title: iCAR, Propylparaben_1uM, 6h, rep2, E02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T9_D3


title: iCAR, Methylparaben_1uM, 6h, rep2, F02

status: Public on Jan 11 2023

type: SRA

city: Mason

first: Yuqing

last: Shan

state: Ohio

address: 8700 mason montgomery road

country: USA

institute: Procter & Gamble

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T8_D3

library_source: transcriptomic

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

molecule: total RNA

organism: Homo sapiens

source_name: heart

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

tag: cell line

value: heart

tag: cell type

value: iCAR

tag: genotype

value: Cardiomyocytes

tag: treatment

tag: time

value: 6h exposure of chemical


title: HDP-004764

city: Lausanne

first: Jean-David

middle: Horacio

last: Morel

state: Vaud

address: Station 15

department: SV/IBI

country: Switzerland

institute: Ecole Ploytechnique Fédérale de Lausanne

description:
CAST/EiJ  Control  Week 6
countMatrix_pass.csv

data_processing:
RNA sequencing was performed on a BGISEQ-500. FastQC (default parameters) was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed. The STAR aligner48 was used for mapping the RNA-Seq data to the C57BL/6J reference genome and determining gene counts. We did not use distinct genomes for each strain due to various genome quality differences between mouse strains that could create bigger artefacts than mapping all strains on the same reference genome in terms of mapping efficiency and gene count estimation.
FastQC (default parameters) was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles FASTA_FILE.fa --sjdbGTFfile GTF_FILE.gtf --sjdbOverhang 99
Map reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 $R2 --outFileNamePrefix ./Data/mapped/$SAMPLE
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
Assembly: rnm10
Supplementary files format and content: tab-delimited text file includes mapped read counts per feature, normalized with the TMM (Trimmed Mean of M-values) method (generated by STAR - per strand and combined strands)
Supplementary files format and content: EdgeR-generated fold changes and adj.pvalues for strain by strain comparisons of diet effects, and comparisons between strains.

organism: Mus musculus

source_name: kidney

growth_protocol: Mouse strains were imported from Charles River and bred at the École Polytechnique Fédérale de Lausanne (EPFL) animal facility for more than two generations before incorporation into the study. All research was approved by the Swiss cantonal veterinary authorities of Vaud under license 30759.The mice were fed a chow diet (Harlan 2018 (6% kCal of fat, 20% kCal of protein, and 74% kCal of carbohydrates). Mice were housed at 2-4 animals per cage under 12 hours light/dark cycle, with ad libitum access to food and water at all times. Body weight was measured weekly from 8 weeks of age until killing. We examined 7 mouse inbred strains.

extract_protocol:
Mice were sacrificed at week 1,2 and 6 (folic acid treated) or weeks 2 and 6 (controls). The sacrifices took place from 8:30 a.m. until 12 a.m., with isoflurane anesthesia followed by a complete blood draw (~1 mL) from the vena cava, followed by perfusion with phosphate-buffered saline. The left kidney and other organs were flash-frozen in liquid nitrogen and stored at -80°C until processing.For mRNA, liver tissue were crushed in liquid nitrogen and then 10 mg of tissues were suspended in TRIzol (Invitrogen) and homogenized with stainless steel beads using a TissueLyser II (Qiagen) at 30 Hz for 2 min. RNA was extracted and purified using Direct-zol-96 RNA kits (Zymo Research). mRNA concentration was measured for all samples. All samples passed a quality check of purity (NanoDrop) and fragmentation (FragmentAnalyzer).
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

treatment_protocol: At 9 weeks of age, 3 groups of mice were treated with 125mg/kg of folic acid in 3M sodium bicarbonate and two groups with bicarbonate alone (vehicle controls). Strains were entered into each group randomly, then observed daily to monitor their health.

tag: tissue

value: kidney

tag: strain

value: CAST/EiJ

value: Control

tag: timepoint

value: Week 6


title: iCAR, Methylparaben_50uM, 6h, rep2, G03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T8_D2


title: iCAR, Methylparaben_500uM, 6h, rep2, D12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T8_D1


title: HDP-004756

description:
CAST/EiJ  Folic Acid  Week 6
countMatrix_pass.csv

value: Folic Acid


title: HDP-004760


title: iCAR, Ethylparaben_1uM, 6h, rep2, H12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T6_D3


title: sIII

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
A total of 15 libraries from NS animals (6 for Cow1, 4 for Cow2 and 5 for Cow3) and 30 from S animals (9 for Cow1, 6 for Cow2 and 15 for Cow3) were generated and prepared for 100bp paired-end sequencing on Illumina HiSeq 2000 and sequenced at 1/20th of a lane per sample.
Reads were trimmed in single-end mode, removing adapter read-through contamination as well as poor quality basecalls. In addition, the first 6bp (on the 5'-end) were clipped off to remove the bias introduced by the 6N pulldown oligos.
Trimmed reads were processed using Bismark v0.20.1 (Krueger and Andrews, 2011; parameters: --non_directional) and deduplicated; methylation calls of Read 1 and Read 2 were merged together and analysed using Seqmonk version 1.45.1.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Bismark CpG coverage report files (ending in .cov.gz) are tab-delimited, use 1-based genomic coordinates for every covered cytosine position in the experiment and are in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>

molecule: genomic DNA

organism: Bos taurus

source_name: cow oocyte from hormonal stimulated ovary

growth_protocol: oocytes were developed in vivo and collected from preovulatory follicles

extract_protocol:
Oocytes were lysed in 5 µl of RLT Plus buffer (Qiagen, Cat. No 1053393) for 10 min at room temperature and bisulfite conversion was carried out directly on the cell lysate to minimise losses using standard manufacture kit (Zymo Research, D5020).
DNA was eluted in first strand synthesis mix containing oligos with Illumina adaptor sequence at the 5’ end and the random nucleotide sequence at the 3′ end to facilitate binding in all genomic locations
Libraries were purified with AMPure XP beads (Beckman Coulter, cat. no. A 63881) and amplified for 13 PCR cycles.

treatment_protocol: after collection of oocytes in non-treated animals, the same animals were superovulated by administrating GnRH (Dalmarelin®, Fatro, Barcelona, Spain – 25mg/mL, 2mL IM) and FSH/LH (Pluset, Calier, Barcelona, Spain - 500 UI FSHp 500IU LHp) as follows: time 0h GnRH administration; 36h, 3.5mL of FSH/LH (IM) and 4mL FSH/LH (SC) and 60h, 2.5mL of FSH/LH (IM)

value: hormonal stimulated ovary

value: Cow MII oocyte


title: s9


title: HDP-004755


title: sO


title: iCAR, Ethylparaben_50uM, 6h, rep2, D08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T6_D2


title: s7


title: s8


title: HDP-004337

description:
129S1/SvImJ  Control  Week 2
countMatrix_pass.csv

value: Week 2


title: sIV


title: HDP-004386

description:
PWK/PhJ  Control  Week 2
countMatrix_pass.csv

value: PWK/PhJ


title: HDP-004761


title: HDP-004381

description:
PWK/PhJ  Folic Acid  Week 2
countMatrix_pass.csv


title: iCAR, Butylparaben_50uM, 6h, rep2, B02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T4_D2


title: HDP-004332


title: iCAR, Ethylparaben_500uM, 6h, rep2, C11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T6_D1


title: HDP-004382


title: HDP-004336

description:
129S1/SvImJ  Folic Acid  Week 2
countMatrix_pass.csv


title: HDP-004331


title: s6


title: iCAR, Butylparaben_1uM, 6h, rep2, H01

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T4_D3


title: HDP-004321

description:
CAST/EiJ  Folic Acid  Week 2
countMatrix_pass.csv


title: HDP-004333


title: s4


title: s32


title: iCAR, theophylline_500uM, 6h, rep2, F05

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T27_D2


title: HDP-004334


title: HDP-004325

description:
CAST/EiJ  Control  Week 2
countMatrix_pass.csv


title: s35


title: s30


title: HDP-004338


title: HDP-004322


title: HDP-005130

description:
C57BL/6J  Folic Acid  Week 2
countMatrix_pass.csv


title: s29


title: iCAR, Butylparaben_500uM, 6h, rep2, A04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T4_D1


title: s3


title: iCAR, theophylline_50uM, 6h, rep2, G02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T27_D3


title: iCAR, theobromine_500uM, 6h, rep2, B04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T26_D2


title: HDP-004142

description:
DBA/2J  Folic Acid  Week 2
countMatrix_pass.csv


title: HDP-004259


title: HDP-004097


title: HDP-004141


title: HDP-004304


title: s25


title: iCAR, paraxanthine_50uM, 6h, rep2, B03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T24_D3


