title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methoxyfenozide, sample 2

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 86

status: Public on Oct 18 2024

type: SRA

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

country: USA

institute: United States Environmental Protection Agency

library_source: transcriptomic

data_processing:
Base calling: Base calling was done by Illumina Real Time Analysis (v3.4.4)
Demultiplex: output was demultiplexed and converted to FastQ format with Bcl2fastq (v2.20.0, Illumina).
Indexing: The fathead minnow reference genome (assembly GCA_016745375.1; Martinson et al., 2022) was indexed with STAR (v2.7.10a, except for the estrone exposure, which used v2.7.9a) and concurrently had in-house gene annotations loaded. The following sample specific parameters were used to generate the genome index: --genomeSAindexNbases 13 --sjdbOverhang 149.
Quality control and trimming: After performing quality control on the raw FastQ data using FastQC and MultiQC (v1.12), raw reads were trimmed using Trim Galore! (v0.6.6) to remove sequencing adapters and low-quality bases and filter out trimmed reads shorter than 20 bp. Trim Galore! is a wrapper script that makes use of the publicly available adapter trimming tool Cutadapt (v4.0).
Mapping: Trimmed reads were then mapped to the indexed genome with STAR version 2.7 using the default parameters except for the use of: --outSAMattributes NH HI AS NM XS.  Samtools (v1.15.1) was used to sort and index the alignment files.
Assign counts: HTSeq (v2.0.1) was used to assign counts to each gene with the following parameters: -f bam -r pos -s no. FastQC and MultiQC (v1.12) were used to assess quality control metrics of the processed reads.  Counts to each gene were parsed, and count data for each exposure condition written to a single tab-delimited matrix file with samples arranged as columns and genes arranged in rows.
Filter counts: Raw counts were first screened to see if any exhibited total counts <2M, and a boxplot of log10 raw counts (+1) for each sample was generated to look for samples with unusual counts distribution. Lowly expressed genes were removed from the raw count matrices using edgeR’s (Robinson et al., 2010) built-in filtering function, filterByExpr(), in version 3.40.2; namely, genes with < 15 reads across all samples and < 10 reads in the smallest group (treatment or control) sample size were filtered out.
Count normalization and filtering: Normalization factors for the filtered count matrices were calculated using the trimmed mean of M-values method via the edgeR function calcNormFactors(). Filtered counts were then normalized by applying a log2 transformation to the counts per million (CPM) read with a pseudo-count of 1 added (to prevent occurrence of any negative count values for downstream analyses, i.e., log2(CPM+1)). Any sample with a filtered, normalized count distribution (assessed via boxplot) that markedly deviated from the rest of the samples within an individual chemical dataset was removed. Multidimensional scaling (MDS) plots were generated to look for possible outliers. Individual samples separated from all remaining replicate samples within the same treatment group on either the first or second principal component by >2x the span of all other samples on the corresponding PC axis were considered strong outliers and removed. If multiple potential outlier samples were present on the same PCA, they were only removed if each outlier sample corresponded to a different treatment group, as such samples were unlikely to represent any reproducible dose-dependent effect.
Assembly: assembly GCA_016745375.1
Supplementary files format and content: *.txt file raw count matrix
Supplementary files format and content: *.txt file count matrix with all filtering, normalization and quality control filters applied. Header rows provide unique sample ID and expsoure concentrations. Starting at row 5, rows are genes and columns are normalized counts with a psuedo-count of 1 added, log2 transformed, and filtered.

molecule: total RNA

organism: Pimephales promelas

source_name: whole body

extract_protocol:
Total RNA was isolated from each homogenate using MagMAX-96 Total RNA Isolation kits (AM1830, Thermo Fisher Scientific, MA, USA) following the manufacturer’s instructions.  All isolated RNA was quantified with spectrophotometry (Synergy HTX plate reader and a Take3 microvolume plate, BioTek, VT, USA) and 16 randomly chosen RNA samples per 96-well plate were analyzed with electrophoresis (4200 Tapestation, Agilent, CA, USA) to confirm quality of the RNA isolation procedure (RINe > 9).
Each cDNA library was prepared from 250 ng of total RNA using commercially available kits that select for mRNA (SENSE mRNA-Seq Library Prep kit, Lexogen, NH, USA) following the manufacturer’s instructions.  The quality and size distribution of libraries was determined using a 4200 TapeStation, and concentrations were measured with a fluorescence-based assay (Quant-iT PicoGreen dsDNA Assay, Thermo Fisher Scientific, MA, USA).

tag: strain

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

value: larvae

tag: tissue

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: mg/L

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment

value: halofenozide (DTXSID4032619)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 87

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by

value: Great Lakes Toxicology & Ecology Division


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 84

tag: strain

tag: age

tag: dev stage

tag: tissue

value: copper sulfate (DTXSID6034479)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 81

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 80

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 82

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 83

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 85

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 79

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 77

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 78

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 76

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 74

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 75

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 73

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 72

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 71

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 92

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 70

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 65

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 66

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 63

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 68

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 67

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 69

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 62

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 59

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 64

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 61

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 58

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 57

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 60

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 56

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 51

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 55

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 49

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 53

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 48

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 47

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 42

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 52

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 50

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 43

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 46

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 44

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 41

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 39

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 40

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 54

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 31

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 30

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 32

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 38

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 37

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 27

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 26

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 35

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 36

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 28

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 33

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 25

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 45

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 22

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 23

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 21

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 34

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 15

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 19

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 20

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 24

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 18

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 29

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 13

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 14

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 12

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 10

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 11

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 8

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 5

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 9

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 4

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 3

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 2

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 93

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name

value: estrone (DTXSID4022367)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 1

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 91

value: less than limit of quantification

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 89

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 92

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 90

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 17

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 16

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 86

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 88

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 87

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 85

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 6

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 84

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 79

tag: strain

tag: age

tag: dev stage

tag: tissue


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 82

tag: Sex

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 80

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to halofenozide, sample 7

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: 337 205771840024_R08C01

type: genomic

city: Warsaw

first: Lukasz

middle: Michal

last: Szafron

address: Roentgena 5

country: Poland

institute: The Maria Sklodowska-Curie National Research Institute of Oncology

description:
337
high-grade serous ovarian carcinoma

hyb_protocol: Bisulphite-converted DNA (with the EZ DNA Methylation Kit, Zymo Research) was hybridized to Infinium MethylationEPIC Beadchip (Illumina) using the standard Illumina protocol.

