title: BSseq_RIL242_rep1

description:
Bisulfite-treated genomic DNA
Read length: 40x40
Processed data file: RIL242_genotypes.bed

source_name: rosette leaves, Col/Cvi RIL242

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol sequenced on 10/03/14 with index TAGCTT.

value: Col/Cvi RIL242


title: BSseq_RIL332_rep2

status: Public on Mar 29 2017

type: SRA

city: Cambridge

first: Mary

last: Gehring

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

description:
Bisulfite-treated genomic DNA
Read length: 40x40, 100x100, 50x50
Processed data file: RIL332_genotypes.bed

library_source: genomic

data_processing:
For all libraries: FastQC was used to examine read quality. Low-quality reads were removed with trim_galore with parameters --clip_R1 8, --clip_R2 8, --stringency 3, -q 25, -r1 32, -r2 32 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/, version from 16 July 2014).
For all libraries: reads were initially aligned to a Col-Cvi “metagenome", created by substituting the Cvi allele of all SNPs into the TAIR10 assembly, then appending this pseudogenome to the TAIR10 (Col) sequence. Reads mapping ambiguously to the metagenome due to lack of SNPs in an area were then remapped to TAIR10. All reads were then filtered based on overlapping SNPs into reads definitively from Col, reads from Cvi, and all other reads. Bisulfite libraries were mapped using bismark v0.16.1 with parameters -N 1 and -L 40, and RNA-seq libraries were mapped using tophat v.2.0.13 with parameters -I 10000, -N 1 and --segment-length 20. All other parameters default.
Mapped bisulfite reads were further filtered to remove presumed PCR duplicates using a custom script provided with Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/), which removes duplicates randomly to minimize bias. Methylation information was then extracted using bismark_methylation_extractor. Resulting data were processed into BED-like format (see file description below) and saved with file format BSseq_{sample}_{context}.txt, where sample is the sample name (e.g. Col_1) and context is CpG, CHG or CHH (see below).
RIL genotypes were reconstructed using the depth of BS-seq reads overlapping SNPs. Coverage of reads overlapping SNPs was determined over 200bp windows for Col reads and Cvi reads separately, then smoothed using a moving average over 51 windows (centered) before calling putative genotype for each region.
htseq-count v0.6.1p1 was used to obtain total read counts for each gene from the mapped RNA-seq reads, with parameters -m union, with --stranded reverse. FPKM values were obtained using Cufflinks v2.2.1 (http://cole-trapnell-lab.github.io/cufflinks/), using a GTF file of the Araport11 A. thaliana annotations, --library-type fr-firststrand and all other parameters default.
Genome_build: Sequence used was A. thaliana TAIR10, annotations used were Araport 11 (https://www.araport.org/data/araport11),
Supplementary_files_format_and_content: BSseq_{sample}_{rep}_{context}.txt = per-cytosine methylation information for each sample (2 reps each) in each context (CpG, CHG and CHH), in BED-like format. First three fields indicate location of the cytosine (BED-like format, 0-based), fourth field is number of unmethylated reads at that position, fifth is number of methylated reads and sixth is % reads methylated. For CG data, data on the positive and negative strand have been combined into a single record by summing the methylated and unmethylated reads on each strand, and a seventh field indicates whether that CG contained data on only the forward strand (1), reverse strand (-1) or both (2).
Supplementary_files_format_and_content: RNAseq_{sample}_stats.txt contains RNA-seq data in tab-delimited format for each sample, with one row per gene. Contains gene ID (gene_id), gene coordinates (locus), FPKM (FPKM) and number of RNA-seq reads aligned to gene (raw_read_counts).
Supplementary_files_format_and_content: RIL{ril}_genotypes.bed contains consensus Col and Cvi regions in the indicated RIL (consensus = same in both replicates) in BED format, where the first three fields indicate a genomic region, and the fourth indicates whether that region is Col- or Cvi-genotype. Regions not covered in this BED file are undetermined - either inconsistent between replicates, unknown (e.g. around centromeres) or heterozygous.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: rosette leaves, Col/Cvi RIL332

growth_protocol: Plants were grown in a greenhouse with 16h light at 21C. Approx. 100mg leaf tissue was harvested from 3-wk-old rosettes.

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol with index GCCAAT sequenced on 03/11/16 (40x40), 03/31/16 (100x100) and 04/13/16 (50x50).

treatment_protocol: No treatment.

tag: strain/background

value: Col/Cvi RIL332

tag: generation

tag: age

value: 3 weeks

tag: tissue

value: rosette leaves


title: Brain_12months_female_0ppb_rep3

status: Public on Nov 30 2017

type: RNA

city: West Lafayette

first: Jennifer

last: Freeman

state: IN

address: 550 Stadium Mall Drive

department: School of Health Sciences

institute: Purdue University

description: Gene expression in 12 months aged brain after a developmental exposure to 0ppb lead

hyb_protocol: Cy3-labeled cDNA samples were mixed with hybridization mix containing 2X Hybridization Buffer, Hybridization Component A, and Alignment Oligo using NimbleGen Hybridization Kit, according to the manufacturers recommendations (Roche NimbleGen, Madison, WI). The samples were incubated at 95°C on a heat block for 5 miniutes for denaturation, and then placed on arrays and hybridized at 42°C overnight on a Thermobrite StatSpin® (Abbott Molecular, Inc., Abbott Park, IL) . Following the hybridization, array slides were washed using Wash Buffer I, II, and III in NimbleGen Wash Buffer Kit (Roche NimbleGen, Madison, WI), and then air-dried briefly.

scan_protocol: Array slides were scanned on SureScan Agilent microarray scanner (G2600D) with one-color scan setting (Scan region, 61 x 21.6 mm; Scan resolution, 2um; Tiff file dyamic range, 20 bit; Dye channel, Green; Green PMT gain, 100%).

data_processing: Array images were extracted with NimbleGen DEVA software (Roche NimbleGen, Madison, WI) in which fluorescence signal intensity values were normalized using quantile normalization and gene calls were generated using the Robust Multichip Average (RMA) algorithm, and then array data were analyzed on Array Star (DNASTAR, Inc., Madison, WI).

molecule: total RNA

organism: Danio rerio

source_name: Brain, 12months old female zebrafish, 0ppb lead, replicate 3

label_protocol: cDNA was labeled using the NimbleGen One-Color DNA Labeling Kit, following the manufacturer's instructions (Roche NimbleGen, Madison, WI). Quality (Yield and specificity) of cy3 labeled cRNA was measured on Drop® ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE).

growth_protocol: Zebrafish (AB stain) were cultured in a Z-Mod System (Aquatic Habitats, Apopka, FL) under a 14:10 light:dark cycle at 28℃. Water quality parameters (conductivity, pH, and temperature) were regulary checked.

extract_protocol: Zebrafish brains dissected at12 months of age were homogenized in Trizol Reagent (Life Technologies, Carlsbad, CA) and stored at -80ºC until RNA isolation. Total RNA was extracted according to established protocols as descrived in Peterson and Freeman (2009) and then purified using the RNeay Mini Kit (Qiagen, Valencia, CA) following manufacturer’s recommendation. Quality and quantity of purified RNA samples were checked on the NanoDrop® ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE).

treatment_protocol: Zebrafish embryos at <2 hours post fertilization (hpf) were developmentally treated with 0ppb or 100ppb lead acetate until 72 hpf. Following the lead exposure, the embryos were washed and transferred to clean aquaria water with no lead treatment. Fish were grown until 12 months of age at which brains were subjected to RNA extraction and then cDNA synthesis for further microarray analysis.

tag: strain

value: AB

value: 12 months old

tag: Sex

value: female

value: brain


title: BSseq_RIL242_rep2

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol sequenced on 10/03/14 with index GGCTAC.


title: BSseq_RIL124_rep2

description:
Bisulfite-treated genomic DNA
Read length: 40x40
Processed data file: RIL124_genotypes.bed

source_name: rosette leaves, Col/Cvi RIL124

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol sequenced on 10/03/14 with index CTTGTA.

value: Col/Cvi RIL124


title: BSseq_RIL124_rep1

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol sequenced on 10/03/14 with index GCCAAT.


title: BSseq_RIL22_rep2

description:
Bisulfite-treated genomic DNA
Read length: 40x40
Processed data file: RIL22_genotypes.bed

source_name: rosette leaves, Col/Cvi RIL22

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol with index ACAGTG sequenced on 12/09/16.

value: Col/Cvi RIL22


title: BSseq_RIL22_rep1

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol with index ATCACG sequenced on 12/09/16.


title: BSseq_RIL84_rep1

description:
Bisulfite-treated genomic DNA
Read length: 40x40
Processed data file: RIL84_genotypes.bed

source_name: rosette leaves, Col/Cvi RIL84

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol with index CGATGT sequenced on 12/09/16.

value: Col/Cvi RIL84


title: BSseq_RIL8_rep2

description:
Bisulfite-treated genomic DNA
Read length: 40x40, 100x100, 50x50
Processed data file: RIL8_genotypes.bed

source_name: rosette leaves, Col/Cvi RIL8

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol with index TAGCTT sequenced on 03/11/16 (40x40), 03/31/16 (100x100), and 04/13/16 (50x50).

value: Col/Cvi RIL8


title: BSseq_RIL84_rep2

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol with index GCCAAT sequenced on 12/09/16 .


title: BSseq_RIL8_rep1

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol with index TGACCA sequenced on 03/11/16 (40x40), 03/31/16 (100x100) and 04/13/16 (50x50).


title: BSseq_Cvi_rep2

description:
Bisulfite-treated genomic DNA
Read length: 40x40, 100x100, 50x50

source_name: rosette leaves, Cvi-0 parent line

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol with index GATCAG sequenced on 03/11/16 (40x40), 03/31/16 (100x100) and 04/13/16 (50x50).

value: Cvi-0 parent line


title: BSseq_Cvi_rep1

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol with index CGATGT sequenced on 03/11/16 (40x40), 03/31/16 (100x100) and 04/13/16 (50x50).


title: BSseq_Col_rep2

source_name: rosette leaves, Col-0 parent line

extract_protocol:
Harvested leaf tissue was pulverized using the Qiagen TissueLyser II. For bisulfite-sequencing, DNA was extracted using the Qiagen DNeasy Plant Mini kit (cat. No. 69104). For RNA-seq, total RNA was isolated using the RNeasy plant mini kit (Qiagen, cat. no. 74903).
For bisulfite sequencing, between 100 and 500ng DNA was bisulfite-converted using the MethylCode bisulfite conversion kit (Invitrogen). Libraries were prepared using the EpiGnome Methyl-seq kit from Epicentre (now the TruSeq DNA methylation kit from Illumina, cat no. EGMK81312), using all bisulfite-converted DNA. Reads were sequenced on an Illumina HiSeq 2000 to obtain 40x40, 50x50 and 100x100bp paired-end reads.
Illumina TruSeq DNA methylation protocol with index TTAGGC sequenced on 03/11/16 (40x40), 03/31/16 (100x100) and 04/13/16 (50x50).

value: Col-0 parent line


title: Wild-type_0 hr_replicate 2

status: Public on Feb 17 2017

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55mL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent custom zebrafish 4X180K Microarrays (060509) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Arrays were scanned on an Agilent Technologies SureScan Microarray Scanner (Agilent Technologies, Santa Clara, CA).

data_processing: Array image data was extracted using Agilent Feature Extraction Software 11.5 (Agilent Technologies, Santa Clara, CA). Array image data was then uploaded to GeneSpring 12.5 (Agilent Technologies, Santa Clara, CA) for statistical analysis. Each gene list was imported into Ingenuity Pathway Analysis (IPA) for gene ontology and molecular pathway analysis (GeneSpring Probe List_* hour.xlsx provided as Series supplementary files).

source_name: Wild-type_0 hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the One-Color Low Input QuickAmp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The zebrafish experiment was conducted in accordance to the internationally accepted standards. The Animal Care and Use Protocol was approved by The Purdue Animal Care and Use Committee (PACUC), adhering to the Guidelines for Use of Zebrafish in the NIH Intramural Research Program (Protocol number: 1401001018).

extract_protocol: Embryos were collected at 0 hpw, 1 hpw, and 6 hpw. Total RNAs were extracted with Trizol (Invitrogen) and further cleaned up with RNeasy MinElute kit (Qiagen). The quality and integrity of RNAs were confirmed using Agiloent Nano RNA QC chip (Sequencing Center of Purdue University).

