 wks gest)

value: Preterm

tag: tissue

value: Peripheral blood leukocytes

tag: data collectin


title: Hel2_2_mRNA

type: SRA

city: Bern

first: Jie

last: Wu

state: Bern

address: Freiestrasse 3

country: Switzerland

institute: Department of Chemistry, Biochemistry and Pharmaceutical Sciences

library_source: transcriptomic

data_processing:
Reads from RNA-seq data were mapped to CDS without adapter trimming using bowtie with the parameters "-n 1 -l 28 -m 1 --no-unal --best --strata". Gene expression for each CDS were quantified with a custom script.
Assembly: sacCer3
Supplementary files format and content: mRNA raw count matrix

organism: Saccharomyces cerevisiae

source_name: MATa his3Δ1 leu2Δ0 ura3Δ0 hel2Δ::LEU2

growth_protocol: Cells were grown in YPD at 30C and 200 RPM

extract_protocol:
Total RNA was extracted with acidic phenol and enriched for mRNAs using the Poly(A) tail
Libraries were prepared using TruSeq stranded mRNA kit

tag: cell line

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 hel2{delta}::LEU2


title: Nurse, rep 2_2, scRNAseq

city: Beijing

first: Xiasang

last: Chen

address: 2 Yuanmingyuan West Road. Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

country: China

institute: State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger mkfastq pipeline within the Cell Ranger software v6.1.1.
Assembly: Amel_HAv3.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Apis mellifera

source_name: honeybee brain

extract_protocol:
Fresh brain tissues were first dissected from the heads of pupae, nurses, and foragers, respectively, and then stored in MACS Tissue Storage Solution on ice to maintain tissue viability. The cell suspension was obtained through enzymatic digestion of the dissected honeybee brain tissue from each biological replicate using a mixture of activated papain solution (50 mg/mL), Liberase TM solution (2.5 mg/L), and DNase I solution (10 mg/mL). The brain tissue underwent two rounds of enzymatic digestion. Prior to digestion, the brain tissue was washed three times with PBS buffer containing 0.4% BSA, each wash lasting 10 minutes.
Library was performed according to the manufacter's instructions(Chromium Single Cell 3’ Reagent Kits v3.1 protocol, 10x Genomics).

value: honeybee brain

value: neural cell

tag: cell type

tag: developmental stage

value: Adult


title: Nurse, rep 3, scRNAseq

description: 10x Genomics


title: 9178 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Term


title: Hel2_1_mRNA


title: H16/510 Diabetic

city: Vizela

first: Marta

middle: Patrícia

last: Ferreira

state: Braga

address: Rua da junuqeira, Santo Adrião

country: Portugal

description: Library name: H16/510

data_processing:
The RNA from each sample was sequenced using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit, panel sequencing for the analysis of RNA expression of ~20.000 genes. Generated files were analyzed using the Transcriptome Analysis Console (TAC) Software to assess the quality metrics of each sequenced sample.
Assembly: GRCh37
Supplementary files format and content: .chp - files to use in Transcriptome Analysis Console (TAC)
Supplementary files format and content: .txt - matrix with rpm

source_name: thyroid tumor

extract_protocol:
The MagMax FFPE DNA/RNA Ultra Kit (Applied Biosystems, Life Technologies, Waltham, MA, USA) was employed for the extraction of RNA from frozen tissue sections, following the manufacturer's protocol.
panel sequencing for the analysis of RNA expression of ~20.000 genes

value: thyroid tumor

tag: age

tag: gender

value: Female

tag: size mm

tag: biological behaviour

value: M

tag: biological behaviour1

tag: biological behaviour2

value: non-B

tag: histologic

value: HCC

tag: growth pattern

value: TRABECULE

tag: peri-tm area

value: MNG

tag: ete mi

value: NO

tag: angioinvasion

value: YES

tag: lymphatic invasion

tag: capsulation

tag: capsul invasion

tag: necrosis

tag: hta

tag: dislipidemia

tag: obesity

tag: treatment type

value: Estatina

tag: cv disease

value: HIGH

tag: atrx

tag: daxx

value: LOW

tag: htc

value: HCT

tag: htc 1

tag: neoplaisa history


title: H15/10986 Non_diabetic

description: Library name: H15/10986

tag: tissue

tag: age

tag: gender

value: Male

tag: size mm

tag: biological behaviour

value: BORDERLINE

tag: biological behaviour1

value: non-M

tag: biological behaviour2

tag: histologic

value: WT-UMP

tag: growth pattern

value: FOLLICULE

tag: peri-tm area

value: N

value: UNEQUIVOCAL

value: Borderline

value: non-HCT


title: Nurse, rep 1_2, scRNAseq

description: 10x Genomics

value: honeybee brain

tag: cell line

value: neural cell

tag: cell type

tag: developmental stage

value: Adult


title: Mouse heart, F_DM 5

city: Galveston

first: Qingjie

last: Li

state: Texas

address: 301 University Boulevard

department: Internal Medicine

institute: UTMB

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the homo sapiens reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by Deseq2 software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: Heart

growth_protocol: Nineteen two-month-old male and female C57BL/6NTac germ-free mice were housed in the UTMB Germ-Free Mouse Facility with a 12-hour light/dark cycle, temperature range of 24-26°C, and a relative humidity of 40-70%.

extract_protocol:
Mice were euthanized under anesthesia and a piece of cardiac tissue was snap-frozen in liquid nitrogen. Total RNAs were isolated from pulverized frozen heart tissue using the PureLink RNA Mini Kit (Thermo Fisher). RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

treatment_protocol: There were four groups of 4 or 5 mice receiving the following treatments: (1) males with normal microbiome (M_NM), (2) males with dysbiotic microbiome (M_DM), (3) females with normal microbiome (F_NM), and (4) females with dysbiotic microbiome (F_DM).

value: Heart

value: Cardiocytes

tag: genotype

value: WT

tag: treatment

value: DM FMT


title: Forager, rep 1, scRNAseq

description: 10x Genomics


title: 9134 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

value: Black/Female

tag: disease state (preterm = <37 wks gest)

value: Term

value: Peripheral blood leukocytes

tag: data collectin


title: H12/28396 Non_diabetic

description: Library name: H12/28396

tag: tissue

value: thyroid tumor

tag: age

value: Female

value: BORDERLINE

value: non-M

value: non-B

value: NIFTP

tag: ete mi

value: NO

tag: angioinvasion

tag: lymphatic invasion

tag: capsulation

value: YES

tag: capsul invasion

tag: necrosis

tag: hta

tag: dislipidemia

tag: obesity

tag: treatment type

tag: cv disease

value: LOW

tag: atrx

tag: daxx

value: HIGH

tag: htc

tag: htc 1

tag: neoplaisa history


title: wt_2_mRNA

source_name: MATa his3Δ1 leu2Δ0 ura3Δ0 met15Δ0

tag: cell line

tag: genotype

value: MATa his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0


title: wt_1_mRNA


title: 9127 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

tag: disease state (preterm = <37 wks gest)

tag: tissue

tag: data collectin


title: ATR+c, G1 phase, quiescent

city: New York

first: Shan

last: Zha

state: NY

address: 1130 Saint Nicholas Ave.

institute: Columbia University

description:
Library name: Bcell-ATRplusC-G1
End-Seq

library_source: genomic

data_processing:
END-seq were aligned to a customized genome containing one copy of rDNA (GenBank accession: BK000964.3) and the mm10 reference genome using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1.
Functions ‘view’ and ‘sort’ of samtools (v.1.11)were used to convert and sort the aligned SAM files to sorted BAM files.
BedGraph files were generated using bedtools genomecov with parameters -5 -bg.
Assembly: A customized genome containing one copy of rDNA (GenBank accession: BK000964.3) and the mm10 reference genome
Supplementary files format and content: BedGraph files as tab-delimited .txt files, separated into plus strand (POS files) and minus strand (NEG files) information. They include a header line with track information in accordance with the UCSC file format guidelines for bedGraph files.

source_name: spleen

growth_protocol: B cells were isolated from the spleens of young adult mice (4-8 weeks). Single-cell suspensions of spleen cells were purified with anti-mouse CD43 magnetic beads (MACS, Miltenyi, 130-042-401). CD43– B cells were cultured at a density of 0.5 × 10^6 in RPMI 1640 medium (Gibco, Cat. 11875093) supplemented with 15% fetal bovine serum (FBS, BenchMark, Cat. 100-106), Minimum Essential Medium (MEM) nonessential amino acids, (Gibco, Cat. 11140050, 100X), 2 mM L-Glutamine (Gibco, Cat, 25030081), 1 mM sodium pyruvate (Gibco, Cat. 11360070), and 50 U/mL penicillin/streptomycin (Gibco, Cat. 15140122), plus 120 μM 2-Mercaptoethanol (Thermo Scientific, 125470100).

extract_protocol:
CD43–splenic B cells were washed with PBS, resuspended in neutralization buffer, embedded in 1% agarose plugs, lysed, and digested with Proteinase K (1 hour at 50°C, followed by 7 hours at 37°C), washed with TE buffer, and then treated with RNase A for 1 hour at 37°C.
End-Seq was performed according to the protocol detailed in Canela, et al. DNA Breaks and End Resection Measured Genome-wide by End Sequencing

treatment_protocol: Cells were cultured in the presence (activated cells) or absence (quiescent cells) of cytokines (25 ng/mL IL-4 (R&D, 404-ML-050) and 1 μg/mL anti-CD40 (BD Pharmingen, 553721) for 24-28 hours.

value: spleen

tag: cell type

value: primary CD43- splenic B cells

tag: treatment


title: Nurse, rep 1_1, scRNAseq

description: 10x Genomics

value: honeybee brain

value: neural cell

tag: developmental stage

value: Adult


title: Pupa, rep 3_2, scRNAseq

description: 10x Genomics

value: Pupa


title: ATR+c, S phase, activated

description:
Library name: Bcell-ATRplusC-S
End-Seq

value: activated (25 ng/mL IL-4 and 1 μg/mL anti-CD40 for 24-28 hours)


title: 9117 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Black/Female

value: Term

value: Peripheral blood leukocytes


title: H13/25071 Diabetic

description: Library name: H13/25071

value: thyroid tumor

tag: age

tag: gender

value: Female

tag: size mm

tag: biological behaviour

value: M

tag: biological behaviour1

tag: biological behaviour2

value: non-B

tag: histologic

value: HCC

tag: growth pattern

value: FOLLICULE

tag: peri-tm area

value: MNG

tag: ete mi

tag: angioinvasion

tag: lymphatic invasion

tag: capsulation

tag: capsul invasion

tag: necrosis

tag: hta

tag: dislipidemia

tag: obesity

value: Insulinotherapy-metformin-estatina

value: HCT


title: 9118 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

tag: disease state (preterm = <37 wks gest)

value: Preterm

tag: tissue

tag: data collectin


title: Mouse heart, F_DM 2

value: Heart

tag: cell type

value: Cardiocytes

tag: genotype

value: WT

tag: treatment

value: DM FMT


title: Papain+OM85, multiome, mRNA

city: Paris

first: Olivier

last: Mirabeau

address: 25-28 rue du Docteur Roux

institute: Institut Pasteur

description:
Library name: Papain_OM85_gex
10x Genomics
OM85 6w no recall_filtered_feature_bc_matrix.h5