scan_protocol: Arrays were imaged with the iScan System (Illumina), using recommended settings.

data_processing:
The data were processed according to protocol published by Maksimovic, J. et al., 2016 (PMID: 27347385), using the R script developed by Szafron LM, available for download from https://github.com/lukszafron/methyl_arrays.r.
Beta values normalized using the normalizeMethyLumiSet function from the methylumi package (DOI: 10.18129/B9.bioc.methylumi)
Unmethylated and methylated raw signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: FFPE

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from snap-frozen samples was extracted and purified using the QIAamp DNA Mini Kit (Qiagen) according to the standard instructions. Genomic DNA from FFPE samples was isolated with the use of MagCoreÂ® Genomic DNA FFPE One-Step Kit (RBC Bioscience).

tag: gender

value: Female

value: OvCa


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 81

tag: strain

value: GLTED-Duluth-wt

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: 500 205771840024_R02C01

description:
500
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 77

tag: age

value: 5-6 dpf

tag: dev stage

tag: tissue

tag: Sex

tag: store cond


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 78

value: larvae

tag: collection date

tag: geo loc_name

tag: exposure duration

tag: measured conc

tag: measured conc_units


title: 464 205771840024_R04C01

description:
464
high-grade serous ovarian carcinoma


title: 565 205771840024_R01C01

description:
565
high-grade serous ovarian carcinoma


title: B10 205771840022_R08C01

description:
B10
serous borderline ovarian tumor without the BRAF V600E mutation

source_name: Frozen

value: BOT


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 75

value: whole body

value: not determined

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 74

tag: strain

value: -80 deg C

value: USA:Minnesota, Duluth

tag: biomaterial provider

tag: birth location

tag: breeding method


title: 303 205771840022_R01C01

description:
303
low-grade serous ovarian carcinoma

tag: gender

value: lgOvCa


title: 270 205771840022_R02C01

description:
270
low-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 73

tag: age

tag: dev stage

tag: tissue

tag: Sex

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

value: mg/L


title: 485 205289440131_R08C01

description:
485
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 72

tag: store cond

tag: collection date

tag: geo loc_name

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 69

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

value: estrone (DTXSID4022367)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 71

tag: strain

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: treatment

value: copper sulfate (DTXSID6034479)


title: 475 205289440131_R07C01

description:
475
high-grade serous ovarian carcinoma

tag: gender

value: Female


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 76

tag: age

tag: dev stage

tag: tissue

tag: Sex

tag: collected by

value: less than limit of quantification


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 70

value: GLTED-Duluth-wt

tag: store cond

tag: collection date

tag: geo loc_name

tag: exposure duration

tag: measured conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 67

value: 5-6 dpf

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 68

tag: strain

value: larvae

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: treatment


title: 451 205289440131_R06C01

description:
451
high-grade serous ovarian carcinoma

tag: gender

value: OvCa


title: 437 205289440131_R04C01

description:
437
high-grade serous ovarian carcinoma


title: 438 205289440131_R05C01

description:
438
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 83

tag: age

tag: dev stage

tag: tissue

value: whole body

tag: Sex

tag: collected by


title: 289 205289440131_R01C01

description:
289
high-grade serous ovarian carcinoma


title: 301 205289440131_R02C01

description:
301
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 65

value: not determined

tag: store cond

tag: collection date

tag: geo loc_name

tag: exposure duration

tag: measured conc


title: 571 205289440072_R07C01

description:
571
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 66

value: -80 deg C

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 62

tag: strain

value: USA:Minnesota, Duluth

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: treatment


title: 530 205289440072_R04C01

description:
530
high-grade serous ovarian carcinoma

tag: gender


title: 545 205289440072_R05C01

description:
545
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 63

tag: age

tag: dev stage

tag: tissue

tag: Sex

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 61

tag: store cond

tag: collection date

tag: geo loc_name

tag: exposure duration

tag: measured conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 60

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: 524 205289440072_R03C01

description:
524
high-grade serous ovarian carcinoma


title: 37 205062740115_R07C01

description:
37
low-grade serous ovarian carcinoma

value: lgOvCa


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 58

tag: strain

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

tag: treatment


title: 286 205062740115_R08C01

description:
286
high-grade serous ovarian carcinoma

tag: gender


title: B84 205062740115_R06C01

description:
B84
serous borderline ovarian tumor with the BRAF V600E mutation


title: B79 205062740115_R05C01

description:
B79
serous borderline ovarian tumor without the BRAF V600E mutation

value: BOT


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 57

tag: age

tag: dev stage

tag: tissue

tag: Sex

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

value: mg/L


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 64

tag: store cond

tag: collection date

tag: geo loc_name

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

value: estrone (DTXSID4022367)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 56

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: B88 205289440072_R08C01

description:
B88
serous borderline ovarian tumor with the BRAF V600E mutation

value: Female


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 55

tag: strain

tag: biomaterial provider

tag: birth location

tag: breeding method

value: less than limit of quantification

tag: treatment


title: B19 204361720089_R02C01

description:
B19
serous borderline ovarian tumor with the BRAF V600E mutation

tag: gender


title: B6 204361720089_R05C01

description:
B6
serous borderline ovarian tumor without the BRAF V600E mutation


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 53

value: GLTED-Duluth-wt

tag: age

tag: dev stage

tag: tissue

tag: Sex

tag: collected by


title: B33 204361720076_R08C01

description:
B33
serous borderline ovarian tumor with the BRAF V600E mutation


title: B35 204361720076_R07C01

description:
B35
serous borderline ovarian tumor without the BRAF V600E mutation


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 51

value: 5-6 dpf

tag: store cond

tag: collection date

tag: geo loc_name

tag: exposure duration

tag: measured conc


title: B37 204361720076_R06C01

description:
B37
serous borderline ovarian tumor with the BRAF V600E mutation


title: B62 204361720075_R06C01

description:
B62
serous borderline ovarian tumor with the BRAF V600E mutation


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 52

value: larvae

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 59

tag: strain

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: treatment

value: copper sulfate (DTXSID6034479)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 49