title: HDP-004258


title: s26


title: iCAR, theophylline_1000uM, 6h, rep2, G04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T27_D1


title: HDP-004257


title: HDP-004067


title: s19


title: HDP-004060


title: iCAR, theobromine_50uM, 6h, rep2, E06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T26_D3


title: iCAR, paraxanthine_1000uM, 6h, rep2, E10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T24_D1


title: HDP-004335


title: HDP-004256


title: s27


title: HDP-004096


title: HDP-004255


title: iCAR, 4-Hydroxybenzoic acid_50uM, 6h, rep2, E03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T17_D2


title: iCAR, theobromine_1000uM, 6h, rep2, C03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T26_D1


title: HDP-004066


title: HDP-003834

description:
WSB/EiJ  Control  Week 2
countMatrix_pass.csv

value: WSB/EiJ


title: HDP-004065


title: iCAR, 4-Hydroxybenzoic acid_500uM, 6h, rep2, G01

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T17_D1


title: HDP-003828

description:
WSB/EiJ  Folic Acid  Week 2
countMatrix_pass.csv


title: HDP-003827


title: iCAR, paraxanthine_500uM, 6h, rep2, C08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T24_D2


title: HDP-004059

description:
PWK/PhJ  Control  Week 2
countMatrix_pass.csv


title: HDP-004064

description:
CAST/EiJ  Control  Week 2
countMatrix_pass.csv


title: s18


title: HDP-003825


title: HDP-004058

description:
PWK/PhJ  Folic Acid  Week 2
countMatrix_pass.csv


title: s16


title: HDP-003833


title: s1


title: s14


title: s13


title: iCAR, Caffeine_50uM, 6h, rep2, A06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T11_D3


title: HDP-003820


title: iCAR, Caffeine_500uM, 6h, rep2, A08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T11_D2


title: s11


title: iCAR, 4-Hydroxybenzoic acid_1uM, 6h, rep2, B10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T17_D3


title: HDP-003817


title: HDP-003815


title: ns9

source_name: cow oocyte from non-stimulated ovary

value: non-stimulated ovary


title: iCAR, Caffeine_1000uM, 6h, rep2, E09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-T11_D1


title: HDP-003810


title: HDP-003809


title: HDP-003818


title: HDP-003753

description:
CAST/EiJ  Folic Acid  Week 6
countMatrix_pass.csv


title: HDP-003792


title: ns8


title: HDP-003791


title: ns20


title: iCAR, DMSO, 6h, rep2, F09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-DMSO-F09

value: vehicle control


title: ns24


title: iCAR, DMSO, 6h, rep2, E05

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-DMSO-E05


title: iCAR, DMSO, 6h, rep2, D10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-DMSO-D10


title: HDP-003743

description:
DBA/2J  Folic Acid  Week 2
countMatrix_pass.csv


title: HDP-003737

description:
DBA/2J  Control  Week 2
countMatrix_pass.csv


title: HDP-003739


title: HDP-003808

description:
WSB/EiJ  Control  Week 2
countMatrix_pass.csv


title: iCAR, DMSO, 6h, rep2, H08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-DMSO-H08


title: HDP-003736


title: ns19


title: HDP-003735


title: iCAR, DMSO, 6h, rep2, D02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-DMSO-D01


title: iCAR, DMSO, 6h, rep2, C07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-DMSO-C07


title: ns17


title: ns23


title: HDP-003698


title: ns16


title: iCAR, DMSO, 6h, rep2, A11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-DMSO-A11


title: HDP-003697


title: HDP-003670


title: HDP-003661

description:
DBA/2J  Folic Acid  Week 1
countMatrix_pass.csv

value: Week 1


title: iCAR, Propylparaben_1uM, 6h, rep1, G12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T9_D3

value: heart


title: ns14


title: HDP-003660


title: HDP-003659


title: HDP-003656


title: ns13


title: iCAR, Propylparaben_50uM, 6h, rep1, E10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T9_D2

value: iCAR


title: ns12


title: HDP-003652


title: iCAR, Propylparaben_500uM, 6h, rep1, H04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T9_D1

value: Cardiomyocytes


title: HDP-003634

description:
CAST/EiJ  Control  Week 6
countMatrix_pass.csv


title: HDP-003631


title: HDP-003575

description:
PWK/PhJ  Control  Week 6
countMatrix_pass.csv


title: HDP-003696


title: ns10


title: iCAR, DMSO, 6h, rep2, B06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW912D-DMSO-B06


title: iCAR, Methylparaben_50uM, 6h, rep1, B11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T8_D2

value: 6h exposure of chemical


title: HDP-003574

value: kidney


title: HDP-003541


title: ns15


title: ns11


title: nBno


title: HDP-003569


title: iCAR, Methylparaben_500uM, 6h, rep1, D03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T8_D1


title: iCAR, Ethylparaben_1uM, 6h, rep1, B12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T6_D3


title: HDP-003540


title: HDP-003539


title: HDP-003640

value: CAST/EiJ


title: pOD13_SuCasO_SuRepeatSpacer

city: Wurzburg

first: Chase

middle: L

last: Beisel

address: Josef-Schneider-Str. 2

country: Germany

institute: Helmholtz Institute for RNA-Based Infection Research

description: crRNA processed by SuCasΩ in E. coli

data_processing:
Illumina reads were quality checked and trimmed using BBDuk (minlength=10 trimmed)
The resulting reads were merged using BBMerge (trimnonoverlapping=f maxratio=0.09 merged) and kept either as full length reads or at maxlength=55
The merged reads were mapped to the reference plus strand sequence using Bowtie2
Supplementary_files_format_and_content: fasta: alignment files containing reads mapped to the crRNA expression locus

organism: Escherichia coli

source_name: Liquid culture

growth_protocol: The cultures containing the plasmid library and either the nuclease-expressing or the control plasmid were grown in LB with antibiotic selection and IPTG as well as L-arabinose to induce nuclease and crRNA expression. The cultures was grown at 37C with constant shaking and harvested once it reached the stationary phase.

extract_protocol:
RNA was extracted using Direct-zol RNA Miniprep Plus (Zymo, R2072)
Ribosomal RNA was removed from the samples using RiboMinus Transcriptome Isolation Kit, bacteria (Invitrogen, K155004). 3'-phosphoryl groups were removed from RNA using T4 polynucleotide kinase (NEB, M0201S). cDNA synthesis and library preparation was performed with NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7330S). Size selection for fragments between 200 bp and 700 bp was performed with Select-a-Size DNA Clean & Concentrator Kit (Zymo, D4080). DNA was cleaned up using AMPure XP beads (Beckman Coulter, A63882) and quantified with DeNovix dsDNA Broad Range Kit on DeNovix DS-11 FX (DeNovix).

treatment_protocol: Prior to extraction the cells were harvested by centrifugation at 14,000 g for 2 min.


