title: MCF10A_woNut_RNA_WT_2 [WT_2]

city: Ramat Gan

first: Ofir

last: Hakim

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

data_processing:
Alignment was done using TopHat.
Reads count on transcripts was done using HTSeq.
Expression and differential analysis was done using 'edgeR' that assigns to each gene a False Discovery Rate (FDR) value and calculates the log Fold Change (logFC) between the two conditions.
Genes with FDR <0.05 and logFC greater than |0.5|were considered differentially expressed
Genome_build: hg19
Supplementary_files_format_and_content: txt file with read counts on genes, generated using HTSeq

growth_protocol: Cells were cultured in DMEM/ Ham's F-12 (Biological Industries) supplemented with 100 ng/ml cholera toxin (Sigma), 20 ng/ml epidermal growth factor (EGF)(corning), 0.01 mg/ml insulin(Sigma), 500 ng/ml hydrocortisone (Sigma), 1% penicillin- streptomycin (Gibco), 5% horse serum (Biological Industries) and kept at 37℃ in a 5% CO2 incubator (Thermo Scientific). Parental and transformed cells were subjected to no more than five passages in culture when used in experiments.

extract_protocol:
Total RNA was extracted from cells using RNA purification kit (GeneAll) according to the manufacturer’s instructions.  RNA quality was measured on a Bioanalyzer (Agilent) and only RNA with RIN score >9 was used for library preparation. Messenger RNA (mRNA) was enriched from 1 μg of total RNA by Poly(A)  mRNA Magnetic Isolation Module (New England Biolabs) according to the manufacturer’s instructions.
cDNA libraries were constructed using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs) following the manufacturer’s protocol. Library concentration was measured by DNA High Sensitivity Kit (Invitrogen) on a Qubit fluorometer (Invitrogen). Library quality and fragment sizes were assessed on a Bioanalyzer (Agilent) or on a Tape station (Agilent). RNA-Seq libraries from at least two biological replicas for each condition were sequenced on Illumina Hi-seq 2000 platform.

treatment_protocol: Cells were treated with 10µM Nutlin-3a (Sigma) or equivalent amount of vehicle (DMSO) for 4 hrs.

tag: tissue source

value: mammary gland; breast

value: epithelial

value: Parental

value: DMSO for 4hrs


title: Group1: 4T1 Control rep1

status: Public on Jan 26 2021

type: SRA

city: Seoul

first: Boksil

last: Hong

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University of Hopsital

library_source: transcriptomic

data_processing:
Reads were aligned them to the Mus musculus (mm10) using Tophat v2.0.13 with Bowtie v2.2.3 algorithm to perform the alignment from McMillan KS et al., Bioinformatics, 2009.
Transcript assembly and abundance estimation using Cufflinks v2.2.1 with a protocol from Trapnel C at al., Nature Biotechnology, 2010 (‘--max-bundle-frags 50000000’ options to correct sequence expression count bias and the ‘-G’ option for making the best use of known gene annotation information).
The transcript-level relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks. Gene-level relative abundances were calculated as the sum of FPKMs of transcripts in the gene.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with FPKM; data2.xlsx contains statistical analysis

molecule: total RNA

organism: Mus musculus

source_name: Murine breast cancer cells

growth_protocol: 4T1 was cultured in RPMI 1640 or Dulbecco’s modified essential medium (Hyclone, Logan, USA) supplemented with 10% FBS and antibiotics/antimycotic, respectively.

extract_protocol:
Total RNA from 4T1 overexpressing miR-204-5p or control was purified using TRIzol reagent (Thermofisher, USA).
A TruSeq RNA library preparation kit (Illumina, San Diego, CA, USA) was used according to the anufacturer’s instructions. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100-nt paired-end sequencing by Illumina HiSeq2500

treatment_protocol: Control or overexpression plasmids for miR-204-5p (Genolution Pharmarceuticals, Seoul, Korea) were transfected to 4T1 using Lipofectamine 3000 (Invitrogen, USA) according to the manufacturer’s instruction and stable clones expressing miR-204-5p were selected using 100 mg/ml Zeoicin, respectively

tag: genotype/variation

value: control

tag: cell line

tag: cell type

value: breast cancer cells


title: MCF-7 ChIP-seq STAT5A PRL+ ACY241+ biological rep 2 technical rep 2

city: Richmond

first: Justin

middle: Michael

last: Craig

state: Virginia

address: 1201 E Marshall St

department: Massey Cancer Center

country: USA

institute: Virginia Commonwealth University

library_source: genomic

data_processing:
NovaSEQ 6000 basecalling for ChIP- and RNA-seq performed by standard Illumina pipeline/software.
ChIP-seq and RNA-seq: ChIP-seq and RNA-seq data were analyzed using the R statistical computing environment and the Galaxy web platform via the public server at usegalaxy.org. Raw reads in .FASTQ file format were assessed for sequence quality, GC content, the presence of adaptors, overrepresented k-mers and duplicated reads utilizing FastQC v0.11.2. Adapters, polyG tails, and 15 bases from 5’ and 3’ tails were trimmed and any low quality reads (>20% bases with phred quality <Q20) or reads less than 60 bases in length (after trimming) were filtered using fastp v0.20.1.
ChIP-seq: Filtered reads were aligned to the hg38 reference genome (GRCh38; excluding the Y chromosome and alternate scaffolds) using Bowtie2 v2.3.4.3. The resultant .BAM files from technical replicates were merged and duplicate reads were removed before biological replicates and corresponding input samples were passed to MACS2 v2.1.1.20160309.6 for peak detection in paired-end mode (-BAMPE) with FDR<0.01.  Peaks in ENCODE blacklist regions were removed. The .BAM files of biological replicates were normalized to sequencing depth and combined to create counts per million (CPM) normalized .BIGWIG files using deepTools bamCoverage module v3.3.2.0.0.
RNA-seq: Filtered reads were aligned to curated RefSeq transcripts (refMrna.fa downloaded from UCSC Table Browser July 27, 2020) utilizing Kallisto quant v0.46.0.4. Gene level summaries of transcript counts were obtained using tximport v0.1. Normalization and differential expression analysis were conducted with limma-voom v3.38.3 using “robust settings” and an FDR<0.05 (Benjamini-Hochberg).
Genome_build: hg38
Supplementary_files_format_and_content: .bigwig files for each experimental condition represent merged technical and biological replicate .BAM files with duplicate reads removed and normalized for sequencing depth as read counts per million (CPM)
Supplementary_files_format_and_content: RNA-seq matrix with gene level read counts for each sample

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MCF-7 cell line was obtained from the American Type Culture Collection (ATCC) and cells were cultured in Dulbecco’s modified Eagles’s medium (DMEM; Life Technologies #11965092) supplemented with 10% fetal bovine serum (FBS; Corning #MT35011CV) and 1% penicillin-streptomycin (ThermoFisher Scientific #15140-122).

extract_protocol:
ChIP-seq:  Approximately 1.0 x 108 cells were used for each experimental condition and biological replicate (n=2 per condition and ChIP target). At the conclusion of ACY-241 treatment and/or prolactin stimulation, chromatin was cross-linked in 1% formaldehyde for 12 minutes, followed by neutralization with 1/20 volume of 2.5 M glycine. Cells were washed twice with ice-cold PBS, scraped and collected in a third volume of PBS, and briefly spun down before pellets were snap-frozen in liquid nitrogen. With the exception of sonication, which was performed using the Covaris M220 Focused-ultrasonicator (Covaris, Inc.), chromatin isolation, immunoprecipitation, and DNA extraction were performed as previously described [Lee, T.I., S.E. Johnstone, and R.A. Young, Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc, 2006. 1(2): p. 729-48]. DNA purity was assessed by spectrophotometry at 260, 270, and 280 nm, and integrity was assessed by capillary electrophoresis utilizing the Agilent 2100 Bioanalyzer.  RNA-seq:  RNA was extracted in phenol: chloroform: isoamyl alcohol (PCA) followed by ethanol precipitation. DNA was enzymatically digested prior to a second round of PCA and ethanol precipitation. RNA purity was assessed by spectrophotometry at 260, 270, and 280 nm, and integrity was assessed by capillary electrophoresis utilizing the Agilent 2100 Bioanalyzer. All samples possessed RIN (RNA Integrity Number) values ≥9.
ChIP-seq:  Library preparation was performed on ≥100 ng DNA using the Ovation Ultralow V2 DNA-Seq Library Preparation Kit (NuGEN) according to the manufacturer’s instructions.  RNA-seq:  Library preparation was performed on ≥500 ng RNA using the Universal Plus mRNA-Seq Library Preparation Kit (NuGEN) according to the manufacturer’s instructions.