tag: age

tag: dev stage

tag: tissue

value: whole body

tag: Sex


title: 312 204361720073_R08C01

description:
312
high-grade serous ovarian carcinoma

tag: gender

value: OvCa


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 48

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

tag: collected by

tag: exposure duration


title: 11 204361720076_R01C01

description:
11
high-grade serous ovarian carcinoma


title: B60 204361720075_R07C01

description:
B60
serous borderline ovarian tumor with the BRAF V600E mutation


title: 314 204361720073_R07C01

description:
314
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 47

value: USA:Minnesota, Duluth

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc


title: B15 204361720089_R03C01

description:
B15
serous borderline ovarian tumor without the BRAF V600E mutation


title: 316 204361720073_R06C01

description:
316
high-grade serous ovarian carcinoma


title: 320 204361720073_R05C01

description:
320
high-grade serous ovarian carcinoma


title: B59 204361720076_R03C01

description:
B59
serous borderline ovarian tumor without the BRAF V600E mutation


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 43

tag: strain

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 50

tag: age

tag: dev stage

tag: tissue

tag: Sex

tag: treatment


title: 348 204361720073_R03C01

description:
348
high-grade serous ovarian carcinoma

tag: gender


title: 351 204361720073_R02C01

description:
351
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 54

tag: store cond

tag: collection date

tag: geo loc_name

tag: collected by

tag: exposure duration


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 39

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 42

tag: strain

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 41

tag: age

tag: dev stage

tag: tissue

tag: Sex

tag: treatment


title: 322 204361720073_R04C01

description:
322
high-grade serous ovarian carcinoma

tag: gender


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 40

tag: store cond

tag: collection date

tag: geo loc_name

tag: collected by

tag: exposure duration


title: 352 204361720073_R01C01

description:
352
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 45

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 38

tag: strain

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 46

tag: age

tag: dev stage

tag: tissue

tag: Sex

tag: treatment


title: 455 204361720060_R06C01

description:
455
high-grade serous ovarian carcinoma

tag: gender


title: 459 204361720060_R05C01

description:
459
high-grade serous ovarian carcinoma


title: 474 204361720060_R01C01

description:
474
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 34

tag: store cond

tag: collection date

tag: geo loc_name

tag: collected by

tag: exposure duration


title: 493 204361720058_R08C01

description:
493
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 44

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 33

tag: strain

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: extrapolated conc_units


title: 461 204361720060_R04C01

description:
461
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 36

tag: age

tag: dev stage

tag: tissue

tag: Sex

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 32

tag: store cond

tag: collection date

tag: geo loc_name

tag: collected by


title: 558 204361720058_R05C01

description:
558
high-grade serous ovarian carcinoma

tag: gender


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 31

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units


title: 607 204361720058_R03C01

description:
607
high-grade serous ovarian carcinoma


title: 610 204361720058_R01C01

description:
610
high-grade serous ovarian carcinoma


title: 470 204361720060_R02C01

description:
470
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 29

tag: strain

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: extrapolated conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 28

tag: age

tag: dev stage

tag: tissue

tag: Sex

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 30

tag: store cond

tag: collection date

tag: geo loc_name

tag: collected by

tag: treatment


title: 609 204361720058_R02C01

description:
609
high-grade serous ovarian carcinoma

tag: gender


title: 408 204361720057_R07C01

description:
408
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 27

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 25

tag: strain

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: extrapolated conc


title: 414 204361720057_R06C01

description:
414
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 26

tag: age

tag: dev stage

tag: tissue

tag: Sex

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 37

tag: store cond

tag: collection date

tag: geo loc_name

tag: collected by

tag: treatment


title: 398 204361720057_R08C01

description:
398
high-grade serous ovarian carcinoma

tag: gender


title: 415 204361720057_R05C01

description:
415
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 24

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units


title: 426 204361720057_R04C01

description:
426
high-grade serous ovarian carcinoma


title: 431 204361720057_R03C01

description:
431
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 22

tag: strain

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: extrapolated conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 23

tag: age

tag: dev stage

tag: tissue

tag: Sex

tag: extrapolated conc_units


title: 569 204361720057_R01C01

description:
569
low-grade serous ovarian carcinoma

value: lgOvCa


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 20

tag: store cond

tag: collection date

tag: geo loc_name

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: treatment


title: 439 204361720057_R02C01

description:
439
high-grade serous ovarian carcinoma

tag: gender


title: B7 204361720051_R06C01

description:
B7
serous borderline ovarian tumor without the BRAF V600E mutation

value: BOT


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 35

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: mg/L

tag: nominal conc

tag: nominal conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 21

tag: strain

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: extrapolated conc

value: estrone (DTXSID4022367)


title: B22 204361720051_R05C01

description:
B22
serous borderline ovarian tumor without the BRAF V600E mutation

value: Female


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 18

value: GLTED-Duluth-wt

tag: age

tag: dev stage

tag: tissue

tag: Sex

value: less than limit of quantification

tag: extrapolated conc_units


title: 611 204361720051_R08C01

description:
611
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 19

value: 5-6 dpf

value: larvae

tag: store cond

tag: collection date

tag: geo loc_name

tag: collected by

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 16

value: whole body

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 15

tag: strain

tag: biomaterial provider

tag: birth location

tag: nominal conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 14

tag: age

tag: dev stage

tag: breeding method

tag: extrapolated conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 17

tag: tissue

tag: Sex

tag: store cond

tag: extrapolated conc_units


title: B31 204361720051_R03C01

description:
B31
serous borderline ovarian tumor without the BRAF V600E mutation

tag: gender


title: B32 204361720051_R02C01

description:
B32
serous borderline ovarian tumor without the BRAF V600E mutation


title: 264 204361720035_R06C01

description:
264
high-grade serous ovarian carcinoma

value: OvCa


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 11

value: not determined

tag: collection date

tag: geo loc_name

tag: collected by

tag: exposure duration

tag: treatment


title: B42 204361720049_R07C01

description:
B42
serous borderline ovarian tumor with the BRAF V600E mutation


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 8

tag: strain

value: -80 deg C

tag: biomaterial provider

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: 266 204361720035_R05C01

description:
266
high-grade serous ovarian carcinoma


title: B48 204361720049_R05C01

description:
B48
serous borderline ovarian tumor with the BRAF V600E mutation


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 9

tag: age

tag: dev stage

value: USA:Minnesota, Duluth

tag: birth location

tag: breeding method

tag: nominal conc_units


title: 253 204361720035_R08C01

description:
253
high-grade serous ovarian carcinoma


title: 280 204361720035_R04C01

description:
280
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 13

tag: tissue

tag: Sex

tag: store cond

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 12

tag: collection date

tag: geo loc_name

tag: collected by

tag: exposure duration


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 5

tag: strain

tag: biomaterial provider

tag: measured conc

tag: treatment


title: 257 204361720035_R07C01

description:
257
high-grade serous ovarian carcinoma

tag: gender


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 10

tag: age

tag: dev stage

tag: birth location

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 6

tag: tissue

tag: Sex

tag: store cond

tag: breeding method

tag: nominal conc_units


title: B41 204361720049_R08C01

description:
B41
serous borderline ovarian tumor without the BRAF V600E mutation


title: 300 204361720035_R02C01

description:
300
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 7

tag: collection date

tag: geo loc_name

tag: collected by

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 4

tag: strain

tag: biomaterial provider

tag: exposure duration

tag: measured conc

tag: treatment


title: 355 204361720030_R08C01

description:
355
high-grade serous ovarian carcinoma

tag: gender


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 3

tag: age

tag: dev stage

tag: birth location

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 1

tag: tissue

tag: Sex

tag: store cond

tag: breeding method

tag: nominal conc_units

value: copper sulfate (DTXSID6034479)