title: HDP-003523

description:
PWK/PhJ  Folic Acid  Week 6
countMatrix_pass.csv


title: HDP-003522


title: pOD49_PAM_lib_deplete_3

description: Control plasmid library without SuCasΩ replicate 3

data_processing:
Library strategy: PAM-assay
Illumina reads were quality checked and trimmed using BBDuk.
Forward sequnces in SuCasΩ depleted library sample 1 were extracted as follows: grep 'TCACC[TCAG][TCAG][TCAG][TCAG][TCAG]' pOD4_PAM_lib_deplete_2_S1_R2_001_trimmed.fasta | cut -c 60-64 | sort | uniq -c | sort -nr | less > pOD4_PAM_lib_deplete_2_S1_R2_001_trimmed_count_5prime.txt
Forward sequnces in SuCasΩ depleted library sample 2 were extracted as follows: grep 'TCACC[TCAG][TCAG][TCAG][TCAG][TCAG]' pOD4_PAM_lib_deplete_3_S2_R2_001_trimmed.fasta | cut -c 60-64 | sort | uniq -c | sort -nr | less > pOD4_PAM_lib_deplete_3_S2_R2_001_trimmed_count_5prime.txt
Forward sequnces in SuCasΩ control library sample 1 were extracted as follows: grep 'TCACC[TCAG][TCAG][TCAG][TCAG][TCAG]' pOD49_PAM_lib_deplete_2_S3_R2_001_trimmed.fasta | cut -c 60-64 | sort | uniq -c | sort -nr | less > pOD49_PAM_lib_deplete_2_S3_R2_001_trimmed_count_5prime.txt
Forward sequnces in SuCasΩ control library sample 2 were extracted as follows: grep 'TCACC[TCAG][TCAG][TCAG][TCAG][TCAG]' pOD4_PAM_lib_deplete_3_S2_R2_001_trimmed.fasta | cut -c 60-64 | sort | uniq -c | sort -nr | less > pOD4_PAM_lib_deplete_3_S2_R2_001_trimmed_count_5prime.txt
Reverse sequnces in SuCasΩ depleted library sample 1 were extracted as follows: grep 'CTCCA[TCAG][TCAG][TCAG][TCAG][TCAG]' pOD4_PAM_lib_deplete_2_S1_R1_001_trimmed.fasta | cut -c 71-75 | sort | uniq -c | sort -nr | less > pOD4_PAM_lib_deplete_2_S1_R1_001_trimmed_count_3prime.txt
Reverse sequnces in SuCasΩ depleted library sample 2 were extracted as follows: grep 'CTCCA[TCAG][TCAG][TCAG][TCAG][TCAG]' pOD4_PAM_lib_deplete_3_S2_R1_001_trimmed.fasta | cut -c 71-75 | sort | uniq -c | sort -nr | less > pOD4_PAM_lib_deplete_3_S2_R1_001_trimmed_count_3prime.txt
Reverse sequnces in SuCasΩ control library sample 1 were extracted as follows: grep 'CTCCA[TCAG][TCAG][TCAG][TCAG][TCAG]' pOD49_PAM_lib_deplete_2_S3_R1_001_trimmed.fasta | cut -c 71-75 | sort | uniq -c | sort -nr | less > pOD49_PAM_lib_deplete_2_S3_R1_001_trimmed_count_3prime.txt
Reverse sequnces in SuCasΩ control library sample 2 were extracted as follows: grep 'CTCCA[TCAG][TCAG][TCAG][TCAG][TCAG]' pOD49_PAM_lib_deplete_3_S4_R1_001_trimmed.fasta | cut -c 71-75 | sort | uniq -c | sort -nr | less > pOD49_PAM_lib_deplete_3_S4_R1_001_trimmed_count_3prime.txt
The depleted sequenes were determined using the following formula: (Total number of control reads/Total number of depleted reads)×(Number depleted reads per sequence/number control reads per cequence)
Supplementary_files_format_and_content: fasta: file containing quality-checked and trimmed sequences
Supplementary_files_format_and_content: txt: file containing sequence counts

molecule: other

source_name: Plasmid DNA from Liquid culture

growth_protocol: The cultures containing the plasmid library and either the nuclease-expressing or the control plasmid were grown in LB with antibiotic selection and IPTG as well as L-arabinose to induce nuclease and crRNA expression. The cultures were grown for 13 hours at 37C with constant shaking.

extract_protocol:
Plasmids were isolated using ZymoPURE II Plasmid Midiprep Kit.
Libraries were constructed by amplifying plasmid DNA region with primers containing Illumina adapters for 25 cycle using Q5 HS High-Fidelity 2X Master Mix. Following amplification, samples were cleaned up with AMPure XP beads. These dsDNAs were then indexed using Nextera barcodes 501, 502, and 707, 708.

treatment_protocol: Prior to extraction the cells were harvested by centrifugation at 4,000 g for 15 min.

value: Control 2


title: HDP-003521

value: Week 6


title: iCAR, Ethylparaben_500uM, 6h, rep1, G08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T6_D1


title: pOD49_PAM_lib_deplete_2

description: Control plasmid library without SuCasΩ replicate 2

value: Control 1


title: iCAR, Methylparaben_1uM, 6h, rep1, F08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T8_D3


title: HDP-003503

description:
WSB/EiJ  Control  Week 6
countMatrix_pass.csv

value: Control


title: HDP-003504

description:
WSB/EiJ  Folic Acid  Week 6
countMatrix_pass.csv

value: Folic Acid


title: pOD4_PAM_lib_deplete_3

description: Depleted plasmid library with SuCasΩ replicate 3

value: Depleted 2


title: HDP-003502


title: iCAR, Butylparaben_1uM, 6h, rep1, D05

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T4_D3


title: iCAR, Butylparaben_50uM, 6h, rep1, B04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T4_D2


title: HDP-003498


title: pOD4_PAM_lib_deplete_2

description: Depleted plasmid library with SuCasΩ replicate 2

value: Depleted 1


title: HDP-003524

value: PWK/PhJ


title: HDP-003501

value: WSB/EiJ


title: HDP-003493


title: HDP-003492


title: iCAR, theophylline_50uM, 6h, rep1, F04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T27_D3


title: iCAR, Butylparaben_500uM, 6h, rep1, C11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T4_D1


title: HDP-003494


title: iCAR, Ethylparaben_50uM, 6h, rep1, H07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T6_D2


title: HDP-003445


title: iCAR, theophylline_500uM, 6h, rep1, A07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T27_D2


title: HDP-003444


title: HDP-003442


title: HDP-003438


title: HDP-003441


title: iCAR, theophylline_1000uM, 6h, rep1, H02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T27_D1


title: HDP-003372

description:
C57BL/6J  Control  Week 6
countMatrix_pass.csv


title: C2C12 cells, KI, Day4 rep3

city: Houston

first: Jun

last: wang

state: Texas

address: 6770 Bertner Ave

institute: Texas Heart Institute

data_processing:
Illumina platform
paired-end reads were generated
DESeq2 R package (1.20.0) was used for data analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: C2C12 cells were maintained in DMEM supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C (designed as day 0, undifferentiated).

extract_protocol:
RNA was harvested using Trizol at day 0 and 4, and sent to Novogene for sequencing libraries construction and analysis..
RNA libraries for RNA-seq were prepared by Novogene using Qubit and qPCR for quantificaiton and bioanalyzer for quality control.

treatment_protocol: Myogenic differentiation was induced by DMEM containing 2% horse serum and antibiotics up to 6 days, and at different time points, i.e. day 2, 4 and 6, cells were collected for analysis.

value: myogenic cells

value: K176R Knockin (KI)

value: myogenic differentiation

value: Day 4


title: HDP-003371

description:
C57BL/6J  Folic Acid  Week 6
countMatrix_pass.csv


title: C2C12 cells, KI, Day4 rep2


title: iCAR, theobromine_50uM, 6h, rep1, G11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T26_D3

value: heart

value: iCAR

value: Cardiomyocytes


title: CM-Dox-2

type: RNA

city: Taipei

first: Yuan-Yuan

last: Cheng

address: Academia road

country: Taiwan

institute: Academia Sinica

description: gene expression

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Genespring sofware

source_name: adult cardiomyocytes after doxycycline treatment for 2 days

label_protocol: Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: αMHC promoter-driven Yamanaka's OSKM factor mice was generated from cross-breeding with αMHC promoter-driven CRE mice and tetO-Yamanaka's OSKM factor mice

extract_protocol: After PBS or doxycycline treatment for 2 days, adult cardiomyocytes were isolated and RNA was extracted for microarray analysis

treatment_protocol: Doxycycline is intraperitoneal injection to induce cardiomyocyte reprogramming in vivo.

tag: gender

value: male

tag: age

value: Doxycycline for 2 days


title: CM-Ctl-2

description: gene expression

source_name: adult cardiomyocytes after PBS treatment for 2 days

value: PBS for 2 days


title: iCAR, theobromine_500uM, 6h, rep1, F02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T26_D2

value: 6h exposure of chemical


title: HDP-003369

value: kidney

value: Control

value: Week 6


title: CM-Dox-1

description: gene expression


title: HDP-003370


title: CM-Ctl-1

description: gene expression


title: C2C12 cells, KI, Day4 rep1


title: HDP-003357

value: Folic Acid


title: C2C12 cells, WT, Day4 rep3

value: WT

value: No differentiation


title: iCAR, paraxanthine_50uM, 6h, rep1, E12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T24_D3


title: HDP-003368


title: iCAR, paraxanthine_500uM, 6h, rep1, H03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T24_D2


title: HDP-003356


title: HDP-003266


title: iCAR, paraxanthine_1000uM, 6h, rep1, F06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T24_D1


title: HDP-003344


title: C2C12 cells, WT, Day4 rep2

value: myogenic cells


title: HDP-003265


title: HDP-003343


title: iCAR, 4-Hydroxybenzoic acid_1uM, 6h, rep1, D11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T17_D3


title: C2C12 cells, WT, Day4 rep1


title: C2C12 cells, KI, Day0 rep3

value: K176R Knockin (KI)