treatment_protocol: ChIP-seq:  MCF-7 cells were grown in 150-mm plates to ~60% confluency in complete medium (as described above) before serum starvation (DMEM, 0.1% BSA) for 20 hours. Cells were treated with either 2 µM ACY-241 or 0.1% DMSO for two hours prior to stimulation with prolactin (250 ng/mL) or an equal volume of 1X PBS for 30 minutes, followed by cell harvest. For each ACY-241/prolactin experimental condition (DMSO/PRL-, DMSO/PRL+, ACY-241/PRL-, ACY-241/PRL+), pooled chromatin was aliquoted for incubation with each antibody immediately prior to the immunoprecipitation step to ensure sampling from an identical cell population and enable robust comparison of the chromatin occupancy of each ChIP target  RNA-seq:  MCF-7 cells were grown in 150-mm plates to ~60% confluency in complete medium (as described above) before serum starvation (DMEM, 0.1% BSA) for 20 hours. Cells were treated with either 2 µM ACY-241 or 0.1% DMSO for two hours prior to stimulation with prolactin (250 ng/mL) or an equal volume of 1X PBS for an additional 2 hours, followed by cell harvest.

value: ER+ breast cancer cells derived from pleural effusion of pt with breast adenocarcinoma

tag: chip antibody

value: STAT5A abcam #ab32043

tag: treatment

value: 30 minutes 250 ng/mL prolactin, 120 minutes 2 uM ACY-241 (Citarinostat)


title: MCF10A_woNut_RNA_WT_3 [WT_3]


title: MCF-7 ChIP-seq STAT5A PRL+ ACY241+ biological rep 2 technical rep 1


title: ADM treatment rep2

city: Hefei

first: Qiang

last: Liu

state: Anhui

address: 443 Huangshan Road

country: China

institute: University of Science and Technology of China

description: processed data file: ADM treatment.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0
Reads Count for each gene in each sample was counted by HTSeq v0.6.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files include normalized abundance measurements for each group

source_name: ADM treatment

growth_protocol: Standard protocol for primary neuron culture for RNA-seq

extract_protocol:
Total RNA was extracted by Trizol.Total amount of 2 μg RNA per sample was used as input material for the RNA   sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA   Library  Prep  Kit  for  Illumina following the manufacturer’s   recommendations  and  index  codes  were  added  to  attribute  sequences  to  each  sample
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: brain

tag: tissue/cell type

value: primary neurons


title: MCF-7 ChIP-seq STAT5A PRL+ ACY241+ biological rep 1 technical rep 2


title: SYC105

city: Chicago

first: Xiao

last: Song

state: IL

address: 303 E Superior St, Lurie 6-250

department: Neurology

institute: Northwestern University Feinberg School of Medicine

data_processing:
Reads were aligned to the human genome GRCh38 using HISAT2 (Version 2.1.0).
Read counts for each gene were quantified using HTSeq-count (Version 0.10.0) and then normalized by DESeq2 (r package, version 1.20.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files include raw counts for each gene of each sample generated from HTSeq-count; csv file includes normalized counts for each gene of all samples for generated from DESeq2.

source_name: glioblastoma tissues

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini kit or Trizol reagent according to the manufacturer's instruction.
Stranded, rRNA-deleted libraries were prepared using the Illumina stranded Total RNA TruSEQ kit according to the manufacturer's instruction.

tag: patient gender

value: Male

tag: patient age

tag: idh1 status

value: Mut

tag: tissue type

value: glioblastoma tissues


title: SYC107

value: Female


title: ADM treatment rep1

description: processed data file: ADM treatment.txt


title: MCF-7 ChIP-seq STAT5A PRL+ ACY241+ biological rep 1 technical rep 1


title: SYC103

value: WT


title: SYC106


title: ADM control rep2

description: processed data file: ADM treatment.txt

source_name: ADM treatment control


title: MCF-7 ChIP-seq STAT5A PRL- ACY241+ biological rep 2 technical rep 2

value: 120 minutes 2 uM ACY-241 (Citarinostat)


title: ApoE particle treatment rep2

description: processed data file: ApoE particle treatment.txt

source_name: ApoE particle treatment


title: MCF10A_RNA_WT_1 [cont_rep1]

value: mammary gland; breast


title: MCF10A_woNut_RNA_WT_1 [WT_1]

value: epithelial


title: SYC102


title: ADM control rep1

description: processed data file: ADM treatment.txt


title: SYC108


title: MCF10A_RNA_HRAS_2 [RAS_rep2]

value: H-RAS Gv12


title: SYC101


title: MCF-7 ChIP-seq STAT5A PRL- ACY241+ biological rep 2 technical rep 1


title: WT_NaCl_rep_4

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

country: Germany

institute: Heidelberg University

data_processing:
Reads were filtered for adapter contamination and quality.
Hisat2 version 2.0.5 was used for mapping.
A custom GTF file consisting of exonic gene regions from Ensembl Mus_musculus.GRCm38.98.chr.gtf.gz and repetitive elements (repeatmasker track for mm10 downloaded from UCSC genome Browser at 2018-07-06) excluding simple repeats and repeat annotations overlapping with exonic regions was prepared.
Read counts were extracted from BAM using featureCounts (v1.6.2) with the following paramters: -s 0 -p -B -Q 20
edgeR v3.26.6 was used for differential expression analysis and FPKM calculation. All genes with coverage were included into the analysis.
Genome_build: Mus_musculus.GRCm38 version 98 and a repeat masker track downloaded from UCSC table browser at 2018-07-06

source_name: NaCl treated mouse cells expressing mouse WT DNMT3A

growth_protocol: DNMT3A R882H Knock-in (KI) mice have been generated by the Mouse Biology Program (MBP) of the University of California (Davis, CA). To achieve inducible expression of DNMT3A R882H, pENTR-Vector (Invitrogen) encoding human DNMT3A with the R882H point mutation preceded by a Lox-Stop-Lox NeoR (LSL) cassette was introduced into C57BL/6N-derived JM8.N4 embryonic stem (ES) cells. After selection on G418, correctly targeted ES cells were injected into BALB/c blastocysts. The resulting chimeric males were bred to C57BL/6N females. DNMT3Afl-R882H/+ mice were crossed to B6.Cg-Tg(Mx1-cre)1Cgn/J mice (referred to as Mx1-Cre)27. Removal of the stop cassette by Cre-mediated excision allows for the expression of the mutant DNMT3AR882H mRNA and protein. All mice were kept in pathogen-free animal facilities at the University Hospital Heidelberg. C57BL/6J (CD45.2) and B6.SJL-PtprcaPepcb/BoyJ (CD45.1”) mice were obtained from The Jackson Laboratory. Age-matched Mx-Cre+// Dnmt3a and Mx-Cre–// Dnmt3a donor animals (Ly5.2) were treated with pI:pC (15 μg/g intraperitoneally [i.p.]) for 3 nonconsecutive days to induce excision of “STOP-cassette”. Donor bone marrow cells was harvested 4 weeks post-pI:pC and mixed in a 1:1 ratio with bone marrow harvested from 45.1 WT donors (B6.SJL-Ptprca Pepcb/BoyJ; Jackson Labs), and was then transplanted into 45.1 recipients for a total of 1 million cells per recipient. Peripheral blood engraftment was assessed by fluorescence-activated cell sorting at 2 weeks post-transplant, at which point recipient mice were divided into treatment groups (n = 7-11 per group) and treated with either AZA (2.5 mg/kg IP; Santa Cruz Biotechnology) or vehicle control (0.9% NaCl) on the following schedule for 2 weeks :  5 days with daily replacement on, 2 days off, 5 days with daily replacement on. MxCre was induced by three intraperitoneal injections (i.p.) of 400µg polyinosinic-polycytidylic acid (poly(I:C)) (Amersham) in PBS on day 0, 3 and 5. Analysis of mice or harvesting of BM cells was performed 10-14 days after the last poly(I:C) injection. In all experiments, recipients transplanted with bone marrow cells were used as controls for nonspecific poly(I:C) effects. In all experiments with D3A-KI we used heterozygous inducible mice because of the dominant effect from a single activated Ctnnb1 allele.