title: 382 204361720030_R05C01

description:
382
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 85

tag: collection date

tag: geo loc_name

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: extrapolated conc

tag: extrapolated conc_units

value: bisphenol A (DTXSID7020182)


title: 383 204361720030_R04C01

description:
383
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 84

tag: strain

tag: biomaterial provider

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 83

tag: age

tag: dev stage

tag: birth location

tag: measured conc_units

value: mg/L


title: 375 204361720030_R06C01

description:
375
high-grade serous ovarian carcinoma

tag: gender


title: 291 204361720035_R03C01

description:
291
high-grade serous ovarian carcinoma


title: B73 204339390014_R05C01

description:
B73
serous borderline ovarian tumor without the BRAF V600E mutation

value: BOT


title: 394 204361720030_R02C01

description:
394
high-grade serous ovarian carcinoma

value: Female


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 82

value: GLTED-Duluth-wt

tag: tissue

tag: Sex

tag: store cond

tag: breeding method

tag: nominal conc


title: 306 204361720035_R01C01

description:
306
high-grade serous ovarian carcinoma


title: B76 204339390014_R03C01

description:
B76
serous borderline ovarian tumor without the BRAF V600E mutation


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 81

tag: collection date

tag: geo loc_name

tag: collected by

tag: nominal conc_units

tag: extrapolated conc


title: 353 204082600082_R07C01

description:
353
low-grade serous ovarian carcinoma

value: lgOvCa


title: B77 204339390014_R02C01

description:
B77
serous borderline ovarian tumor with the BRAF V600E mutation


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 79

tag: strain

value: 5-6 dpf

tag: biomaterial provider

tag: exposure duration

tag: measured conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to E1, sample 2

tag: age

tag: dev stage

value: larvae

tag: birth location

tag: measured conc_units

tag: treatment

value: estrone (DTXSID4022367)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 76

tag: tissue

value: whole body

tag: Sex

tag: store cond

tag: breeding method


title: B83 204339390014_R01C01

description:
B83
serous borderline ovarian tumor with the BRAF V600E mutation

tag: gender


title: 369 204082600082_R05C01

description:
369
high-grade serous ovarian carcinoma

value: OvCa


title: 387 204361720030_R03C01

description:
387
high-grade serous ovarian carcinoma


title: 360 204082600082_R06C01

description:
360
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 78

value: not determined

value: -80 deg C

tag: collection date

tag: geo loc_name

tag: collected by

tag: nominal conc

tag: nominal conc_units


title: 404 204082600082_R04C01

description:
404
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 75

tag: strain

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: exposure duration

tag: measured conc

tag: extrapolated conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 72

tag: age

tag: dev stage

tag: birth location

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: measured conc_units

tag: extrapolated conc_units


title: 127 204082600042_R07C01

description:
127
high-grade serous ovarian carcinoma


title: 421 204082600082_R03C01

description:
421
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 74

tag: tissue

tag: Sex

tag: store cond

tag: breeding method

tag: treatment

value: bisphenol A (DTXSID7020182)