value: Day 0


title: HDP-003160

description:
129S1/SvImJ  Control  Week 6
countMatrix_pass.csv


title: iCAR, 4-Hydroxybenzoic acid_50uM, 6h, rep1, C05

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T17_D2


title: HDP-003350


title: HDP-003157

description:
129S1/SvImJ  Folic Acid  Week 6
countMatrix_pass.csv


title: C2C12 cells, WT, Day0 rep3


title: C2C12 cells, KI, Day0 rep1

value: myogenic differentiation


title: iCAR, 4-Hydroxybenzoic acid_500uM, 6h, rep1, E09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T17_D1

value: heart


title: HDP-003110

description:
DBA/2J  Folic Acid  Week 6
countMatrix_pass.csv


title: HDP-003111


title: HDP-003109


title: HDP-003126


title: C2C12 cells, WT, Day0 rep2


title: HDP-003101

description:
DBA/2J  Control  Week 6
countMatrix_pass.csv


title: iCAR, theobromine_1000uM, 6h, rep1, G01

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T26_D1

value: iCAR


title: C2C12 cells, WT, Day0 rep1


title: HDP-003100


title: HDP-003355


title: HDP-003159


title: iCAR, Caffeine_1000uM, 6h, rep1, E08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T11_D1

value: Cardiomyocytes


title: HDP-003099


title: C2C12 cells, KI, Day0 rep2


title: HDP-003098


title: HDP-003097


title: HDP-003096


title: OVX6

city: Saarbrücken

first: Kathrin

last: Kattler-Lackes

state: non-US Resident

address: Campus A2.4 Raum 0.13

department: Epigenetics

institute: Saarland University

data_processing:
After a quality control with FastQC version 0.11.2 (www.bioinformatics.bbsrc.ac.uk/projects/fastqc/), reads were adapter-trimmed (Q < 20) with Cutadapt (version 1.4.132) using Trim Galore! version 0.3.3 (www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Reads were aligned to mm10 assembly with the grape-nf pipeline (https://github.com/guigolab/grape-nf) wrapping STAR version 2.4.0j33 (76) and RSEM version 1.2.2134 (77).
Read counts were normalized as CPM values.
Assembly: mm10
Supplementary files format and content: CPM count matrix

source_name: liver

extract_protocol:
whole liver was digested with Papain and total RNA was extracted
NEB Next Ultra RNA Library preparation kit (Ipswich)

treatment_protocol: all animals were OVX and put on high fat diet. One group (FSH) was treated with FSH, the other group (OVCX) with saline.

value: liver

tag: Sex

value: female

value: >12 weeks

value: WT C57BL/6

value: Saline


title: iCAR, DMSO, 6h, rep1, H08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-DMSO-H08

value: vehicle control


title: OVX5


title: HDP-003095

value: kidney

value: Control

value: Week 6


title: iCAR, Caffeine_50uM, 6h, rep1, C03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T11_D3

value: 6h exposure of chemical


title: iCAR, DMSO, 6h, rep1, F09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-DMSO-F09


title: iCAR, DMSO, 6h, rep1, E05

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-DMSO-E05


title: HDP-003079

value: Folic Acid


title: HDP-003080


title: HDP-003081


title: OVX4


title: HDP-003102


title: iCAR, Caffeine_500uM, 6h, rep1, G02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-T11_D2


title: OVX3


title: HDP-003750

description:
CAST/EiJ  Folic Acid  Week 6
countMatrix_pass.csv

value: CAST/EiJ


title: HDP-003010


title: HDP-002997


title: iCAR, DMSO, 6h, rep1, C07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-DMSO-C07


title: HDP-002995


title: HDP-002931

description:
PWK/PhJ  Folic Acid  Week 1
countMatrix_pass.csv

value: PWK/PhJ

value: Week 1


title: OVX2


title: OVX1


title: HDP-002930


title: HDP-002907

description:
A/J  Control  Week 6
countMatrix_pass.csv

value: A/J


title: HDP-002906


title: iCAR, DMSO, 6h, rep1, A11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-DMSO-A11

value: heart

value: iCAR


title: HDP-002905


title: iCAR, DMSO, 6h, rep1, D10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-DMSO-D10

value: Cardiomyocytes


title: FSH6

value: liver

value: female

value: FSH


title: HDP-002880

description:
A/J  Folic Acid  Week 6
countMatrix_pass.csv


title: FSH3

value: >12 weeks

value: WT C57BL/6


title: HDP-002879

value: kidney


title: HDP-002877


title: FSH2


title: HDP-002878


title: HDP-002876


title: HDP-002996

description:
129S1/SvImJ  Control  Week 6
countMatrix_pass.csv

value: Control


title: A549, Propylparaben_1uM, 6h, rep3, H03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T9_D3

source_name: Lung

value: Lung

value: epithelial cell

value: Carcinoma


title: FSH1


title: HDP-002875

value: Week 6


title: A549, Propylparaben_50uM, 6h, rep3, A08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T9_D2

value: 6h exposure of chemical


title: A549, Propylparaben_500uM, 6h, rep3, E09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T9_D1


title: HDP-002873

value: Folic Acid


title: iCAR, DMSO, 6h, rep1, B06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-DMSO-B06

value: vehicle control


title: Hypoxia Co-culture

city: Oegstgeest

first: Marlene

last: Geyer

state: Please Select

address: De Limes 7

country: Netherlands

institute: Mimetas

data_processing:
Reads were aligned to the Homo sapiens (hg38) reference transcriptome using BWA MEM [Li and Durbin, 2009; PMID 20080505].
Reads that mapped equally well to multiple locations were discarded.
Mapping and generation of count tables was done using the MapAndGo script1.
Assembly: hg38
Supplementary files format and content: tab separated file containing gene ID including chromosomal location and a gene count value for each sample

source_name: pancreatic cancer

growth_protocol: PDAC organoids were grown either in monoculture or co-culture with pancreatic stellate cells on an OrganoPlate® 2-Lane and RNA was isolated using the RNeasy Micro Kit from Quiagen.

extract_protocol:
RNA was harvested using Rneasy(R) Micro Kit (Qiagen). 20ng/ul of total RNA was used for the construction of sequencing libraries.
Sequencing was performed at Single Cell Discoveries, a sequencing service provider. mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq [Hashimshony et al. 2012; PMID: 22939981 and Simini et al, 2014; PMID: 25500896]. In brief, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers. The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles). located in the Netherlands using an adapted version of the CEL-seq protocol.

treatment_protocol: The cells were either grown in normoxia (20% oxygen content) or hypoxia (1% oxygen content).

value: pancreatic cancer

value: PDAC organoid Pat.65 and Klon 2.2 PSC

value: pancreatic cancer organoids and pancreatic stellate cells

value: WT

value: hypoxia


title: FSH4

value: liver

value: female

value: FSH


title: HDP-002872

value: kidney

value: A/J


title: A549, Methylparaben_50uM, 6h, rep3, E12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T8_D2

value: Lung


title: HDP-002847

description:
CAST/EiJ  Folic Acid  Week 1
countMatrix_pass.csv

value: CAST/EiJ

value: Week 1


title: HDP-002871

value: Week 6


title: Normoxia Co-culture

value: normoxia


title: A549, Methylparaben_500uM, 6h, rep3, D08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T8_D1

value: epithelial cell

value: Carcinoma

value: 6h exposure of chemical


title: HDP-002841

value: Folic Acid


title: HDP-002838

value: PWK/PhJ


title: HDP-002842


title: Normoxia Monoculture

value: pancreatic cancer

value: PDAC organoid Pat.65

value: Pancreatic cancer organoids

value: WT


title: HDP-002837


title: A549, Ethylparaben_1uM, 6h, rep3, D03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T6_D3


title: HDP-002832


title: A549, Ethylparaben_500uM, 6h, rep3, H09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T6_D1


title: HDP-002836


title: HDP-002804

description:
129S1/SvImJ  Folic Acid  Week 1
countMatrix_pass.csv


title: HDP-002830


title: Hypoxia Monoculture

value: hypoxia


title: A549, Butylparaben_1uM, 6h, rep3, A10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T4_D3


title: A549, Methylparaben_1uM, 6h, rep3, F10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T8_D3


title: HDP-002803

value: kidney


title: HDP-002796


title: A549, Butylparaben_50uM, 6h, rep3, F08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T4_D2


title: 28-3-M-0b-5

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

institute: University of Zurich

data_processing:
Demultiplexing with Illumina bcl2fastq
Adapter trimming with TrimGalore!
Alignment against hg19 with STAR aligner
Peak calling with MOSAiCS
Assembly: hg19
Supplementary files format and content: ChIP peaks

source_name: in vitro macrophages

growth_protocol: M1-macrophages were differentiated according to the standardized Promocell method C-28055