extract_protocol:
RNA was isolated from sorted LSK cells using the RNeasy Micro kit (Qiagen). RNA quality was checked using the Bioanalyzer Pico kit. RNA with a RIN value of <8 was excluded from library preparation.
Double-stranded cDNA was synthesized and amplified using the SMARTer Ultra Low RNA kit (Clontech). The cDNA samples were sheared by the Covaris system. Sheared fragments were end-repaired, A-tailed, and ligated to sequencing adaptors. A size selection to about 200 bp insert size was performed before PCR enrichment.

value: LSK sorted bone marrow cells

value: NaCl

tag: dnmt3a status

value: mouse WT DNMT3A +/+


title: MCF-7 ChIP-seq STAT5A PRL- ACY241+ biological rep 1 technical rep 2

value: ER+ breast cancer cells derived from pleural effusion of pt with breast adenocarcinoma


title: WT_NaCl_rep_3


title: MCF10A_RNA_WT_2 [cont_rep2]

value: Parental


title: SYC95


title: SYC100


title: MCF10A_RNA_HRAS_1 [RAS_rep1]


title: MCF10A_Nut_RNA_WT_2 [WT_2_NUT]

value: 10µM Nutlin-3a 4hrs


title: MCF10A_Nut_RNA_WT_3 [WT_3_NUT]


title: MCF-7 ChIP-seq STAT5A PRL- ACY241+ biological rep 1 technical rep 1

value: STAT5A abcam #ab32043


title: SYC94


title: WT_NaCl_rep_2


title: MCF10A_Nut_RNA_WT_1 [WT_1_NUT]


title: SYC93


title: MCF-7 ChIP-seq STAT5A PRL+ ACY241- biological rep 2 technical rep 2

value: 30 minutes 250 ng/mL prolactin, 120 minutes 0.1% DMSO


title: MCF10A_HRAS_input_p53_2

data_processing:
Alignment was done using Bowtie, allowing only unique reads to be considered.
For detecting regions of local read enrichment (peaks), MACS algorithm was applied with default parameters for ChIP-seq.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak file that were generated by MACS

extract_protocol:
Cells were cross-linked for 10 min at 37°C in 1% formaldehyde followed by quenching with 125 mM glycine for 10 min. Fixed cells were lysed with SDS Lysis Buffer (1% SDS, 50mM Tris pH 8.1, 10mM EDTA) supplemented with protease inhibitor and sonicated for 560 seconds (ME220 sonicator, Covaris). Cleared chromatin was diluted 1:10 with dilution Buffer (16.7mM Tris-HCl 8.1; 1.2mM EDTA; 167mM NaCl; 1.1% Triton) and incubated over night with 5 ug α-p53 (DO-1, Santa-Cruz) bound to magnetic beads (Dynabeads Protein G). Chromatin was washed with low salt buffer (20mM Tris-HCl 8.1; 2mM EDTA; 150mM NaCl; 1% triton; 0.1% SDS), high salt buffer (20mM Tris-HCl 8.1; 2mM EDTA; 500mM NaCl; 1% triton; 0.1% SDS), LiCl buffer (10mM Tris-HCl 8.1; 1mM EDTA; 1% NP-40; 250mM LiCl) at 4°C, and twice with TE (10mM Tris-HCl 8.1; 1mM EDTA) at room temp. Complexes were eluted with Elution buffer (10mM Tris-HCl 8.1; 1mM EDTA; 200mM NaCl; 1% SDS). Crosslinks were reversed with 1 mg/mL Proteinase K overnight at 65°C.
Purified DNA was used to prepare sequencing libraries using NEBNext UltraII DNA Library Prep Kit (New England Biolabs). Library concentration was measured by DNA High Sensitivity Kit (Invitrogen) on a Qubit fluorometer (Invitrogen). Library quality and fragment sizes were assessed on a Bioanalyzer (Agilent).

treatment_protocol: The p53 samples were treated with nutlin before the fixation.


title: SYC92


title: WT_NaCl_rep_1


title: MCF-7 ChIP-seq STAT5A PRL+ ACY241- biological rep 2 technical rep 1


title: MCF-7 ChIP-seq STAT5A PRL+ ACY241- biological rep 1 technical rep 2


title: MCF10A_HRAS_p53_2

value: α-p53 (DO-1, Santa-Cruz)


title: SYC91

value: Male


title: MCF-7 ChIP-seq STAT5A PRL+ ACY241- biological rep 1 technical rep 1


title: WT_Azacitidine_rep_3

source_name: Azacytidine treated mouse cells expressing mouse WT DNMT3A

value: Azacytidine


title: WT_Azacitidine_rep_1


title: WT_Azacitidine_rep_2


title: MCF-7 ChIP-seq STAT5A PRL- ACY241- biological rep 2 technical rep 2

value: 120 minutes 0.1% DMSO


title: SYC90

value: WT

value: glioblastoma tissues


title: MCF10A_HRAS_input_p53_1

value: mammary gland; breast


title: DNMT3A_R882H_NaCl_rep_4

source_name: NaCl treated mouse cells expressing mouse WT DNMT3A and human R882H DNMT3A

value: mouse WT DNMT3A + human DNMT3A R882H


title: MCF10A_HRAS_p53_1

value: epithelial

value: H-RAS Gv12


title: SYC86


title: DNMT3A_R882H_NaCl_rep_3

value: LSK sorted bone marrow cells

value: NaCl


title: MCF-7 ChIP-seq STAT5A PRL- ACY241- biological rep 1 technical rep 2

value: ER+ breast cancer cells derived from pleural effusion of pt with breast adenocarcinoma


title: MCF-7 ChIP-seq STAT5A PRL- ACY241- biological rep 2 technical rep 1


title: SYC83

source_name: Normal brain tissues

value: Normal brain tissues


title: DNMT3A_R882H_NaCl_rep_2


title: SYC82


title: MCF-7 ChIP-seq INPUT biological rep 2 technical rep 2


title: MCF-7 ChIP-seq STAT5A PRL- ACY241- biological rep 1 technical rep 1


title: SYC81


title: MCF-7 ChIP-seq INPUT biological rep 2 technical rep 1


title: SYC78


title: DNMT3A_R882H_Azacitidine_rep_5

source_name: Azacytidine treated mouse cells expressing mouse WT DNMT3A and human R882H DNMT3A


title: MCF-7 ChIP-seq INPUT biological rep 1 technical rep 2


title: SYC77


title: DNMT3A_R882H_Azacitidine_rep_3


title: DNMT3A_R882H_Azacitidine_rep_4


title: MCF-7 ChIP-seq INPUT biological rep 1 technical rep 1


title: SYC76


title: MCF10A_HRAS_CTCF_2

value: α-CTCF (Millipore 07-729)


title: H1299 cells-K571

city: Shanghai

first: Jianxiu

last: Yu

address: 280 South Chongqing Road, Shanghai 200025, China

department: Department of Biochemistry and Molecular Cell Biology

institute: shanghai jiaotong university school of medicine

description:
total RNA
H1299 cells-K571

data_processing:
3’ adaptor-trimming and low quality reads were removed by cutadapt software (v1.9.3)
clean reads of all libraries were aligned to the reference genome (hg19)  by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software
Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNAs were figured out and choosed by home-made scripts.
cuffdiff software (v2.2.1, part of cufflinks) was used to get the transcript level and gene level FPKM, and fold change and p-value were calculated , differentially bound or expressed mRNAs were identified.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM, counts

source_name: H1299 cells

extract_protocol:
MeRIP-seq:m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq,China) with anti-m6A antiboy. Both the input sample without immunoprecipitation and the m6A IP samples were used for library generation with  NEBNext® Ultra II  Directional RNA Library Prep Kit (New England Biolabs).
RIP-seq:RNA immunoprecipitation was performed with the GenSeqTM RIP Kit (GenSeq,China) with anti-Flag antiboy. RNA extracted by Trizol (Invitrogen, UK).rRNAs were removed from the immunoprecipitated RNA and input RNA samples by using Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego,CA, USA).
RNA-seq:Total RNA harvested by Trizol reagent was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
MeRIP-seq:The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.
RIP-seq:Libraries were controlled for quality and uantified using the BioAnalyzer 2100 system (Agilent Technologies). Library sequencing was performed on the Illumina Hiseq instrument with 150bp paired-end reads according to the manufacturer’s instructions
RNA-seq:Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired end reads