title: 130 204082600042_R06C01

description:
130
low-grade serous ovarian carcinoma

tag: gender


title: 30 204082600042_R08C01

description:
30
low-grade serous ovarian carcinoma


title: 396 204361720030_R01C01

description:
396
high-grade serous ovarian carcinoma


title: 175 204082600042_R05C01

description:
175
high-grade serous ovarian carcinoma


title: 192 204082600042_R04C01

description:
192
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 68

tag: collection date

tag: geo loc_name

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: nominal conc

tag: nominal conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 71

tag: strain

tag: biomaterial provider

tag: exposure duration

tag: measured conc

value: mg/L

tag: extrapolated conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 70

tag: age

tag: dev stage

tag: birth location

tag: measured conc_units

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 69

tag: tissue

tag: Sex

tag: store cond

tag: breeding method

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 66

tag: collection date

tag: geo loc_name

tag: collected by

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 65

tag: strain

tag: biomaterial provider

tag: exposure duration

tag: nominal conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 77

tag: age

tag: dev stage

tag: measured conc

tag: extrapolated conc


title: 271 204082600042_R03C01

description:
271
high-grade serous ovarian carcinoma

tag: gender


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 64

tag: tissue

tag: Sex

tag: birth location

tag: measured conc_units

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 73

tag: store cond

tag: collection date

tag: geo loc_name

tag: breeding method

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 63

tag: strain

tag: biomaterial provider

tag: collected by

tag: exposure duration

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 67

tag: age

tag: dev stage

tag: measured conc

tag: nominal conc_units

tag: extrapolated conc


title: 313 204082600042_R02C01

description:
313
high-grade serous ovarian carcinoma

tag: gender


title: 319 203916360006_R05C01

description:
319
high-grade serous ovarian carcinoma


title: 281 203916360006_R07C01

description:
281
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 80

tag: tissue

tag: Sex

tag: birth location

tag: measured conc_units

tag: extrapolated conc_units


title: 255 203916360006_R08C01

description:
255
high-grade serous ovarian carcinoma


title: 328 204082600042_R01C01

description:
328
high-grade serous ovarian carcinoma


title: 299 203916360006_R06C01

description:
299
high-grade serous ovarian carcinoma


title: 340 203916360006_R03C01

description:
340
high-grade serous ovarian carcinoma


title: 323 203916360006_R04C01

description:
323
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 61

tag: store cond

tag: collection date

tag: geo loc_name

tag: breeding method

tag: treatment


title: 405 203916360006_R01C01

description:
405
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 59

tag: strain

tag: biomaterial provider

tag: collected by

tag: exposure duration

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 58

tag: age

tag: dev stage

tag: measured conc

tag: nominal conc_units

tag: extrapolated conc


title: 389 203916360006_R02C01

description:
389
high-grade serous ovarian carcinoma

tag: gender


title: 8 203916360004_R08C01

description:
8
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 57

tag: tissue

tag: Sex

tag: birth location

tag: measured conc_units

tag: extrapolated conc_units


title: 67 203916360004_R07C01

description:
67
high-grade serous ovarian carcinoma


title: 70 203916360004_R06C01

description:
70
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 55

tag: store cond

tag: collection date

tag: geo loc_name

tag: breeding method

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 62

tag: strain

tag: biomaterial provider

tag: collected by

tag: exposure duration

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 54

tag: age

tag: dev stage

tag: measured conc

tag: nominal conc_units

tag: extrapolated conc


title: 100 203916360004_R05C01

description:
100
high-grade serous ovarian carcinoma

tag: gender


title: 145 203916360004_R04C01

description:
145
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 53

tag: tissue

tag: Sex

tag: birth location

tag: measured conc_units

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 51

tag: store cond

tag: collection date

tag: geo loc_name

tag: breeding method

tag: treatment


title: 160 203916360004_R03C01

description:
160
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 52

tag: strain

tag: biomaterial provider

tag: collected by

tag: exposure duration

tag: nominal conc


title: 174 203916360004_R02C01

description:
174
high-grade serous ovarian carcinoma


title: 508 203911080047_R07C01

description:
508
high-grade serous ovarian carcinoma


title: Human Sertoli cells, prophylactic IFNε treatment, 48h, MOI 5, replicate 2

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Base calling was performed using Dragen BCLConvert (v3.10.11).
RNA-seq read alignment and UMI counting was performed in R (v4.1.2). The scPipe package (v1.14.0) was employed to process the data. Multiplex RNA-seq FASTQ files had already been demultiplexed and contained the I1 index and UMI sequences in the read header, but headers were reformatted using awk for compatibility with scPipe.
Read alignment was performed using the RSubread package (v2.6.4). An index was built using the Ensembl Homo sapiens GRCh38 primary assembly genome file and alignment was performed with default settings.
Aligned reads were mapped to exons using the sc_exon_mapping function with the Ensembl Homo sapiens GRCh38 v110 GFF3 genome annotation file. BAM files were processed and reads mapping to exons were associated with each individual sample using the sc_demultiplex function, taking the UMI into account, and an overall count for each gene for each was sample was generated using the sc_gene_counting function (with UMI_cor = 1).
Additional gene annotation was obtained using the biomaRt package (v2.50.1) and a DGEList object was created with the counts and gene annotation using the edgeR package (v3.36.0). A design matrix was constructed, grouping samples by treatment regime (IFNε or buffer; therapeutic or prophylactic), viral dose (MOI 5 or 10) and infection time (24 or 48 hours). Lowly expressed genes were removed using the filterByExpr function and normalisation factors were calculated using the TMM method. Counts were transformed using the voom method and a linear model was fit using the edgeR voomLmFit function.
Differential gene expression analyses were performed using the limma (v3.50.0) package. Groups were compared using the contrasts.fit function and moderated t-statistics were calculated using the eBayes function. Differentially expressed genes were determined using a false discovery rate (FDR)-adjusted p-value < 0.05.
Assembly: hg38
Supplementary files format and content: Comma-separated text fiile with UMI-corrected counts for every gene and every sample

source_name: Sertoli cells

growth_protocol: Cells were grown in Sertoli Cell Medium (ScienCell Research Laboratories Cat. #4521) at 37°C in 5% CO2, and passaged at 95% confluency (~every 3 days) using mild trypsinization as per company recommendations. Cells grown up to passage 4 were used in all experiments.

extract_protocol:
Cells were harvested 24h or 48h post-infection, using a cell scraper. Harvested cells were centrifuged to remove media, and were immediately snap frozen. RNA extraction was carried out using the RNeasy lipid tissue kit (Qiagen GmBH, Hilden, Germany) according to the manufacturer’s instructions. On-column DNAse treatment was performed using DNAse I reagent. Total RNA samples were assessed by Qubit and Bioanalyzer. Samples with a RIN over 7 were selected for RNA-seq.
Libraries were generated using an in-house multiplex RNA-seq method (version 01/09/2021) and were prepared using 25 ng of total RNA input. An 8 bp sample index and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template switching oligonucleotide. Illumina P5 was added by tagmentation by Nextera transposase and PCR and Illumina P7 was added by PCR. The library was designed so that the forward read (R1) used the standard R1 primer to sequence the cDNA in the sense direction for transcript identification. The index read (I1) used the standard i7 primer to sequence directly into the sample index and then the 10 bp UMI. Samples were prepared as two libraries, so an additional index read (I2) sequenced the i5 library index. Sequencing (R1 61 bp; I1 18 bp; I2 8 bp) was performed on a NextSeq 2000 (Illumina) P3 50 cycle run, as per the manufacturer’s instructions. On-board denaturing and clustering were done using 900 pM of library pool (Illumina Protocol 1000000109376 v3 Nov2020).

treatment_protocol: At 70% confluency, the cells were infected with Zika virus (strain PRVABC59) at a multiplicity of infection (MOI) of 5 or 10. Cultures were treated with 100IU recombinant human IFNɛ 12h before infection (prophylactic-IFNɛ) or 1h after infection (therapeutic-IFNɛ), or diluent alone (controls). (IFNɛ was generated in house as described in Stifter et al 2017; specific activity 3.62 x 104 IU/ml). Cultures were incubated for either 24 or 48 hours post virus infection.