extract_protocol:
Cells were washed with PBS/Igepal and once with PBS/Igepal/PMSF, pelleted and stored at -80°C. Then the ActiveMotif ChipIT Express kit was applied
Standard Illumina DNA random library was utilized

treatment_protocol: attached macrophages were in 200ml Nutrimix bags. Formaldehyde at a final concentration of 0.05% was added at the end of the corresponding flight phase. After 2h, crosslinking was quenched with glycine/PBS

value: in vitro macrophages

value: Peripheral blood monocytic cell

value: M1 macrophage

tag: biological replicate

tag: chip antibody

value: RNA Pol II


title: 28-3-M-0a-5


title: HDP-002656

description:
A/J  Folic Acid  Week 1
countMatrix_pass.csv

value: A/J

value: Week 1


title: 28-2-M-0-4

value: ug


title: 28-3-M-G-5


title: A549, Butylparaben_500uM, 6h, rep3, G07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T4_D1

value: Lung

value: epithelial cell

value: Carcinoma


title: 28-3-M-0-5


title: HDP-002795

value: Folic Acid


title: HDP-002655


title: 28-2-M-0-3


title: HDP-002596

description:
C57BL/6J  Folic Acid  Week 1
countMatrix_pass.csv


title: A549, theophylline_50uM, 6h, rep3, E10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T27_D3

value: 6h exposure of chemical


title: HDP-002595


title: HDP-002797


title: A549, theophylline_500uM, 6h, rep3, D06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T27_D2


title: 28-2-M-0b-3


title: A549, Ethylparaben_50uM, 6h, rep3, F12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T6_D2


title: A549, theophylline_1000uM, 6h, rep3, C05

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T27_D1


title: HDP-002563

description:
WSB/EiJ  Folic Acid  Week 1
countMatrix_pass.csv

value: WSB/EiJ


title: 28-2-M-0b-4


title: HDP-002593


title: HDP-002794


title: HDP-002591


title: HDP-002562


title: A549, theobromine_50uM, 6h, rep3, C04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T26_D3


title: HDP-002592


title: HDP-002594


title: HDP-002561


title: 28-2-M-0a-3


title: A549, theobromine_500uM, 6h, rep3, F07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T26_D2


title: 28-2-M-0a-4


title: 28-2-M-G-4


title: A549, theobromine_1000uM, 6h, rep3, D09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T26_D1


title: 28-2-M-G-3


title: HDP-002559


title: HDP-002560


title: A549, paraxanthine_50uM, 6h, rep3, D04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T24_D3


title: HDP-002549


title: HDP-002550


title: HDP-002165


title: 28-1-M-0-7


title: A549, paraxanthine_1000uM, 6h, rep3, B12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T24_D1


title: HDP-002163


title: A549, paraxanthine_500uM, 6h, rep3, G09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T24_D2


title: 28-1-M-0-2


title: musNASH20

city: Xiamen

first: Qiuhong

last: Liu

address: The First Affiliated Hospital, Xiamen University. No.55 Zhenhai Road, Xiamen, China

country: China

institute: Xiamen Medical College

data_processing:
The raw data was filtered with SOAPnuke (v1.5.2)
The clean data were mapped to the reference genome by HISAT (v2.1.0)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5)
The expression level of genes was calculated by RSEM (v1.2.8)
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM，TPM and read count values for each Sample

source_name: Liver

extract_protocol:
RNA was harvested by crushing lysis and purification. Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using sample QC, mRNA isolation, mRNA fragmentation, cDNA synthesis, end repair, add A and adaptor ligation, PCR, library QC, circularization, sequencing.

value: Liver

value: male

value: Ath diet


title: musNASH19

value: WT


title: A549, 4-Hydroxybenzoic acid_1uM, 6h, rep3, H12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T17_D3


title: 28-1-M-0-1

value: in vitro macrophages


title: musEXE22

value: EXE+Ath diet


title: A549, 4-Hydroxybenzoic acid_50uM, 6h, rep3, A09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T17_D2


title: musNASH5


title: A549, Caffeine_50uM, 6h, rep3, B11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T11_D3


title: musEXE8


title: musCTR29

value: Con


title: 28-1-M-0b-7

value: Peripheral blood monocytic cell

value: M1 macrophage


title: A549, 4-Hydroxybenzoic acid_500uM, 6h, rep3, G06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T17_D1


title: A549, Caffeine_500uM, 6h, rep3, E07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T11_D2


title: iCAR, DMSO, 6h, rep1, D02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_iCAR_cts.txt
R-BSW911D-DMSO-D01

value: heart

value: iCAR

value: Cardiomyocytes

value: vehicle control


title: 28-1-M-0b-2


title: HDP-002166

description:
A/J  Folic Acid  Week 1
countMatrix_pass.csv

value: kidney

value: A/J

value: Week 1


title: musCTR4


title: 28-1-M-0a-2


title: 28-1-M-0a-7


title: A549, Caffeine_1000uM, 6h, rep3, A02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-T11_D1

value: Lung

value: epithelial cell

value: Carcinoma

value: 6h exposure of chemical


title: TED T30

city: Anyang

first: MIN JOUNG

last: LEE

address: 22 Gwanpyeong-ro

department: Ophthalmology

country: South Korea

institute: Hallym University Sacred Heart Hospital

description: MicroRNA

hyb_protocol: Total RNA was processed using the Nanostring nCounter v3.0a array.

scan_protocol: Arrays were scanned using the Nanostring scanner.

data_processing: Nanostring nCounter arrays were normalized using the top 100 genes without background substraction using the generic mean in the nSolver Analysis Software v3.

label: Biotin

source_name: TED

extract_protocol: Total RNA was extracted from the serum of every sample using an miRNeasy Serum/Plasma Kit (Qiagen, Germantown, MD, USA) according to the manufacturer’s instructions.12 RNA quality was measured using a NanoDrop 2000 spectrophotometer (Thermo ScientificTM, Waltham, MA, USA).

tag: disease state

value: TED-Inactive

value: serum


title: TED T33

description: MicroRNA

label_protocol: Total RNA was processed using the Nanostring nCounter v3.0a array.


title: TED T24

description: MicroRNA

value: TED-Active


title: A549, DMSO, 6h, rep3, H08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-DMSO-H08


title: 28-1-M-0a-1

value: in vitro macrophages

value: RNA Pol II


title: musEXE18

value: Liver

value: WT

value: male

value: EXE+Ath diet


title: TED T21

description: MicroRNA


title: TED T23

description: MicroRNA


title: 28-1-M-G-7

value: Peripheral blood monocytic cell

value: M1 macrophage


title: musCTR3

value: Con


title: TED T19

description: MicroRNA


title: 28-1-M-0b-1


title: TED T17

description: MicroRNA


title: A549, DMSO, 6h, rep3, E05

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-DMSO-E05

value: vehicle control


title: A549, DMSO, 6h, rep3, F09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-DMSO-F09

value: Lung


title: TED T14

description: MicroRNA


title: 28-1-M-G-2


title: 28-1-M-G-1


title: A549, DMSO, 6h, rep3, D02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-DMSO-D01

value: epithelial cell


title: TED T5

description: MicroRNA


title: Healthy Control C5

description: MicroRNA

source_name: Healthy Control

value: Healthy Control


title: TED T2

description: MicroRNA


title: Healthy Control C3

description: MicroRNA


title: Healthy Control C2

description: MicroRNA


title: Patient 15

first: Ce

last: Gao

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
FASTQ files were obtained by Illumina bcl2fastq2.
STAR and RSEM were used to align to GRCh38 and to calculate the raw counts for genes, respectively.
Assembly: GRCh38
Supplementary files format and content: raw counts and TPM in csv

source_name: peripheral blood

extract_protocol:
RNA was obtained using the Qiagen RNeasy Micro Kit
RNA-Seq libraries from mDC were generated as previously described by Trombetta JJ et al Current Protocols in molecular biology, 2014

treatment_protocol: samples were not treated correspond to primary cells isolated ex vivo

value: peripheral blood

value: HAART


title: Patient 14


title: Patient 13


title: A549, DMSO, 6h, rep3, C07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-DMSO-C07

value: Carcinoma


title: A549, DMSO, 6h, rep3, B06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-DMSO-B06


title: Healthy Control C1

description: MicroRNA

value: serum


title: A549, Propylparaben_1uM, 6h, rep2, E02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T9_D3

value: 6h exposure of chemical


title: Patient 12


title: A549, DMSO, 6h, rep3, D10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-DMSO-D10


title: Patient 11


title: A549, DMSO, 6h, rep3, A11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW913B-DMSO-A11


title: control_rep2

city: nanjing

first: yuxi

last: liu

address: Dingjiaqiao Road 87,Nanjing,China

institute: Southeast university

description: CircRNA expression in control cartilage

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 4 out of 8 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.
When comparing the two groups of profile differences (OA versus control), the “fold change” (the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes ＞=2 and p-values＜0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: Cartilage, control, replicate 2

label_protocol: Sample labeling was performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: 1.Homogenization of above pulverized cartilage tissues using the Mini-Bead-Beater-16 (Biospec)v and TRIzol® Reagent (Invitrogen life technologies). 2.Phase separation using chloroform. 3.RNA precipitation using isopropyl alcohol. 4.RNA wash using 75% ethanol. 5.Redissolving the RNA using RNase-free water.