data_processing:
The data were processed using the Cell Ranger suite (v7.2.0) from 10X Genomics. Specifically, raw base call (BCL) files generated by Illumina sequencers were demultiplexed into fastq files for GEX and ATAC-seq using the cellranger mkfastq and cellranger-arc mkfastq commands. Cellranger-arc count (v2.0.0) was then used to process these fastq files, performing alignment, filtering, barcode counting, peak calling, and quantification of both GEX and ATAC molecules, following the 10X Genomics guidelines.
Assembly: mm10
Supplementary files format and content: Outputs of Cellranger-arc: sample_filtered_feature_bc_matrix.h5: An hdf5 file storing the count matrices related to gene expression and atac-seq data sample_atac_fragments.tsv.gz: A compressed tab-delimited file containing ATAC-seq fragments. sample_atac_fragments.tsv.gz.tbi: index file associated with sample_atac_fragments.tsv.gz sample_atac_peaks.bed: A standard BED file format listing genomic peaks identified during the Cellranger ATAC-seq pipeline. sample_per_barcode_metrics.csv: A comma-separated file summarizing metrics per nuclei, used for QC and filtering of nuclei

molecule: polyA RNA

source_name: Lung

extract_protocol:
Single-cell suspensions of hematopoietic and non-hematopoietic lung cells were prepared using distinct digestion protocols. Hematopoietic cells were isolated after a 45-minute digestion at 37°C in digestion buffer (RPMI 1640 supplemented with 1 mg/ml collagenase D, 1 U/ml DNase I, and 25 µg/ml liberase TL). Following digestion, CD45+ hematopoietic cells were enriched via positive magnetic sorting. Non-hematopoietic cells were prepared by digesting lung tissue for 45 minutes at room temperature (RT) in PBS containing 25 mg/ml dispase and 1% low-melting-point agarose. The lungs were subsequently transferred to RPMI 1640 media with 2.4 U/ml DNase I, teased apart, and incubated on a shaker at 37°C for 10 minutes. Non-hematopoietic cells were enriched via negative magnetic sorting for CD45-. Purified cells were pooled together to proceed with scMulti-omics experiments.
Library was performed using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) according to manufacturer’s instructions. Briefly, nuclei suspensions were incubated with a transposase, which fragmented the DNA in open regions of the chromatin and added the adapter sequences to the ends of the DNA fragments. The transposed nuclei were loaded onto Chromium Next GEM chip with partitioning oil and barcoded single-cell gel beads, followed by PCR amplification. The ATAC library and gene expression library were then prepared separately. Libraries were then pooled evenly and paired-end sequencing was performed on an Illumina NextSeq 550 Instrument.
scMulti-omics

value: Lung

value: CD45- enriched cells

tag: strain

value: C57BL/6j mice (WT)

tag: age

value: 7-9 weeks

tag: Sex

value: 20 µg papain+750 µg OM85 at day 1, sacrifice at day 42


title: H14/25793 Non_diabetic

description: Library name: H14/25793

value: thyroid tumor

tag: gender

value: Female

tag: size mm

tag: biological behaviour

value: M

tag: biological behaviour1

tag: biological behaviour2

tag: histologic

tag: growth pattern

tag: peri-tm area

tag: ete mi

value: NO

tag: angioinvasion

value: YES

tag: lymphatic invasion

tag: treatment type

tag: cv disease

value: LOW

tag: atrx

value: HIGH

tag: daxx

tag: htc

tag: htc 1

tag: neoplaisa history


title: Pupa, rep 2, scRNAseq

description: 10x Genomics

tag: tissue

value: honeybee brain

tag: cell line

value: neural cell

tag: cell type

tag: developmental stage

value: Pupa


title: Nurse, rep 2_1, scRNAseq

description: 10x Genomics

value: Adult


title: H12/25496 Non_diabetic

description: Library name: H12/25496

tag: age

tag: gender

tag: size mm

tag: biological behaviour

value: BORDERLINE

tag: biological behaviour1

value: non-M

tag: biological behaviour2

value: non-B

tag: histologic

value: WT-UMP

value: FOLLICULE

value: CLT

tag: capsulation

tag: capsul invasion

value: UNEQUIVOCAL

tag: necrosis

tag: hta

tag: dislipidemia

tag: obesity

value: Borderline

value: non-HCT


title: 9150 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

value: Black/Female

tag: disease state (preterm = <37 wks gest)

value: Preterm

tag: tissue

value: Peripheral blood leukocytes

tag: data collectin


title: H10/9873 Non_diabetic

description: Library name: H10/9873

value: thyroid tumor

tag: age

value: Male

tag: growth pattern

tag: peri-tm area

tag: ete mi

value: NO

tag: angioinvasion

tag: lymphatic invasion

value: YES

tag: treatment type

value: Estatina

tag: cv disease

value: HIGH

tag: atrx

tag: daxx

value: LOW

tag: htc

tag: htc 1

tag: neoplaisa history


title: Pupa, rep 3_1, scRNAseq

description: 10x Genomics

value: honeybee brain

tag: cell line

value: neural cell

tag: cell type

tag: developmental stage

value: Pupa


title: Papain+OM85, multiome, ATAC

description:
Library name: Papain_OM85_atac
10x Genomics
OM85 6w no recall_filtered_feature_bc_matrix.h5

library_source: genomic single cell

tag: tissue

value: Lung

value: CD45- enriched cells

tag: strain

value: C57BL/6j mice (WT)

value: 7-9 weeks

tag: Sex

value: Female

tag: treatment

value: 20 µg papain+750 µg OM85 at day 1, sacrifice at day 42


title: 9109 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

value: Black/Female

tag: disease state (preterm = <37 wks gest)

value: Preterm

value: Peripheral blood leukocytes

tag: data collectin


title: Pupa, rep 1, scRNAseq

description: 10x Genomics


title: H11/28272 Non_diabetic

description: Library name: H11/28272

value: thyroid tumor

tag: age

tag: gender

tag: size mm

tag: biological behaviour

value: M

tag: biological behaviour1

tag: biological behaviour2

value: non-B

tag: histologic

value: HCC

tag: growth pattern

value: TRABECULE

tag: peri-tm area

value: MNG

tag: ete mi

tag: angioinvasion

tag: lymphatic invasion

tag: capsulation

tag: capsul invasion

tag: necrosis

tag: hta

tag: dislipidemia

tag: obesity

tag: treatment type

value: NO

value: HCT


title: Aptamers, 2' FY-RNA , pyoverdine

city: Ames

first: Marit

last: Nilsen-Hamilton

state: Iowa

address: 2437 Pammel Dr

department: BBMB

institute: Iowa State University

library_source: other

data_processing:
Raw data are demultiplexed and assigned to respective rounds by open source software AptaSuite. Barcodes ATCACG, TAGCTT, GGCTAC, AGTCAA, ATGTCA, GTCCGC, CTTGTA were used to assign initial pool, rounds 4,5,6,7,8 and 9 respectively. Quality control was performed by allowing a zero-nucleotide mismatch between the reference and matched barcodes, and 2 mismatches between the reference and matched primers. Any reads not conforming to these standards were excluded from downstream analysis. Aptamer families (clusters) were consequently extracted from each round using AptaCluster. We performed a total of 10 iterations of locality sensitive hashing, sampling 40% of the indices in the randomized regions and allowing no more than 10 nucleotide mismatches between the seed sequence of a cluster to each remaining member
Supplementary files format and content: S_1502 results summary.xlsx (contains the information about barcodes, pool size , count of unique fraction, singletons and enriched species. Also contains the seed sequences from top 10K clusters)
Supplementary files format and content: S1502.tar.xz (contains demultiplexed and clustered output analyzed by aptasuite program)

molecule: other

organism: synthetic construct

source_name: not applicable

extract_protocol:
PCR purification
PCR amplified libraries were prepared for NGS using Nextera Illumina sequencing primers and the appropriate bar coding.

tag: tissue

value: not applicable

tag: cell line

tag: cell type

tag: sample type

value: aptamer library


title: 9104 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

tag: disease state (preterm = <37 wks gest)

value: Term

tag: data collectin


title: H14/270931 Non_diabetic

description: Library name: H14/270931

tag: age

tag: gender

tag: size mm

tag: biological behaviour

value: B

tag: biological behaviour1

value: non-M

tag: biological behaviour2

tag: histologic

value: HCA

tag: growth pattern

value: FOLLICULE

tag: peri-tm area

tag: ete mi

value: YES

value: Estatina

tag: cv disease

value: LOW

tag: atrx

value: HIGH

tag: daxx

tag: htc

tag: htc 1

tag: neoplaisa history


title: Papain+CPG, multiome, ATAC

description:
Library name: Papain_CPG_atac
10x Genomics
papain_CPG 6w no recall_filtered_feature_bc_matrix.h5

tag: tissue

value: Lung

tag: cell type

value: CD45- enriched cells

tag: strain

value: C57BL/6j mice (WT)

value: 7-9 weeks

tag: Sex

value: Female

tag: treatment

value: 20 µg papain+8 µg CpG at day 1, sacrifice at day 42


title: CF52.Tr_SKD_10mg/mL_2

city: Jeongeup-Si

first: Ju Young

last: Lee

address: 30 Baekhak 1 Gil,

country: South Korea

institute: Korea institute of toxicology

description: Library name: CF_10mg_2

data_processing:
Illumina bcl2fastq2 (Version 2.20) used for basecalling.
Sequenced reads were trimmed for adapter sequences and low-quality filtered using bbduk 39.01.
the clean reads were mapped to the reference genome using STAR 2.7.10b.
The quantification of reads was processed using HTSeq-count 2.0.2.
Assembly: UU Cfam GSD 1.0
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Canis lupus familiaris

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen) according to the manufacturer’ instructions.