treatment_protocol:
H1299-shYTHDF2-WT cells (endogenous YTHDF2 was silenced by shYTHDF2 and then re-expressed Flag-tagged YTHDF2-WT) were treated with Ginkgolic acid for 12h
H1299-shYTHDF2-WT cells (endogenous YTHDF2 was silenced by shYTHDF2 and then re-expressed Flag-tagged YTHDF2-WT) were treated with 2-D08 for 24h

value: lung

tag: antibody/kit

value: untreated


title: DNMT3A_R882H_Azacitidine_rep_2


title: MCF10A_HRAS_input_CTCF_2


title: SYC73


title: MCF10A_HRAS_input_CTCF_1


title: DNMT3A_R882H_Azacitidine_rep_1


title: H1299 cells-WT

description:
total RNA
H1299 cells-WT


title: DNMT3A_R882H_NaCl_rep_1


title: MCF10A_HRAS_CTCF_1


title: MCF10A_WT_input_CTCF_2

value: Parental


title: NRF2KO_SFN_rep2

city: Tianjin

first: Zhiheng

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

institute: Tianjin Medical University

data_processing:
HISAT2 (version 2.1.0) was used to align paired-end reads to human (hg38) genome. Only unique mapped reads were used in further analysis.
FeatureCounts (version 1.6.0) was used to count reads number for each sample.
R package DESeq2 was used to identify differentially expressed genes, cut-offs were set at foldchange = 1.5 and FDR at 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

molecule: polyA RNA

source_name: WT 9-12 cell

extract_protocol:
Total RNA isolation was performed using TRIzol (Invitrogen). Total RNAs from whole kidney were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was completed by Novogene company (Beijing, China).

tag: cell line background

value: immortalized epithelial cell line obtained from patients with ADPKD

value: Nrf2 knockout

value: Nrf2 activator sulforaphane (SFN)


title: Pax3_2

city: Shenzhen

first: Huo

last: Bingqing

state: Guangdong

address: Lianhua Road

institute: Shenzhen PKU-HKUST Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample

source_name: Neuro-2a cells

growth_protocol: Mouse neuroblastoma Neuro-2a cells were purchased from ATCC (Manassas, USA), and maintained in Dulbecco’s modified Eagle’s medium (DMEM; Gibco Inc., USA) supplemented with penicillin (100U/mL), streptomycin (100mg/mL), and 10% fetal bovine serum (FBS, Gibco). Cells were cultured at 37℃ in cell culture flasks with 5% CO2.

extract_protocol:
The Pax3 overexpression adenoviral infected Cells were harvested from each group,and then placed in cryopreservation tubes and immediately immersed in liquid nitrogen (−196°C) for preservation.Total RNA from each sample was isolated using the TRIzol Reagent kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We use Pax3 overexpression adenoviral to infect Neuro-2a cells for 48h.

value: Pax3 overexpression


title: MCF10A_WT_CTCF_2


title: SYC70


title: Pax3_1


title: NC_2

value: control


title: SYC69


title: NC_1


title: MCF10A_WT_input_CTCF_1

value: mammary gland; breast


title: NRF2KO_SFN_rep1


title: NRF2KO_DMSO_rep2

value: vehicle


title: MCF10A_WT_CTCF_1

value: epithelial


title: NRF2KO_DMSO_rep1


title: SFN_rep2


title: MCF10A_ATAC_HRAS_1

data_processing:
Alignment was done using Bowtie, allowing only unique reads to be considered.
For detecting regions of local read enrichment (peaks), MACS algorithm was applied. Read start site was adjusted to represent  the center of the transposon binding event and the following parameters for MACS were  applied – --tsize=51 --nomodel --shiftsize=75 --llocal=25000 -p 1e-04
Genome_build: hg19
Supplementary_files_format_and_content: bed file of peaks that were generated by MACS

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro 2013). Briefly, cells were lysed and nuclei counted. Transposition reaction was performed on 105 nuclei using 5l of Nextera TDEI enzyme (Illumina) for 30 minutes at 37°C
Library was amplified using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs). Library concentration was measured by DNA High Sensitivity Kit (Invitrogen) on a Qubit fluorometer (Invitrogen). Library quality and fragment sizes were assessed on a Bioanalyzer (Agilent)

value: H-RAS Gv12


title: SYC66


title: MCF10A_ATAC_WT_2


title: SYC72


title: SYC71


title: DMSO_rep2


title: MCF10A_ATAC_WT_1


title: DMSO_rep1


title: RC_10

status: Public on Jan 25 2021

city: Cambridge

first: Guy

last: Slater

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

description: Ras Celecoxib

data_processing:
Fastq files were quality checked using FastQC [Babraham Institute, Simon Andrews], trimmed using cutadapt 1.16 [https://doi.org/10.14806/ej.17.1.200] with -m 20 --match-read-wildcards -q 30,30
Reads were aligned with hisat2 [Kim, Langmead and Salzberg 2015, Nature Methods] using default parameters and samtools [Li et al. 2009, Bioinformatics] was used for selecting only uniquely mapping reads and removing duplicates.
Alignment files corresponding to multiple lanes were merged using samtools [Li et al. 2009, Bioinformatics].
Counts of reads corresponding to genes from gencode v19 were generated using featureCounts v1.6.2 from the Subread package [Liao, Smyth and Shi, Bioinformatics 2014] with -t exon -g gene_id -F SAF -s 0
Genome_build: hg19
Supplementary_files_format_and_content: A space-delimited matrix containing counts for all samples.

source_name: ER:RAS IMR90 cell line

growth_protocol: DMEM + 10% FCS + Pen / Strep

extract_protocol:
Qiagen RNAeasy plus kit
Truseq stranded mRNA kit

treatment_protocol: 6 days of 100nM 4-OHT or 40uM Celecoxib or both

value: 4OHT 100 nM + Celecoxib 10 uM

tag: passage


title: SYC64


title: RC_8

description: Ras Celecoxib


title: RC_9

description: Ras Celecoxib


title: SYC68


title: RC_2

description: Ras Celecoxib


title: RC_5

description: Ras Celecoxib


title: RC_6

description: Ras Celecoxib


title: RC_7

description: Ras Celecoxib


title: C_9

description: Celecoxib

value: Celecoxib 10 uM


title: C_10

description: Celecoxib


title: MCF10A_ATAC_HRAS_2


title: SYC67


title: C_8

description: Celecoxib


title: SFN_rep1


title: C_6

description: Celecoxib


title: C_7

description: Celecoxib


title: C_5

description: Celecoxib


title: C_1

description: Celecoxib


title: C_2

description: Celecoxib


title: R_10

description: Ras

value: 4OHT 100 nM


title: R_9

description: Ras


title: R_8

description: Ras


title: RC_1

description: Ras Celecoxib


title: MDS-L-CON

type: RNA

first: Zheng

last: Zhang

address: YiShan Road 600

institute: Shanghai Jiao Tong University

description: Gene expression data from MDS-L treated with DMSO

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: MDS-L cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cell lines were cultured in RPMI 1640 containing 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2. In addition, IL-3 (100 U/ml) is essential for MDS-L cells.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: cells were seeded at a density of 5×10^5 cells/ well in 6-well plates and treated with five 24-h pulses of 1 μM DAC (Selleck Chemicals LLC, Houston TX, USA) and harvested after the treatment.

value: MDS-L

value: DMSO


title: R_6

description: Ras


title: R_7

description: Ras


title: SKM-1-DAC

description: Gene expression data from SKM-1 treated with decitabine

source_name: SKM-1 cell line

value: decitabine


title: R_5

description: Ras


title: SKM-1-CON

description: Gene expression data from SKM-1 treated with DMSO


title: R_2

description: Ras


title: G_9

description: Growing


title: G_8

description: Growing


title: G_6

description: Growing


title: G_2

description: Growing


title: G_7

description: Growing


title: G_5

description: Growing


title: R_1

description: Ras


title: MDS-L-DAC

description: Gene expression data from MDS-L treated with decitabine


title: G_1

description: Growing


title: 837siSTAT3poolQplusn1_Grade_S46

city: Goettingen

first: Andreas

last: Leha

address: Humboldtallee 32

department: Medical Statistics

institute: University Medical Center Goettingen

data_processing:
Illumina Casava software was used for basecalling.
Sequences were aligned to the human reference genome (assembly GRCh38) using STAR (version 2.5.2b).
Transcript level quantifications were generated using the ensembl transcript annotation (release 93) via RSEM (version 1.2.19). The resulting quantifications have been translated to gene level abundance estimates using tximport (version 1.12.3).
Abundance estimatios per gene were analyzed using edgeR (version 3.26.6) describing gene expression as a generalized linear model including condition (combined knockdown [siSTAT3pool, siNEG] and stimulation [IL6, control]) and kit [Dharmacon, Qiagen] as full model; comparisons in stimulation (IL6 vs control) or in knockdown (siSTAT3pool vs siNeg) were performed as contrast tests.
Data analysis was performed in R (version 3.4.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file with counts per million for each sample

source_name: SW837 cells

growth_protocol: The human colorectal cancer cell line SW837 was obtained from the American Type Culture Collection (ATCC) and cultured in Leibovitz L-15 medium (Invitrogen), supplemented with 10% fetal bovine serum (FBS; Biochrom) and 2 mM L-glutamine (BioWhittaker) at 37 °C.