tag: cell type

value: Sertoli cells

value: prophylactic IFNepsilon

tag: time

tag: dose

value: MOI 5

tag: replicate


title: Human Sertoli cells, prophylactic IFNε treatment, 48h, MOI 5, replicate 3


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 50

value: GLTED-Duluth-wt

tag: age

tag: dev stage

tag: tissue

tag: Sex

tag: birth location

tag: measured conc

tag: nominal conc_units

tag: extrapolated conc


title: 197 203916360004_R01C01

description:
197
high-grade serous ovarian carcinoma

tag: gender

value: Female


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 49

tag: strain

value: 5-6 dpf

value: larvae

tag: store cond

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: breeding method

tag: measured conc_units

tag: extrapolated conc_units

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 46

tag: age

tag: dev stage

value: whole body

tag: collected by

tag: exposure duration

tag: nominal conc


title: Human Sertoli cells, prophylactic IFNε treatment, 48h, MOI 5, replicate 1

tag: cell type

tag: time

tag: dose

tag: replicate


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 56

tag: strain

tag: tissue

tag: Sex

tag: store cond

tag: birth location

tag: measured conc

tag: nominal conc_units

tag: extrapolated conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 60

tag: age

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: breeding method

tag: measured conc_units

tag: extrapolated conc_units

tag: treatment


title: Human Sertoli cells, prophylactic IFNε treatment, 48h, MOI 10, replicate 3

tag: cell type

tag: time

tag: dose

value: MOI 10

tag: replicate


title: 136400_WT, control cerebral organoid day27, scRNAseq

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Analysis was done using 10x Cell Ranger 5.0.1 workflow, reference refdata-gex-GRCh38-2020-A and Seurat 4.0.1.
Fastq files were subsetted to the filtered cellular barcodes, therefore in Cell Ranger v5.0.1 reanalysis please  --force-cells 3488 for 136400_WT, --force-cells 3414 for 136401_m8neg, and --force-cells 3426 for 136401_m8pos.
Assembly: hg38
Supplementary files format and content: rds file containing integrated seurat object: integrated_seurat_object.rds

source_name: cerebral organoid

growth_protocol: Cerebral organoids were generated and cultured until day 27 as described in Hagelkruys et al, 2022 (https://doi.org/10.1126/sciadv.abo7247).

extract_protocol:
Single-cell suspensions from two cerebral organoids per condition were prepared at day 27 using 0.9×:1× Accutase/Trypsin (Gibco, 11538876) and incubated for 15 min on 37°C while shaking and dissociating manually by pipetting every 5 min. Digestion was stopped by gradually adding two volumes of cold DMEM/F-12, washed with DPBS−/− (Thermo Fisher Scientific, 14190094) plus 0.04% BSA (VWR, 9048-46-8). Cells were then filtered through a cell strainer, counted, and loaded onto a 10x Genomics controller in DPBS−/− plus 0.04% BSA according to the manufacturer’s protocol with a target cell number of 4000 cells.
Library was performed according to the manufacturer's instruction (Single Cell 3' v3, 10X Genomics)

tag: tissue

value: cerebral organoid


title: 498 203911080047_R08C01

description:
498
high-grade serous ovarian carcinoma

tag: gender

value: OvCa


title: Human Sertoli cells, prophylactic IFNε treatment, 48h, MOI 10, replicate 2


title: 136401_m8pos, MORC2-deficient cerebral organoid day27, scRNAseq

description: 10X Genomics


title: 136401_m8neg, MPHOSPH8-deficient cerebral organoid day27, scRNAseq

description: 10X Genomics


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 48

tag: strain

tag: dev stage

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

value: USA:Minnesota, Duluth

tag: birth location

tag: collected by

tag: exposure duration

tag: measured conc

tag: nominal conc


title: 509 203911080047_R06C01

description:
509
high-grade serous ovarian carcinoma


title: Human Sertoli cells, prophylactic IFNε treatment, 48h, MOI 10, replicate 1


title: Human Sertoli cells, prophylactic buffer treatment, 48h, MOI 5, replicate 3

value: prophylactic buffer


title: Human Sertoli cells, prophylactic buffer treatment, 48h, MOI 5, replicate 2


title: B2 203911080047_R04C01

description:
B2
serous borderline ovarian tumor without the BRAF V600E mutation

value: BOT


title: Human Sertoli cells, prophylactic buffer treatment, 48h, MOI 10, replicate 2


title: 410 203911080046_R08C01

description:
410
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 47

tag: age

tag: collection date

tag: geo loc_name

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: measured conc_units

value: mg/L

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

value: bisphenol A (DTXSID7020182)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 43

tag: strain

value: GLTED-Duluth-wt

tag: dev stage

tag: tissue

value: Great Lakes Toxicology & Ecology Division

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 45

value: 5-6 dpf

tag: Sex

tag: store cond

tag: birth location

tag: collected by

value: copper sulfate (DTXSID6034479)


title: Human Sertoli cells, prophylactic buffer treatment, 48h, MOI 5, replicate 1

tag: cell type

value: Sertoli cells

tag: time

tag: dose

value: MOI 5

tag: replicate


title: Human Sertoli cells, prophylactic buffer treatment, 48h, MOI 10, replicate 1

value: MOI 10


title: 605 203911080047_R05C01

description:
605
high-grade serous ovarian carcinoma

tag: gender

value: Female

value: OvCa


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 44

tag: age

value: larvae

value: whole body

value: not determined

value: -80 deg C

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: breeding method

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: Human Sertoli cells, prophylactic buffer treatment, 48h, MOI 10, replicate 3

tag: treatment

value: prophylactic buffer


title: 416 203911080046_R07C01

description:
416
high-grade serous ovarian carcinoma


title: Human Sertoli cells, therapeutic buffer treatment, 48h, MOI 5, replicate 3

value: therapeutic buffer


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 40

tag: strain

tag: dev stage

tag: tissue

tag: Sex

tag: store cond

value: USA:Minnesota, Duluth

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

value: mg/L

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 42

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: collection date

tag: geo loc_name

tag: collected by

value: Great Lakes Toxicology & Ecology Division

value: bisphenol A (DTXSID7020182)


title: Human Sertoli cells, therapeutic IFNε treatment, 48h, MOI 5, replicate 2

tag: cell type

value: Sertoli cells

value: therapeutic IFNepsilon

tag: time

tag: dose

value: MOI 5

tag: replicate


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 39

tag: strain

value: larvae

tag: biomaterial provider

tag: breeding method

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc

tag: treatment


title: Human Sertoli cells, therapeutic IFNε treatment, 48h, MOI 5, replicate 3


title: Human Sertoli cells, therapeutic IFNε treatment, 48h, MOI 10, replicate 3

value: MOI 10


title: Human Sertoli cells, therapeutic buffer treatment, 48h, MOI 5, replicate 2


title: 430 203911080046_R05C01

description:
430
high-grade serous ovarian carcinoma

tag: gender

value: Female

value: OvCa


title: Human Sertoli cells, therapeutic buffer treatment, 48h, MOI 5, replicate 1


title: Human Sertoli cells, therapeutic buffer treatment, 48h, MOI 10, replicate 3