tag: cell line


title: 9103 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

value: Black/Female

tag: disease state (preterm = <37 wks gest)

value: Preterm

value: Peripheral blood leukocytes

tag: data collectin


title: H11/11208 Non_diabetic

description: Library name: H11/11208

value: thyroid tumor

tag: age

tag: gender

tag: size mm

tag: biological behaviour

value: M

tag: biological behaviour1

tag: biological behaviour2

value: non-B

tag: histologic

value: OV-PTC

tag: growth pattern

value: TRABECULE

tag: peri-tm area

value: N

value: NO

tag: angioinvasion

tag: lymphatic invasion

tag: capsulation

tag: capsul invasion

tag: necrosis

tag: hta

tag: dislipidemia

tag: obesity

tag: treatment type

value: s/info

value: PTC

value: non-HCT


title: Papain condition, multiome, mRNA

description:
Library name: Papain_gex
10x Genomics
papain 6w no recall_filtered_feature_bc_matrix.h5

tag: tissue

value: Lung

tag: cell type

value: CD45- enriched cells

tag: strain

value: C57BL/6j mice (WT)

tag: age

tag: Sex

tag: treatment

value: 20 µg papain at day 1, sacrifice at day 42


title: 9097 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

value: Black/Female

tag: disease state (preterm = <37 wks gest)

value: Term

tag: data collectin


title: Papain condition, multiome, ATAC

description:
Library name: Papain_atac
10x Genomics
papain 6w no recall_filtered_feature_bc_matrix.h5

value: 7-9 weeks

value: Female


title: CF52.Tr_Negativecontrol_2

description: Library name: CF_NC_2

tag: cell line


title: 9081 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Peripheral blood leukocytes


title: Control condition, multiome, mRNA

description:
Library name: Control_gex
10x Genomics
control_6w_no_recall_filtered_feature_bc_matrix.h5

value: no treatment


title: H11/17561 Non_diabetic

description: Library name: H11/17561

value: thyroid tumor

tag: gender

tag: size mm

tag: biological behaviour

value: B

tag: biological behaviour1

value: non-M

tag: biological behaviour2

tag: histologic

value: HCA

tag: growth pattern

value: FOLLICULE

tag: peri-tm area

tag: ete mi

tag: angioinvasion

tag: lymphatic invasion

tag: capsulation

value: YES

value: Estatina

tag: cv disease

value: LOW

tag: atrx

value: HIGH

tag: daxx

tag: htc

value: HCT

tag: htc 1

tag: neoplaisa history


title: 9110 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

tag: disease state (preterm = <37 wks gest)

tag: tissue

tag: data collectin


title: 9065 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: H10/19529 Non_diabetic

description: Library name: H10/19529

tag: age

tag: gender

tag: size mm

tag: biological behaviour

tag: biological behaviour1

tag: biological behaviour2

tag: histologic

value: MNG

value: NO

tag: capsul invasion

tag: necrosis

tag: hta

tag: dislipidemia

tag: obesity

tag: treatment type


title: CF52.Tr_Negativecontrol_1

description: Library name: CF_NC_1

tag: cell line


title: H10/11914 Non_diabetic

description: Library name: H10/11914

value: Male

value: M

value: non-B

value: HCC

tag: growth pattern

value: TRABECULE

tag: peri-tm area

tag: ete mi

tag: angioinvasion

tag: lymphatic invasion

tag: capsulation

tag: cv disease

tag: atrx

tag: daxx

tag: htc

tag: htc 1

tag: neoplaisa history


title: 9064 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

value: Black/Female

tag: disease state (preterm = <37 wks gest)

value: Preterm

tag: tissue

value: Peripheral blood leukocytes

tag: data collectin


title: H08/7704 Non_diabetic

description: Library name: H08/7704

value: thyroid tumor

tag: age

tag: gender

value: Female

tag: size mm

tag: biological behaviour

value: B

tag: biological behaviour1

value: non-M

tag: biological behaviour2

tag: histologic

value: HCA

tag: capsul invasion

tag: necrosis

tag: hta

tag: dislipidemia

tag: obesity

tag: treatment type


title: Control condition, multiome, ATAC

description:
Library name: Control_atac
10x Genomics
control_6w_no_recall_filtered_feature_bc_matrix.h5

value: Lung

tag: cell type

value: CD45- enriched cells

tag: strain

value: C57BL/6j mice (WT)

value: 7-9 weeks

tag: Sex

tag: treatment

value: no treatment


title: 9061 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

tag: disease state (preterm = <37 wks gest)

tag: tissue

tag: data collectin


title: MDCK_SKD_10mg/mL_2

description: Library name: 10mg_2

source_name: MDCK (NBL-2) - CCL-34

tag: cell line

value: MDCK (NBL-2) - CCL-34


title: Papain+CPG, multiome, mRNA

description:
Library name: Papain_CPG_gex
10x Genomics
papain_CPG 6w no recall_filtered_feature_bc_matrix.h5

tag: age

value: 20 µg papain+8 µg CpG at day 1, sacrifice at day 42


title: papain_recall, scRNAseq

description:
Library name: papain_recall
10x Genomics

data_processing:
Data were processed using the Cell Ranger pipeline (v6.0.1). The cellranger count command was used to align the reads, generate feature-barcode matrices, and quantify gene expression. The filtered_feature_bc_matrix output from Cellranger was used.
Assembly: mm10
Supplementary files format and content: There are 3 gzipped files per sample. The sample_features.tsv.gz file is a gzipped tab-delimited file containing the gene names. The sample_barcodes.tsv.gz file is a gzipped one-column tab-delimited file containing the cell barcodes which passed the Cell Ranger filter. The sample_matrix.mtx.gz file is a gzipped Matrix Market file (Matrix Market Format) that contains gene-by-cell counts represented in a dense matrix format.

extract_protocol:
Single-cell suspensions of hematopoietic and non-hematopoietic lung cells were prepared using distinct digestion protocols. Hematopoietic cells were isolated after a 45-minute digestion at 37°C in digestion buffer (RPMI 1640 supplemented with 1 mg/ml collagenase D, 1 U/ml DNase I, and 25 µg/ml liberase TL). Following digestion, CD45+ hematopoietic cells were enriched via positive magnetic sorting. Non-hematopoietic cells were prepared by digesting lung tissue for 45 minutes at room temperature (RT) in PBS containing 25 mg/ml dispase and 1% low-melting-point agarose. The lungs were subsequently transferred to RPMI 1640 media with 2.4 U/ml DNase I, teased apart, and incubated on a shaker at 37°C for 10 minutes. Non-hematopoietic cells were enriched via negative magnetic sorting for CD45-. Hematopoietic and non-hematopoietic cells were then labeled with TotalSeq-B anti-mouse hashtag 1 and hashtag 2 antibodies, respectively. The labeled samples were pooled together for scRNA-seq experiments.
Library was performed on the 10x Genomics Chromium platform using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1-Dual Index (10x Genomics) according to the manufacturer’s instructions. Briefly, 20,000 single cells were partitioned into Gel Beads in Emulsion (GEMs) in the GemCode instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, shearing and 5’ adaptor and sample index attachment. Barcoded single cell transcriptome libraries were sequenced with 38 bp paired-end reads on an Illumina NextSeq 500 Instrument.

value: 20 µg papain at day 1-3 and 41 (recall), sacrifice at day 42


title: MDCK_SKD_10mg/mL_1

description: Library name: 10mg_1


title: papain_cpg_recall, scRNAseq

description:
Library name: papain_cpg_recall
10x Genomics

value: 20 µg papain+8 µg CpG at day 1-3 and 41 (recall), sacrifice at day 42


title: H08/2820 Diabetic

description: Library name: H08/2820

tag: gender

tag: size mm

tag: biological behaviour

tag: biological behaviour1

tag: biological behaviour2

tag: histologic

tag: growth pattern

value: FOLLICULE

tag: peri-tm area

value: CLT

tag: ete mi

value: NO

tag: angioinvasion

tag: lymphatic invasion

tag: capsulation

value: YES

value: Insulinotherapy-metformin-estatina

tag: cv disease

value: LOW

tag: atrx

value: HIGH

tag: daxx

tag: htc

value: HCT

tag: htc 1

tag: neoplaisa history


title: 9060 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

value: Black/Female

tag: disease state (preterm = <37 wks gest)

value: Preterm

tag: tissue

value: Peripheral blood leukocytes

tag: data collectin


title: MDCK_Negativecontrol_2

description: Library name: NC_2

tag: cell line


title: H05/4287 Non_diabetic

description: Library name: H05/4287

value: thyroid tumor

tag: age

tag: gender

value: Female

tag: size mm

tag: biological behaviour

value: M

tag: biological behaviour1

tag: biological behaviour2

value: non-B

tag: histologic

value: HCC

tag: growth pattern

value: TRABECULE

value: MNG

tag: capsul invasion

tag: necrosis

tag: hta

tag: dislipidemia

tag: obesity

tag: treatment type


title: papain_cpg_no_recall, scRNAseq

description:
Library name: papain_cpg_no_recall
10x Genomics

tag: tissue

value: Lung

tag: strain

value: C57BL/6j mice (WT)

value: 7-9 weeks

tag: Sex

tag: treatment

value: 20 µg papain+8 µg CpG at day 1-3, sacrifice at day 42


title: MDCK_Negativecontrol_1

description: Library name: NC_1

tag: cell line

value: MDCK (NBL-2) - CCL-34


title: CF52.Tr_SKD_10mg/mL_1

description: Library name: CF_10mg_1


title: 9057 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

tag: disease state (preterm = <37 wks gest)

tag: data collectin


title: H05/11608 Non_diabetic

description: Library name: H05/11608

tag: age

tag: gender

tag: size mm

tag: biological behaviour

tag: biological behaviour1

tag: biological behaviour2

value: FOLLICULE

tag: peri-tm area

value: N

tag: ete mi

value: NO

tag: angioinvasion

value: YES

tag: lymphatic invasion

tag: capsulation

tag: cv disease

value: LOW

tag: atrx

value: HIGH

tag: daxx

tag: htc

tag: htc 1

tag: neoplaisa history


title: papain_no_recall, scRNAseq

description:
Library name: papain_no_recall
10x Genomics

tag: tissue

tag: strain

tag: age

tag: Sex

value: Female

tag: treatment

value: 20 µg papain at day 1-3, sacrifice at day 42


title: 9052 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

value: Black/Female

tag: disease state (preterm = <37 wks gest)

value: Preterm

value: Peripheral blood leukocytes

tag: data collectin


title: papain_cpg_d3 condition, scRNAseq

description:
Library name: papain_cpg_d3
10x Genomics

value: 20 µg papain+8 µg CpG at day 1-3, sacrifice at day 3


title: liver_day29_Cyclobutrifluram_800ppm_50C

city: Bracknell

first: Liam

last: Doonan

state: Berkshire

address: Jealott's Hill International Research Centre

country: United Kingdom

institute: Syngenta

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916364_S01_GE1_107_Sep09_1_2

hyb_protocol: Purified cRNA was fragmented (Agilent gene expression hybridisation kit, 5188-5242) and hybridised to Agilent mouse whole genome expression microarrays (G4852/G4853).

scan_protocol: The arrays were washed in Agilent Gene Expression Wash Buffer 1 and Agilent Gene Expression Wash Buffer 2. Scanning and image analysis was performed using the Agilent DNA Microarray Scanner equipped with extended dynamic range (XDR) software according to the Agilent one Colour Gene Expression Protocol (December 2015; P/N G4140-90040).

data_processing:
Extraction from raw microarray image files was performed by using Agilent Feature Extraction Software (Version 10.7.1.1.) to generate raw microarray data. The matrix on sheet2 was generated with LIMMA read.maimages(source="agilent",  green.only=TRUE)
Gprocessed signal

source_name: liver, day29, Cyclobutrifluram, 800ppm

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared using the Agilent low input labelling kit (5190-2305) from 200 ng total RNA and purified using the Qiagen RNeasy mini kit (74104). Quantification of cRNA yields and specific activity (pmol Cy3 per μg cRNA) were measured by NanoDrop spectroscopy.

extract_protocol: Liver samples (40 – 60 mg each) were taken from the left lateral lobe, snap frozen in liquid nitrogen, and  processed for whole genome microarray analysis. Total RNA was extracted from each sample using the Qiagen miRNeasy Mini Kit (217004, v 12/2014) according to the manufacturer’s instructions.