extract_protocol:
Cells were lysed by adding 350 µl RLT buffer (Qiagen) directly on the well and total RNA was extracted using the Rneasy Mini Kit (Qiagen) according to the manufacturers instructions for extraction of total RNA from human cells.
RNA-seq libraries were performed using 500 ng mRNA of a non-stranded RNA Seq, massively-parallel mRNA sequencing approach from Illumina (TruSeq RNA Library Preparation Kit v2, Set A; 48 samples, 12 indexes). Specifically we first optimized the ligation step diluting the adapters concentration to increase ligation efficiency (>94%), and finally we reduce the number of PCR cycles (10 cycles) to avoid PCR duplication artefacts as well as primer dimers in the final library product. Libraries were prepared on the automation (Beckman Coulters Biomek FXP workstation). For accurate quantitation of cDNA libraries a fluorometric-based system, the QuantiFluordsDNA System from Promega, was used. The size of final cDNA libraries was determined by using the dsDNA 905 Reagent Kit (Fragment Analyzer Advanced Bioanalytical) exhibiting a sizing of 300 bp in average. Libraries were pooled and sequenced on the Illumina HiSeq 4000 (SE; 1 x 50 bp; 30-35 Mio reads/sample).

treatment_protocol: SW837 cells were transfected with siRNA pools targeting STAT3 and the respective non-targeting control siRNAs (Dharmacon Horizon Discovery; Qiagen) using lipid-based transfection (Lipofectamine® RNAiMAX Transfection Reagent; Invitrogen). For Hy-IL-6 stimulation, cells were treated overnight by 20 ng/ml Hy-IL-6 at 37 °C. Additionally, total RNA was isolated from unstimulated SW837 cells for each transfection condition.

value: colorectal cancer cell line SW837

tag: kit

value: Qiagen

tag: knockdown

tag: stimulation


title: 837siSTAT3poolQplusn3_Grade_S48

tag: cell line


title: 837siSTAT3poolQ-n1_Grade_S40


title: 837siSTAT3poolDplusn3_Grade_S36

value: Dharmacon


title: 837siSTAT3poolQ-n3_Grade_S42


title: 837siSTAT3poolDplusn2_Grade_S35


title: 837siSTAT3poolDplusn1_Grade_S34


title: 837siSTAT3poolD-n3_Grade_S57


title: 837siSTAT3poolD-n2_Grade_S56


title: 837siSTAT3poolQplusn2_Grade_S47


title: 837siNegQplusn1_Grade_S43

value: siNeg


title: G_10

description: Growing


title: 837siNegQplusn3_Grade_S45


title: 837siNegQplusn2_Grade_S44


title: 837siNegDplusn3_Grade_S33


title: 837siNegDplusn1_Grade_S31


title: 837siNegDplusn2_Grade_S32


title: 837siNegQ-n3_Grade_S39


title: 837siNegDn2_Grade_S53


title: 837siNegDn1_Grade_S52


title: 837siSTAT3poolQ-n2_Grade_S41


title: usp9x_low_K27_rep2

city: Toronto

first: Miguel

last: Ramalho-Santos

state: ON

address: 25 Orde Street

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description: H3K27me3 ChIP-seq in ES cells

data_processing:
Raw sequence fastq files were trimmed using trim_galore v0.4.0 to remove residual Illumina adapter sequences and check library quality.
For RNA-seq, trimmed fq files were aligned to the mm10 transcriptome using tophat v2.1.1 (options -p 8 -g 20 --no-coverage-search --library-type fr-firststrand --no-novel-indels).     For ChIP-seq, trimmed fq files were aligned to the mm10 genome using bowtie2 v2.2.5 for genomic alignment (-p 8 --local --very-sensitive-local --no-unal).
Aligned files were sorted using samtools sort.
ChIP-seq bam files were deduplicated using picard MarkDuplicates (REMOVE_DUPLICATES=true) and indexed using samtools.
Reads were imported into R/Bioconductor for further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq read counts over genes were obtained using featureCounts (-t exon -T 8 -s 2 -g gene_id) and a .gtf file for the mm10 transcriptome. Processed ChIP-seq files were converted to normalized bigwig (bw) files using the bamCoverage (--scaleFactor <> --binSize 10 -p max) and replicates merged by bigwigCompare (-of --operation add --binSize 10 -p max), both in the deepTools package. Peaks were called in ChIPseq replicates using epic2 (-gn mm10 -d chrM) and shared peaks determined by bedtools intersect. Peaks within 3kb were merged using bedtools (merge -d 3000).

organism:
Homo sapiens
Mus musculus

source_name: ES cells

growth_protocol: E14 ES cells were cultured in DMEM GlutaMAX with Na Pyruvate, 15% FBS, 0.1 mM Non-essential amino acids, 50 U/ml Penicillin/Streptomycin, 0.1 mM EmbryoMax 2-Mercaptoethanol, and 1000 U/ml ESGRO supplement (LIF).   Animal experiments were performed with 5-8-week-old female and 2-6-month-old male C57BL/6J mice.

extract_protocol:
For ES cells, RNA was extracted from the same number of cells using Qiagen RNeasy mini columns. Synthetic RNAs from the Exteral RNAs Control Consortium (ERCC) were spiked in at known concentrations to the same volume of RNA.    For ChIP in ES cells, 1 million cells were sorted and cross-linked for 10 min a room temperature in 1% formaldehyde/PBS. Cross-links were quenched with glycine (final 125 mM) for 5 min at room temperature. Cell pellets were washed in cold PBS, snap frozen, and stored at -80˚C. All subsequent steps were performed on ice or at 4˚C. Fixed cell pellets were thawed and lysed in 1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8 with protease inhibitors (1x Protease inhibitor cocktail, 1 mM PMSF, 1 mM NaF) for for 30 min. Chromatin was sheared to 200-500 bp fragments on a Covaris S220 with settings PIP 105, duty 2, cpb 200 for 9 min. Chromatin lysates were clarified by centrifugation and diluted 1:10 in dilution buffer (1% Triton X-100, 2 mM EDTA, 167 mM NaCl, 20 mM Tris-HCl pH 8) with protease inhibitors. Inputs were collected at the same time. IPs were performed overnight using 2.5 ug of antibody (CST #9733 H3K27me3) per equivalent of 500,000 cells, rotating at 4˚C. The next day, immunocomplexes were precipitated by incubation with pre-washed Protein A Dynabeads for 2h. Beads were washed 4x10 min in low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl pH 8), 1x10 min in high-salt buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 500 mM NaCl, 20 mM Tris-HCl pH 8), 1x10 min in LiCl buffer (0.25 M LiCl, 0.5% NP-40, 0.5% Na deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8), and 1x fast in TE. ChIP and input samples were eluted in fresh ChIP elution buffer (1% SDS, 50 mM NaHCO3, 50 mM Tris-HCl pH 8, 1 mM EDTA) and treated with RNase A for 1h at 37˚C. Cross-links were reversed by shaking overnight at 65˚C with Proteinase K.    For embryos, RNA was extracted from whole E8.5 embryos cleaned of extraembryonic tissues using Qiagen RNeasy mini columns.
For ES cells, RNA-seq libraries were constructed starting from 1 ug of total RNA using the NEBNext Directional II Directional RNA Library Kit for Illumina (NEB #E7760S) and Poly(A) mRNA Magnetic Isolation Module (NEB #E7490S). Libraries were indexed with NEBNext Multiplex Oligos for Illumina and sequenced as a pool.     ChIP-seq libraries were constructed using the NEBNext Ultra II DNA Library Kit for Illumina (NEB #E7645S). Libraries were indexed with NEBNext Multiplex Oligos for Illumina and sequenced as a pool.     For embryos, RNA-seq libraries were constructed starting from 300 ng of total RNA using the NEBNext Directional II Directional RNA Library Kit for Illumina (NEB #E7760S) and Poly(A) mRNA Magnetic Isolation Module (NEB #E7490S). Libraries were indexed with NEBNext Multiplex Oligos for Illumina and sequenced as a pool.