title: Human Sertoli cells, therapeutic IFNε treatment, 48h, MOI 10, replicate 2


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 41

tag: age

tag: dev stage

tag: tissue

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

tag: birth location

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 37

tag: strain

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: collected by


title: 454 203911080046_R03C01

description:
454
high-grade serous ovarian carcinoma


title: 492 203911080046_R02C01

description:
492
high-grade serous ovarian carcinoma


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 38

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: mg/L

tag: nominal conc


title: Human Sertoli cells, therapeutic buffer treatment, 48h, MOI 10, replicate 2

tag: cell type

tag: treatment

value: therapeutic buffer

tag: time

tag: dose

tag: replicate


title: Human Sertoli cells, therapeutic IFNε treatment, 48h, MOI 5, replicate 1


title: Human Sertoli cells, therapeutic IFNε treatment, 48h, MOI 10, replicate 1


title: Human Sertoli cells, therapeutic buffer treatment, 48h, MOI 10, replicate 1


title: 495 203911080046_R01C01

description:
495
high-grade serous ovarian carcinoma

tag: gender


title: 420 203911080046_R06C01

description:
420
high-grade serous ovarian carcinoma


title: Human Sertoli cells, prophylactic IFNε treatment, 24h, MOI 5, replicate 3

value: prophylactic IFNepsilon


title: Human Sertoli cells, prophylactic IFNε treatment, 24h, MOI 10, replicate 2


title: Human Sertoli cells, prophylactic IFNε treatment, 24h, MOI 5, replicate 1


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 36

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

tag: tissue

tag: Sex

tag: store cond

tag: birth location

value: Great Lakes Toxicology & Ecology Division

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

value: bisphenol A (DTXSID7020182)


title: Human Sertoli cells, prophylactic IFNε treatment, 24h, MOI 10, replicate 1

value: Sertoli cells


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 35

tag: strain

value: larvae

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: breeding method

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units


title: UT-TERT cells PFOS treated2

city: Omaha

first: Kendra

last: Clark

state: Nebraska

address: 560 South 45th street

institute: University of Nebraska Medical Center

data_processing:
The nf-core pipeline trim the fastq files using cutadapt (Martin & Marcel 2011) and trimgalore to remove adapters, terminal unknown bases (Ns) and low-quality 3’ regions (Phred score < 30).
The trimmed fastq files were mapped to the hg38 Human reference genome using the nf-core v3.14.0 (Ewels et al., 2020) pipeline in Nextflow v23.10.1 (Di Tommaso et al., 2017) to perform the RNAseq analysis.
Assembly: GRCh38.p14 (GCA_000001405.29)
Supplementary files format and content: The text files give normalized expression abundance in Count, TPM and FPKM values for all the available genes.

source_name: UT-TERT

extract_protocol:
Total RNA was isolated from control and PFAS treated cells using the Zymo Direct-zol Microprep Kit
Libraries were prepped using 75 Universal Plus™ mRNA-Seq with NuQuant (Tecan Genomics, Morgan Hill, CA). Starting amount of RNA was 50 ng and procedure followed per manufacturers recommendations.

tag: cell line

value: UT-TERT

tag: treatment

value: PFAS -PFOS


title: Human Sertoli cells, prophylactic IFNε treatment, 24h, MOI 10, replicate 3

tag: cell type

tag: time

tag: dose

value: MOI 10

tag: replicate


title: 452 203911080046_R04C01

description:
452
high-grade serous ovarian carcinoma

tag: gender

value: Female

value: OvCa


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 34

tag: age

tag: dev stage

tag: tissue

value: whole body

tag: Sex

value: not determined

tag: store cond

value: -80 deg C

value: USA:Minnesota, Duluth

tag: birth location

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

value: copper sulfate (DTXSID6034479)


title: UT-TERT cells PFOS treated3

tag: cell line


title: Human Sertoli cells, prophylactic buffer treatment, 24h, MOI 5, replicate 2

tag: treatment

value: prophylactic buffer

value: MOI 5


title: Human Sertoli cells, prophylactic buffer treatment, 24h, MOI 5, replicate 1

tag: cell type


title: UT-TERT cells PFOS treated1


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 33

tag: strain

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: collection date

tag: geo loc_name

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: mg/L


title: Human Sertoli cells, prophylactic buffer treatment, 24h, MOI 5, replicate 3

value: Sertoli cells

tag: time

tag: dose

tag: replicate


title: Human Sertoli cells, prophylactic buffer treatment, 24h, MOI 10, replicate 2


title: UT-TERT cells PFOA treated3

value: UT-TERT

value: PFAS -PFOA


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 31

tag: age

tag: dev stage

value: larvae

tag: tissue

tag: Sex

tag: store cond

tag: birth location

value: Great Lakes Toxicology & Ecology Division

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

value: bisphenol A (DTXSID7020182)


title: Human Sertoli cells, prophylactic buffer treatment, 24h, MOI 10, replicate 1

tag: cell type

tag: treatment

value: MOI 10


title: Human Sertoli cells, prophylactic buffer treatment, 24h, MOI 10, replicate 3


title: Human Sertoli cells, prophylactic IFNε treatment, 24h, MOI 5, replicate 2

value: prophylactic IFNepsilon


title: Human Sertoli cells, therapeutic IFNε treatment, 24h, MOI 5, replicate 3

value: therapeutic IFNepsilon


title: UT-TERT cells PFOA treated1

tag: cell line


title: Human Sertoli cells, therapeutic IFNε treatment, 24h, MOI 5, replicate 2


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 30

tag: strain

value: whole body

value: not determined

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

tag: breeding method

tag: collected by

tag: exposure duration

tag: measured conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 29

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

tag: tissue

tag: Sex

tag: store cond

tag: measured conc_units


title: Human Sertoli cells, therapeutic IFNε treatment, 24h, MOI 10, replicate 3

tag: cell type

tag: treatment

tag: time

tag: dose

tag: replicate


title: UT-TERT cells PFBS treated2

tag: cell line

value: PFAS -PFBS


title: Human Sertoli cells, therapeutic IFNε treatment, 24h, MOI 10, replicate 1


title: Human Sertoli cells, therapeutic buffer treatment, 24h, MOI 5, replicate 3

value: therapeutic buffer

value: MOI 5


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 28

tag: strain

tag: collection date

tag: geo loc_name

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

value: mg/L

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc


title: Human Sertoli cells, therapeutic IFNε treatment, 24h, MOI 10, replicate 2

value: Sertoli cells


title: UT-TERT cells PFBS treated1

value: UT-TERT


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 27

tag: age

tag: dev stage

value: larvae

tag: tissue

tag: Sex

tag: store cond

tag: collected by

value: Great Lakes Toxicology & Ecology Division

tag: exposure duration

tag: measured conc

tag: extrapolated conc_units

value: bisphenol A (DTXSID7020182)


title: Human Sertoli cells, therapeutic buffer treatment, 24h, MOI 5, replicate 2

tag: cell type

tag: treatment

tag: time

tag: dose

tag: replicate


title: Human Sertoli cells, therapeutic buffer treatment, 24h, MOI 10, replicate 2

value: MOI 10


title: UT-TERT cells PFOA treated2

tag: cell line

value: PFAS -PFOA


title: UT-TERT cells mix treated3

value: PFAS -MIX


title: Human Sertoli cells, therapeutic buffer treatment, 24h, MOI 10, replicate 3


title: Human Sertoli cells, therapeutic buffer treatment, 24h, MOI 5, replicate 1