treatment_protocol:
To generate a miR-223 deficient fish line, two individual single guide RNAs (sgRNAs) targeting pre-miR-223 were designed: sgRNA1 binding site: 5’-TTAGAGTATTTGACAGACTG-3’, and sgRNA2 binding site: 5’-TTTGTCAAATACCCCAAGAG-3’. The T7 promoter and the scaffold were added using overlapping PCR with the following primers listed from 5’ to 3’:
sgRNA1-P1: GCGGCCTCTAATACGACTCACTATAGGGTTAGAGTATTTGACAGACTGGTTTTAGAGCTA, sgRNA1-P2: TGACAGACTGGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC, sgRNA1-P3: GATCCGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACT; sgRNA2-P1: GCGGCCTCTAATACGACTCACTATAGGGTTTGTCAAATACCCCAAGAGGTTTTAGAGCTA, sgRNA2-P2: ACCCCAAGAGGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC, sgRNA2-P3: GATCCGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACT. sgRNAs were synthesized by in vitro transcription using MEGAshortscript T7 kit (Invitrogen) using the purified PCR products as template. To make cas9 mRNA, the plasmid pT3TS-nCas9n (Addgene Plasmid #46757)1 was linearized by XbaI and purified. Cas9 mRNA was generated using mMESSAGE mMACHINE T3 kit (Invitrogen). The mix of sgRNA1 (100 ng/ul), sgRNA2 (100 ng/ul) and cas9 mRNA (150 ng/ul) was injected into one-cell stage embryos. The embryos were raised to sexual maturity and the F1s were screened by sequencing the miR-223 locus. The homozygous mutant were obtained after several generations of backcross and incross.
To generate transgenic zebrafish lines, plasmids containing the tol2 backbone was coinjected with transposase mRNA into embryos at one-cell stage as described2. The construct tol2-lyzC-Gal4-Vp16-cyrs-CFP was generated with Gateway Cloning (Thermo Fisher) using the tol2 kit to make Tg(lyzc: Gal4-Vp16; crys: CFP)pu8. Founders were screened with green eyes.
To generate a miR-223 over expression line, Tg(lyzC: RFP-miR-223) pu9, a 317 bp genomic DNA sequence containing miR-223 was PCR amplified using the following primers listed from 5’ to 3’: forward CTGGCAGTACGGGCTCAGGAGGAAGAGGGAGGAGTAAAATTGAAT, reverse TAACAGCAGTTGGCTAATGAATGTTGTCATCCTCCACATTTTGCA, and cloned into the BbsI site in the intron of the vector3. GFP was replaced by RFP and then inserted into a Tol2 backbone with lyzC promoter. A transgenic line expressing the empty backbone, Tg(lyzC: RFP) pu10 was generated as the control.
To generate miR223 sponge line, Tg(krt4: RFP-miR-223 sponge)pu12, a sequence containing six copies of bulged miR-223 binding sites was synthesized as a gBlocks Gene Fragment (Integrated DNA Technologies) and inserted downstream of RFP in a pME construct. The final construct was generated by Gateway Cloning. Founders were selected with red apical epithelial cells. A line with RFP Tg(krt4: RFP) pu13 was made as the control. The line Tg(krt4: GFP) pu11 was also generated for cell sorting.
More than one founders were obtained for each line and their offspring display similar phenotypes.
To generate a miR-223 deficient fish line, two individual single guide RNAs (sgRNAs) targeting pre-miR-223 were designed: sgRNA1 binding site: 5’-TTAGAGTATTTGACAGACTG-3’, and sgRNA2 binding site: 5’-TTTGTCAAATACCCCAAGAG-3’. The T7 promoter and the scaffold were added using overlapping PCR with the following primers listed from 5’ to 3’:
sgRNA1-P1: GCGGCCTCTAATACGACTCACTATAGGGTTAGAGTATTTGACAGACTGGTTTTAGAGCTA, sgRNA1-P2: TGACAGACTGGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC, sgRNA1-P3: GATCCGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACT; sgRNA2-P1: GCGGCCTCTAATACGACTCACTATAGGGTTTGTCAAATACCCCAAGAGGTTTTAGAGCTA, sgRNA2-P2: ACCCCAAGAGGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC, sgRNA2-P3: GATCCGCACCGACTCGGTGCCACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACT. sgRNAs were synthesized by in vitro transcription using MEGAshortscript T7 kit (Invitrogen) using the purified PCR products as template. To make cas9 mRNA, the plasmid pT3TS-nCas9n (Addgene Plasmid #46757)1 was linearized by XbaI and purified. Cas9 mRNA was generated using mMESSAGE mMACHINE T3 kit (Invitrogen). The mix of sgRNA1 (100 ng/ul), sgRNA2 (100 ng/ul) and cas9 mRNA (150 ng/ul) was injected into one-cell stage embryos. The embryos were raised to sexual maturity and the F1s were screened by sequencing the miR-223 locus. The homozygous mutant were obtained after several generations of backcross and incross.
To generate transgenic zebrafish lines, plasmids containing the tol2 backbone was coinjected with transposase mRNA into embryos at one-cell stage as described2. The construct tol2-lyzC-Gal4-Vp16-cyrs-CFP was generated with Gateway Cloning (Thermo Fisher) using the tol2 kit to make Tg(lyzc: Gal4-Vp16; crys: CFP)pu8. Founders were screened with green eyes.
To generate a miR-223 over expression line, Tg(lyzC: RFP-miR-223) pu9, a 317 bp genomic DNA sequence containing miR-223 was PCR amplified using the following primers listed from 5’ to 3’: forward CTGGCAGTACGGGCTCAGGAGGAAGAGGGAGGAGTAAAATTGAAT, reverse TAACAGCAGTTGGCTAATGAATGTTGTCATCCTCCACATTTTGCA, and cloned into the BbsI site in the intron of the vector3. GFP was replaced by RFP and then inserted into a Tol2 backbone with lyzC promoter. A transgenic line expressing the empty backbone, Tg(lyzC: RFP) pu10 was generated as the control.
To generate miR223 sponge line, Tg(krt4: RFP-miR-223 sponge)pu12, a sequence containing six copies of bulged miR-223 binding sites was synthesized as a gBlocks Gene Fragment (Integrated DNA Technologies) and inserted downstream of RFP in a pME construct. The final construct was generated by Gateway Cloning. Founders were selected with red apical epithelial cells. A line with RFP Tg(krt4: RFP) pu13 was made as the control. The line Tg(krt4: GFP) pu11 was also generated for cell sorting.
More than one founders were obtained for each line and their offspring display similar phenotypes.

tag: genotype/variation

value: wild type

value: Embryo

value: 0 hpw


title: Wild-type_1 hr_replicate 2

source_name: Wild-type_1 hr

value: 1 hpw


title: Wild-type_1 hr_replicate 4


title: Wild-type_0 hr_replicate 4


title: Wild-type_6 hr_replicate 3

source_name: Wild-type_6 hr

value: 6 hpw


title: Wild-type_1 hr_replicate 1


title: Knock-out_6 hr_replicate 4

source_name: Knock-out_6 hr

value: miR-223 deficient; knock-out


title: 46.3 um - replicate 1

status: Public on Feb 20 2017

type: genomic

description:
72 hours = ~1.5 cell cycle lengths
46.3_R1

hyb_protocol: Hybridization was performed following Agilent's protocol (version 7.3) for two color hybridization.

scan_protocol: Arrays were scanned on a SureScan microarray scanner (Agilent Technologies, Santa Clara, CA) at 3 microns.

data_processing:
Array image data was extracted using Agilent Feature Extraction Software 11.5 (Agilent Technologies, Santa Clara, CA).  Microarray analysis was performed following MIAME guidelines. aCGH analysis was completed using Agilent Genomic Workbench 7.0.4 following the aberration detection method 2 (ADM2) algorithm. ADM2 identifies all aberrant intervals in a given sample with consistently high or low log ratios based on statistical score. The ADM2 algorithm searches for intervals in which a statistical score based on the average quality weighted log ratio of the sample and reference channels exceeds a user specific threshold and reports contiguous genomic regions as aberrant regions.
Calls were determined which contained at least six consecutive probes to obtain a high degree of confidence (Agilent Technologies, Santa Clara, CA).

source_name: Zebrafish fibroblast cells exposed to 46.3 um atrazine for 72 hours

label_protocol: Labeling was performed following Agilent's protocol (version 7.3) for two color hybridization. Test DNA was labeled with Cy5 and the control treatment labeled with Cy3.

growth_protocol: 7.5 x 10^5 cells were initially seeded into each petri dish. After set-up, petri dishes were placed in an incubator at 28°C and 5% CO2 for 72 hours (the equivalent of 1.5 cell cycle lengths).

extract_protocol: After 72 hours, cells were harvested and genomic DNA was isolated following a standard phenol:chloroform isolation method.

treatment_protocol: Cells were exposed to either 0, 0.463, 4.63, or 46.3 um atrazine for 72 hours.

tag: agent

value: atrazine

tag: dose

tag: cell type

value: fibroblast

source_name: Zebrafish fibroblast cells exposed to 0 um atrazine

value: control


title: Knock-out_0 hr_replicate 4

source_name: Knock-out_0 hr


title: 4.63 um - replicate 1

description:
72 hours = ~1.5 cell cycle lengths
4.63_R1

source_name: Zebrafish fibroblast cells exposed to 4.63 um atrazine for 72 hours


title: Wild-type_0 hr_replicate 3


title: Knock-out_1 hr_replicate 3

source_name: Knock-out_1 hr


title: Knock-out_1 hr_replicate 2


title: Wild-type_6 hr_replicate 1


title: Knock-out_6 hr_replicate 3


title: Wild-type_0 hr_replicate 1


title: Knock-out_6 hr_replicate 2


title: Knock-out_0 hr_replicate 3


title: Knock-out_0 hr_replicate 2


title: Wild-type_1 hr_replicate 3


title: 0.463 um - replicate 1

description:
72 hours = ~1.5 cell cycle lengths
0.463_R1

source_name: Zebrafish fibroblast cells exposed to 0.463 um atrazine for 72 hours


title: 0.463 um - replicate 3

description:
72 hours = ~1.5 cell cycle lengths
0.463_R3


title: Wild-type_6 hr_replicate 2


title: Knock-out_1 hr_replicate 4


title: Wild-type_6 hr_replicate 4


title: 46.3 um - replicate 2

description:
72 hours = ~1.5 cell cycle lengths
46.3_R2


title: 46.3 um - replicate 3

description:
72 hours = ~1.5 cell cycle lengths
46.3_R3


title: 0.463 um - replicate 2

description:
72 hours = ~1.5 cell cycle lengths
0.463_R2


title: 4.63 um - replicate 2

description:
72 hours = ~1.5 cell cycle lengths
4.63_R2


title: 4.63 um - replicate 3

description:
72 hours = ~1.5 cell cycle lengths
4.63_R3


title: Male brain_5-6mpf_3 ppb_replicate 5

status: Public on Jul 01 2016

description: Gene expression 5-6 mpf following embryonic atrazine exposure

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55mL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent custom zebrafish 4X180K Microarrays (060509) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Arrays were scanned at 5 microns on an Agilent Technologies SureScan Microarray Scanner (Agilent Technologies, Santa Clara, CA).

data_processing: Array image data was extracted using Agilent Feature Extraction Software 11.5 (Agilent Technologies, Santa Clara, CA). Array image data was then uploaded to GeneSpring 12.5 (Agilent Technologies, Santa Clara, CA) for statistical analysis. Each gene list was imported into Ingenuity Pathway Analysis (IPA) for gene ontology and molecular pathway analysis.

source_name: Male brian, 3 ppb, replicate 5

growth_protocol: Zebrafish (wild-type AB strain) were housed in a Z-Mod System (Aquatic Habitats, Apopka, FL) on a 14:10 hour light:dark cycle and maintained at 28ºC ± 1°C with a pH of 7.0-7.2 and conductivity range of 470-520 µS.

extract_protocol: Total RNA (Brain tissue) was isolated by the RNeasy Mini Kit (Qiagen, Venlo, Limburg).

treatment_protocol: Embryos were dosed with 0, 0.3, 3, or 30 ppb atrazine (CAS #1912-24-9; Chem Service, 98% purity) from 1-72 hours post fertilization (hpf) as previously described (Weber et al. 2013; Wirbisky et al., 2015). After the exposure, larvae were rinsed with clean fish system water, housed in 4-liter tanks in the system with 20-30 fish per tank, and allowed to mature under normal growing conditions.