treatment_protocol: Auxin was added to ES cells at a final concentration of 500 uM for 8h or 48h, as indicated. Water was used as vehicle control. ES cells were sorted prior to RNA or chromatin extraction.

tag: cell type

value: E14 embryonic stem cells

value: 8h auxin

tag: spike-in

value: HEK293 gDNA

tag: chip antibody

value: anti-H3K27me3 (Cell Signaling Technology #9733)


title: usp9x_high_K27_rep2

description: H3K27me3 ChIP-seq in ES cells

tag: treatment


title: usp9x_low_K27_rep1

description: H3K27me3 ChIP-seq in ES cells


title: usp9x_high_K27_rep1

description: H3K27me3 ChIP-seq in ES cells


title: 837siSTAT3poolD-n1_Grade_S55

value: control


title: neg_K27_rep2

description: H3K27me3 ChIP-seq in ES cells

value: vehicle


title: neg_K27_rep1

description: H3K27me3 ChIP-seq in ES cells


title: input_K27_rep2

description: none (input)

value: none (input)


title: Mature sperm Veh14

city: Lexington

first: Wesley

middle: N

last: Saintilnord

state: KY

address: 741 South Limestone, Biological Biomedical Sciences Research Building

department: Molecular and Cellular Biochemistry

institute: University of Kentucky College of Medicine

data_processing:
base calling pipeline: HiSeq Control Software HD 3.4.0.38, RTA 2.7.7, bcl2fastq2.17 v2.17.1.14
Adapters and low-quality bases from raw data files were removed using trim_galore  version 0.5.0
Pre-processed fastq files were aligned to murine mm10/GRCm38 using bismark  v0.22.3
Methylation calling was done to create browser tracks for CpG sites for each sample using the bismark_methylation_extractor funtionnality (bismrak version 0.22.3)
CpG data was further filtered to eliminate coverage less than 10X in all samples and extremily high coverage was discarded to eliminate potential PCR bias using the R package MethylKit (version 1.12.0)
Genome_build: mm10/GRCm38 from UCSC
Supplementary_files_format_and_content: tsv files containing the following tab-separetd information for each sample : chromosome, coordinate of the CpG position, strand, methylation level (from 0 to 1) and coverage of the CpG

source_name: Cauda epididymis

growth_protocol: Thirty C57BL/6J male mice were purchased from The Jackson Laboratory at seven weeks of age. They were housed singly in an environmental controlled vivarium between 68-72ºF under a controlled photoperiod (14/10 light dark cycle) and acclimated for a week during which they were fed 10% Kcal from fat diet. Mice were fed the same 10% Kcal diet for the duration of the study to ensure purity of ingredients and matched nutritional exposure (and to decrease the risk of any cadmium being present in the food).

extract_protocol: Mature sperm was isolated from both cauda epididymides rinsed in a petri dish containing PBS and pelleted in PBS with 1% BSA. The supernatant was collected and centrifuged at 4000 rpm for 10 min at 4°C to pellet sperm and re-suspended in pure sperm wash. Genomic DNA was extracted from sperm using the Qiagen DNeasy Tissue Kit according to the manufaturer's protocol.

treatment_protocol: Mice in the vehicle (control) group were given RO water. Cd-exposed group were given RO water with 0.9 PPM (0.9 mg/L) of cadmium (prepared from cadmium chloride). Mice were allowed ad libitum access to their respective water formulations over the course of the study. Average dose was 0.68mg Cd/kg of body weight.

tag: strain

tag: tissue

value: Cauda epididymis

value: sperm

value: RO water

tag: age

value: Initially 7 weeks old; 9 weeks post treament


title: Mature sperm Veh15


title: 837siNegQ-n2_Grade_S38


title: Mature sperm Veh12


title: 837siNegQ-n1_Grade_S37


title: Mature sperm Veh11


title: Mature sperm Veh10


title: 837siNegDn3_Grade_S54


title: Mature sperm Veh9


title: Mature sperm Veh6


title: Mature sperm Veh4


title: Mature sperm Veh5


title: Mature sperm Veh8


title: Mature sperm Veh7


title: Mature sperm Veh2


title: Mature sperm Veh3


title: Mature sperm Cad14

value: RO water with 0.9 ppm of cadmium


title: Mature sperm Veh1


title: input_K27_rep1

description: none (input)


title: Mature sperm Cad10


title: Mature sperm Cad9


title: Mature sperm Veh13


title: Mature sperm Cad13


title: Mature sperm Cad11


title: Mature sperm Cad6


title: Mature sperm Cad8


title: Mature sperm Cad7


title: Mature sperm Cad5


title: Mature sperm Cad12


title: Mmu_lps_bal_cells

city: Biberach

middle: Thaddaeus

last: Wohnhaas

address: Birkendorfer Straße 65

institute: Boehringer Ingelheim

data_processing:
Reads: Read 1: 26 bp (cell barcode and UMI), Index read: 8, Read 2: 98 (sequence read)
Data were processed with Cell Ranger version 2.1.1. Raw base BCL files were demultiplexed using "cellranger mkfastq" and bcl2fastq v2.17.1.14. FASTQ files generated from "cellranger mkfastq" were further processed by "cellranger count"  which made use of STAR  to align the 98 bp sequence read against GRCm38. Filtering for valid cell barcodes and quantification of cell barcodes as well as unique molecular identifiers (UMIs) was also performed using "cellranger count".
Genome_build: GRCm38
Supplementary_files_format_and_content: Market Exchange format containing three files: tab-separated values files containing barcodes and annotated genes, respectively, matrix file containing UMI counts and indices for the barcode and gene tsv files

source_name: Immune cells

extract_protocol:
Bronchoalveolar lavage was performed by flushing lungs twice with 0.8 mL of Hanks solution containing 0.6 mM EDTA. BAL cells of eight animals were equally pooled for further analysis. Droplet-based single-cell partitioning of washed immune cells was performed using the 10X Genomics Chromium Controller.
Single-cell RNA-Seq libraries were generated using the Chromium Single-Cell 3' Reagent v2 Kit (10X Genomics, Pleasanton, CA) according to the manufacturer's instructions.

treatment_protocol: Mice were exposed once to a single dose of aerosolized Escherichia coli lipopolysaccharide (LPS) in PBS (1mg/ml) for 30min and mice were sacrificed 4 hours post LPS inhalation.

tag: stimulus

value: LPS

value: Bronchoalveolar lavage cells


title: Mature sperm Cad4


title: Mature sperm Cad1


title: Mature sperm Cad3


title: Mature sperm Cad2


title: usp9x_high_48h_rep2

description: RNA-seq in ES cells

value: 8h auxin + 48h recovery

value: ERCC


title: usp9x_high_48h_rep3

description: RNA-seq in ES cells


title: usp9x_high_48h_rep1

description: RNA-seq in ES cells


title: Mature sperm Cad15


title: usp9x_low_48h_rep3

description: RNA-seq in ES cells


title: usp9x_low_48h_rep2

description: RNA-seq in ES cells


title: usp9x_high_8h_rep1

description: RNA-seq in ES cells


title: usp9x_low_8h_rep3

description: RNA-seq in ES cells


title: usp9x_low_8h_rep2

description: RNA-seq in ES cells


title: Ctrl_neg_rep1

description: RNA-seq in ES cells


title: L-ESCs.WGBS.r1

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

institute: Southern Medical University

description: bisulfite treated  genomic DNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove adaptor sequences and low quality bases;
For whole genome bisulfite sequencing (WGBS), the clean reads were first mapped to mouse reference genome mm10 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module.
For WGBS, methylation level of covered cytosines, including CpG, CHH and CHG were estimated using comstomized perl scripts.
Genome_build: mm10
Supplementary_files_format_and_content: Methylation calling txt files include the methylation level of covered cytosines, including CpG, CHH and CHG context.