value: liver

tag: gender

value: male

value: cyclobutrifluram

tag: dose (ppm)

tag: duration (days)


title: 9049 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: liver_day29_Cyclobutrifluram_800ppm_49C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916362_S01_GE1_107_Sep09_1_1


title: papain_d3 condition, scRNAseq

description:
Library name: papain_d3
10x Genomics

value: Lung

value: C57BL/6j mice (WT)

value: 7-9 weeks

value: 20 µg papain at day 1-3, sacrifice at day 3


title: liver_day29_Cyclobutrifluram_800ppm_47C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916353_S01_GE1_107_Sep09_1_3


title: liver_day29_Cyclobutrifluram_800ppm_48C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916354_S01_GE1_107_Sep09_2_2


title: liver_day29_Cyclobutrifluram_800ppm_46C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916346_S01_GE1_107_Sep09_2_4


title: NPC cells, BIHi043-A, control, vehicle [0.1% DMSO] treated for 6 hours, replicate 3

city: Berlin

first: Markus

last: Schuelke

state: Berlin

address: Augustenburger Platz 1

department: Neuropediatrics

country: Germany

institute: Charite

description:
Library name: XM001_DMSO_06C
Column_name in FPKM_joined.tab: FPKM_XM001_DMSO_06C

data_processing:
The DNB library was then paired-end sequenced on the DNBSEQ-500 platform (DNBSEQ Technology, BGI, Beijing, China) with a read length of 150 bp. After removing of the sequencing adapters, the resulting FASTQ files were finally filtered for the desired length of 150 bp and for quality scores of Phred+33. FASTQ files were aligned to the human genome (GeneCode GRCh38.p14_47) using STAR v2.7.11a with the following settings: --runThreadN 36 --outReadsUnmapped Fastx --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --seedSearchStartLmax 75 --outFilterMatchNmin 250 --alignSoftClipAtReferenceEnds No --outSAMattrIHstart 0 --alignEndsType EndToEnd --twopassMode Basic. The resulting *.bam file was sorted and indexed using samtools v1.17.
The sorted *.bam file was passed to StringTie v2.2.1 with the following settings: -u -p 36. The resulting *.gtf files were merged using stringtie merge and normalized read counts (TPM and FPKM) were generated using stringtie ballgown. The read counts of all experimental samples were then concatenated into a single table: output.tpm.csv and output.fpkm.csv.
Assembly: GeneCode GRCh38.p14_47
Supplementary files format and content: Stringtie ballgown output files: *.cov.refs.ballgown.gtf => contains details of the transcripts that StringTie assembles from RNA-Seq data in the GTF format; *.gene_abund.ballgown.tab => contains gene abundance counts as normalized FPKM and TPM values as a CSV table; *.out.ballgown.gtf => This is a file listing all the transcripts in the reference annotation that are fully covered, end to end, by reads. The output format is a GTF file as described above. Each line of the GTF is corresponds to a gene or transcript in the reference annotation.
Supplementary files format and content: FPKM_joined.tab, FPKM_joined.csv, TPM_joined.tab, TPM_joined.csv => fused tables with all the samples of the experiment in CSV and EXCEL format provided as TPM and FPK values.

source_name: NPC generated from iPSC

growth_protocol: Neuronal Progenitor Cells (NPCs) were generated from iPSCs from controls and of patients with MT-ATP6 mutations using a protocol described by Zink et al., 2021 (https://doii.org/10.21769/BioProtoc.3939). NPCs were then maintained on Geltrex [Thermo Fisher Scientific, Gibco, #A1413302]-coated 6-well plates at 37°C and 5% CO2 with media changes every other day according to the published protocol from Reinhardt et al., 2013 (https://doi.org/10.1371/journal.pone.0059252) and Zink et al., 2021. NPCs were maintained in 4.5 mM glucose-containing media consisting of the following components: 0.5x Neurobasal without glucose [Thermo Fisher Scientific, Waltham, MA, USA, Gibco, A2477501], 0.5x DMEM/F12 without glucose [Elabscience, EP-CM-L0128], 0.5x N2 [Thermo Fisher Scientific, Gibco, #17502-048], 0.5x B27 without vitamin A [Thermo Fisher Scientific, Gibco #12587010], 2 mM L-Glutamine [Invitrogen, 25030-02425], 1x MycoZap Plus-CL [Lonza, Basel, Switzerland, #VZA-2012] with the addition of 0.5 µM PMA [Miltenyi Biotech, #130-104-465], 3 µM CHIR 99021 [Cayman Chemical, Ann Arbor, MI, USA, #13122], 150 µM ascorbic acid [Sigma-Aldrich, St. Louis, MO, USA, #A92902], 0.115 mM sodium pyruvate [Thermo Fisher Scientific, Gibco, #11360070]  and 4.5 mM glucose [Sigma-Aldrich, #G-5400].

extract_protocol:
RNA was purified using the NucleoSpin RNA Plus kit (Macherey-Nagel, Düren, Germany, #740984) and eluted in 30 µL RNase-free H2O. The RNA concentration was measured using the NanoDrop 2000 photometer and aliquots of 1-2 µg RNA were snap-frozen in liquid nitrogen and stored at -80°C.
The construction of the eukaryotic strand-specific transcriptome library was performed according to the „DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing“ protocol of the  Beijing Genetics Institute (BGI). Briefly, 500 ng total RNA was enriched for polyA-carrying molecules using oligo-dT beads. The RNA was then fragmented and the first cDNA strand was synthesized using random primers. Second strand cDNA was synthesized using dUTP instead of dTTP and the synthesized cDNA was subjected to end repair and 3' adenylation. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments, which were then amplified by PCR. After quality control, the library was circularized and amplified to produce DNA nanoballs (DNBs).

treatment_protocol: NPCs were seeded at a density of 500,000 cells/well in neural progenitor medium containing 4.5 mM glucose on Geltrex-coated or Matrigel-coated 6-well plates and incubated at 37°C and 5% CO2 with medium change every other day. After reaching 70% confluence, the medium was supplemented with 0.1% DMSO (vehicle) or 1 µM or 10 µM Sildenafil (Selleckchem, Cologne, Germany, #S4684) dissolved in 0.1% DMSO and incubated at 37°C and 5% CO2 for 6 or 24 hours (in triplicates). Control cells were grown without additives (in triplicate). At the end of the incubation period, the medium was aspirated and the cells were washed twice with Dulbecco's Phosphate-Buffered Saline (DPBS). Cells were then rapidly scraped in 1 mL DPBS. The cell suspension was collected in a 1.5 mL Eppendorf tube and centrifuged at 8,000 x g for 5 minutes at 4°C. The supernatant was aspirated and the cell pellet was flash-frozen in liquid nitrogen and stored at -80°C.

value: NPC generated from iPSC

tag: cell line

tag: cell type

value: Neuronal precursor cells (NPCs)

tag: genotype

value: wildtype

value: 0.1% DMSO for 6 hours

tag: biological replicate


title: NPC cells, BIHi043-A, control, vehicle [0.1% DMSO] treated for 24 hours, replicate 2

description:
Library name: XM001_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_XM001_DMSO_24B

value: 0.1% DMSO for 24 hours


title: wild type, glucose/NH4, biol rep3

city: Warsaw

first: Agnieszka

last: Dzikowska

address: Pawinskiego 5A

department: Biology

country: Poland

institute: University of Warsaw

description: 2x100 bp paired-end sequencing

data_processing:
Raw single reads were subjected to sequence quality control using FastQC.
Raw sequences were trimmed using Trimmomatic (versin 0.39) (Bolger et al., 2014),
Optical duplicates were removed using MarkDuplicates from GATK package (wersja 4.1.2.0) (McKenna et al., 2010)
Reads were aligned and count using HTSeq-count (version 0.9.1) (Anders et al., 2015)
Differentially expressed genes were selected using DESeq2 package (version 1.16.1) (Love et al., 2014).
Assembly: Reads were aligned to the Aspergillus nidulansreference sequence version s10-m04-r16 (Aspergillus Genome Database - AspGD; http://www.aspergillusgenome.org/).
Supplementary files format and content: Relative expression (areB deletion strain vs. wild-type), xlsx output from the DESeq2.

organism: Aspergillus nidulans

source_name: mycellium

growth_protocol: Mycelia were grown in minimal medium for 9-11h at 37oC under carbon repressing (1% glucose) or non-repressing (0.1% fructose); and under nitrogen repressing (10 mM ammonium tartrate) or non-repressing (5mM urea) conditions.

extract_protocol:
Total RNAs were isolated according to (Schmitt et al., 1990) and then treated with TURBO™ DNase (Invitrogen). Ribosomal RNA was depleted with Ribominus™ Transcriptome Isolation Kit Yeast (Invitrogen). Sample quality was assessed using an Agilent 2100 Bioanalyzer and RNA 6000 Pico kit.
24 RNA-Seq libreries were constructed using rRNA-depleted RNAs and KAPA RNA HyperPrep (Kapa Biosciences) kit and Illumina TruSeqTM DNA UD Indexes (Illumina). 14 cycles of cDNA amplification were applied. The size distribution was assessed using the Agilent 2100 Bioanalyzer and High Sensitvity DNA kit (Agilent). The quantity of each library was assessed by qPCR using the Kapa Library Quantification kit (Kapa Biosciences). The libraries were sequenced on the Illumina NovaSeq 6000 instrument using NovaSeq 6000 S1 Reagent Kit (200 cycles) (Illumina) (2x100 bp paired-end).

value: mycellium

value: 1% glucose, 10 mM ammonium tartrate

tag: replicate

value: biological replicate 3


title: NPC cells, BIHi043-A, control, vehicle [0.1% DMSO] treated for 24 hours, replicate 1

description:
Library name: XM001_DMSO_24A
Column_name in FPKM_joined.tab: FPKM_XM001_DMSO_24A


title: liver_day29_Cyclobutrifluram_800ppm_45C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916343_S01_GE1_107_Sep09_2_1


title: wild type, glucose/NH4, biol rep2

description: 2x100 bp paired-end sequencing

value: biological replicate 2


title: 9033 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Black/Female

value: Preterm

value: Peripheral blood leukocytes


title: liver_day3_Cyclobutrifluram_800ppm_45A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916342_S01_GE1_107_Sep09_2_1

source_name: liver, day3, Cyclobutrifluram, 800ppm

value: liver

value: male

value: cyclobutrifluram


title: NPC cells, BIHi043-A, control, vehicle [0.1% DMSO] treated for 6 hours, replicate 2

description:
Library name: XM001_DMSO_06B
Column_name in FPKM_joined.tab: FPKM_XM001_DMSO_06B


title: wild type, glucose/NH4, biol rep1

description: 2x100 bp paired-end sequencing

value: biological replicate 1


title: liver_day29_Cyclobutrifluram_800ppm_44C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916342_S01_GE1_107_Sep09_1_2


title: NPC cells, BIHi043-A, control, vehicle [0.1% DMSO] treated for 6 hours, replicate 1

description:
Library name: XM001_DMSO_06A
Column_name in FPKM_joined.tab: FPKM_XM001_DMSO_06A


title: 9018 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Term


title: 9019 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: H05/1044 Diabetic

description: Library name: H05/1044

value: thyroid tumor

value: Female

tag: size mm

tag: biological behaviour

value: M

tag: biological behaviour1

tag: biological behaviour2

value: non-B

tag: histologic

value: OV-PTC

tag: growth pattern

value: FOLLICULE

tag: peri-tm area

value: CLT

tag: ete mi

value: NO

tag: angioinvasion

value: YES

tag: lymphatic invasion

tag: capsulation

tag: capsul invasion

tag: necrosis

tag: hta

tag: dislipidemia

tag: obesity

tag: treatment type

value: controlled with diet

tag: cv disease

value: HIGH

tag: atrx

tag: daxx

value: LOW

tag: htc

value: PTC

tag: htc 1

value: non-HCT

tag: neoplaisa history


title: 9050 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

tag: race/sex

value: Black/Female

tag: disease state (preterm = <37 wks gest)