value: wild-type AB strain

tag: gender

value: Male

value: 3 ppb

value: Brain

value: 5-6 mpf


title: Male brain_5-6mpf_0.3 ppb_replicate 5

source_name: Male brain, 0.3 ppb, replicate 5

value: 0.3 ppb


title: Male brain_5-6mpf_30 ppb_replicate 4

source_name: Male brain, 30 ppb, replicate 4

value: 30 ppb


title: Male brain_5-6mpf_30 ppb_replicate 6

source_name: Male brain, 30 ppb, replicate 6


title: Knock-out_0 hr_replicate 1


title: Male brain_5-6mpf_30 ppb_replicate 3

source_name: Male brain, 30 ppb, replicate 3


title: Male brain_5-6mpf_0.3 ppb_replicate 6

source_name: Male brain, 0.3 ppb, replicate 6


title: Male brain_5-6mpf_3 ppb_replicate 4

source_name: Male brain, 3 ppb, replicate 4


title: Male brain_5-6mpf_0.3 ppb_replicate 2

source_name: Male brain, 0.3 ppb, replicate 2


title: Male brain_5-6mpf_30 ppb_replicate 5

source_name: Male brain, 30 ppb, replicate 5


title: Male brain_5-6mpf_0 ppb_replicate 2

source_name: Male brain, 0 ppb, replicate 2

value: 0 ppb


title: Male brain_5-6mpf_0 ppb_replicate 4

source_name: Male brain, 0 ppb, replicate 4


title: Male brain_5-6mpf_30 ppb_replicate 2

source_name: Male brain, 30 ppb, replicate 2


title: Male brain_5-6mpf_0.3 ppb_replicate 1

source_name: Male brain, 0.3 ppb, replicate 1


title: Male brain_5-6mpf_0 ppb_replicate 5

source_name: Male brain, 0 ppb, replicate 5


title: Male brain_5-6mpf_0.3 ppb_replicate 3

source_name: Male brain, 0.3 ppb, replicate 3


title: Male brain_5-6mpf_0 ppb_replicate 6

source_name: Male brain, 0 ppb, replicate 6


title: Male testes_5-6mpf_0 ppb_replicate 6

source_name: Male testes, 0 ppb, replicate 6

extract_protocol: Total RNA (Male testes) was isolated by the RNeasy Mini Kit (Qiagen, Venlo, Limburg).

value: Testes


title: Male brain_5-6mpf_3 ppb_replicate 1

source_name: Male brain, 3 ppb, replicate 1


title: Male brain_5-6mpf_3 ppb_replicate 2

source_name: Male brain, 3 ppb, replicate 2


title: Male brain_5-6mpf_0 ppb_replicate 3

source_name: Male brain, 0 ppb, replicate 3


title: Male brain_5-6mpf_30 ppb_replicate 1

source_name: Male brain, 30 ppb, replicate 1


title: Male brain_5-6mpf_0.3 ppb_replicate 4

source_name: Male brain, 0.3 ppb, replicate 4


title: Knock-out_6 hr_replicate 1

source_name: Knock-out_6 hr

value: Embryo


title: Male testes_5-6mpf_0.3 ppb_replicate 6

source_name: Male testes, 0.3 ppb, replicate 6


title: Male brain_5-6mpf_0 ppb_replicate 1

source_name: Male brain, 0 ppb, replicate 1


title: Male brain_5-6mpf_3 ppb_replicate 3

source_name: Male brain, 3 ppb, replicate 3


title: Male testes_5-6mpf_30 ppb_replicate 6

source_name: Male testes, 30 ppb, replicate 6


title: Male testes_5-6mpf_3 ppb_replicate 6

source_name: Male testes, 3 ppb, replicate 6


title: Male brain_5-6mpf_3 ppb_replicate 6

source_name: Male brain, 3 ppb, replicate 6


title: Male testes_5-6mpf_3 ppb_replicate 5

source_name: Male testes, 3 ppb, replicate 5


title: Male testes_5-6mpf_30 ppb_replicate 5

source_name: Male testes, 30 ppb, replicate 5


title: Male testes_5-6mpf_0 ppb_replicate 5

source_name: Male testes, 0 ppb, replicate 5


title: Male testes_5-6mpf_0 ppb_replicate 3

source_name: Male testes, 0 ppb, replicate 3


title: Male testes_5-6mpf_0.3 ppb_replicate 3

source_name: Male testes, 0.3 ppb, replicate 3


title: Male testes_5-6mpf_3 ppb_replicate 2

source_name: Male testes, 3 ppb, replicate 2


title: Male testes_5-6mpf_0.3 ppb_replicate 1

source_name: Male testes, 0.3 ppb, replicate 1


title: Male testes_5-6mpf_30 ppb_replicate 3

source_name: Male testes, 30 ppb, replicate 3


title: Larvae_3 dpf_0 ppb_replicate 4

status: Public on Apr 21 2016

hyb_protocol: Dried samples were resuspended in nuclease-free water and prepared for hybridization using GE Blocking Agent and Hi-RPM Hybridization Buffer. Samples were loaded onto a custom designed 8X60K Agilent miRNA array in which all human and zebrafish miRNAs were included (based on miRBase release 18.0). Arrays were loaded into SureHyb chambers and hybridized at 55oC for 20 hours in an Agilent Microarray Hybridization Oven.

scan_protocol: The following day, arrays were removed from the oven, washed with Agilent Gene Expression Wash Buffers and scanned on an Agilent SureScan Microarray scanner.

data_processing: Probe information was extracted from generated tif images using Feature Extraction image analysis software 9.5.3 using QC Metric Set to evaluate the quality of labeling and hybridization. Data were background-subtracted, normalized to the 90th percentile, and analyzed for differential expression in GeneSpring 12.5 software using a one-way analysis of variance (ANOVA) with a Tukey’s post hoc test (p<0.05) to determine which atrazine treatment groups were different from the control.

source_name: Larvae_0 ppb

label_protocol: Samples were dephosphorylated using Calf Intestinal Phosphatase and then denatured with dimethyl sulfoxide. Following denaturation, samples were cooled and subsequently labeled with Cyanine 3-pCp using a T4 RNA Ligase. Labeled samples were purified using MicroBioSpin 6 columns (Bio-Rad, Hercules, CA) and dried using a Savant Speed Vac on medium-high heat for 1 hour.

extract_protocol: Total RNA (whole zebrafish larvae) was isolated by the miRNeasy Kit (Qiagen, Venlo, Limburg).

treatment_protocol: Embryos were dosed with 0, 0.3, 3, or 30 ppb atrazine (CAS #1912-24-9; Chem Service, 98% purity) from 1-72 hours post fertilization (hpf) as previously described (Weber et al. 2013; Wirbisky et al., 2015). After the exposure, total RNA was extracted and miRNA microarray was peformed.

value: Larvae

value: 3 dpf

tag: treated with

value: 0 parts per billion (ppb) atrazine


title: Larvae_3 dpf_0.3 ppb_replicate 3

source_name: Larvae_0.3 ppb

value: 0.3 parts per billion (ppb) atrazine


title: Larvae_3 dpf_3 ppb_replicate 3

source_name: Larvae_3 ppb

value: 3 parts per billion (ppb) atrazine


title: Larvae_3 dpf_30 ppb_replicate 4

source_name: Larvae_30 ppb

value: 30 parts per billion (ppb) atrazine


title: Male testes_5-6mpf_0 ppb_replicate 4

source_name: Male testes, 0 ppb, replicate 4

value: control


title: Larvae_3 dpf_0 ppb_replicate 3


title: Larvae_3 dpf_0.3 ppb_replicate 4


title: Larvae_3 dpf_3 ppb_replicate 4


title: Larvae_3 dpf_30 ppb_replicate 3


title: Male testes_5-6mpf_3 ppb_replicate 3

source_name: Male testes, 3 ppb, replicate 3

value: wild-type AB strain

value: atrazine


title: Male testes_5-6mpf_0.3 ppb_replicate 5

source_name: Male testes, 0.3 ppb, replicate 5

value: Male


title: Male testes_5-6mpf_30 ppb_replicate 2

source_name: Male testes, 30 ppb, replicate 2


title: Male testes_5-6mpf_0 ppb_replicate 1

source_name: Male testes, 0 ppb, replicate 1


title: Male testes_5-6mpf_30 ppb_replicate 1

source_name: Male testes, 30 ppb, replicate 1


title: Larvae_3 dpf_0 ppb_replicate 2


title: Larvae_3 dpf_3 ppb_replicate 2


title: Male testes_5-6mpf_0.3 ppb_replicate 2

source_name: Male testes, 0.3 ppb, replicate 2


title: Larvae_3 dpf_0.3 ppb_replicate 2


title: Male testes_5-6mpf_0 ppb_replicate 2

source_name: Male testes, 0 ppb, replicate 2


title: Larvae_3 dpf_3 ppb_replicate 1


title: Larvae_3 dpf_30 ppb_replicate 2


title: Male testes_5-6mpf_30 ppb_replicate 4

source_name: Male testes, 30 ppb, replicate 4


title: Male testes_5-6mpf_3 ppb_replicate 4

source_name: Male testes, 3 ppb, replicate 4

value: 3 ppb


title: Larvae_3 dpf_0 ppb_replicate 1


title: Male testes_5-6mpf_3 ppb_replicate 1

source_name: Male testes, 3 ppb, replicate 1

value: 5-6 mpf


title: Female ovaries_5-6mpf_0.3 ppb_replicate 4

status: Public on Mar 02 2016

source_name: Female ovaries, 0.3 ppb, replicate 4

extract_protocol: Total RNA (ovarian tissue) was isolated by the RNeasy Mini Kit (Qiagen, Venlo, Limburg).

value: AB

tag: genotype

value: wildtype

value: Female

value: Ovaries


title: Female ovaries_5-6mpf_3 ppb_replicate 6

source_name: Female ovaries, 3 ppb, replicate 6


title: Female ovaries_5-6mpf_30 ppb_replicate 4

source_name: Female ovaries, 30 ppb, replicate 4


title: Female ovaries_5-6mpf_30 ppb_replicate 6

source_name: Female ovaries, 30 ppb, replicate 6


title: Male testes_5-6mpf_0.3 ppb_replicate 4

source_name: Male testes, 0.3 ppb, replicate 4

value: 0.3 ppb

value: Testes


title: Female ovaries_5-6mpf_3 ppb_replicate 3

source_name: Female ovaries, 3 ppb, replicate 3


title: Female ovaries_5-6mpf_30 ppb_replicate 3

source_name: Female ovaries, 30 ppb, replicate 3


title: Female ovaries_5-6mpf_3 ppb_replicate 1

source_name: Female ovaries, 3 ppb, replicate 1


title: Female ovaries_5-6mpf_0 ppb_ replicate 2

source_name: Female ovaries, 0 ppb, replicate 2


title: Female ovaries_5-6mpf_3 ppb_replicate 4

source_name: Female ovaries, 3 ppb, replicate 4


title: Female ovaries_5-6mpf_0 ppb_replicate 4

source_name: Female ovaries, 0 ppb, replicate 4


title: Female ovaries_5-6mpf_0.3 ppb_replicate 3

source_name: Female ovaries, 0.3 ppb, replicate 3


title: Female ovaries_5-6mpf_30 ppb_replicate 2

source_name: Female ovaries, 30 ppb, replicate 2


title: Female ovaries_5-6mpf_0.3 ppb_replicate 6

source_name: Female ovaries, 0.3 ppb, replicate 6


title: Female ovaries_5-6mpf_0 ppb_replicate 5

source_name: Female ovaries, 0 ppb, replicate 5


title: Female ovaries_5-6mpf_30 ppb_replicate 1

source_name: Female ovaries, 30 ppb, replicate 1


title: Female ovaries_5-6mpf_0.3 ppb_replicate 5

source_name: Female ovaries, 0.3 ppb, replicate 5


title: Female ovaries_5-6mpf_3 ppb_replicate 5

source_name: Female ovaries, 3 ppb, replicate 5


title: Female ovaries_5-6mpf_0 ppb_replicate 3

source_name: Female ovaries, 0 ppb, replicate 3


title: Female ovaries_5-6mpf_0 ppb_replicate 1

source_name: Female ovaries, 0 ppb, replicate 1


title: Female ovaries_5-6mpf_0.3 ppb_replicate 2

source_name: Female ovaries, 0.3 ppb, replicate 2


title: Female ovaries_5-6mpf_30 ppb_replicate 5

source_name: Female ovaries, 30 ppb, replicate 5


title: Female ovaries_5-6mpf_3 ppb_replicate 2

source_name: Female ovaries, 3 ppb, replicate 2


title: Female ovaries_5-6mpf_0 ppb_replicate 6

source_name: Female ovaries, 0 ppb, replicate 6


title: Female ovaries_5-6mpf_0.3 ppb_replicate 1

source_name: Female ovaries, 0.3 ppb, replicate 1


title: Brain_12months_male_10ppb_rep2

status: Public on Feb 08 2016

description: Gene expression in 12 months aged brain after a developmental exposure to 10ppb lead

hyb_protocol: Cy3-labeled cRNA samples  (1.65 μg) were mixed with fragmentation mix containing Gene Expression Blocking Agent, Nuclease-free water, Fragmentation Buffer (Ailent) and then incubated at 60°C for 30 minutes to fragment RNA, according to the manufacturers recommendations. The fragmented cRNA samples were mixed with Hi-RPM Hybridizatoin Buffer (Agilent) and then hybridized on a custom designed zebrafish microarrays  65°C for 17 hours in a Agilent hybridization oven with gentle rotation.  Following the hybridization, microarrays were washed in Agilent Gene Expressoin Wash Buffer 1 and 2, and then air-dried briefly.

scan_protocol: Slides were scanned on SureScan Agilent microarray scanner (G2600D) with one-color scan setting (Scan region, 61 x 21.6 mm; Scan resolution, 2um; Tiff file dyamic range, 20 bit; Dye channel, Green; Green PMT gain, 100%).

data_processing: Scanned images were extracted with Feature Extraction Software  version 11.5 (Agilent).