source_name: Embryonic stem cell

extract_protocol:
The isolated genomic DNA were used to construct the WGBS library, as previously described (Zhang et al., 2017).
Following the manufacturer’s instructions, genomic DNA was extracted from stem cells using the DNeasy Blood & Tissue Kit (Qiagen). Remaining RNA was removed by treating with RNase A. Three replicated samples from each of these stem cells were used for library preparation to ensure repeatability of experiment. In short, 2 μg of genomic DNA spiked with 10 ng of lambda DNA were fragmented to about 300 bp with Covaris S220. Next, end repair and A-ligation were performed to the DNA fragments. Methylated Adaptor (NEB) was then ligated to the DNA fragments. In order to reach >99% bisulfite conversion, the adaptor-ligated DNA was treated twice using EZ-96 DNA Methylation-Direct™ MagPrep (Zymo Research). The resulting single-strand DNA fragments were amplified by 4 PCR cycles using the KAPA HiFi HotStart Uracil+ ReadyMix (2×). At last, the libraries were sequenced on HiSeq4000 platform to generate 150-bp paired-end reads.

value: Embryonic stem cell

tag: passages


title: L-ESCs.WGBS.r3

description: bisulfite treated  genomic DNA


title: Ctrl_flag_rep2

description: RNA-seq in ES cells

value: E14 embryonic stem cells


title: Ctrl_neg_rep2

description: RNA-seq in ES cells


title: usp9x_low_8h_rep1

description: RNA-seq in ES cells

value: 8h auxin


title: Ctrl_neg_rep3

description: RNA-seq in ES cells


title: L-ESCs.WGBS.r2

description: bisulfite treated  genomic DNA


title: usp9x_low_48h_rep1

description: RNA-seq in ES cells


title: Ctrl_flag_rep1

description: RNA-seq in ES cells


title: usp9x_high_8h_rep2

description: RNA-seq in ES cells


title: TP0001651B04_5_3.000000uM_DMEM_6h_TC00283209_P19

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description:
TP0001651B04_5_3.000000uM_DMEM_6h
TC00283209_P19

data_processing:
[Read alignment]  Each FASTQ file was aligned to the probe sequences in the hWTv1 assay using HISAT2 v2.1.0 with spliced alignment disabled.
[Probe counts]  Aligned reads in SAM format were processed with SAMtools v1.9 to compute the number of uniquely aligned reads for each probe. Probe counts and associated meta-data for each well were stored for analysis using MongoDB v3.6.14.
Genome_build: hWTv1
Supplementary_files_format_and_content: httr_mcf7_pilot_count_data.csv - processed data provided as a single table of counts for all probes x all samples
hWTv1_mcf7_probes.csv - contains the targeted probes for the TempO-seq assay

source_name: MCF7 Cells

growth_protocol: Five vials of cryopreserved MCF7 (HTB-22TM) cells were purchased from American Tissue Culture Collection, designated as passage 0 (P0) and stored in vapor phase liquid nitrogen prior to initial thawing and expansion. A passage 3 (P3) MCF7 cryostock was generated by thawing and pooling all five original source vials and culturing through three consecutive passages in complete growth medium (DMEM + 10% FBS + 1% PSG). At each passage, cells from different culture vessels were pooled prior to re-seeding for subsequent expansion. At P3, cells were cryopreserved at 4 million cells per mL in complete growth medium + 5% DMSO according to manufacturer’s protocol. MCF7 cultures used in all phases of this study were maintained in humidified incubators with 5% CO2 atmosphere and internal temperature of 37°C. For chemical screening, MCF7 cells were thawed and subjected to a uniform expansion protocol from P3 to P6 through increasingly larger sizes of tissue culture vessels (T25 to T75 to T225) prior to plating in 384-well format. The three cultures were initiated on consecutive days and subject to uniform handling procedures to ensure that dosing and sample collection also occurred on consecutive days. All chemical screening experiments were performed on P7 cells.

extract_protocol:
Six hours after chemical treatment, HTTr assay plates were removed from the incubator and media in each assay well was drained to a residual volume of 10 µL using MultiFlo FX microdispenser equipped with a vacuum-driven aspiration manifold. To create cell lysates, 10 µL volumes of 2X BioSpyder lysis buffer were dispensed into each assay well using the same MultiFlo FX instrument equipped with 1 µL peristaltic pump dispensing cassette. Then, 20 µL volumes of UHRR, HBRR, BLDSMO, BLTSA and Lysis Buffer reference material were manually dispensed into duplicate wells of column 1 of each assay plate. The plates were sealed with an adhesive aluminum plate cover and incubated at room temperature, protected from light, for 30 minutes. The plates were then stored at -80°C prior to shipment to BioSpyder, Inc.
Samples were analyzed by BioSpyder using a custom-attenuated version of the TempO-Seq human whole transcriptome version 1 (hWTv1) assay, which includes 21,111 probes covering 19,287 genes. Lysates were processed as described in (House et al. 2017). In brief, 2 µL of each lysate was hybridized with 2 µL of detector oligos from the hWTv1 assay using the following thermal cycler protocol: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, terminating with 45°C incubation for 16-24 hours. Excess oligos were then removed via nuclease digestion (90 min at 37°C) and hybridized detector oligos were ligated (60 min at 37°) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured and 10 µL of each ligation product was transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification (10 min at 37°C, 2 min at 95°C, 6 cycles of 95°C for 30 s, 54°C for 30 s, 72°C for 120 s, 16 cycles of 95°C for 30s and 72°C for 120s, followed by 72°C for 60 s) with well coordinate-specific “barcoded” primer pairs containing universal adaptors for sequencing. Samples were then pooled into a series of three sequencing libraries (1 for each plate). Pooled sequencing libraries were then distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA).

treatment_protocol: DMSO-solubilized chemical stock solutions were received frozen from the US EPA ToxCast chemical inventory management contractor (EvoTec, Princeton, NJ) and stored at -80°C prior to dose plate preparation. An eight-point dilution series (1/2 log10 spacing) of test chemicals was prepared in a LabCyte Echo-qualified 384-well polypropylene (384PP) plate at 200x the desired nominal test concentration for screening (0.03 – 100 µM). Singleton wells of dosing solutions for each test chemical concentration were arrayed in columns 2 through 23 of the dose plate (Figure 1A). Transcriptomics reference chemicals (genistein, trichostatin A, sirolimus) were solubilized as 200x dosing solutions corresponding to nominal test concentrations of 10, 1 and 0.1 µM, respectively. Triplicate wells of dosing solutions for each of the transcriptomic reference chemicals were added to the dose plate (column 24) along with quadruplicate wells of pure DMSO as a vehicle control. At 24 h post-plating, 200 nL of 200x dosing solutions were transferred to the assay plates using a LabCyte Echo 550 acoustic dispenser. The final concentration of DMSO in all treatment, reference treatment and vehicle control wells was 0.5%.  Well coordinates on each assay plate were uniquely randomized with respect to treatment so that any potential edge-well effects were distributed in an unbiased manner across all possible treatment conditions.