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 26

tag: strain

value: whole body

value: not determined

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units


title: UT-TERT cells mix treated1


title: Testis, wild type, mouse WT28, batch 2

data_processing:
Base calling was performed using Dragen BCLConvert (v3.10.11).
RNA-seq read alignment and UMI counting was performed in R (v4.1.2). The scPipe package (v1.14.0) was employed to process the data. Multiplex RNA-seq FASTQ files had already been demultiplexed and contained the I1 index and UMI sequences in the read header, but headers were reformatted using awk for compatibility with scPipe.
Read alignment was performed using the RSubread package (v2.6.4). An index was built using the Ensembl Mus musculus GRCm39 top level genome file and alignment was performed with default settings.
Aligned reads were mapped to exons using the sc_exon_mapping function with the Ensembl Mus musculus GRCm39 v109 GFF3 genome annotation file. BAM files were processed and reads mapping to exons were associated with each individual sample using the sc_demultiplex function, taking the UMI into account, and an overall count for each gene for each was sample was generated using the sc_gene_counting function (with UMI_cor = 1).
Additional gene annotation was obtained using the biomaRt package (v2.50.1) and a DGEList object was created with the counts and gene annotation using the edgeR package (v3.36.0). A design matrix was constructed, grouping samples by genotype (WT or Ifne KO), also incorporating the sequencing batch. Lowly expressed genes were removed using the filterByExpr function and normalisation factors were calculated using the TMM method. Counts were transformed using the voom method and a linear model was fit using the edgeR voomLmFit function. Sample weights were incorporated and donor was used as a blocking factor, as there were technical replicates of mice WT10, Ifne13 and Ifne16 across the two sequencing batches.
Differential gene expression analyses were performed using the limma (v3.50.0) package. Groups were compared using the contrasts.fit function and moderated t-statistics were calculated using the eBayes function. Differentially expressed genes were determined using a false discovery rate (FDR)-adjusted p-value < 0.05.
Assembly: mm39
Supplementary files format and content: Comma-separated text fiile with UMI-corrected counts for every gene and every sample

organism: Mus musculus

source_name: Testis

growth_protocol: Sexually mature male mice aged between 8–12 weeks were used in these experiments. IFNε-/- mice on C57BL/6J background were maintained in standard specific pathogen-free (SPF) conditions. Age matched C57BL/6J (WT) mice were used as controls, since the colony was maintained as a homozygous only colony, and therefore obtaining littermate controls was not possible. WT mice were purchased from Monash Animal Services Animals and were acclimatised for one week. All animal experiments were approved by the Monash Medical Centre Animal Ethics Committee and the Monash Animal Research Platform Animal Ethics Committee, and were performed in strict accordance with the National Health and Medical Research Council Code of Practice for the Care and Use of Animals for Experimental Purposes.

extract_protocol:
Total cellular RNA was extracted from snap frozen testes, using the RNeasy mini kit (QIAGEN GmBH, Hilden, Germany) with on-column DNAse treatment, following manufacturer's instructions. Total RNA concentration was quantified by Qubit (Invitrogen) and quality checked by Bioanalyzer (Agilent) or capillary electrophoresis (BiOptic QSep100). RNA samples with an RNA integrity number ≥7.0 were used for RNA-seq analysis.
Libraries were generated using an in-house multiplex RNA-seq method (version 01/09/2021) and were prepared using 25 ng (batch 1) or 30 ng (batch 2) of total RNA input. An 8 bp sample index and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template switching oligonucleotide. Illumina P5 was added by tagmentation by Nextera transposase and PCR and Illumina P7 was added by PCR. The library was designed so that the forward read (R1) used the standard R1 primer to sequence the cDNA in the sense direction for transcript identification. The index read (I1) used the standard i7 primer to sequence directly into the sample index and then the 10 bp UMI. Sequencing (R1 up to 111 bp; I1 18 bp) was performed on a NextSeq 2000 (Illumina) P2 100 cycle run, as per the manufacturer’s instructions. On-board denaturing and clustering were done using 900 pM of library pool (Illumina Protocol 1000000109376 v3 Nov2020).

treatment_protocol: Adult wildtype mice (WT) and Ifne-/- mice lacking IFNe were culled using carbon dioxide overdose at the age of 8–12 weeks. Serum and reproductive tract organs were collected for analysis.

tag: tissue

value: Testis

tag: genotype

value: WT

value: PBS

tag: donor

tag: batch


title: Human Sertoli cells, therapeutic buffer treatment, 24h, MOI 10, replicate 1

tag: cell type

tag: treatment

value: therapeutic buffer

tag: time


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 24

value: GLTED-Duluth-wt

tag: age

value: 5-6 dpf

tag: dev stage

tag: Sex

tag: store cond

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

value: mg/L

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to bisphenol A, sample 25

tag: strain

value: larvae

tag: collection date

tag: geo loc_name

tag: biomaterial provider

tag: birth location

tag: breeding method

value: Great Lakes Toxicology & Ecology Division

tag: measured conc_units

tag: nominal conc

tag: nominal conc_units

value: bisphenol A (DTXSID7020182)


title: UT-TERT cells genx treated3

tag: cell line

value: UT-TERT

tag: treatment

value: PFAS -GENX


title: Human Sertoli cells, therapeutic IFNε treatment, 24h, MOI 5, replicate 1

tag: cell type

value: Sertoli cells

value: therapeutic IFNepsilon

tag: time

tag: dose

value: MOI 5

tag: replicate


title: Testis, wild type, mouse WT29, batch 2

tag: tissue

value: Testis

tag: genotype

tag: donor

tag: batch