source_name: Brain, 12months old male zebrafish, 10ppb lead, replicate 2

label_protocol: Labeling of cRNA with cyanine 3 (cy3) was conducted using the Low Input Quick Amp Labeling Kit (Agilent), following the manufacturer's guideline.  Quality (Yield and specificity) of cy3 labeled cRNA was measured on Drop® ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE).

growth_protocol: Zebrafish (AB strain) were maintained in a Z-Mod System (Aquatic Habitats, Apopka, FL) with a 14:10 light:dark cycle at 28℃. Water quality was regulary monitored by checking conductivity, pH, and temperature.

extract_protocol: Brains obtained from 12 months aged zebrafish were homogenized in Trizol Reagent (Life Technologies, Carlsbad, CA) and stored at -80ºC until RNA isolation. Total RNA was extracted following established protocols descrived in Peterson and Freeman (2009). Extracted total RNA samples were purified on the RNeay Mini Kit (Qiagen, Valencia, CA) according to manufacturer’s protocol and then subjected to RNA quality and quantity measurements on the NanoDrop® ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE).

treatment_protocol: Zebrafish embryos were developmentally treated with 0ppb or 10ppb lead acetate from <2 hours post fertilization (hpf) thorugh 72 hpf, and then washed and transferred to clean aquaria water with no lead treatment. Fish were grown until they reached the age of 12 months at which brains were dissected for RNA isolatoin.

value: 12 months old

value: male

value: brain


title: Brain_12months_male_0ppb_rep4

description: Gene expression in 12 months aged brain after a developmental exposure to 0ppb lead

source_name: Brain, 12months old male zebrafish, 0ppb lead, replicate 4


title: Larvae_3 dpf_0.3 ppb_replicate 1

source_name: Larvae_0.3 ppb

value: Larvae

value: 3 dpf

value: 0.3 parts per billion (ppb) atrazine


title: Brain_12months_male_10ppb_rep3

source_name: Brain, 12months old male zebrafish, 10ppb lead, replicate 3


title: Brain_12months_male_10ppb_rep1

source_name: Brain, 12months old male zebrafish, 10ppb lead, replicate 1


title: Brain_12months_female_10ppb_rep1

source_name: Brain, 12months old female zebrafish, 10ppb lead, replicate 1

value: female


title: 48-3 RNA-Seq

status: Public on Feb 01 2016

city: Eugene

first: Hans

middle: Christian

last: Dreyer

state: Oregon

address: 1240 University of Oregon

department: Human Physiology

institute: University of Oregon

library_source: transcriptomic

data_processing:
Sequencing and basecalling by Illumina HiSeq Control Software 2.2.58
BCL conversion and demultiplexing by Illumina CASAVA 1.8.2
FASTQ files aligned to Homo_sapiens.GRCh38.dna.toplevel.fa genome assembly obtained from ENSEMBL.  The Homo_sapiens.GRCh38.78.gtf file from ENSEMBL was used for annotation.  Alignments were performed with STAR 2.4.0i.
Gene count tables were generated from STAR-produced SAM files using HTSeq-count 0.6.1
genome build: Homo_sapiens.GRCh38.dna.toplevel.fa
.counts files: Gene count tables generated by HTSeq-count from each .sam file for each sample

organism: Homo sapiens

source_name: 2hr after surgery and tourniquet

extract_protocol: Lexogen QuantSeq mRNA-seq kit

value: Muscle biopsy 2hr after surgery and tourniquet


title: Brain_12months_male_0ppb_rep3

source_name: Brain, 12months old male zebrafish, 0ppb lead, replicate 3


title: 42-1 RNA-Seq

source_name: Immediately before surgery

value: Muscle biopsy immediately before surgery


title: 42-3 RNA-Seq


title: 45-3 RNA-Seq


title: 39-3 RNA-Seq


title: 43-3 RNA-Seq


title: 43-1 RNA-Seq


title: 45-1 RNA-Seq


title: 48-1 RNA-Seq


title: Brain_12months_female_0ppb_rep2

source_name: Brain, 12months old female zebrafish, 0ppb lead, replicate 2


title: 38-3 RNA-Seq


title: Brain_12months_female_10ppb_rep3

source_name: Brain, 12months old female zebrafish, 10ppb lead, replicate 3


title: 38-1 RNA-Seq


title: 37-3 RNA-Seq


title: 39-1 RNA-Seq


title: Zebrafish larvae_72 hpf_0 ppb_replicate 4

description: Gene expression at 72 hpf following embryonic 10 ppb trichloroethylene exposure

scan_protocol: Arrays were scanned  on an Agilent Technologies SureScan Microarray Scanner (Agilent Technologies, Santa Clara, CA).

data_processing: Array image data was extracted using Agilent Feature Extraction Software 11.5 (Agilent Technologies, Santa Clara, CA). Array image data was then uploaded to GeneSpring 12.5 (Agilent Technologies, Santa Clara, CA) for statistical analysis. Each gene list was imported into Ingenuity Pathway Analysis (IPA) for gene ontology and molecular pathway analysis.   Supplementary table of probes altered in zebrafish larvae following embryonic trichloroethylene exposure of 10 ppb is available on the series record: Supplemental Table_GEO_091015.xlsx.

source_name: Larvae, 0 ppb, replicate 4

growth_protocol: Zebrafish (wild-type AB strain) were housed in a Z-Mod System (Aquatic Habitats, Apopka, FL) on a 14:10 hour light:dark cycle and maintained at 28ºC ± 1°C with a pH of 7.0-7.2 and conductivity range of 470-520 µS. Adult fish were bred in cages and embryos were collected and staged following established protocols (Peterson et al., 2011; Westerfield, 2007).

extract_protocol: Total RNA was isolated by the RNeasy Mini Kit (Qiagen, Venlo, Limburg).

treatment_protocol: Embryos were dosed with 0 or 10 ppb trichloroethylene (99.5% purity) (Sigma-Aldrich, St. Louis, MO) from 1-72 hours post fertilization (hpf). After the 72 hpf dosing period, the zebrafish larvae were collected from the glass vials and pooled to 50 embryos per sample (considered as one biological replicate). Four biological replicates were completed (n=4).

value: Whole larvae

value: 72 hpf


title: Zebrafish larvae_72 hpf_0 ppb_replicate 2

source_name: Larvae, 0 ppb, replicate 2

value: AB


title: Brain_12months_female_0ppb_rep1

source_name: Brain, 12months old female zebrafish, 0ppb lead, replicate 1


title: Zebrafish larvae_72 hpf_0 ppb_replicate 3

source_name: Larvae, 0 ppb, replicate 3


title: 37-1 RNA-Seq


title: Zebrafish larvae_72 hpf_0 ppb_replicate 1

source_name: Larvae, 0 ppb, replicate 1


title: Brain_12months_female_10ppb_rep2

source_name: Brain, 12months old female zebrafish, 10ppb lead, replicate 2


title: Zebrafish larvae_72 hpf_10 ppb_replicate 4

source_name: Larvae, 10 ppb, replicate 4


title: Zebrafish larvae_72 hpf_10 ppb_replicate 3

source_name: Larvae, 10 ppb, replicate 3


title: Zebrafish larvae_72 hpf_10 ppb_replicate 2

source_name: Larvae, 10 ppb, replicate 2


title: 36-3 RNA-Seq


title: Brain_12months_male_0ppb_rep1

source_name: Brain, 12months old male zebrafish, 0ppb lead, replicate 1


title: Brain_12months_female_0ppb_rep3

source_name: Brain, 12months old female zebrafish, 0ppb lead, replicate 3


title: 36-1 RNA-Seq


title: 33-1 RNA-Seq


title: 34-3 RNA-Seq


title: 33-3 RNA-Seq


title: 34-1 RNA-Seq


title: Zebrafish larvae_72 hpf_10 ppb_replicate 1

source_name: Larvae, 10 ppb, replicate 1


title: Kidney, 10 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3

status: Public on Dec 31 2015

city: Durham

first: Scott

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

hyb_protocol: Affymetrix GeneChips were hybridized labeled cRNA  and then, washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual

scan_protocol: Standard Affymetrix procedures

data_processing: The raw microarray data (.CEL files) were normalized by applying the RMA algorithm provided by the genomics analysis tool, GeneSpring GX 12.6 (Agilent Technology, Foster City, CA); all microarrays from this series were normalized together

label: Biotin

organism: Rattus norvegicus

label_protocol: Purified total RNA (260/280 = 2.02 - 2.19) was hybridized to individual Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization

extract_protocol: Total RNA extracted using TRI Reagent (Molecular Research Center Inc., Cincinnati, OH) according to manufacturer’s protocol

value: Harlan Sprague-Dawley

value: Kidney

tag: compound

value: 10 mg/kg

tag: time

value: 5 days

tag: route

value: Gavage

value: Male


title: Kidney, 100 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4

value: 100 mg/kg


title: Kidney, 300 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1

value: 300 mg/kg


title: Kidney, 500 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2

value: 500 mg/kg


title: Kidney, 500 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4


title: Kidney, 100 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1


title: Kidney, 300 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4


title: Kidney, 500 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1


title: Kidney, 1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4

value: 1 mg/kg


title: Kidney, 10 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4


title: Kidney, 300 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3


title: Kidney, 10 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2


title: Kidney, 1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3


title: Kidney, 100 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3


title: Kidney, 0.1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3

value: 0.1 mg/kg


title: Kidney, 1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1


title: Kidney, 300 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2


title: Kidney, 500 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3


title: Kidney, 0 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4

value: 0 mg/kg


title: Kidney, 0.1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4


title: Kidney, 0 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3


title: Kidney, 100 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2


title: Kidney, 10 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1


title: Kidney, 1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2


title: Kidney, 0 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 5


title: Kidney, 0 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2


title: Brain_12months_male_0ppb_rep2

source_name: Brain, 12months old male zebrafish, 0ppb lead, replicate 2

value: 12 months old

value: male

value: brain


title: Kidney, 0 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1


title: Kidney, 0.1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2


title: Kidney, 0.1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1


title: Liver, 500 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1

value: Liver


title: Liver, 300 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4


title: Liver, 500 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3


title: Liver, 500 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2


title: Liver, 300 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1


title: Liver, 300 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3


title: Liver, 500 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4


title: Liver, 100 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1


title: Liver, 10 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4


title: Liver, 100 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2


title: Liver, 100 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3


title: Liver, 10 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2


title: Liver, 10 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1


title: Liver, 300 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2


title: Liver, 10 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3


title: Liver, 100 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4


title: Liver, 1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2


title: Liver, 0.1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3


title: Liver, 1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3


title: Liver, 0.1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4


title: Liver, 1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4


title: Liver, 0 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 5


title: Liver, 1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1


title: Liver, 0.1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2


title: Liver, 0 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 3


title: Liver, 0 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 4


title: Liver, 0 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 2


title: Liver, 1000 mg/kg, PPH, Biological Rep 3

hyb_protocol: Affymetrix GeneChips were hybridized to 5 ug of labeled cRNA  and then, washed, and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual

source_name: Liver, 1000 mg/kg, PPH

label_protocol: Purified total RNA (260/280 = 2.00 - 2.20) was hybridized to individual Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization

growth_protocol: Male Harlan Sprague Dawley (Hsd:Sprague Dawley SD) rats (Harlan) were placed on NTP-2000 diet. The rats were housed five animals per cage. After a 10 to 14 day quarantine period, 6-8 week old animals were randomly assigned to treatment and control groups.

treatment_protocol: The dose levels were 0, 1, 10, 100, 500, 1000 and 2000 mg/kg of MCHM in corn oil. The test agent via gavage for five consecutive days and sacrificed the day after the final dose. The dosing volume was 5 mL/kg. The 2000 mg/kg dose group was moribund sacrificed before the last dose was administered and tissue samples  these animals were not collected.