value: Preterm

tag: tissue

value: Peripheral blood leukocytes

tag: data collectin


title: wild type, glucose/urea, biol rep3

description: 2x100 bp paired-end sequencing

value: mycellium

tag: treatment

value: 1% glucose, 5mM urea

tag: genotype

tag: replicate

value: biological replicate 3


title: 9017 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Term


title: liver_day29_Cyclobutrifluram_800ppm_43C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916337_S01_GE1_107_Sep09_2_3

value: liver

tag: gender

value: male

value: cyclobutrifluram

tag: dose (ppm)

tag: duration (days)


title: Vehicle, 24 hours post-treatment, scRNAseq

city: Bonn

first: Tobias

last: Bald

address: Venusberg-Campus 1

department: Institute for Experimental Oncology

institute: University Hospital Bonn

description: 10x Genomics

data_processing:
The raw 10x data were quantified using cellCounts function in Rsubread package. The mouse reference genome GRCm38/mm10 and RefSeq gene annotation (build 38.1) were used in the quantification. Cells with as low as 50 UMIs (Unique Molecular Identifiers) were included in the analysis to allow neutrophils to be detected and included in the analysis. Cells with >20% mitochondrial content or >40% ribosomal content were excluded from analysis. Cells expressing >8,000 genes were also excluded to remove potential doublets. Genes that failed to express in at least 3 cells in at least one sample were excluded from analysis. Mitochondrial genes, ribosomal genes and genes with no valid symbols were also excluded. Dimension reduction and clustering of the data were performed using the Seurat package. Cell type annotation based on the ImmGen database was determined using the SingleR package.
Assembly: GRCm38/mm10
Supplementary files format and content: rds file containing counts table after alignment and rds file containing seurat object with metadata

source_name: EMT6.5 mammary tumor

extract_protocol:
Tumors were initially minced with scissors and resuspended in a 0.8% Collagenase A solution (in serum-free DMEM) followed by dissociation for 40 minutes, 37°C with gentle agitation using the gentleMACS dissociator (Mitenyi Biotech, San Diego, CA). Upon digestion, samples were neutralized with the addition of 2 volumes of DMEM (10%FCS) and strained through 70μm and 22μm filters prior to centrifugation at 4°C, 400rpm for 2 minutes. Red blood cells were removed from the samples by the addition of a red cell lysis buffer (150 mmol/L NH4Cl, 1 mmol/L KHCO3, 100 mmol/L EDTA, pH 8) for 2 minutes, and then clarified by centrifugation. Samples were resuspended in DMEM 2% FCS and evaluated for viability by trypan blue staining and hemocytometer count. Dissociated viable cells (3x106) were pooled from three independent tumors per treatment, labelled with Sytox Green viability dye (Thermo Fisher, Waltham, MA). Viable cells (20,000) were recovered by flow cytometry (BD FACS Aria; BD Biosciences, Franklin Lakes, NJ) and loaded onto a Chromium Single Cell Chip (10x Genomics, Pleasanton, CA).
The cDNA preparation was prepared according to the Single Cell 3′ V 3.0 Protocol.The barcoded cDNA was purified using solid‐phase reversible immobilization (SPRI) beads and amplified in a PCR step. The Read 1 (R1) primer was added during the Gel Beads-in-emulsion (GEM) generation. The P5, P7 and Read 2 (R2) primers were added via end repair, A‐tailing, adaptor ligation, and PCR. The sequencing was completed on an Illumina Nextseq500 platform (Illumina, San Diego, CA) using recommended sequencing parameters.

treatment_protocol: Female Balb/c mice bearing orthotopic EMT6.5 mammary tumors received a single intravenous treatment of saline or AXA-042 (10 μg/mouse), 10 days after implantation of 1x105 cells, when tumors were ~300mm3. Mice were culled 24h later and tumors recovered for single cell transcriptomic analysis.

value: EMT6.5 mammary tumor

tag: strain

value: Balb/c

tag: Sex

value: female

value: intravenous saline


title: NPC cells, BIHi043-A, control, untreated for 24 hours, replicate 3

description:
Library name: XM001_basal_24C
Column_name in FPKM_joined.tab: FPKM_XM001_basal_24C

value: NPC generated from iPSC

tag: cell line

tag: cell type

value: Neuronal precursor cells (NPCs)

value: wildtype

value: no additives for 24 hours

tag: biological replicate


title: AXA-042 treated, 24 hours post-treatment, scRNAseq

description: 10x Genomics

value: intravenous AXA-042 10 ug/mouse


title: wild type, glucose/urea, biol rep2

description: 2x100 bp paired-end sequencing

value: biological replicate 2


title: liver_day29_Cyclobutrifluram_800ppm_42C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916336_S01_GE1_107_Sep09_1_4


title: 9037 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Black/Female

value: Peripheral blood leukocytes


title: 9012 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: NPC cells, BIHi043-A, control, vehicle [0.1% DMSO] treated for 24 hours, replicate 3

description:
Library name: XM001_DMSO_24C
Column_name in FPKM_joined.tab: FPKM_XM001_DMSO_24C

value: 0.1% DMSO for 24 hours


title: 9010 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Preterm


title: wild type, glucose/urea, biol rep1

description: 2x100 bp paired-end sequencing

value: mycellium

value: 1% glucose, 5mM urea

value: biological replicate 1


title: NPC cells, BIHi043-A, control, untreated for 24 hours, replicate 2

description:
Library name: XM001_basal_24B
Column_name in FPKM_joined.tab: FPKM_XM001_basal_24B


title: liver_day29_Cyclobutrifluram_800ppm_41C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916364_S01_GE1_107_Sep09_2_1

value: liver

value: male

value: cyclobutrifluram


title: wild type, fructose/NH4, biol rep3

description: 2x100 bp paired-end sequencing

value: 0.1% fructose, 10 mM ammonium tartrate

value: biological replicate 3


title: NPC cells, BIHi043-A, control, untreated for 6 hours, replicate 3

description:
Library name: XM001_basal_06C
Column_name in FPKM_joined.tab: FPKM_XM001_basal_06C

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)

value: no additives for 6 hours


title: 9008 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Term


title: NPC cells, BIHi043-A, control, untreated for 6 hours, replicate 2

description:
Library name: XM001_basal_06B
Column_name in FPKM_joined.tab: FPKM_XM001_basal_06B

value: wildtype


title: wild type, fructose/NH4, biol rep2

description: 2x100 bp paired-end sequencing

value: biological replicate 2


title: wild type, fructose/NH4, biol rep1

description: 2x100 bp paired-end sequencing


title: 9007 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Black/Female

value: Peripheral blood leukocytes


title: liver_day8_Cyclobutrifluram_800ppm_49B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916361_S01_GE1_107_Sep09_2_1

source_name: liver, day8, Cyclobutrifluram, 800ppm


title: liver_day8_Cyclobutrifluram_800ppm_48B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916354_S01_GE1_107_Sep09_1_2


title: NPC cells, BIHi043-A, control, untreated for 6 hours, replicate 1

description:
Library name: XM001_basal_06A
Column_name in FPKM_joined.tab: FPKM_XM001_basal_06A


title: 9005 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: 9002 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: wild type, fructose/urea, biol rep3

description: 2x100 bp paired-end sequencing

value: 0.1% fructose, 5mM urea


title: liver_day8_Cyclobutrifluram_800ppm_47B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916352_S01_GE1_107_Sep09_2_3


title: NPC cells, BIHi043-A, control, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 3

description:
Library name: XM001_1um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_XM001_1um_DRUG_24C


title: 7155 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Preterm


title: liver_day8_Cyclobutrifluram_800ppm_46B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480915114_S01_GE1_107_Sep09_1_1


title: wild type, fructose/urea, biol rep2

description: 2x100 bp paired-end sequencing

value: mycellium


title: wild type, fructose/urea, biol rep1

description: 2x100 bp paired-end sequencing

value: biological replicate 1


title: NPC cells, BIHi043-A, control, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 2

description:
Library name: XM001_1um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_XM001_1um_DRUG_24B


title: liver_day8_Cyclobutrifluram_800ppm_45B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916343_S01_GE1_107_Sep09_1_1

value: liver


title: NPC cells, BIHi043-A, control, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 1

description:
Library name: XM001_1um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_XM001_1um_DRUG_24A


title: NPC cells, BIHi043-A, control, untreated for 24 hours, replicate 1

description:
Library name: XM001_basal_24A
Column_name in FPKM_joined.tab: FPKM_XM001_basal_24A

value: no additives for 24 hours


title: liver_day8_Cyclobutrifluram_800ppm_50B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916364_S01_GE1_107_Sep09_1_3

value: male

value: cyclobutrifluram


title: 7090 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: liver_day8_Cyclobutrifluram_800ppm_44B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916341_S01_GE1_107_Sep09_2_2


title: NPC cells, BIHi043-A, control, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: XM001_1um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_XM001_1um_DRUG_06C


title: areBΔ, glucose/NH4, biol rep2

description: 2x100 bp paired-end sequencing

value: 1% glucose, 10 mM ammonium tartrate

value: areB{delta}::A.f. pyrG, pyrG89; argB2; nkuA{delta}::argB, pabaB22; riboB2


title: liver_day8_Cyclobutrifluram_800ppm_43B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916337_S01_GE1_107_Sep09_1_3


title: NPC cells, BIHi043-A, control, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: XM001_1um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_XM001_1um_DRUG_06B

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)


title: 7078 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: 7086 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Term


title: areBΔ, glucose/NH4, biol rep1

description: 2x100 bp paired-end sequencing


title: liver_day8_Cyclobutrifluram_800ppm_42B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916129_S01_GE1_107_Sep09_2_2


title: NPC cells, BIHi043-A, control, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: XM001_1um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_XM001_1um_DRUG_06A

value: wildtype


title: NPC cells, BIHi043-A, control, 10 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 3

description:
Library name: XM001_10um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_XM001_10um_DRUG_24C


title: areBΔ, glucose/urea, biol rep3

description: 2x100 bp paired-end sequencing

value: 1% glucose, 5mM urea

value: biological replicate 3


title: 7067 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Black/Female

value: Peripheral blood leukocytes


title: liver_day8_Cyclobutrifluram_800ppm_41B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916365_S01_GE1_107_Sep09_2_1


title: 7065 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

value: Preterm


title: liver_day3_Cyclobutrifluram_800ppm_50A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916364_S01_GE1_107_Sep09_1_4


title: areBΔ, glucose/urea, biol rep1

description: 2x100 bp paired-end sequencing

value: mycellium


title: 9042 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: 7060 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: NPC cells, BIHi043-A, control, 10 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 1

description:
Library name: XM001_10um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_XM001_10um_DRUG_24A


title: liver_day3_Cyclobutrifluram_800ppm_49A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916361_S01_GE1_107_Sep09_1_1


title: areBΔ, glucose/urea, biol rep2

description: 2x100 bp paired-end sequencing

value: biological replicate 2


title: areBΔ, fructose/NH4, biol rep3

description: 2x100 bp paired-end sequencing

value: 0.1% fructose, 10 mM ammonium tartrate


title: 7121 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: liver_day3_Cyclobutrifluram_800ppm_48A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916353_S01_GE1_107_Sep09_2_2