treatment_protocol: All cartilage samples were immediately frozen in liquid nitrogen before RNA isolation. Cryo pulverization of fresh cartilage tissues using the Biopulverizer (Biospec).

value: Cartilage

value: control (traumatic fracture)


title: control_rep3

description: CircRNA expression in control cartilage

source_name: Cartilage, control, replicate 3


title: Patient 10


title: control_rep4

description: CircRNA expression in control cartilage

source_name: Cartilage, control, replicate 4


title: OA_rep3

description: CircRNA expression in OA cartilage

source_name: Cartilage, OA, replicate 3

value: osteoarthritis


title: HFD/ FGFR4 rep4

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp.
Trimmed sequence reads were pseudoaligned to mouse transcriptome (Ensembl version 94) using kallisto.
Transcript counts were collapsed into gene counts using tximport.
Assembly: GRCm38/Ensembl 94
Supplementary files format and content: CSV file includes gene counts for all samples

source_name: Ileum

extract_protocol:
Total RNA was extracted from ileum biopsies in a mix of Trizol and chloroform and then precipitated with 70% of ethanol. RNA purification was performed using RNeasy Mini Kit columns (QIAGEN, catalog 74106).
RNA libraries for RNA-seq were prepared using the KAPA HyperPrep Kit with Ribo-Erase following manufacturer's protocols.

value: Ileum

tag: diet

value: HFD


title: HFD/ FGFR4 rep2


title: A549, Methylparaben_1uM, 6h, rep2, F02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T8_D3


title: Patient 9


title: HFD rep4

value: Control


title: control_rep1

description: CircRNA expression in control cartilage

source_name: Cartilage, control, replicate 1


title: Healthy Control C4

description: MicroRNA


title: A549, Propylparaben_50uM, 6h, rep2, H06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T9_D2


title: A549, Methylparaben_50uM, 6h, rep2, G03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T8_D2


title: HFD/ FGFR4 rep1


title: Patient 7


title: HFD/ FGFR4 rep3


title: HFD rep3


title: HFD rep2


title: HFD rep1


title: OA_rep2

description: CircRNA expression in OA cartilage

source_name: Cartilage, OA, replicate 2


title: OA_rep1

description: CircRNA expression in OA cartilage

source_name: Cartilage, OA, replicate 1


title: A549, Propylparaben_500uM, 6h, rep2, F07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T9_D1


title: Patient 6


title: Chow/ FGFR4 rep3

value: Chow


title: A549, Methylparaben_500uM, 6h, rep2, D12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T8_D1


title: Patient 8


title: Chow/ FGFR4 rep2


title: Patient 5


title: OA_rep4

description: CircRNA expression in OA cartilage

source_name: Cartilage, OA, replicate 4


title: Patient 4


title: Chow/ FGFR4 rep1


title: A549, Ethylparaben_50uM, 6h, rep2, D08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T6_D2


title: Chow rep4


title: Chow rep3


title: A549, Butylparaben_50uM, 6h, rep2, A06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T4_D2


title: Chow rep1


title: A549, Butylparaben_1uM, 6h, rep2, H01

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T4_D3


title: Patient 1


title: RNA-seq, C42B, rep3

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

description: RNA-seq in C42B cells

data_processing:
RNA-seq data was first trimmed with Trimgalore, and aligned to hg38 using STAR.
The bam files generated from STAR were then quantified using Rsem.
Assembly: hg38
Supplementary files format and content: .tsv

extract_protocol:
The human prostate cancer C42B cells were obtained from ViroMed Laboratories (Minneapolis, MN, USA) Cells were grown at 37 °C in 5% CO2. It was grown in RPMI1640 culture medium, and supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher Scientific, Waltham, MA, USA) and 1% penicillin and streptomycin. All cell stocks were authenticated at the USC Norris Cancer Center cell culture facility by comparison to the ATCC and/or published genomic criteria for that specific cell line; all cells were documented as free of mycoplasma.
RNA was extracted with Trizol reagent. RNA-seq libraries were prepared with KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (Cat # KK8421; Kapa Biosystems, Woburn, MA, USA) then sequenced on an Illumina NextSeq 500 with 75 bp single end reads.

value: Human prostate cancer cells


title: A549, Ethylparaben_500uM, 6h, rep2, C11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T6_D1


title: A549, Ethylparaben_1uM, 6h, rep2, H12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T6_D3


title: Chow rep2


title: A549, theophylline_50uM, 6h, rep2, G02

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T27_D3


title: A549, Butylparaben_500uM, 6h, rep2, A04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T4_D1


title: PD-L1 low beta cells from n = 2 replicate.

city: Paris

first: Masaya

last: OSHIMA

address: 123 boulevard de Port Royal

country: France

institute: INSERM U1016

data_processing:
Sequencing reads were mapped to the mouse genome version GenCode M23 (RRID: SCR_014966 and GRCm38.p6 release 93) using STAR v2.5.2b. Transcripts were quantified using the RSEM software tool.
Normalization and differential gene expression DGE analyses were performed with R package DESeq2 v1.32.0.
Assembly: GRCm38.p6 release 93

source_name: Pancreas

extract_protocol:
RNA was isolated using the RNeasy Micro kit ( #74004, Qiagen)
For library construction, 5 ng of high quality (RIN >7) total RNA was processed using an Ovation Solo RNA-seq Kit.

value: Pancreas

value: Beta cells (PD-L1 low)

value: IFNγ 50pg.mL, 20h


title: Control, untreated beta cells from n = 3 replicate.

value: Beta cells


title: Control, untreated beta cells from n = 4 replicate.


title: Patient 2

value: peripheral blood


title: PD-L1 high beta cells from n = 2 replicate.

value: Beta cells (PD-L1 high)


title: RNA-seq, C42B, rep1

description: RNA-seq in C42B cells

growth_protocol: RPMI1640 culture medium, and supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher Scientific, Waltham, MA, USA) and 1% penicillin and streptomycin.


title: RNA-seq, C42B, rep2

description: RNA-seq in C42B cells


title: PD-L1 high beta cells from n = 3 replicate.


title: PD-L1 low beta cells from n = 4 replicate.


title: Chow/ FGFR4 rep4


title: A549, theophylline_500uM, 6h, rep2, F05

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T27_D2

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

source_name: Lung

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

value: Lung

value: epithelial cell

value: Carcinoma


title: Control, untreated beta cells from n = 1 replicate.


title: Patient 3

value: HAART


title: PD-L1 high beta cells from n = 1 replicate.


title: PD-L1 high beta cells from n = 4 replicate.


title: chronic study, mouse heart, doxo+NMN rep6

city: Nyon

first: Nicolas

last: Hulo

address: Avenue Reverdil 4

institute: Nuvamid SA

description:
Chronic_Doxo-NMN-25-Heart
Doxo-NMN-25-Heart

data_processing:
Sequenced reads were mapped to mm10 genome using STAR (v2.7.3a) with default parameter. The bam output files were then passed to featureCounts (v2.0.0) with the mm10 gencode gtf file to generate the count table
Supplementary files format and content: Acute_Doxo_Heart.csv, csv files of count table for Acute experiment
Supplementary files format and content: Chronic_Doxo_Heart.csv, csv files of count table for Chronic experiment

source_name: Heart

extract_protocol:
Frozen heart samples from the acute and chronic toxicity studies were submitted to Genewiz (Leipzig, Germany) or Azenta (former Genewiz, NJ, USA), respectively
Sequencing was performed on an Illumina NovaSeqTM 6000 platform after total RNA extraction, poly(A) selection and library generation.
Approximately 30 million single-end reads per sample were obtained

value: Heart

value: WT

value: Doxo beta-NMN (500 mg/kg)


title: PD-L1 low beta cells from n = 3 replicate.