value: Propylene glycol phenyl ether


title: Liver, 1000 mg/kg, PPH, Biological Rep 4

value: Harlan Sprague-Dawley


title: Liver, 0 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1


title: Liver, 500 mg/kg, PPH, Biological Rep 3

source_name: Liver, 500 mg/kg, PPH


title: Liver, 500 mg/kg, PPH, Biological Rep 4


title: Liver, 1000 mg/kg, PPH, Biological Rep 2


title: Liver, 1000 mg/kg, PPH, Biological Rep 1


title: Liver, 500 mg/kg, PPH, Biological Rep 2


title: Liver, 100 mg/kg, PPH, Biological Rep 1

source_name: Liver, 100 mg/kg, PPH


title: Liver, 100 mg/kg, PPH, Biological Rep 2


title: Liver, 10 mg/kg, PPH, Biological Rep 4

source_name: Liver, 10 mg/kg, PPH


title: Liver, 10 mg/kg, PPH, Biological Rep 1


title: Liver, 100 mg/kg, PPH, Biological Rep 3


title: Liver, 1 mg/kg, PPH, Biological Rep 2

source_name: Liver, 1 mg/kg, PPH


title: Liver, 100 mg/kg, PPH, Biological Rep 4


title: Liver, 1 mg/kg, PPH, Biological Rep 4


title: Liver, 500 mg/kg, PPH, Biological Rep 1


title: Liver, 1 mg/kg, PPH, Biological Rep 3


title: Liver, 1 mg/kg, PPH, Biological Rep 1


title: Liver, 0 mg/kg, PPH, Biological Rep 5

source_name: Liver, 0 mg/kg, PPH


title: Liver, 10 mg/kg, PPH, Biological Rep 3


title: Liver, 0 mg/kg, PPH, Biological Rep 2


title: Liver, 0 mg/kg, PPH, Biological Rep 1


title: Liver, 0 mg/kg, PPH, Biological Rep 3


title: Liver, 0 mg/kg, PPH, Biological Rep 4


title: Liver, 10 mg/kg, PPH, Biological Rep 2


title: Kidney, 1000 mg/kg, PPH, Biological Rep 3

source_name: Kidney, 1000 mg/kg, PPH

value: Kidney


title: Liver, 0.1 mg/kg, 4-Methylcyclohexanemethanol, Biological Rep 1


title: Kidney, 1000 mg/kg, PPH, Biological Rep 2


title: Kidney, 500 mg/kg, PPH, Biological Rep 3

source_name: Kidney, 500 mg/kg, PPH


title: Kidney, 100 mg/kg, PPH, Biological Rep 4

source_name: Kidney, 100 mg/kg, PPH


title: Kidney, 500 mg/kg, PPH, Biological Rep 2


title: Kidney, 500 mg/kg, PPH, Biological Rep 1


title: Kidney, 1000 mg/kg, PPH, Biological Rep 4


title: Kidney, 100 mg/kg, PPH, Biological Rep 3


title: Kidney, 100 mg/kg, PPH, Biological Rep 1


title: Kidney, 10 mg/kg, PPH, Biological Rep 4

source_name: Kidney, 10 mg/kg, PPH

value: 10 mg/kg


title: Kidney, 10 mg/kg, PPH, Biological Rep 1

value: 5 days


title: Kidney, 10 mg/kg, PPH, Biological Rep 3

value: Gavage


title: Kidney, 10 mg/kg, PPH, Biological Rep 2

value: Male


title: Kidney, 1 mg/kg, PPH, Biological Rep 3

source_name: Kidney, 1 mg/kg, PPH


title: Kidney, 1 mg/kg, PPH, Biological Rep 2


title: Kidney, 0 mg/kg, PPH, Biological Rep 3

source_name: Kidney, 0 mg/kg, PPH


title: Liver, Crude MCHM, 500 mg/kg, Biological Rep 4

source_name: Liver, Crude MCHM, 500 mg/kg

label_protocol: Purified total RNA (260/280 = 1.98 - 2.21) was hybridized to individual Affymetrix GeneChip® Rat Genome 230 2.0 plus microarrays according to the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com). Double stranded cDNA was synthesized from RNA using reverse transcriptase and an oligo-dT primer. Biotinylated RNA (labeled cRNA) served as the microarray target. cRNA was fragmented using heat and magnesium (Mg+2) reducing the cRNA to 25-200 base fragments to facilitate efficient and reproducible hybridization

treatment_protocol: The dose levels were 0, 0.1, 1, 10, 100, 300 and 500 mg/kg of MCHM in corn oil. The test agent via gavage for five consecutive days and sacrificed the day after the final dose. The dosing volume was 5 mL/kg.

value: Crude MCHM


title: Kidney, 0 mg/kg, PPH, Biological Rep 2


title: Kidney, 0 mg/kg, PPH, Biological Rep 4


title: Liver, Crude MCHM, 300 mg/kg, Biological Rep 2

source_name: Liver, Crude MCHM, 300 mg/kg

value: 300 mg/kg


title: Kidney, 0 mg/kg, PPH, Biological Rep 5


title: Liver, Crude MCHM, 100 mg/kg, Biological Rep 1

source_name: Liver, Crude MCHM, 100 mg/kg

value: 100 mg/kg


title: Liver, Crude MCHM, 500 mg/kg, Biological Rep 3

value: 500 mg/kg


title: Liver, Crude MCHM, 300 mg/kg, Biological Rep 3


title: Kidney, 1000 mg/kg, PPH, Biological Rep 1


title: Kidney, 100 mg/kg, PPH, Biological Rep 2


title: Liver, Crude MCHM, 10 mg/kg, Biological Rep 4

source_name: Liver, Crude MCHM, 10 mg/kg


title: Kidney, 1 mg/kg, PPH, Biological Rep 4

value: 1 mg/kg


title: Liver, Crude MCHM, 500 mg/kg, Biological Rep 2


title: Liver, Crude MCHM, 100 mg/kg, Biological Rep 2


title: Liver, Crude MCHM, 100 mg/kg, Biological Rep 3


title: Liver, Crude MCHM, 300 mg/kg, Biological Rep 1


title: Kidney, 1 mg/kg, PPH, Biological Rep 1


title: Liver, Crude MCHM, 10 mg/kg, Biological Rep 1


title: Liver, Crude MCHM, 300 mg/kg, Biological Rep 4


title: Liver, Crude MCHM, 1 mg/kg, Biological Rep 2

source_name: Liver, Crude MCHM, 1 mg/kg


title: Kidney, 0 mg/kg, PPH, Biological Rep 1

value: 0 mg/kg


title: Liver, Crude MCHM, 10 mg/kg, Biological Rep 3


title: Liver, Crude MCHM, 1 mg/kg, Biological Rep 1


title: Liver, Crude MCHM, 10 mg/kg, Biological Rep 2


title: Liver, Crude MCHM, 500 mg/kg, Biological Rep 1


title: Liver, Crude MCHM, 0.1 mg/kg, Biological Rep 3

source_name: Liver, Crude MCHM, 0.1 mg/kg

value: 0.1 mg/kg


title: Liver, Crude MCHM, 100 mg/kg, Biological Rep 4


title: Liver, Crude MCHM, 1 mg/kg, Biological Rep 4


title: Liver, Crude MCHM, 1 mg/kg, Biological Rep 3


title: Kidney, Crude MCHM, 500 mg/kg, Biological Rep 3

source_name: Kidney, Crude MCHM, 500 mg/kg


title: Liver, Crude MCHM, 0.1 mg/kg, Biological Rep 1


title: Liver, Crude MCHM, 0 mg/kg, Biological Rep 3

source_name: Liver, Crude MCHM, 0 mg/kg


title: Kidney, Crude MCHM, 500 mg/kg, Biological Rep 2


title: Liver, Crude MCHM, 0 mg/kg, Biological Rep 4


title: Kidney, Crude MCHM, 100 mg/kg, Biological Rep 2

source_name: Kidney, Crude MCHM, 100 mg/kg


title: Kidney, Crude MCHM, 300 mg/kg, Biological Rep 2

source_name: Kidney, Crude MCHM, 300 mg/kg


title: Liver, Crude MCHM, 0 mg/kg, Biological Rep 1


title: Liver, Crude MCHM, 0.1 mg/kg, Biological Rep 2


title: Kidney, Crude MCHM, 300 mg/kg, Biological Rep 3


title: Liver, Crude MCHM, 0 mg/kg, Biological Rep 2


title: Kidney, Crude MCHM, 10 mg/kg, Biological Rep

source_name: Kidney, Crude MCHM, 10 mg/kg


title: Kidney, Crude MCHM, 1 mg/kg, Biological Rep 2

source_name: Kidney, Crude MCHM, 1 mg/kg


title: Kidney, Crude MCHM, 300 mg/kg, Biological Rep 1


title: Kidney, Crude MCHM, 0.1 mg/kg, Biological Rep 1

source_name: Kidney, Crude MCHM, 0.1 mg/kg


title: Kidney, Crude MCHM, 0.1 mg/kg, Biological Rep 2


title: Kidney, Crude MCHM, 10 mg/kg, Biological Rep 1


title: Kidney, Crude MCHM, 0 mg/kg, Biological Rep 2

source_name: Kidney, Crude MCHM, 0 mg/kg


title: Kidney, Crude MCHM, 100 mg/kg, Biological Rep 1


title: Kidney, Crude MCHM, 500 mg/kg, Biological Rep 1


title: Kidney_S040721-029_Hexachloro-1,3-Butadiene_50 mg/kg_3d

status: Public on Aug 18 2014

description: Complete Drug Matrix dataset for primary rat hepatocytes; more details can be found at http://cebs.niehs.nih.gov/ under accession number 004-00008-0000-000-2

hyb_protocol: Ten micrograms of the fragmented cRNA was hybridized to each Uniset Rat I Expression BioArray (Amersham Biosciences) for 20 h at 37 ◦C, while shaking at 300 rpm.

scan_protocol: All processed slides were scanned using the Axon GenePix Scanner (Axon Instrument, Union City, CA) with the laser set to 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10_m.  The data were analyzed using the CodeLinkTM Expression Analysis Software Version 2.2.25 (Amersham Biosciences).

data_processing: Data was extracted from the Probe Value column of background-subtracted files, and quantile-normalized, without baseline transformation in GeneSpring GX 11.5.1.  Data artifacts (probes with -2 as the probe value) were removed (set to empty) before normalization. Probe values that were blank were left blank.

molecule: polyA RNA

source_name: Kidney, Hexachloro-1,3-Butadiene, 3d

label_protocol: The methods used for cRNA preparation are described in the CodeLinkTM manual v2.1 as supplied by Amersham Biosciences using the Qiagen BioRobot 9604 (Valencia, CA).

growth_protocol: Male Sprague–Dawley (Crl:CD® (SD)|GS BR) rats(aged 6–8 weeks) were purchased from Charles River Laboratories (Wilmington, MA). They were housed in plastic cages for 1 week for acclimation to the laboratory environment of a ventilated room (temperature, 22±3 ◦C; humidity 30–70%; 12-h light:12-h dark cycle per day, 6:00 a.m.–6:00 p.m.) until use. Certified Rodent Diet #5002 (PMI Feeds Inc.) and chlorinated tap water was available ad libitum.

extract_protocol: Poly A(+) RNA was isolated using the MagNA Pure LC robot (Roche, Basel, Switzerland) in combination with the MagNA Pure LC mRNA Isolation kit I (Roche, Basel, Switzerland), concentrated by ethanol precipitation, resuspend in 7 ul DEPC-treated water, quantified by ribogreen fluorescence using Wallac Victor2 fluorometer (Perkin Elmer, Fremont CA) and transcribed to cDNA

treatment_protocol: The 0.25 and 1-day time points were harvested starting at 1:00 p.m. and completed within 1–2 h, whereas the 3 and 5-day time points were harvested starting at 7:00 a.m. and completed within 2–4 h; all harvests used an appropriately staggered schedule so that the harvest times were accurate to ±30 min of the designed dose-to-harvest interval.