value: liver


title: NPC cells, BIHi043-A, control, 10 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 2

description:
Library name: XM001_10um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_XM001_10um_DRUG_24B


title: 7057 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: NPC cells, BIHi043-A, control, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: XM001_10um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_XM001_10um_DRUG_06C


title: areBΔ, glucose/NH4, biol rep3

description: 2x100 bp paired-end sequencing


title: areBΔ, fructose/NH4, biol rep2

description: 2x100 bp paired-end sequencing


title: NPC cells, BIHi043-A, control, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: XM001_10um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_XM001_10um_DRUG_06B


title: areBΔ, fructose/NH4, biol rep1

description: 2x100 bp paired-end sequencing

value: biological replicate 1


title: liver_day3_Cyclobutrifluram_800ppm_46A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916345_S01_GE1_107_Sep09_2_4

value: male

value: cyclobutrifluram


title: NPC cells, BIHi043-A, control, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: XM001_10um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_XM001_10um_DRUG_06A


title: 7032 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: areBΔ, fructose/urea, biol rep3

description: 2x100 bp paired-end sequencing

value: 0.1% fructose, 5mM urea

value: areB{delta}::A.f. pyrG, pyrG89; argB2; nkuA{delta}::argB, pabaB22; riboB2


title: 7007 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age


title: liver_day3_Cyclobutrifluram_800ppm_44A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916341_S01_GE1_107_Sep09_1_2


title: areBΔ, fructose/urea, biol rep2

description: 2x100 bp paired-end sequencing


title: liver_day3_Cyclobutrifluram_800ppm_43A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916336_S01_GE1_107_Sep09_2_3


title: FFPE tissue of glioblastoma, case 30

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

description:
207253360019_R01C01
30

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to either Illumina Infinium MethylationGPL21145 v1 or Illumina Infinium MethylationGPL33022 v2 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan

data_processing: RStudio (R package ChAMP v2.26.0)

label: Cy5 and Cy3

source_name: FFPE tissue of glioblastoma

extract_protocol: We extracted DNA from unstained sections of paraffin blocks containing at least 50% tumour cells, using MagPurix FFPE DNA Extraction Kit (Zzinexts).

tag: score os

value: favorable

tag: score pfs

tag: mgmt promoter status

value: unmethylated

tag: dna methylation class

value: MC Glioblastoma IDH-wildtype mesenchymal subtype

value: FFPE tissue of glioblastoma


title: areBΔ, fructose/urea, biol rep1

description: 2x100 bp paired-end sequencing

tag: tissue


title: liver_day3_Cyclobutrifluram_800ppm_42A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916335_S01_GE1_107_Sep09_1_4


title: liver_day3_Cyclobutrifluram_800ppm_41A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480916365_S01_GE1_107_Sep09_1_1


title: FFPE tissue of glioblastoma, case 27

description:
207253360097_R07C01
27

value: unfavorable

value: MC Glioblastoma IDH-wildtype RTK1 subtype


title: NPC cells, HHUUKDi009-A, control, vehicle [0.1% DMSO] treated for 24 hours, replicate 1

description:
Library name: TFBJ_DMSO_24A
Column_name in FPKM_joined.tab: FPKM_TFBJ_DMSO_24A

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)

value: wildtype

value: 0.1% DMSO for 24 hours


title: liver_day29_Cyclobutrifluram_400ppm_40C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916363_S01_GE1_107_Sep09_2_1

source_name: liver, day29, Cyclobutrifluram, 400ppm


title: Rat_CIA_chon

city: Shenzhen

first: Yan

last: WANG

address: 1068 Xueyuan Ave

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

data_processing:
The gene expression matrices were generated from raw reads using scopetools (https://anaconda.org/singleronbio/scopetools). The first step involved filtering out reads without polyT tails and extracting cell barcodes and unique molecular identifiers (UMIs). Adapters and polyA tails were trimmed before aligning the reads to the pre-mRNA reference. Then reads with the same cell barcode, UMI, and gene were grouped together to count the number of UMIs per gene per cell.
Assembly: scRNA-seq: mRatBN7.2
Supplementary files format and content: scRNA-seq: barcodes.tsv, genes.tsv, and matrix.mtx

organism: Rattus norvegicus

source_name: cartilage

extract_protocol:
Cartilage were lysesd and pelleted by centrifugation at 300 g for 3 minutes at 4 °C and washed with cold PBS. Tissues were resuspended in 1 mL pre-warmed (37 °C) TrypLE, and rotated at 37 °C for 15 to 30 minutes until tissues were dissociated into single cells via microscope). Cells were pelleted at 300 g for 3 minutes at 4 °C, and washed with cold PBS.
Chromium Single Cell 3' Reagents Kits version 2

value: cartilage

value: Lewis

value: type II collagen and Complete Freund's Adjuvant before Day 14 collection


title: NPC cells, HHUUKDi009-A, control, vehicle [0.1% DMSO] treated for 6 hours, replicate 3

description:
Library name: TFBJ_DMSO_06C
Column_name in FPKM_joined.tab: FPKM_TFBJ_DMSO_06C

value: 0.1% DMSO for 6 hours


title: Rat_Ctrl_chon


title: FFPE tissue of glioblastoma, case 25

description:
207253360001_R03C01
25

value: MC Glioblastoma IDH-wildtype mesenchymal subtype subclass B (novel)


title: liver_day3_Cyclobutrifluram_800ppm_47B

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 800 ppm
US45102884_257480915114_S01_GE1_107_Sep09_2_4

value: liver

value: male

value: cyclobutrifluram


title: 7042 DNA_pregnant_peripheral blood_8-18 wks gestation_18-45 yrs age

source_name: Peripheral blood leukocytes

tag: race/sex

value: Black/Female

tag: disease state (preterm = <37 wks gest)

value: Term

value: Peripheral blood leukocytes

tag: data collectin


title: Liver, adult (3 months), H3K27me3, rep4

city: La Jolla

first: Aditya

last: Parmar

state: California

address: 9500 Gilman Dr.

department: Pathology

institute: University of California San Diego

description: Library name: Adult, liver, H3K27me3, replicate 4

data_processing:
Raw FASTQ reads were trimmed using Trimmomatic v0.39.
Trimmed reads were aligned to the mm10 genome with Bowtie2 v2.3.4.1.
BAM files were sorted and unmapped reads were removed with SAMtools v1.14
BigWig files were generated using bamCoverage (DeepTools v3.5.0) with 50 bp bins
A blacklist of alignment artifact regions was removed prior to normalization
BigWigs were normalized based on 99th percentile peak height, using scaling factors to correct for differences in sequencing depth.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Run

source_name: liver

extract_protocol:
For native CUT&RUN nuclei were extracted using conventional methods.
CUT&RUN libraries were prepared using the NEB Ultra™ II DNA Library Prep Kit for Illumina. Reactions were performed at half scale using between 10 ng and 30 ng of DNA  starting material. The amount of inut was kept consistent across a given histone modification.  Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 200-500 bp in length using SPRIselect beads from Beckman Coulter. Libraries were validated using tapestation.

tag: developmental timepoint

value: adult (3 months)

tag: antibody


title: NPC cells, HHUUKDi009-A, control, vehicle [0.1% DMSO] treated for 6 hours, replicate 1

description:
Library name: TFBJ_DMSO_06A
Column_name in FPKM_joined.tab: FPKM_TFBJ_DMSO_06A

tag: genotype

tag: treatment


title: NPC cells, HHUUKDi009-A, control, vehicle [0.1% DMSO] treated for 6 hours, replicate 2

description:
Library name: TFBJ_DMSO_06B
Column_name in FPKM_joined.tab: FPKM_TFBJ_DMSO_06B


title: FFPE tissue of glioblastoma, case 22

description:
207705780029_R01C01
22

value: favorable

value: unmethylated

value: MC Glioblastoma IDH-wildtype mesenchymal subtype

value: FFPE tissue of glioblastoma


title: liver_day29_Cyclobutrifluram_400ppm_39C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916362_S01_GE1_107_Sep09_1_2

tag: gender

tag: dose (ppm)

tag: duration (days)


title: liver_day29_Cyclobutrifluram_400ppm_38C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916354_S01_GE1_107_Sep09_2_3


title: FFPE tissue of glioblastoma, case 21

description:
207253360103_R04C01
21


title: Liver, adult (3 months), H3K27me3, rep3

description: Library name: Adult, liver, H3K27me3, replicate 3


title: NPC cells, HHUUKDi009-A, control, untreated for 24 hours, replicate 3

description:
Library name: TFBJ_basal_24C
Column_name in FPKM_joined.tab: FPKM_TFBJ_basal_24C

value: NPC generated from iPSC

tag: cell line

tag: cell type

value: Neuronal precursor cells (NPCs)

value: wildtype

value: no additives for 24 hours


title: NPC cells, HHUUKDi009-A, control, vehicle [0.1% DMSO] treated for 24 hours, replicate 3

description:
Library name: TFBJ_DMSO_24C
Column_name in FPKM_joined.tab: FPKM_TFBJ_DMSO_24C

value: 0.1% DMSO for 24 hours

tag: biological replicate


title: liver_day29_Cyclobutrifluram_400ppm_37C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916353_S01_GE1_107_Sep09_1_4


title: FFPE tissue of glioblastoma, case 18

description:
207253360097_R02C01
18

tag: score os

value: unfavorable

tag: score pfs


title: Liver, embryonic day 16, H3K27me3, rep4

description: Library name: Embryo, liver, H3K27me3, replicate 4

value: liver

value: embryonic day 16


title: NPC cells, HHUUKDi009-A, control, vehicle [0.1% DMSO] treated for 24 hours, replicate 2

description:
Library name: TFBJ_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_TFBJ_DMSO_24B


title: NPC cells, HHUUKDi009-A, control, untreated for 24 hours, replicate 2

description:
Library name: TFBJ_basal_24B
Column_name in FPKM_joined.tab: FPKM_TFBJ_basal_24B


title: FFPE tissue of glioblastoma, case 28

description:
207253360149_R01C01
28

tag: mgmt promoter status

value: methylated

tag: dna methylation class


title: Liver, embryonic day 16, H3K27me3, rep3

description: Library name: Embryo, liver, H3K27me3, replicate 3

tag: tissue


title: NPC cells, HHUUKDi009-A, control, untreated for 24 hours, replicate 1

description:
Library name: TFBJ_basal_24A
Column_name in FPKM_joined.tab: FPKM_TFBJ_basal_24A


title: liver_day29_Cyclobutrifluram_400ppm_35C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916343_S01_GE1_107_Sep09_2_2

value: male

value: cyclobutrifluram


title: Liver, adult (3 months), H3K27ac, rep4

description: Library name: Adult, liver, H3K27ac, replicate 4


title: Liver, adult (3 months), H3K27ac, rep3

description: Library name: Adult, liver, H3K27ac, replicate 3


title: FFPE tissue of glioblastoma, case 15

description:
207253360103_R03C01
15

value: MC Glioblastoma IDH-wildtype RTK2 subtype


title: FFPE tissue of glioblastoma, case 17

description:
207253360107_R05C01
17


title: NPC cells, HHUUKDi009-A, control, untreated for 6 hours, replicate 3

description:
Library name: TFBJ_basal_06C
Column_name in FPKM_joined.tab: FPKM_TFBJ_basal_06C