title: A549, theobromine_50uM, 6h, rep2, E06

first: Yuqing

last: Shan

address: 8700 mason montgomery road

institute: Procter & Gamble

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T26_D3

value: 6h exposure of chemical


title: chronic study, mouse heart, doxo+NMN rep4

description:
Chronic_Doxo-NMN-23-Heart
Doxo-NMN-23-Heart


title: chronic study, mouse heart, doxo+NMN rep3

description:
Chronic_Doxo-NMN-20-Heart
Doxo-NMN-20-Heart


title: chronic study, mouse heart, doxo+NMN rep1

description:
Chronic_Doxo-NMN-17-Heart
Doxo-NMN-17-Heart


title: A549, theobromine_1000uM, 6h, rep2, C03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T26_D1


title: chronic study, mouse heart, doxo+NMN rep2

description:
Chronic_Doxo-NMN-19-Heart
Doxo-NMN-19-Heart


title: chronic study, mouse heart, doxo rep5

description:
Chronic_Doxo-27-Heart
Doxo-27-Heart

value: Doxo


title: A549, paraxanthine_50uM, 6h, rep2, B03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T24_D3


title: chronic study, mouse heart, doxo rep4

description:
Chronic_Doxo-26-Heart
Doxo-26-Heart


title: chronic study, mouse heart, doxo rep1

description:
Chronic_Doxo-17-Heart
Doxo-17-Heart


title: A549, paraxanthine_1000uM, 6h, rep2, E10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T24_D1


title: A549, paraxanthine_500uM, 6h, rep2, C08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T24_D2


title: chronic study, mouse heart, control rep5

description:
Chronic_CTRL-24-Heart
CTRL-24-Heart

value: Vehicle


title: A549, theophylline_1000uM, 6h, rep2, B12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T27_D1


title: chronic study, mouse heart, control rep4

description:
Chronic_CTRL-23-Heart
CTRL-23-Heart


title: chronic study, mouse heart, doxo rep3

description:
Chronic_Doxo-22-Heart
Doxo-22-Heart


title: chronic study, mouse heart, doxo rep2

description:
Chronic_Doxo-21-Heart
Doxo-21-Heart


title: chronic study, mouse heart, control rep2

description:
Chronic_CTRL-20-Heart
CTRL-20-Heart


title: chronic study, mouse heart, control rep3

description:
Chronic_CTRL-22-Heart
CTRL-22-Heart


title: chronic study, mouse heart, doxo+NMN rep5

description:
Chronic_Doxo-NMN-24-Heart
Doxo-NMN-24-Heart


title: A549, 4-Hydroxybenzoic acid_1uM, 6h, rep2, B10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T17_D3


title: chronic study, mouse heart, control rep1

description:
Chronic_CTRL-17-Heart
CTRL-17-Heart


title: acute study, mouse heart, control rep14

description:
Acute_Heart_CTRL_40
Heart_53


title: acute study, mouse heart, control rep13

description:
Acute_Heart_CTRL_39
Heart_52


title: A549, 4-Hydroxybenzoic acid_50uM, 6h, rep2, E03

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T17_D2


title: A549, 4-Hydroxybenzoic acid_500uM, 6h, rep2, G01

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T17_D1


title: Control, untreated beta cells from n = 2 replicate.

value: Control


title: A549, theobromine_500uM, 6h, rep2, B04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T26_D2


title: A549, Caffeine_50uM, 6h, rep2, H04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T11_D3


title: acute study, mouse heart, doxo rep13

description:
Acute_Heart_Doxo_38
Heart_51


title: chronic study, mouse heart, doxo rep6

description:
Chronic_Doxo-28-Heart
Doxo-28-Heart


title: acute study, mouse heart, doxo rep12

description:
Acute_Heart_Doxo_37
Heart_49


title: acute study, mouse heart, doxo+NMN rep13

description:
Acute_Heart_Doxo-NMN_36
Heart_46

value: Doxo beta-NMN (180 mg/kg)


title: A549, Caffeine_500uM, 6h, rep2, A08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T11_D2


title: acute study, mouse heart, doxo+NMN rep12

description:
Acute_Heart_Doxo-NMN_35
Heart_44


title: acute study, mouse heart, doxo+NMN rep11

description:
Acute_Heart_Doxo-NMN_34
Heart_43


title: A549, DMSO, 6h, rep2, H08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-DMSO-H08

value: vehicle control


title: acute study, mouse heart, doxo+NMN rep10

description:
Acute_Heart_Doxo-NMN_33
Heart_42


title: A549, Caffeine_1000uM, 6h, rep2, E09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-T11_D1


title: acute study, mouse heart, doxo rep9

description:
Acute_Heart_Doxo_30
Heart_38


title: acute study, mouse heart, doxo rep10

description:
Acute_Heart_Doxo_31
Heart_39


title: A549, DMSO, 6h, rep2, F09

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-DMSO-F09


title: A549, DMSO, 6h, rep2, E05

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-DMSO-E05


title: acute study, mouse heart, doxo+NMN rep8

description:
Acute_Heart_Doxo-NMN_27
Heart_33


title: acute study, mouse heart, doxo+NMN rep9

description:
Acute_Heart_Doxo-NMN_28
Heart_35


title: A549, DMSO, 6h, rep2, D10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-DMSO-D10


title: cG13_WGBS

city: Napoli

first: Maria

middle: Rosaria

last: Matarazzo

address: Via Pietro Castellino 111

country: Italy

institute: Institute of Genetics and Biophysics "ABT"

data_processing:
The quality of sequenced PE reads was assessed using FastQC. The low quality raw read pairs were filtered out and the Illumina adapters were trimmed using Cutadapt with the following settings: -u 7 ; -U 7; -q > 30; -m > 40.
Bismark program was utilised for bisulfite-conversion and indexing of the reference genome (canonical chromosomes including chr 1-22; X and Y), alignment of PE reads and removal of PCR duplication. Per-base cytosine methylation report  was obtained using the Bismark methylation extractor command (parameters: -p --no_overlap --counts --zero_based –cutoff 2 --cytosine_report –CX_context). For DMR identification, we tiled the genome into 1kb windows with minimum 2Cs, 5x read coverage and called the DMRs using the MethylKit R package (difference=25, qvalue=0.01, type="hypo").
Genome_build: hg38
Supplementary_files_format_and_content: Text file with columns: chr, start, end, strand, count_methylated, count_unmethylated, CX_context, trinucleotide_context

source_name: iPSCs

growth_protocol: The iPSC lines were cultured on Geltrex™ LDEV-Free Reduced Growth Factor Basement Membrane Matrix (A1413302, Gibco™) coated plates and maintained in StemMACS™ iPS-Brew XF, human medium (130-104-368, Miltenyi Biotec).

extract_protocol:
Genomic DNA was extracted from WT1 iPSC, ICF1 iPSCs and their respective corrected clones, using the Wizard® Genomic DNA Purification Kit (A1125, Promega).
WGBS libraries were prepared and sequenced according to Illumina's instructions.

value: iPSCs

tag: condition

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/ p.S780L)


title: acute study, mouse heart, doxo rep6

description:
Acute_Heart_Doxo_25
Heart_29


title: cG50_WGBS


title: acute study, mouse heart, control rep12

description:
Acute_Heart_CTRL_24
Heart_28


title: acute study, mouse heart, doxo rep7

description:
Acute_Heart_Doxo_26
Heart_30


title: acute study, mouse heart, doxo rep8

description:
Acute_Heart_Doxo_29
Heart_37


title: A549, DMSO, 6h, rep2, D02

city: Mason

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-DMSO-D01


title: acute study, mouse heart, control rep10

description:
Acute_Heart_CTRL_22
Heart_26


title: acute study, mouse heart, control rep11

description:
Acute_Heart_CTRL_23
Heart_27


title: pG_WGBS

value: ICF1 patient (DNMT3B p. I41fsX42 / p.S780L)


title: cR35_WGBS

value: ICF1 cells with corrected DNMT3B (DNMT3B p. wt/wt)


title: acute study, mouse heart, doxo+NMN rep6

description:
Acute_Heart_Doxo-NMN_19
Heart_22


title: acute study, mouse heart, control rep9

description:
Acute_Heart_CTRL_21
Heart_25


title: cR7_WGBS


title: A549, DMSO, 6h, rep2, B06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-DMSO-B06

value: Lung


title: pR_WGBS

value: ICF1 patient (DNMT3B p. D817G / p. D817G)


title: acute study, mouse heart, doxo+NMN rep7

description:
Acute_Heart_Doxo-NMN_20
Heart_23


title: A549, DMSO, 6h, rep2, A11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-DMSO-A11