value: Sprague Dawley, CD-IGS

value: 50 mg/kg

value: 3 d

tag: vehicle

value: Corn Oil

value: Intraperitoneal

tag: rna extraction date

tag: hybridization date


title: Kidney_S040707-085_Chlorobenzene_500 mg/kg_3d

source_name: Kidney, Chlorobenzene, 3d

value: Kidney

value: Chlorobenzene

value: CMC

value: Oral Gavage


title: Kidney, Crude MCHM, 0 mg/kg, Biological Rep 3

value: Harlan Sprague-Dawley

value: 5 days

value: Gavage

value: Male


title: Kidney_S040721-031_Hexachloro-1,3-Butadiene_50 mg/kg_5d

source_name: Kidney, Hexachloro-1,3-Butadiene, 5d

value: 5 d


title: Kidney_S040707-088_Chlorobenzene_500 mg/kg_5d

source_name: Kidney, Chlorobenzene, 5d

value: 500 mg/kg


title: Kidney_S040721-026_Hexachloro-1,3-Butadiene_50 mg/kg_1d

source_name: Kidney, Hexachloro-1,3-Butadiene, 1d

value: 1 d


title: Kidney, Crude MCHM, 0 mg/kg, Biological Rep 1

value: Crude MCHM

value: 0 mg/kg


title: Kidney_S040721-081_Trichloroethylene_1230 mg/kg_1d

source_name: Kidney, Trichloroethylene, 1d

value: Sprague Dawley, CD-IGS

value: Trichloroethylene


title: Kidney, Crude MCHM, 1 mg/kg, Biological Rep 1

value: 1 mg/kg


title: Kidney_S040707-055_4-Chloroaniline_75 mg/kg_1d

source_name: Kidney, 4-Chloroaniline, 1d

value: 75 mg/kg


title: Kidney_S040707-058_4-Chloroaniline_75 mg/kg_3d

source_name: Kidney, 4-Chloroaniline, 3d

value: Kidney

value: 3 d


title: Kidney_S040707-061_4-Chloroaniline_75 mg/kg_5d

source_name: Kidney, 4-Chloroaniline, 5d

value: CMC


title: Kidney_S040707-009_Saline_0 mg/kg_3d

source_name: Kidney, Saline, 3d

value: Saline

value: Intraperitoneal


title: Kidney_S040707-068_Benzyl Acetate_1868 mg/kg_1d

source_name: Kidney, Benzyl Acetate, 1d

value: Benzyl Acetate

value: Oral Gavage


title: Kidney_S040707-057_4-Chloroaniline_75 mg/kg_3d

value: Male


title: Kidney_S040707-071_Benzyl Acetate_1868 mg/kg_3d

source_name: Kidney, Benzyl Acetate, 3d


title: Kidney_S040707-003_Saline_0 mg/kg_1d

source_name: Kidney, Saline, 1d


title: Kidney_S040707-054_4-Chloroaniline_75 mg/kg_1d


title: Kidney_S040707-044_4-Chloro-2-Nitroaniline_1200 mg/kg_3d

source_name: Kidney, 4-Chloro-2-Nitroaniline, 3d


title: Kidney_S040707-082_Chlorobenzene_500 mg/kg_1d

source_name: Kidney, Chlorobenzene, 1d

value: Chlorobenzene


title: Kidney_S040707-046_4-Chloro-2-Nitroaniline_1200 mg/kg_5d

source_name: Kidney, 4-Chloro-2-Nitroaniline, 5d

value: 5 d


title: Kidney_S040707-043_4-Chloro-2-Nitroaniline_1200 mg/kg_3d


title: Kidney_S040707-015_Saline_0 mg/kg_5d

source_name: Kidney, Saline, 5d


title: Kidney_S040721-084_Trichloroethylene_1230 mg/kg_3d

source_name: Kidney, Trichloroethylene, 3d


title: Kidney_S040707-041_4-Chloro-2-Nitroaniline_1200 mg/kg_1d

source_name: Kidney, 4-Chloro-2-Nitroaniline, 1d

value: 1 d


title: Kidney_S040707-087_Chlorobenzene_500 mg/kg_5d

value: 500 mg/kg


title: Kidney_S040707-047_4-Chloro-2-Nitroaniline_1200 mg/kg_5d


title: Kidney_S040707-084_Chlorobenzene_500 mg/kg_3d

source_name: Kidney, Chlorobenzene, 3d


title: Kidney_S040707-040_4-Chloro-2-Nitroaniline_1200 mg/kg_1d


title: Kidney_S040707-081_Chlorobenzene_500 mg/kg_1d


title: Kidney_S040707-074_Benzyl Acetate_1868 mg/kg_5d

source_name: Kidney, Benzyl Acetate, 5d


title: Kidney_S040707-053_4-Chloroaniline_75 mg/kg_1d


title: Kidney_S040707-042_4-Chloro-2-Nitroaniline_1200 mg/kg_3d


title: Kidney_S040707-059_4-Chloroaniline_75 mg/kg_5d


title: Kidney_S020909-216_Tolazamide_1500 mg/kg_5d

source_name: Kidney, Tolazamide, 5d

value: Tolazamide


title: Kidney_S040707-067_Benzyl Acetate_1868 mg/kg_1d

value: Sprague Dawley, CD-IGS


title: Kidney_S040707-008_Saline_0 mg/kg_3d

value: 0 mg/kg


title: Kidney_S020909-212_Tolazamide_1500 mg/kg_3d

source_name: Kidney, Tolazamide, 3d


title: Kidney_S040707-039_4-Chloro-2-Nitroaniline_1200 mg/kg_1d


title: Kidney_S040707-056_4-Chloroaniline_75 mg/kg_3d


title: Kidney_S020909-263_Levofloxacin_739 mg/kg_5d

source_name: Kidney, Levofloxacin, 5d

value: Levofloxacin

value: 739 mg/kg

value: Water


title: Kidney_S040707-007_Saline_0 mg/kg_3d

value: Kidney

value: 3 d


title: Kidney_S040707-013_Saline_0 mg/kg_5d

value: Saline


title: Kidney_S040707-045_4-Chloro-2-Nitroaniline_1200 mg/kg_5d

value: CMC


title: Kidney_S040707-073_Benzyl Acetate_1868 mg/kg_5d

value: Benzyl Acetate


title: Kidney_S040707-001_Saline_0 mg/kg_1d

value: Intraperitoneal


title: Kidney_S040707-002_Saline_0 mg/kg_1d

value: Male


title: Kidney_S020708-262_Mevastatin_1200 mg/kg_5d

source_name: Kidney, Mevastatin, 5d

value: Mevastatin

value: Oral Gavage


title: Kidney_S040707-014_Saline_0 mg/kg_5d

value: 5 d


title: Kidney_S020909-160_Isoeugenol_1560 mg/kg_1d

source_name: Kidney, Isoeugenol, 1d

value: Isoeugenol

value: 1 d


title: Kidney_S020422-040_2-Acetylaminofluorene_30 mg/kg_1d

source_name: Kidney, 2-Acetylaminofluorene, 1d

value: Sprague Dawley, CD-IGS

value: 30 mg/kg


title: Kidney_S020506-312_Irinotecan_5 mg/kg_5d

source_name: Kidney, Irinotecan, 5d

value: Irinotecan

value: 5 mg/kg

value: Intravenous


title: Kidney_S020506-309_Irinotecan_5 mg/kg_3d

source_name: Kidney, Irinotecan, 3d

value: Kidney


title: Kidney_S020617-305_Pravastatin_1200 mg/kg_1d

source_name: Kidney, Pravastatin, 1d

value: Pravastatin

value: Corn Oil


title: Kidney_R020924-186_Trimethadione_535 mg/kg_1d

source_name: Kidney, Trimethadione, 1d

value: Trimethadione

value: 535 mg/kg

value: Water


title: Kidney_S020506-306_Irinotecan_5 mg/kg_1d

source_name: Kidney, Irinotecan, 1d

value: Saline

value: Male


title: Kidney_S020909-262_Levofloxacin_739 mg/kg_5d

value: Levofloxacin

value: 739 mg/kg

value: Oral Gavage


title: Kidney_S011204-191_Etoposide_188 mg/kg_5d

source_name: Kidney, Etoposide, 5d

value: Etoposide

value: 188 mg/kg

value: 5 d


title: Kidney_S020715-137_Propylene Glycol_2000 mg/kg_1d

source_name: Kidney, Propylene Glycol, 1d

value: Sprague Dawley, CD-IGS

value: Propylene Glycol

value: 1 d


title: Kidney_S011204-186_Etoposide_188 mg/kg_1d

source_name: Kidney, Etoposide, 1d

value: Kidney


title: Kidney_S020422-381_Venlafaxine_320 mg/kg_3d

source_name: Kidney, Venlafaxine, 3d

value: Venlafaxine

value: 320 mg/kg

value: 3 d


title: Kidney_S020311-048_Camptothecin_5 mg/kg_5d

source_name: Kidney, Camptothecin, 5d

value: Camptothecin

value: 5 mg/kg

value: Intravenous


title: Kidney_S020506-311_Irinotecan_5 mg/kg_5d

value: Irinotecan

value: Saline

value: Male


title: Kidney_S011204-189_Etoposide_188 mg/kg_3d

source_name: Kidney, Etoposide, 3d

value: Corn Oil

value: Oral Gavage


title: Kidney_S020311-045_Camptothecin_5 mg/kg_3d

source_name: Kidney, Camptothecin, 3d


title: Kidney_S011204-192_Etoposide_188 mg/kg_5d

value: Etoposide

value: 188 mg/kg


title: Kidney_S020909-264_Levofloxacin_739 mg/kg_5d

value: Sprague Dawley, CD-IGS

value: Levofloxacin

value: 739 mg/kg

value: 5 d

value: Water


title: Kidney_S020909-261_Levofloxacin_739 mg/kg_3d

source_name: Kidney, Levofloxacin, 3d

value: Kidney


title: Kidney_S011127-185_Thioguanine_24 mg/kg_1d

source_name: Kidney, Thioguanine, 1d

value: Thioguanine

value: 24 mg/kg

value: 1 d


title: Kidney_S011127-189_Thioguanine_24 mg/kg_3d

source_name: Kidney, Thioguanine, 3d

value: 3 d


title: Kidney_S011127-186_Thioguanine_24 mg/kg_1d


title: Kidney_S020909-258_Levofloxacin_739 mg/kg_1d

source_name: Kidney, Levofloxacin, 1d


title: Kidney_S011127-188_Thioguanine_24 mg/kg_3d


title: Kidney_S020909-167_Isoeugenol_1560 mg/kg_5d

source_name: Kidney, Isoeugenol, 5d

value: Isoeugenol

value: CMC


title: Kidney_S020422-384_Venlafaxine_320 mg/kg_5d

source_name: Kidney, Venlafaxine, 5d

value: Venlafaxine

value: 320 mg/kg

value: Male


title: Kidney_S011127-192_Thioguanine_24 mg/kg_5d

source_name: Kidney, Thioguanine, 5d

value: Corn Oil

value: Oral Gavage


title: Kidney_S020311-042_Camptothecin_5 mg/kg_1d

source_name: Kidney, Camptothecin, 1d

value: Sprague Dawley, CD-IGS

value: Camptothecin

value: 5 mg/kg

value: Saline

value: Intravenous


title: Kidney_S020909-213_Tolazamide_1500 mg/kg_3d

source_name: Kidney, Tolazamide, 3d

value: Kidney

value: Tolazamide


title: Kidney_S020909-164_Isoeugenol_1560 mg/kg_3d

source_name: Kidney, Isoeugenol, 3d


title: Kidney_S020909-162_Isoeugenol_1560 mg/kg_1d

source_name: Kidney, Isoeugenol, 1d


title: Kidney_S020909-165_Isoeugenol_1560 mg/kg_3d


title: Kidney_S020909-210_Tolazamide_1500 mg/kg_1d

source_name: Kidney, Tolazamide, 1d


title: Kidney_S020909-168_Isoeugenol_1560 mg/kg_5d

value: 5 d


title: Kidney_S020715-138_Propylene Glycol_2000 mg/kg_1d

source_name: Kidney, Propylene Glycol, 1d

value: Propylene Glycol

value: 1 d

value: Water


title: Kidney_S020715-141_Propylene Glycol_2000 mg/kg_3d

source_name: Kidney, Propylene Glycol, 3d

value: 3 d


title: Kidney_S020311-044_Camptothecin_5 mg/kg_3d


title: Kidney_S020311-041_Camptothecin_5 mg/kg_1d


title: Kidney_S011127-191_Thioguanine_24 mg/kg_5d

value: Thioguanine

value: 24 mg/kg


title: Kidney_S020708-261_Mevastatin_1200 mg/kg_3d

source_name: Kidney, Mevastatin, 3d

value: Mevastatin

value: CMC

value: Male


title: Kidney_S020708-264_Mevastatin_1200 mg/kg_5d

source_name: Kidney, Mevastatin, 5d

value: Sprague Dawley, CD-IGS

value: Oral Gavage


title: Kidney_S020318-168_Sulfaphenazole_1695 mg/kg_5d

source_name: Kidney, Sulfaphenazole, 5d

value: Sulfaphenazole


title: Kidney_S020708-258_Mevastatin_1200 mg/kg_1d

source_name: Kidney, Mevastatin, 1d


title: Kidney_S020311-047_Camptothecin_5 mg/kg_5d

source_name: Kidney, Camptothecin, 5d

value: Camptothecin

value: 5 mg/kg

value: Saline


title: Kidney_R020924-188_Trimethadione_535 mg/kg_3d

source_name: Kidney, Trimethadione, 3d

value: Kidney

value: Trimethadione

value: 535 mg/kg


title: Kidney_S020909-260_Levofloxacin_739 mg/kg_3d

source_name: Kidney, Levofloxacin, 3d

value: Levofloxacin

value: 739 mg/kg


title: Kidney_R020924-185_Trimethadione_535 mg/kg_1d