value: no additives for 6 hours


title: liver_day29_Cyclobutrifluram_400ppm_33C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916129_S01_GE1_107_Sep09_2_1


title: Liver, embryonic day 16, H3K27ac, rep4

description: Library name: Embryo, liver, H3K27ac, replicate 4


title: NPC cells, HHUUKDi009-A, control, untreated for 6 hours, replicate 2

description:
Library name: TFBJ_basal_06B
Column_name in FPKM_joined.tab: FPKM_TFBJ_basal_06B


title: FFPE tissue of glioblastoma, case 13

description:
207253360149_R08C01
13

value: MC Diffuse paediatric-type high grade glioma MYCN subtype


title: liver_day29_Cyclobutrifluram_400ppm_34C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916342_S01_GE1_107_Sep09_1_3


title: NPC cells, HHUUKDi009-A, control, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 3

description:
Library name: TFBJ_1um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_TFBJ_1um_DRUG_24C


title: FFPE tissue of glioblastoma, case 11

description:
207253360133_R07C01
11

value: favorable


title: NPC cells, HHUUKDi009-A, control, untreated for 6 hours, replicate 1

description:
Library name: TFBJ_basal_06A
Column_name in FPKM_joined.tab: FPKM_TFBJ_basal_06A


title: liver_day29_Cyclobutrifluram_400ppm_32C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916366_S01_GE1_107_Sep09_2_1


title: Liver, embryonic day 16, H3K27ac, rep3

description: Library name: Embryo, liver, H3K27ac, replicate 3


title: FFPE tissue of glioblastoma, case 8

description:
207253360149_R06C01
8

value: unmmethylated

value: MC Glioblastoma IDH-wildtype mesenchymal subtype


title: Liver, adult (3 months), H3K9ac, rep4

description: Library name: Adult, liver, H3K9ac, replicate 4

value: adult (3 months)


title: liver_day8_Cyclobutrifluram_400ppm_40B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916363_S01_GE1_107_Sep09_1_1

source_name: liver, day8, Cyclobutrifluram, 400ppm


title: FFPE tissue of glioblastoma, case 5

description:
207253360107_R01C01
5

value: FFPE tissue of glioblastoma


title: liver_day8_Cyclobutrifluram_400ppm_39B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916361_S01_GE1_107_Sep09_2_2


title: liver_day29_Cyclobutrifluram_400ppm_36C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916345_S01_GE1_107_Sep09_1_1


title: NPC cells, HHUUKDi009-A, control, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 2

description:
Library name: TFBJ_1um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_TFBJ_1um_DRUG_24B

value: NPC generated from iPSC

value: Neuronal precursor cells (NPCs)

value: wildtype


title: Liver, adult (3 months), H3K9ac, rep3

description: Library name: Adult, liver, H3K9ac, replicate 3


title: NPC cells, HHUUKDi009-A, control, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 1

description:
Library name: TFBJ_1um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_TFBJ_1um_DRUG_24A


title: Liver, embryonic day 16, H3K9ac, rep3

description: Library name: Embryo, liver, H3K9ac, replicate 3


title: FFPE tissue of glioblastoma, case 3

description:
207253360149_R03C01
3

value: unfavorable

value: MC Glioblastoma IDH-wildtype with primitive neuronal component (novel)


title: liver_day8_Cyclobutrifluram_400ppm_38B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916354_S01_GE1_107_Sep09_1_3

value: liver


title: FFPE tissue of glioblastoma, case 2

description:
207253360019_R04C01
2

value: methylated

value: MC Glioblastoma IDH-wildtype RTK1 subtype


title: NPC cells, HHUUKDi009-A, control, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: TFBJ_1um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_TFBJ_1um_DRUG_06C


title: NPC cells, HHUUKDi009-A, control, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: TFBJ_1um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_TFBJ_1um_DRUG_06B


title: liver_day8_Cyclobutrifluram_400ppm_37B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480915114_S01_GE1_107_Sep09_2_2

value: male

value: cyclobutrifluram


title: Liver, adult (3 months), H3K4me3, rep4

description: Library name: Adult, liver, H3K4me3, replicate 4


title: NPC cells, HHUUKDi009-A, control, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: TFBJ_1um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_TFBJ_1um_DRUG_06A


title: FFPE tissue of glioblastoma, case 10

description:
207253360133_R02C01
10

value: unmethylated


title: liver_day8_Cyclobutrifluram_400ppm_36B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916344_S01_GE1_107_Sep09_2_1


title: NPC cells, HHUUKDi009-A, control, 10 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 3

description:
Library name: TFBJ_10um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_TFBJ_10um_DRUG_24C


title: liver_day29_Cyclobutrifluram_400ppm_31C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916330_S01_GE1_107_Sep09_1_2


title: NPC cells, HHUUKDi009-A, control, 10 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 2

description:
Library name: TFBJ_10um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_TFBJ_10um_DRUG_24B


title: Liver, adult (3 months), H3K4me3, rep3

description: Library name: Adult, liver, H3K4me3, replicate 3


title: liver_day8_Cyclobutrifluram_400ppm_35B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916129_S01_GE1_107_Sep09_1_2


title: liver_day8_Cyclobutrifluram_400ppm_34B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916341_S01_GE1_107_Sep09_2_3


title: Liver, embryonic day 16, H3K9ac, rep4

description: Library name: Embryo, liver, H3K9ac, replicate 4

value: embryonic day 16


title: Liver, embryonic day 16, H3K4me3, rep3

description: Library name: Embryo, liver, H3K4me3, replicate 3


title: NPC cells, HHUUKDi009-A, control, 10 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 1

description:
Library name: TFBJ_10um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_TFBJ_10um_DRUG_24A


title: Kidney, adult (3 months), H3K27me3, rep4

description: Library name: Adult, kidney, H3K27me3, replicate 4

source_name: kidney

value: kidney


title: Liver, embryonic day 16, H3K4me3, rep4

description: Library name: Embryo, liver, H3K4me3, replicate 4


title: liver_day8_Cyclobutrifluram_400ppm_33B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480915114_S01_GE1_107_Sep09_1_2


title: Kidney, adult (3 months), H3K27me3, rep3

description: Library name: Adult, kidney, H3K27me3, replicate 3


title: liver_day8_Cyclobutrifluram_400ppm_32B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916366_S01_GE1_107_Sep09_1_1


title: NPC cells, HHUUKDi009-A, control, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: TFBJ_10um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_TFBJ_10um_DRUG_06B


title: Kidney, embryonic day 16, H3K27me3, rep4

description: Library name: Embryo, kidney, H3K27me3, replicate 4


title: liver_day8_Cyclobutrifluram_400ppm_31B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916365_S01_GE1_107_Sep09_2_2


title: Kidney, adult (3 months), H3K27ac, rep4

description: Library name: Adult, kidney, H3K27ac, replicate 4


title: liver_day3_Cyclobutrifluram_400ppm_39A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916361_S01_GE1_107_Sep09_1_2

source_name: liver, day3, Cyclobutrifluram, 400ppm


title: NPC cells, HHUi002-A, MILS patient, vehicle [0.1% DMSO] treated for 24 hours, replicate 2

description:
Library name: TDA3_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_TDA3_DMSO_24B

value: m.9185T>C Mutation (homoplasmy)

value: 0.1% DMSO for 24 hours


title: NPC cells, HHUUKDi009-A, control, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: TFBJ_10um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_TFBJ_10um_DRUG_06A


title: Kidney, adult (3 months), H3K27ac, rep3

description: Library name: Adult, kidney, H3K27ac, replicate 3

value: adult (3 months)


title: liver_day3_Cyclobutrifluram_400ppm_38A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916353_S01_GE1_107_Sep09_2_3


title: NPC cells, HHUi002-A, MILS patient, vehicle [0.1% DMSO] treated for 24 hours, replicate 1

description:
Library name: TDA3_DMSO_24A
Column_name in FPKM_joined.tab: FPKM_TDA3_DMSO_24A


title: liver_day3_Cyclobutrifluram_400ppm_40A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916362_S01_GE1_107_Sep09_2_1


title: Kidney, embryonic day 16, H3K27ac, rep4

description: Library name: Embryo, kidney, H3K27ac, replicate 4


title: NPC cells, HHUUKDi009-A, control, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: TFBJ_10um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_TFBJ_10um_DRUG_06C


title: NPC cells, HHUi002-A, MILS patient, vehicle [0.1% DMSO] treated for 6 hours, replicate 3

description:
Library name: TDA3_DMSO_06C
Column_name in FPKM_joined.tab: FPKM_TDA3_DMSO_06C

value: 0.1% DMSO for 6 hours


title: liver_day3_Cyclobutrifluram_400ppm_37A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916352_S01_GE1_107_Sep09_1_4


title: liver_day3_Cyclobutrifluram_400ppm_36A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916344_S01_GE1_107_Sep09_1_1


title: NPC cells, HHUi002-A, MILS patient, vehicle [0.1% DMSO] treated for 6 hours, replicate 2

description:
Library name: TDA3_DMSO_06B
Column_name in FPKM_joined.tab: FPKM_TDA3_DMSO_06B

value: NPC generated from iPSC


title: Kidney, embryonic day 16, H3K27me3, rep3

description: Library name: Embryo, kidney, H3K27me3, replicate 3


title: NPC cells, HHUi002-A, MILS patient, vehicle [0.1% DMSO] treated for 24 hours, replicate 3

description:
Library name: TDA3_DMSO_24C
Column_name in FPKM_joined.tab: FPKM_TDA3_DMSO_24C

value: Neuronal precursor cells (NPCs)


title: Kidney, adult (3 months), H3K9ac, rep4

description: Library name: Adult, kidney, H3K9ac, replicate 4


title: liver_day3_Cyclobutrifluram_400ppm_35A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916342_S01_GE1_107_Sep09_2_2


title: NPC cells, HHUi002-A, MILS patient, vehicle [0.1% DMSO] treated for 6 hours, replicate 1

description:
Library name: TDA3_DMSO_06A
Column_name in FPKM_joined.tab: FPKM_TDA3_DMSO_06A


title: Kidney, adult (3 months), H3K9ac, rep3

description: Library name: Adult, kidney, H3K9ac, replicate 3


title: liver_day3_Cyclobutrifluram_400ppm_34A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916341_S01_GE1_107_Sep09_1_3


title: liver_day3_Cyclobutrifluram_400ppm_33A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916336_S01_GE1_107_Sep09_2_4


title: Kidney, embryonic day 16, H3K9ac, rep4

description: Library name: Embryo, kidney, H3K9ac, replicate 4


title: NPC cells, HHUi002-A, MILS patient, untreated for 24 hours, replicate 3

description:
Library name: TDA3_basal_24C
Column_name in FPKM_joined.tab: FPKM_TDA3_basal_24C

value: no additives for 24 hours


title: Kidney, embryonic day 16, H3K27ac, rep3

description: Library name: Embryo, kidney, H3K27ac, replicate 3


title: Kidney, embryonic day 16, H3K9ac, rep3

description: Library name: Embryo, kidney, H3K9ac, replicate 3


title: Kidney, adult (3 months), H3K4me3, rep4

description: Library name: Adult, kidney, H3K4me3, replicate 4


title: NPC cells, HHUi002-A, MILS patient, untreated for 24 hours, replicate 1

description:
Library name: TDA3_basal_24A
Column_name in FPKM_joined.tab: FPKM_TDA3_basal_24A


title: NPC cells, HHUi002-A, MILS patient, untreated for 6 hours, replicate 3

description:
Library name: TDA3_basal_06C
Column_name in FPKM_joined.tab: FPKM_TDA3_basal_06C

value: no additives for 6 hours


title: liver_day3_Cyclobutrifluram_400ppm_31A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916365_S01_GE1_107_Sep09_1_2


title: PBMC_nonBOS_Sam30

city: Chicago

first: Wei

last: Zhang

state: Illinois

address: 840 S. Wood Street

department: Pediatrics & Institute of Human Genetics

institute: University of Illinois

hyb_protocol: Total RNA was processed using the Illumina Total prep kit (Ambion) according to the manufacturer’s protocol. Illumina array hybridizations, washing, etc.