value: epithelial cell

value: Carcinoma


title: acute study, mouse heart, doxo rep11

description:
Acute_Heart_Doxo_32
Heart_41

value: Heart


title: A549, Propylparaben_50uM, 6h, rep1, E10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW911B-T9_D2


title: acute study, mouse heart, control rep8

description:
Acute_Heart_CTRL_16
Heart_16

value: WT


title: acute study, mouse heart, doxo rep5

description:
Acute_Heart_Doxo_17
Heart_17


title: A549, Propylparaben_1uM, 6h, rep1, G12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW911B-T9_D3


title: WT1_WGBS

value: healthy control (DNMT3B wt/wt)


title: acute study, mouse heart, control rep5

description:
Acute_Heart_CTRL_13
Heart_13


title: acute study, mouse heart, control rep6

description:
Acute_Heart_CTRL_14
Heart_14


title: A549, DMSO, 6h, rep2, C07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW912B-DMSO-C07


title: acute study, mouse heart, control rep7

description:
Acute_Heart_CTRL_15
Heart_15


title: A549, Propylparaben_500uM, 6h, rep1, H04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW911B-T9_D1

value: 6h exposure of chemical


title: acute study, mouse heart, doxo+NMN rep3

description:
Acute_Heart_Doxo-NMN_11
Heart_11


title: acute study, mouse heart, doxo+NMN rep2

description:
Acute_Heart_Doxo-NMN_10
Heart_10


title: acute study, mouse heart, doxo+NMN rep4

description:
Acute_Heart_Doxo-NMN_12
Heart_12


title: HG-SOC endothelin and macitentan treated replicate 3

city: Torino

first: Ivan

last: Molineris

state: TO

address: Via Nizza 52

department: Life Science and System Biology

institute: University of Turin

data_processing:
Sequencing reads were aligned to human reference genome (version GRCh38.p10) using STAR v2.5.3a [PMID:23104886] (with parameters --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04) and providing a list of known splice sites extracted from GENCODE comprehensive annotation (version 27)
Read that align on ribosomal gene or ribosomal repeated sequences in the genome are removed
Gene expression levels were quantified with featureCounts v1.6.3 [PMID:24227677] (options: -t exon -g gene_name) using GENCODE gene annotation (version 27 basic). Multi-mapped reads were excluded from quantification.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: raw gene count

molecule: polyA RNA

source_name: Patient-derived HG-SOC primary cells

growth_protocol: Patient-derived high-grade serous ovarian cancer (HG-SOC) primary cells were isolated from the ascitic fluid of a HG-SOC patient through Ficoll-Histopaque 1077 (Sigma-Aldrich, St. Louis, Missouri,USA). Interface cells were washed in culture medium, and 5×106 viable cells were seeded in 75-cm2 culture flasks, in RPMI 1640 (Gibco, Grovemont Cir, Gaithersburg, USA) containing 1% penicillin streptomycin and 10% fetal bovine serum. All experiments were conducted between the first and second in vitro passage. The purity of primary cultures was assessed by immunophenotyping with a panel of monoclonal Abs (including WT1, keratin 7, calretinin and OCT-125) recognizing ovarian tumor-associated antigens by the alkaline phosphatase-peroxidase-antiperoxidase method. The early passage HG-SOC patient-derived cell line is named PMOV10 where PM stands for Preclinical Models, OV stands for ovarian serous cancer, and # is the order in which the cell line was established

extract_protocol:
Total RNA was isolated using the RNeasy Quick Start kit (Qiagen), according to the manufacturer’s protocol. Quantity and quality of the starting RNA were checked by NanoDrop (Thermo Scientific).
Before starting with library prep, RNA quality was determined running samples on Tapestation 4100 (Agilent). Only RNA samples with RIN above 7 were used in the next steps. To generate the NGS libraries, we exploited the TruSeq Stranded mRNA (Illumina) kit, starting from 100ng of total RNA. Libraries were barcoded, pooled, and sequenced on an Illumina NextSeq 500 sequencing system, in order to obtain for each sample ~ 20-30M single-end reads, 100 nt long.

treatment_protocol: Patient-derived HG-SOC cells (PMOV10) were seeded 1x106 cells/75-cm2 culture flask and incubated at 37°C for 24 hours, then were starved for 24 hours and stimulated with endothelin-1 (ET-1, 100 nM), or with macitentan (MAC, 1µM), alone or in combination with ET-1, or with acetic acid (1% in H20) as vehicle (CTR) for 24 hours.

tag: mac

value: Y


title: HG-SOC endothelin and macitentan treated replicate 2


title: acute study, mouse heart, doxo+NMN rep1

description:
Acute_Heart_Doxo-NMN_9
Heart_9


title: A549, Methylparaben_50uM, 6h, rep1, B11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW911B-T8_D2

tag: cell line


title: acute study, mouse heart, doxo+NMN rep5

description:
Acute_Heart_Doxo-NMN_18
Heart_21


title: A549, Methylparaben_1uM, 6h, rep1, F08

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW911B-T8_D3

tag: cell type


title: HG-SOC endothelin and macitentan treated replicate 1


title: HG-SOC macitentan treated replicate 4

value: N


title: A549, Methylparaben_500uM, 6h, rep1, A06

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW911B-T8_D1

tag: genotype


title: acute study, mouse heart, doxo rep3

description:
Acute_Heart_Doxo_7
Heart_7

tag: treatment

value: Doxo


title: acute study, mouse heart, doxo rep2

description:
Acute_Heart_Doxo_6
Heart_6


title: A549, Ethylparaben_1uM, 6h, rep1, G04

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW911B-T6_D3

tag: time


title: HG-SOC macitentan treated replicate 3


title: acute study, mouse heart, control rep4

description:
Acute_Heart_CTRL_4
Heart_4

tag: tissue

value: Vehicle


title: acute study, mouse heart, doxo rep1

description:
Acute_Heart_Doxo_5
Heart_5


title: A549, Ethylparaben_50uM, 6h, rep1, H07

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0204_A549_cts.txt
R-BSW911B-T6_D2


title: acute study, mouse heart, control rep3

description:
Acute_Heart_CTRL_3
Heart_3


title: HG-SOC macitentan treated replicate 2


title: Ahr_KO_CD8_LmOVA_R2

city: Gainesville

first: Liang

last: Zhou

state: FL

address: 2015 SW 16th Ave

department: IDI

institute: University of Florida

data_processing:
FastQC was used to ensure high per-base sequence quality of reads.
[RNA-seq] Sequenced reads were mapped and raw count values quantified with STAR (v2.7.4a) to the Mus musculus genome (GRCm38/mm10 assembly) and filtered for uniquely mapped reads. Quantitated mRNA expression levels, FPKM aligned reads, were calculated based on exon regions using RSEM (v1.2.25)
[ChIP-seq] ChIP-seq reads were mapped to the mouse genome (mm10) with bowtie2 (Langmead and Salzberg, 2012). The mapped reads were filtered using samtools (Li et al., 2009), keeping only the uniquely aligned reads, and bedgraph files (scaled to 10 million reads) were made with bedtools (Quinlan and Hall, 2010).  CHIP-seq peak locations were identified using Homer (Heinz et al., 2010)
[scRNA-seq] Alignment, quantification, and quality control were performed using the Cell Ranger Software (v3.1.0) and default parameters. After quality control and removal of dead cells, doublets, and contaminating melanoma cells (Pmel mRNA count > 0) a total of 9726 cells remained for downstream analysis. Normalization, cell clustering (resolution = 2), dimensionality reduction, differential expression, visualization, and pseudotime analysis were performed using the R packages Seurat (Butler et al., 2018) and Monocle (Trapnell et al., 2014). The 3000 most variable features identified with the variance-stabilizing transformation (vst)-method were used for principal component analysis (PCA). Upon inspection of elbowplot and jackstraw plot, the first 20 principal components (PCs) were used for further analysis. Cell type annotation was performed manually by assessment of cluster marker genes.
Assembly: GRCm38/mm10
Supplementary files format and content: [RNA-seq] text file of raw counts for all samples, [ChIP-seq] bedgraph files for each sample, [scRNAseq] single cell barcodes, features, and matrix files for each sample

source_name: Small Intestine IEL CD8+ T cell

extract_protocol:
RNA was extracted using RNAeasy Micro Kit, followed by cDNA generation with SMART-Seq® HT Kit (TaKaRa).
cDNA generation was performed with SMART-Seq® HT Kit (Takara). Sequencing libraries were generated with Nextera® XT DNA Library Preparation Kit (Illumina).

value: Small Intestine IEL

value: CD8+ T cell

tag: strain

value: Ahr-/-


title: acute study, mouse heart, control rep1

description:
Acute_Heart_CTRL_1
Heart_1