source_name: Kidney, Trimethadione, 1d

value: 1 d

value: Water


title: Kidney_S011127-187_Thioguanine_24 mg/kg_3d

source_name: Kidney, Thioguanine, 3d

value: Thioguanine

value: 24 mg/kg

value: 3 d

value: Corn Oil


title: Kidney_S011127-184_Thioguanine_24 mg/kg_1d

source_name: Kidney, Thioguanine, 1d

value: Sprague Dawley, CD-IGS

value: Male


title: Kidney_S020708-257_Mevastatin_1200 mg/kg_1d

value: Mevastatin

value: CMC

value: Oral Gavage


title: Kidney_S020909-209_Tolazamide_1500 mg/kg_1d

value: Tolazamide


title: Kidney_S020617-308_Pravastatin_1200 mg/kg_3d

source_name: Kidney, Pravastatin, 3d

value: Kidney

value: Pravastatin


title: Kidney_S020909-257_Levofloxacin_739 mg/kg_1d

source_name: Kidney, Levofloxacin, 1d


title: Kidney_S020715-144_Propylene Glycol_2000 mg/kg_5d

source_name: Kidney, Propylene Glycol, 5d

value: Propylene Glycol

value: 5 d


title: Kidney_S020708-263_Mevastatin_1200 mg/kg_5d


title: Kidney_S020909-259_Levofloxacin_739 mg/kg_3d

value: Levofloxacin

value: 739 mg/kg


title: Kidney_S020909-214_Tolazamide_1500 mg/kg_5d

source_name: Kidney, Tolazamide, 5d


title: Kidney_S020715-140_Propylene Glycol_2000 mg/kg_3d

value: Water


title: Kidney_S020909-161_Isoeugenol_1560 mg/kg_1d

source_name: Kidney, Isoeugenol, 1d

value: Isoeugenol

value: 1 d


title: Kidney_S020311-043_Camptothecin_5 mg/kg_3d

source_name: Kidney, Camptothecin, 3d

value: Camptothecin

value: 5 mg/kg

value: 3 d

value: Saline

value: Intravenous


title: Kidney_S020617-311_Pravastatin_1200 mg/kg_5d

source_name: Kidney, Pravastatin, 5d

value: Sprague Dawley, CD-IGS

value: Corn Oil

value: Male


title: Kidney_S011127-190_Thioguanine_24 mg/kg_5d

source_name: Kidney, Thioguanine, 5d

value: Kidney

value: Thioguanine

value: 24 mg/kg

value: Oral Gavage


title: Kidney_S020715-143_Propylene Glycol_2000 mg/kg_5d

value: Propylene Glycol

value: 5 d


title: Kidney_S020909-208_Tolazamide_1500 mg/kg_1d

source_name: Kidney, Tolazamide, 1d

value: Tolazamide

value: CMC


title: Kidney_R020924-191_Trimethadione_535 mg/kg_5d

source_name: Kidney, Trimethadione, 5d

value: Trimethadione

value: 535 mg/kg

value: Water


title: Kidney_S020617-306_Pravastatin_1200 mg/kg_1d

source_name: Kidney, Pravastatin, 1d

value: Pravastatin

value: 1 d


title: Kidney_S020708-260_Mevastatin_1200 mg/kg_3d

source_name: Kidney, Mevastatin, 3d

value: Mevastatin

value: 3 d


title: Kidney_S020909-215_Tolazamide_1500 mg/kg_5d

value: Sprague Dawley, CD-IGS


title: Kidney_S020909-256_Levofloxacin_739 mg/kg_1d

value: Levofloxacin

value: 739 mg/kg

value: Male


title: Kidney_S020909-166_Isoeugenol_1560 mg/kg_5d

source_name: Kidney, Isoeugenol, 5d

value: Kidney

value: Isoeugenol


title: Kidney_S020422-383_Venlafaxine_320 mg/kg_5d

source_name: Kidney, Venlafaxine, 5d

value: Venlafaxine

value: 320 mg/kg

value: Oral Gavage


title: Kidney_S020422-380_Venlafaxine_320 mg/kg_3d

source_name: Kidney, Venlafaxine, 3d


title: Kidney_R020924-184_Trimethadione_535 mg/kg_1d

source_name: Kidney, Trimethadione, 1d


title: Kidney_S020422-378_Venlafaxine_320 mg/kg_1d

source_name: Kidney, Venlafaxine, 1d


title: Kidney_S020422-379_Venlafaxine_320 mg/kg_3d


title: Kidney_R020924-187_Trimethadione_535 mg/kg_3d

source_name: Kidney, Trimethadione, 3d


title: Kidney_S020311-040_Camptothecin_5 mg/kg_1d

source_name: Kidney, Camptothecin, 1d

value: Camptothecin

value: 5 mg/kg

value: Saline

value: Intravenous


title: Kidney_R020924-190_Trimethadione_535 mg/kg_5d

value: Trimethadione

value: 535 mg/kg

value: 5 d

value: Water


title: Kidney_S020325-405_Ofloxacin_3000 mg/kg_3d

source_name: Kidney, Ofloxacin, 3d

value: Sprague Dawley, CD-IGS

value: Ofloxacin

value: 3 d


title: Kidney_R020924-069_Dexfenfluramine_29 mg/kg_3d

source_name: Kidney, Dexfenfluramine, 3d

value: Dexfenfluramine

value: 29 mg/kg

value: Male


title: Kidney_S020909-211_Tolazamide_1500 mg/kg_3d

source_name: Kidney, Tolazamide, 3d

value: Kidney

value: Tolazamide

value: CMC


title: Kidney_S020715-142_Propylene Glycol_2000 mg/kg_5d

source_name: Kidney, Propylene Glycol, 5d

value: Propylene Glycol

value: Oral Gavage


title: Kidney_S020617-307_Pravastatin_1200 mg/kg_3d

source_name: Kidney, Pravastatin, 3d

value: Pravastatin

value: Corn Oil


title: Kidney_S020909-163_Isoeugenol_1560 mg/kg_3d

source_name: Kidney, Isoeugenol, 3d

value: Isoeugenol


title: Kidney_S020715-139_Propylene Glycol_2000 mg/kg_3d

source_name: Kidney, Propylene Glycol, 3d


title: Kidney_S020708-259_Mevastatin_1200 mg/kg_3d

value: Mevastatin


title: Kidney_S020422-377_Venlafaxine_320 mg/kg_1d

value: Venlafaxine

value: 320 mg/kg

value: 1 d


title: Kidney_S020617-310_Pravastatin_1200 mg/kg_5d

source_name: Kidney, Pravastatin, 5d

value: Sprague Dawley, CD-IGS

value: 5 d


title: Kidney_R020924-142_Sulfadiazine_1170 mg/kg_5d

source_name: Kidney, Sulfadiazine, 5d

value: Sulfadiazine

value: Water


title: Kidney_S020708-256_Mevastatin_1200 mg/kg_1d

source_name: Kidney, Mevastatin, 1d

value: Male


title: Kidney_S020325-400_Ofloxacin_3000 mg/kg_1d

source_name: Kidney, Ofloxacin, 1d

value: Kidney

value: Ofloxacin


title: Kidney_S020325-403_Ofloxacin_3000 mg/kg_3d

value: 3 d


title: Kidney_S020715-136_Propylene Glycol_2000 mg/kg_1d

source_name: Kidney, Propylene Glycol, 1d

value: Propylene Glycol


title: Kidney_S020325-406_Ofloxacin_3000 mg/kg_5d

source_name: Kidney, Ofloxacin, 5d

value: Oral Gavage


title: Kidney_S020311-046_Camptothecin_5 mg/kg_5d

source_name: Kidney, Camptothecin, 5d

value: Camptothecin

value: 5 mg/kg

value: Saline

value: Intravenous


title: Kidney_S020422-382_Venlafaxine_320 mg/kg_5d

source_name: Kidney, Venlafaxine, 5d

value: Venlafaxine


title: Kidney_S020325-408_Ofloxacin_3000 mg/kg_5d


title: Kidney_S020617-304_Pravastatin_1200 mg/kg_1d

source_name: Kidney, Pravastatin, 1d

value: Pravastatin

value: Corn Oil


title: Kidney_S020311-384_Mefenamic Acid_93 mg/kg_5d

source_name: Kidney, Mefenamic Acid, 5d

value: Sprague Dawley, CD-IGS

value: Mefenamic Acid

value: 93 mg/kg


title: Kidney_R040528-003_Corn Oil_0 mg/kg_5d

source_name: Kidney, Corn Oil, 5d

value: 0 mg/kg

value: 5 d


title: Kidney_R020924-136_Sulfadiazine_1170 mg/kg_1d

source_name: Kidney, Sulfadiazine, 1d

value: Kidney

value: Sulfadiazine

value: 1 d

value: Water

value: Male


title: Kidney_S020429-382_Salicylamide_1300 mg/kg_5d

source_name: Kidney, Salicylamide, 5d

value: Salicylamide

value: CMC

value: Oral Gavage


title: Kidney_R020924-139_Sulfadiazine_1170 mg/kg_3d

source_name: Kidney, Sulfadiazine, 3d

value: 3 d


title: Kidney_S020205-333_Sulfathiazole_2629 mg/kg_3d

source_name: Kidney, Sulfathiazole, 3d

value: Sulfathiazole


title: Kidney_S020205-330_Sulfathiazole_2629 mg/kg_1d

source_name: Kidney, Sulfathiazole, 1d


title: Kidney_S020318-166_Sulfaphenazole_1695 mg/kg_5d

source_name: Kidney, Sulfaphenazole, 5d

value: Sulfaphenazole


title: Kidney_S020318-165_Sulfaphenazole_1695 mg/kg_3d

source_name: Kidney, Sulfaphenazole, 3d


title: Kidney_S020205-336_Sulfathiazole_2629 mg/kg_5d

source_name: Kidney, Sulfathiazole, 5d


title: Kidney_S020318-162_Sulfaphenazole_1695 mg/kg_1d

source_name: Kidney, Sulfaphenazole, 1d


title: Kidney_S020318-164_Sulfaphenazole_1695 mg/kg_3d


title: Kidney_R040528-022_Diclofenac_3.5 mg/kg_5d

source_name: Kidney, Diclofenac, 5d

value: Diclofenac

value: 3.5 mg/kg

value: Corn Oil


title: Kidney_R021008-192_Thalidomide_113 mg/kg_5d

source_name: Kidney, Thalidomide, 5d

value: Sprague Dawley, CD-IGS

value: Thalidomide

value: 113 mg/kg


title: Kidney_R021008-186_Thalidomide_113 mg/kg_1d

source_name: Kidney, Thalidomide, 1d

value: Kidney


title: Kidney_S020205-335_Sulfathiazole_2629 mg/kg_5d

value: 5 d


title: Kidney_S020318-161_Sulfaphenazole_1695 mg/kg_1d

value: 1 d


title: Kidney_S020205-331_Sulfathiazole_2629 mg/kg_3d

value: Water


title: Kidney_S020205-328_Sulfathiazole_2629 mg/kg_1d

value: Male


title: Kidney_S020318-163_Sulfaphenazole_1695 mg/kg_3d


title: Kidney_S020205-334_Sulfathiazole_2629 mg/kg_5d


title: Kidney_R040528-001_Corn Oil_0 mg/kg_5d

value: 0 mg/kg


title: Kidney_S020318-160_Sulfaphenazole_1695 mg/kg_1d


title: Kidney_S020205-329_Sulfathiazole_2629 mg/kg_1d


title: Kidney_R040528-021_Diclofenac_3.5 mg/kg_5d


title: Kidney_R021008-165_Roxithromycin_312 mg/kg_3d

source_name: Kidney, Roxithromycin, 3d

value: Roxithromycin

value: 312 mg/kg

value: CMC


title: Kidney_S020311-382_Mefenamic Acid_93 mg/kg_5d

value: Mefenamic Acid

value: 93 mg/kg

value: Oral Gavage


title: Kidney_R021008-162_Roxithromycin_312 mg/kg_1d

source_name: Kidney, Roxithromycin, 1d


title: Kidney_R021008-168_Roxithromycin_312 mg/kg_5d

source_name: Kidney, Roxithromycin, 5d


title: Kidney_S020617-246_Oxcarbazepine_1600 mg/kg_1d

source_name: Kidney, Oxcarbazepine, 1d

value: Oxcarbazepine


title: Kidney_S020617-249_Oxcarbazepine_1600 mg/kg_3d

source_name: Kidney, Oxcarbazepine, 3d

value: 3 d


title: Kidney_S020205-332_Sulfathiazole_2629 mg/kg_3d

value: Sprague Dawley, CD-IGS

value: Sulfathiazole


title: Kidney_S020415-264_Nateglinide_625 mg/kg_5d

source_name: Kidney, Nateglinide, 5d

value: Nateglinide

value: 625 mg/kg


title: Kidney_S030120-068_Bromfenac_5 mg/kg_3d

source_name: Kidney, Bromfenac, 3d

value: Kidney

value: Bromfenac

value: 5 mg/kg


title: Kidney_S020916-288_Streptomycin_120 mg/kg_5d

source_name: Kidney, Streptomycin, 5d

value: Streptomycin

value: 120 mg/kg

value: 5 d

value: Saline

value: Intravenous

value: Male


title: Kidney_R021008-189_Thalidomide_113 mg/kg_3d

source_name: Kidney, Thalidomide, 3d

value: Thalidomide

value: 113 mg/kg

value: CMC


title: Kidney_S020415-258_Nateglinide_625 mg/kg_1d

source_name: Kidney, Nateglinide, 1d

value: 1 d

value: Oral Gavage


title: Kidney_R040528-020_Diclofenac_3.5 mg/kg_5d

value: Sprague Dawley, CD-IGS

value: Diclofenac

value: 3.5 mg/kg