scan_protocol: Scanning were performed according to standard protocols provide by Illumina using a HiScan

data_processing: The raw microarray data were background corrected and quantile normalized across all samples using the Illumina Genome Studio. Gene expression of samples obtained from ‘BOS’ group was compared to non-‘BOS’ group using independent and unpaired T-test correction for multiple comparisons to estimate a false discovery rate as implemented in multiple variables linear regression analysis (MLR). Genes were retained for further analyses if FDR < 5%.

label: Cy3, Cy5

source_name: PBMCs

label_protocol: Same to Sample name. 52 pieces of PBMC cells mRNA (100 ng/ul) was randomized before undergoing hybridization to the Human HT-12 v4 Expression BeadChip Kit.

extract_protocol: PBMC cells were separated from patient blood samples using the Ficoll method (Amersham). Total RNA of PBMC cells was isolated using RNeasy Mini Kit according to the manufacturer’s directions (Qiagen).

tag: recipient

value: lung transplant recipient

value: Female

tag: age


title: Kidney, adult (3 months), H3K4me3, rep3

description: Library name: Adult, kidney, H3K4me3, replicate 3

tag: developmental timepoint


title: NPC cells, HHUi002-A, MILS patient, untreated for 24 hours, replicate 2

description:
Library name: TDA3_basal_24B
Column_name in FPKM_joined.tab: FPKM_TDA3_basal_24B


title: NPC cells, HHUi002-A, MILS patient, untreated for 6 hours, replicate 2

description:
Library name: TDA3_basal_06B
Column_name in FPKM_joined.tab: FPKM_TDA3_basal_06B


title: liver_day29_Cyclobutrifluram_120ppm_30C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916363_S01_GE1_107_Sep09_2_2

source_name: liver, day29, Cyclobutrifluram, 120ppm

value: liver


title: PBMC_nonBOS_Sam29

value: Male


title: PBMC_nonBOS_Sam25


title: NPC cells, HHUi002-A, MILS patient, untreated for 6 hours, replicate 1

description:
Library name: TDA3_basal_06A
Column_name in FPKM_joined.tab: FPKM_TDA3_basal_06A


title: liver_day3_Cyclobutrifluram_400ppm_32A

description:
liver gene expression after 3 days exposed to Cyclobutrifluram 400 ppm
US45102884_257480916330_S01_GE1_107_Sep09_2_1

value: male


title: PBMC_nonBOS_Sam28


title: liver_day29_Cyclobutrifluram_120ppm_29C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916362_S01_GE1_107_Sep09_1_3

value: cyclobutrifluram


title: PBMC_nonBOS_Sam26


title: liver_day29_Cyclobutrifluram_120ppm_28C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916354_S01_GE1_107_Sep09_2_4


title: PBMC_nonBOS_Sam27


title: NPC cells, HHUi002-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 3

description:
Library name: TDA3_1um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_TDA3_1um_DRUG_24C


title: PBMC_nonBOS_Sam23


title: PBMC_nonBOS_Sam21


title: liver_day29_Cyclobutrifluram_120ppm_26C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916345_S01_GE1_107_Sep09_1_2


title: NPC cells, HHUi002-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 2

description:
Library name: TDA3_1um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_TDA3_1um_DRUG_24B


title: Brain, adult (3 months), H3K27me3, rep3

description: Library name: Adult, brain, H3K27me3, replicate 3

source_name: brain

value: brain

tag: antibody


title: PBMC_nonBOS_Sam19


title: Kidney, embryonic day 16, H3K4me3, rep3

description: Library name: Embryo, kidney, H3K4me3, replicate 3

value: embryonic day 16


title: liver_day29_Cyclobutrifluram_120ppm_25C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916343_S01_GE1_107_Sep09_2_3


title: liver_day29_Cyclobutrifluram_120ppm_27C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916346_S01_GE1_107_Sep09_2_1


title: NPC cells, HHUi002-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: TDA3_1um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_TDA3_1um_DRUG_06C

tag: genotype


title: Brain, adult (3 months), H3K27me3, rep4

description: Library name: Adult, brain, H3K27me3, replicate 4


title: Kidney, embryonic day 16, H3K4me3, rep4

description: Library name: Embryo, kidney, H3K4me3, replicate 4

value: kidney


title: PBMC_nonBOS_Sam20


title: NPC cells, HHUi002-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 1

description:
Library name: TDA3_1um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_TDA3_1um_DRUG_24A

value: m.9185T>C Mutation (homoplasmy)

tag: treatment


title: PBMC_nonBOS_Sam22

tag: gender


title: PBMC_nonBOS_Sam24


title: Brain, embryonic day 16, H3K27me3, rep4

description: Library name: Embryo, brain, H3K27me3, replicate 4


title: PBMC_nonBOS_Sam18


title: Brain, embryonic day 16, H3K27me3, rep3

description: Library name: Embryo, brain, H3K27me3, replicate 3


title: PBMC_nonBOS_Sam17


title: NPC cells, HHUi002-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 2

description:
Library name: TDA3_1um_DRUG_06B
Column_name in FPKM_joined.tab: FPKM_TDA3_1um_DRUG_06B


title: genomic DNA from 3h_1

city: Xiangyang

first: Ya-nan

last: Zhu

address: No.136, Jingzhou Road, Xiangcheng District

institute: Xiangyang Central Hospital

description: changes of genome-wide DNA methylation at 3hrs in placental trophoblast

hyb_protocol: Bisulfite-converted DNA was isothermally amplified and enzymatically fragmented, followed by purification and hybridization with the Infinium MethylationEPIC (850K) BeadChip (Illumina).

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

data_processing: Idat files were imported and then preprocessed with ChAMP (version 2.12.4) package in R to get the raw data. The raw data was normalized with the Beta-Mixture Quantile dilation (BMIQ) algorithm.

source_name: placenta

growth_protocol: Standard Illumina Protocol

extract_protocol: Total DNA was extracted from primary cultured placental cytotroblasts and syncytiotrophoblasts using a Qiagen DNA kit (Qiagen, Germany)

value: cytotrophoblasts


title: liver_day29_Cyclobutrifluram_120ppm_23C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916336_S01_GE1_107_Sep09_1_1

tag: dose (ppm)


title: liver_day29_Cyclobutrifluram_120ppm_24C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916342_S01_GE1_107_Sep09_1_4

tag: duration (days)


title: NPC cells, HHUi002-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 3

description:
Library name: TDA3_10um_DRUG_24C
Column_name in FPKM_joined.tab: FPKM_TDA3_10um_DRUG_24C

source_name: NPC generated from iPSC

tag: cell line


title: Brain, embryonic day 16, H3K27ac, rep4

description: Library name: Embryo, brain, H3K27ac, replicate 4


title: Brain, adult (3 months), H3K27ac, rep4

description: Library name: Adult, brain, H3K27ac, replicate 4

value: adult (3 months)


title: NPC cells, HHUi002-A, MILS patient, 1 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 1

description:
Library name: TDA3_1um_DRUG_06A
Column_name in FPKM_joined.tab: FPKM_TDA3_1um_DRUG_06A

tag: cell type


title: genomic DNA from 48h_2

description: changes of genome-wide DNA methylation at 48hrs in placental trophoblast

value: syncytiotrophoblasts


title: liver_day29_Cyclobutrifluram_120ppm_21C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916330_S01_GE1_107_Sep09_1_3


title: NPC cells, HHUi002-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 2

description:
Library name: TDA3_10um_DRUG_24B
Column_name in FPKM_joined.tab: FPKM_TDA3_10um_DRUG_24B

value: NPC generated from iPSC

tag: biological replicate


title: Brain, adult (3 months), H3K27ac, rep3

description: Library name: Adult, brain, H3K27ac, replicate 3


title: NPC cells, HHUi002-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 24 hours, replicate 1

description:
Library name: TDA3_10um_DRUG_24A
Column_name in FPKM_joined.tab: FPKM_TDA3_10um_DRUG_24A

value: Neuronal precursor cells (NPCs)


title: Brain, embryonic day 16, H3K27ac, rep3

description: Library name: Embryo, brain, H3K27ac, replicate 3


title: PBMC_nonBOS_Sam16


title: liver_day8_Cyclobutrifluram_120ppm_30B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916363_S01_GE1_107_Sep09_1_2

source_name: liver, day8, Cyclobutrifluram, 120ppm


title: genomic DNA from 48h_3


title: liver_day29_Cyclobutrifluram_120ppm_22C

description:
liver gene expression after 29 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916366_S01_GE1_107_Sep09_2_2


title: genomic DNA from 48h_4


title: PBMC_nonBOS_Sam15


title: Brain, adult (3 months), H3K9ac, rep4

description: Library name: Adult, brain, H3K9ac, replicate 4


title: PBMC_nonBOS_Sam12


title: NPC cells, HHUi002-A, MILS patient, 10 µM Sildenafil in 0.1% DMSO for 6 hours, replicate 3

description:
Library name: TDA3_10um_DRUG_06C
Column_name in FPKM_joined.tab: FPKM_TDA3_10um_DRUG_06C


title: PBMC_nonBOS_Sam14


title: Brain, adult (3 months), H3K9ac, rep3

description: Library name: Adult, brain, H3K9ac, replicate 3


title: liver_day8_Cyclobutrifluram_120ppm_29B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916361_S01_GE1_107_Sep09_2_3


title: Brain, embryonic day 16, H3K9ac, rep4

description: Library name: Embryo, brain, H3K9ac, replicate 4


title: Brain, embryonic day 16, H3K9ac, rep3

description: Library name: Embryo, brain, H3K9ac, replicate 3


title: liver_day8_Cyclobutrifluram_120ppm_28B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916129_S01_GE1_107_Sep09_2_3


title: liver_day8_Cyclobutrifluram_120ppm_27B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916346_S01_GE1_107_Sep09_1_1


title: Brain, adult (3 months), H3K4me3, rep4

description: Library name: Adult, brain, H3K4me3, replicate 4


title: liver_day8_Cyclobutrifluram_120ppm_25B

description:
liver gene expression after 8 days exposed to Cyclobutrifluram 120 ppm
US45102884_257480916343_S01_GE1_107_Sep09_1_3


title: genomic DNA from 3h_2

description: changes of genome-wide DNA methylation at 3hrs in placental trophoblast


title: NPC cells, CRMi003-A, control, vehicle [0.1% DMSO] treated for 24 hours, replicate 2

description:
Library name: NCRM1_DMSO_24B
Column_name in FPKM_joined.tab: FPKM_NCRM1_DMSO_24B

value: wildtype

value: 0.1% DMSO for 24 hours