value: Corn Oil


title: Kidney_S020916-285_Streptomycin_120 mg/kg_3d

source_name: Kidney, Streptomycin, 3d

value: Kidney

value: 3 d


title: Kidney_R020813-188_Rifampin_99 mg/kg_3d

source_name: Kidney, Rifampin, 3d

value: Rifampin

value: 99 mg/kg


title: Kidney_R021008-167_Roxithromycin_312 mg/kg_5d

value: Roxithromycin

value: 312 mg/kg

value: 5 d


title: Kidney_R020813-186_Rifampin_99 mg/kg_1d

source_name: Kidney, Rifampin, 1d

value: Male


title: Kidney_S020415-261_Nateglinide_625 mg/kg_3d

source_name: Kidney, Nateglinide, 3d

value: Nateglinide

value: 625 mg/kg


title: Kidney_S020617-252_Oxcarbazepine_1600 mg/kg_5d

source_name: Kidney, Oxcarbazepine, 5d

value: Oxcarbazepine

value: CMC


title: Kidney_R020813-192_Rifampin_99 mg/kg_5d

source_name: Kidney, Rifampin, 5d

value: Oral Gavage


title: Kidney_R020924-066_Dexfenfluramine_29 mg/kg_1d

source_name: Kidney, Dexfenfluramine, 1d

value: Sprague Dawley, CD-IGS

value: Dexfenfluramine

value: 29 mg/kg

value: 1 d

value: Water


title: Kidney_R020924-072_Dexfenfluramine_29 mg/kg_5d

source_name: Kidney, Dexfenfluramine, 5d

value: Kidney


title: Kidney_S020923-048_Foscarnet_350 mg/kg_5d

source_name: Kidney, Foscarnet, 5d

value: Foscarnet

value: 350 mg/kg

value: Saline

value: Intravenous


title: Kidney_S020729-240_Lamotrigine_26 mg/kg_5d

source_name: Kidney, Lamotrigine, 5d

value: Lamotrigine

value: 26 mg/kg

value: 5 d


title: Kidney_S020729-237_Lamotrigine_26 mg/kg_3d

source_name: Kidney, Lamotrigine, 3d

value: 3 d

value: Male


title: Kidney_S020708-165_Erythromycin_1500 mg/kg_3d

source_name: Kidney, Erythromycin, 3d

value: Erythromycin

value: CMC


title: Kidney_S020923-045_Foscarnet_350 mg/kg_3d

source_name: Kidney, Foscarnet, 3d

value: Sprague Dawley, CD-IGS


title: Kidney_S020729-234_Lamotrigine_26 mg/kg_1d

source_name: Kidney, Lamotrigine, 1d

value: Oral Gavage


title: Kidney_S020708-168_Erythromycin_1500 mg/kg_5d

source_name: Kidney, Erythromycin, 5d


title: Kidney_S020923-042_Foscarnet_350 mg/kg_1d

source_name: Kidney, Foscarnet, 1d


title: Kidney_S020708-162_Erythromycin_1500 mg/kg_1d

source_name: Kidney, Erythromycin, 1d


title: Kidney_S020311-378_Mefenamic Acid_93 mg/kg_1d

source_name: Kidney, Mefenamic Acid, 1d

value: Mefenamic Acid

value: 93 mg/kg

value: Corn Oil


title: Kidney_S020325-141_Methyl Salicylate_444 mg/kg_3d

source_name: Kidney, Methyl Salicylate, 3d

value: Kidney

value: Methyl Salicylate

value: 444 mg/kg


title: Kidney_S020311-381_Mefenamic Acid_93 mg/kg_3d

source_name: Kidney, Mefenamic Acid, 3d


title: Kidney_S020422-048_2-Acetylaminofluorene_30 mg/kg_5d

source_name: Kidney, 2-Acetylaminofluorene, 5d

value: 30 mg/kg


title: Kidney_S020318-184_6-Mercaptopurine_25 mg/kg_1d

source_name: Kidney, 6-Mercaptopurine, 1d

value: 25 mg/kg

value: 1 d


title: Kidney_S020325-138_Methyl Salicylate_444 mg/kg_1d

source_name: Kidney, Methyl Salicylate, 1d


title: Kidney_S020722-257_4-Methylpyrazole_155 mg/kg_1d

source_name: Kidney, 4-Methylpyrazole, 1d

value: 155 mg/kg

value: Saline

value: Intravenous


title: Kidney_R021008-161_Roxithromycin_312 mg/kg_1d

source_name: Kidney, Roxithromycin, 1d

value: Roxithromycin

value: 312 mg/kg

value: Male


title: Kidney_R021008-164_Roxithromycin_312 mg/kg_3d

source_name: Kidney, Roxithromycin, 3d

value: Sprague Dawley, CD-IGS

value: 3 d

value: CMC


title: Kidney_R021008-166_Roxithromycin_312 mg/kg_5d

source_name: Kidney, Roxithromycin, 5d

value: 5 d

value: Oral Gavage


title: Kidney_S020729-236_Lamotrigine_26 mg/kg_3d

source_name: Kidney, Lamotrigine, 3d

value: Kidney

value: Lamotrigine

value: 26 mg/kg


title: Kidney_S020325-144_Methyl Salicylate_444 mg/kg_5d

source_name: Kidney, Methyl Salicylate, 5d

value: Methyl Salicylate

value: 444 mg/kg

value: Corn Oil


title: Kidney_S020429-044_3-Acetamidophenol_700 mg/kg_3d

source_name: Kidney, 3-Acetamidophenol, 3d

value: 700 mg/kg


title: Kidney_S020923-047_Foscarnet_350 mg/kg_5d

source_name: Kidney, Foscarnet, 5d

value: Foscarnet

value: 350 mg/kg

value: Saline


title: Kidney_S020729-239_Lamotrigine_26 mg/kg_5d

source_name: Kidney, Lamotrigine, 5d


title: Kidney_S020415-263_Nateglinide_625 mg/kg_5d

source_name: Kidney, Nateglinide, 5d

value: Nateglinide

value: 625 mg/kg


title: Kidney_S020617-248_Oxcarbazepine_1600 mg/kg_3d

source_name: Kidney, Oxcarbazepine, 3d

value: Sprague Dawley, CD-IGS

value: Oxcarbazepine

value: Male


title: Kidney_S020729-233_Lamotrigine_26 mg/kg_1d

source_name: Kidney, Lamotrigine, 1d

value: 1 d

value: CMC


title: Kidney_S020617-251_Oxcarbazepine_1600 mg/kg_5d

source_name: Kidney, Oxcarbazepine, 5d

value: Kidney

value: 5 d

value: Oral Gavage


title: Kidney_S020617-245_Oxcarbazepine_1600 mg/kg_1d

source_name: Kidney, Oxcarbazepine, 1d


title: Kidney_S020325-137_Methyl Salicylate_444 mg/kg_1d

value: Methyl Salicylate


title: Kidney_S020415-260_Nateglinide_625 mg/kg_3d

source_name: Kidney, Nateglinide, 3d

value: 3 d


title: Kidney_S020429-042_3-Acetamidophenol_700 mg/kg_1d

source_name: Kidney, 3-Acetamidophenol, 1d

value: Corn Oil


title: Kidney_S020325-143_Methyl Salicylate_444 mg/kg_5d

value: 444 mg/kg


title: Kidney_S020311-383_Mefenamic Acid_93 mg/kg_5d

source_name: Kidney, Mefenamic Acid, 5d

value: Mefenamic Acid

value: 93 mg/kg


title: Kidney_S020415-257_Nateglinide_625 mg/kg_1d

source_name: Kidney, Nateglinide, 1d


title: Kidney_S020311-380_Mefenamic Acid_93 mg/kg_3d

source_name: Kidney, Mefenamic Acid, 3d


title: Kidney_S020325-140_Methyl Salicylate_444 mg/kg_3d

source_name: Kidney, Methyl Salicylate, 3d


title: Kidney_R020924-071_Dexfenfluramine_29 mg/kg_5d

source_name: Kidney, Dexfenfluramine, 5d

value: Dexfenfluramine

value: 29 mg/kg

value: Water


title: Kidney_S020311-377_Mefenamic Acid_93 mg/kg_1d

source_name: Kidney, Mefenamic Acid, 1d

value: Sprague Dawley, CD-IGS


title: Kidney_S020506-308_Irinotecan_5 mg/kg_3d

source_name: Kidney, Irinotecan, 3d

value: Irinotecan

value: 5 mg/kg

value: Saline

value: Intravenous


title: Kidney_S020708-167_Erythromycin_1500 mg/kg_5d

source_name: Kidney, Erythromycin, 5d

value: Kidney

value: Erythromycin

value: CMC

value: Male


title: Kidney_R020924-065_Dexfenfluramine_29 mg/kg_1d

source_name: Kidney, Dexfenfluramine, 1d

value: 1 d

value: Oral Gavage


title: Kidney_S020708-164_Erythromycin_1500 mg/kg_3d

source_name: Kidney, Erythromycin, 3d

value: 3 d


title: Kidney_R020924-068_Dexfenfluramine_29 mg/kg_3d

source_name: Kidney, Dexfenfluramine, 3d


title: Kidney_S020923-041_Foscarnet_350 mg/kg_1d

source_name: Kidney, Foscarnet, 1d

value: Foscarnet

value: 350 mg/kg


title: Kidney_S011204-187_Etoposide_188 mg/kg_3d

source_name: Kidney, Etoposide, 3d

value: Etoposide

value: 188 mg/kg

value: Corn Oil


title: Kidney_S011204-190_Etoposide_188 mg/kg_5d

source_name: Kidney, Etoposide, 5d

value: Sprague Dawley, CD-IGS

value: 5 d


title: Kidney_S011204-184_Etoposide_188 mg/kg_1d

source_name: Kidney, Etoposide, 1d


title: Kidney_S020708-161_Erythromycin_1500 mg/kg_1d

source_name: Kidney, Erythromycin, 1d


title: Kidney_S020506-310_Irinotecan_5 mg/kg_5d

source_name: Kidney, Irinotecan, 5d

value: Irinotecan

value: 5 mg/kg


title: Kidney_S020506-307_Irinotecan_5 mg/kg_3d

value: Saline

value: Intravenous


title: Kidney_S020506-304_Irinotecan_5 mg/kg_1d

source_name: Kidney, Irinotecan, 1d

value: Kidney


title: Kidney_R020924-192_Trimethadione_535 mg/kg_5d

source_name: Kidney, Trimethadione, 5d

value: Trimethadione

value: 535 mg/kg

value: Water


title: Kidney_S011204-185_Etoposide_188 mg/kg_1d

value: 1 d

value: Oral Gavage

value: Male


title: Kidney_S020325-402_Ofloxacin_3000 mg/kg_1d

source_name: Kidney, Ofloxacin, 1d

value: Ofloxacin


title: Kidney_R020924-189_Trimethadione_535 mg/kg_3d

source_name: Kidney, Trimethadione, 3d

value: 3 d


title: Kidney_S011204-188_Etoposide_188 mg/kg_3d

value: Etoposide

value: 188 mg/kg


title: Kidney_S020617-312_Pravastatin_1200 mg/kg_5d

source_name: Kidney, Pravastatin, 5d

value: Sprague Dawley, CD-IGS

value: Pravastatin

value: Corn Oil


title: Kidney_R020924-141_Sulfadiazine_1170 mg/kg_3d

source_name: Kidney, Sulfadiazine, 3d

value: Sulfadiazine


title: Kidney_R020924-144_Sulfadiazine_1170 mg/kg_5d

source_name: Kidney, Sulfadiazine, 5d

value: 5 d


title: Kidney_S020429-384_Salicylamide_1300 mg/kg_5d

source_name: Kidney, Salicylamide, 5d

value: Salicylamide

value: CMC


title: Kidney_S020506-305_Irinotecan_5 mg/kg_1d

value: Kidney

value: Irinotecan

value: 5 mg/kg

value: Saline

value: Intravenous


title: Kidney_S020325-407_Ofloxacin_3000 mg/kg_5d

source_name: Kidney, Ofloxacin, 5d

value: Water

value: Oral Gavage

value: Male


title: Kidney_R020924-138_Sulfadiazine_1170 mg/kg_1d

source_name: Kidney, Sulfadiazine, 1d

value: 1 d


title: Kidney_S020617-309_Pravastatin_1200 mg/kg_3d

source_name: Kidney, Pravastatin, 3d

value: 3 d


title: Kidney_S020429-377_Salicylamide_1300 mg/kg_1d

source_name: Kidney, Salicylamide, 1d

value: Sprague Dawley, CD-IGS


title: Kidney_S020325-401_Ofloxacin_3000 mg/kg_1d

value: Ofloxacin


title: Kidney_S020422-376_Venlafaxine_320 mg/kg_1d

source_name: Kidney, Venlafaxine, 1d

value: Venlafaxine

value: 320 mg/kg


title: Kidney_S020429-383_Salicylamide_1300 mg/kg_5d

value: 5 d


title: Kidney_S020429-380_Salicylamide_1300 mg/kg_3d

source_name: Kidney, Salicylamide, 3d

value: Salicylamide


title: Kidney_S020325-404_Ofloxacin_3000 mg/kg_3d

source_name: Kidney, Ofloxacin, 3d


title: Kidney_S020429-379_Salicylamide_1300 mg/kg_3d

value: CMC


title: Kidney_S020318-167_Sulfaphenazole_1695 mg/kg_5d

source_name: Kidney, Sulfaphenazole, 5d

value: Kidney

value: Sulfaphenazole


title: Kidney_R021008-163_Roxithromycin_312 mg/kg_3d

source_name: Kidney, Roxithromycin, 3d

value: Roxithromycin

value: 312 mg/kg


title: Kidney_R020924-140_Sulfadiazine_1170 mg/kg_3d

value: Sulfadiazine