tag: media

value: DMEM + 10% HI-FBS

value: 6h exposure of 3 uM of Propiconazole

tag: chemical name

value: Propiconazole

tag: chemical sample id

tag: chemical concentration

value: 3 uM

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate well


title: TP0001651F01_3_0.300000uM_DMEM_6h_TC00283209_P15

description:
TP0001651F01_3_0.300000uM_DMEM_6h
TC00283209_P15

tag: cell line

value: 6h exposure of 0.3 uM of Tetrac

value: Tetrac


title: TP0001651D02_8_100.000000uM_DMEM_6h_TC00283209_P16

description:
TP0001651D02_8_100.000000uM_DMEM_6h
TC00283209_P16

value: 6h exposure of 100 uM of PFOA

value: PFOA


title: TP0001651D05_1_0.030000uM_DMEM_6h_TC00283209_P18

description:
TP0001651D05_1_0.030000uM_DMEM_6h
TC00283209_P18

value: 6h exposure of 0.03 uM of Thiram

value: Thiram


title: TP0001651F04_5_3.000000uM_DMEM_6h_TC00283209_P21

description:
TP0001651F04_5_3.000000uM_DMEM_6h
TC00283209_P21

value: 6h exposure of 3 uM of Fulvestrant

value: Fulvestrant


title: TP0001651G04_1_0.030000uM_DMEM_6h_TC00283209_P24

description:
TP0001651G04_1_0.030000uM_DMEM_6h
TC00283209_P24

value: 6h exposure of 0.03 uM of Cladribine

value: Cladribine


title: Ctrl_flag_rep3

description: RNA-seq in ES cells

tag: cell type

value: 8h auxin + 48h recovery

tag: spike-in

value: ERCC


title: TSA_DMEM_6h_TC00283209_P20

description:
TSA_DMEM_6h
TC00283209_P20

tag: treatment

value: 6h exposure of 1 uM of Trichostatin A

value: Trichostatin A

value: 1 uM


title: TP0001651A01_6_10.000000uM_DMEM_6h_TC00283209_P23

description:
TP0001651A01_6_10.000000uM_DMEM_6h
TC00283209_P23

value: DMEM + 10% HI-FBS

value: 6h exposure of 10 uM of Pyraclostrobin

value: Pyraclostrobin

value: 10 uM


title: TP0001651A03_3_0.300000uM_DMEM_6h_TC00283209_P22

description:
TP0001651A03_3_0.300000uM_DMEM_6h
TC00283209_P22

value: 6h exposure of 0.3 uM of Butafenacil

value: Butafenacil


title: TP0001651E04_7_30.000000uM_DMEM_6h_TC00283209_P14

description:
TP0001651E04_7_30.000000uM_DMEM_6h
TC00283209_P14

value: 6h exposure of 30 uM of Farglitazar

value: Farglitazar

value: 30 uM


title: TP0001651G01_7_30.000000uM_DMEM_6h_TC00283209_P17

description:
TP0001651G01_7_30.000000uM_DMEM_6h
TC00283209_P17

value: 6h exposure of 30 uM of Vinclozolin

value: Vinclozolin


title: TP0001651A05_5_3.000000uM_DMEM_6h_TC00283209_P13

description:
TP0001651A05_5_3.000000uM_DMEM_6h
TC00283209_P13

value: 6h exposure of 3 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)

value: 3 uM


title: TP0001651D04_3_0.300000uM_DMEM_6h_TC00283209_P12

description:
TP0001651D04_3_0.300000uM_DMEM_6h
TC00283209_P12

value: 6h exposure of 0.3 uM of Clofibrate

value: Clofibrate


title: TP0001651A03_6_10.000000uM_DMEM_6h_TC00283209_P11

description:
TP0001651A03_6_10.000000uM_DMEM_6h
TC00283209_P11

value: 6h exposure of 10 uM of Butafenacil


title: TP0001651F01_4_1.000000uM_DMEM_6h_TC00283209_P09

description:
TP0001651F01_4_1.000000uM_DMEM_6h
TC00283209_P09

value: DMEM + 10% HI-FBS

value: 6h exposure of 1 uM of Tetrac

value: Tetrac

value: 1 uM


title: TP0001651H02_4_1.000000uM_DMEM_6h_TC00283209_P10

description:
TP0001651H02_4_1.000000uM_DMEM_6h
TC00283209_P10

value: 6h exposure of 1 uM of Maneb

value: Maneb


title: GEN_DMEM_6h_TC00283209_P07

description:
GEN_DMEM_6h
TC00283209_P07

value: 6h exposure of 10 uM of Genistein

value: Genistein

value: 10 uM


title: TP0001651A05_1_0.030000uM_DMEM_6h_TC00283209_P08

description:
TP0001651A05_1_0.030000uM_DMEM_6h
TC00283209_P08

value: 6h exposure of 0.03 uM of Clomiphene citrate (1:1)


title: TP0001651B06_2_0.100000uM_DMEM_6h_TC00283209_P06

description:
TP0001651B06_2_0.100000uM_DMEM_6h
TC00283209_P06

value: 6h exposure of 0.1 uM of Troglitazone

value: Troglitazone


title: TP0001651H03_2_0.100000uM_DMEM_6h_TC00283209_P05

description:
TP0001651H03_2_0.100000uM_DMEM_6h
TC00283209_P05

value: 6h exposure of 0.1 uM of Fomesafen

value: Fomesafen


title: TP0001651F03_1_0.030000uM_DMEM_6h_TC00283209_P02

description:
TP0001651F03_1_0.030000uM_DMEM_6h
TC00283209_P02

value: 6h exposure of 0.03 uM of 4-Cumylphenol


title: TP0001651G01_2_0.100000uM_DMEM_6h_TC00283209_P04

description:
TP0001651G01_2_0.100000uM_DMEM_6h
TC00283209_P04

value: 6h exposure of 0.1 uM of Vinclozolin

value: Vinclozolin


title: Untrtd_DMEM_6h_TC00283209_O24

description:
Untrtd_DMEM_6h
TC00283209_O24

value: DMEM + 10% HI-FBS

value: untreated


title: TP0001651B05_2_0.100000uM_DMEM_6h_TC00283209_O22

description:
TP0001651B05_2_0.100000uM_DMEM_6h
TC00283209_O22

value: 6h exposure of 0.1 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride


title: TP0001651D05_3_0.300000uM_DMEM_6h_TC00283209_O21

description:
TP0001651D05_3_0.300000uM_DMEM_6h
TC00283209_O21

value: 6h exposure of 0.3 uM of Thiram

value: Thiram


title: TP0001651D03_2_0.100000uM_DMEM_6h_TC00283209_O20

description:
TP0001651D03_2_0.100000uM_DMEM_6h
TC00283209_O20

value: 6h exposure of 0.1 uM of Cypermethrin

value: Cypermethrin


title: TP0001651H05_6_10.000000uM_DMEM_6h_TC00283209_O19

description:
TP0001651H05_6_10.000000uM_DMEM_6h
TC00283209_O19

value: 6h exposure of 10 uM of Trifloxystrobin

value: Trifloxystrobin

value: 10 uM


title: TP0001651D02_1_0.030000uM_DMEM_6h_TC00283209_O18

description:
TP0001651D02_1_0.030000uM_DMEM_6h
TC00283209_O18

value: 6h exposure of 0.03 uM of PFOA

value: PFOA


title: DMSO_DMEM_6h_TC00283209_O08

description:
DMSO_DMEM_6h
TC00283209_O08

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: TP0001651A06_1_0.030000uM_DMEM_6h_TC00283209_O16

description:
TP0001651A06_1_0.030000uM_DMEM_6h
TC00283209_O16

value: 6h exposure of 0.03 uM of Cyproconazole

value: Cyproconazole


title: TP0001651E01_2_0.100000uM_DMEM_6h_TC00283209_O14

description:
TP0001651E01_2_0.100000uM_DMEM_6h
TC00283209_O14

value: DMEM + 10% HI-FBS

value: 6h exposure of 0.1 uM of Bifenthrin

value: Bifenthrin


title: TP0001651H05_1_0.030000uM_DMEM_6h_TC00283209_O13

description:
TP0001651H05_1_0.030000uM_DMEM_6h
TC00283209_O13

value: 6h exposure of 0.03 uM of Trifloxystrobin


title: TP0001651C04_8_100.000000uM_DMEM_6h_TC00283209_O06

description:
TP0001651C04_8_100.000000uM_DMEM_6h
TC00283209_O06

value: 6h exposure of 100 uM of Simvastatin

value: Simvastatin


title: TP0001651H05_8_100.000000uM_DMEM_6h_TC00283209_O15

description:
TP0001651H05_8_100.000000uM_DMEM_6h
TC00283209_O15

value: 6h exposure of 100 uM of Trifloxystrobin


title: TP0001651H01_4_1.000000uM_DMEM_6h_TC00283209_O07

description:
TP0001651H01_4_1.000000uM_DMEM_6h
TC00283209_O07

value: 6h exposure of 1 uM of Flutamide

value: Flutamide

value: 1 uM


title: TP0001651A02_8_100.000000uM_DMEM_6h_TC00283209_O11

description:
TP0001651A02_8_100.000000uM_DMEM_6h
TC00283209_O11

value: 6h exposure of 100 uM of Imazalil

value: Imazalil


title: TP0001651C03_3_0.300000uM_DMEM_6h_TC00283209_O05

description:
TP0001651C03_3_0.300000uM_DMEM_6h
TC00283209_O05

value: 6h exposure of 0.3 uM of Simazine

value: Simazine


title: TP0001651H03_5_3.000000uM_DMEM_6h_TC00283209_O03

description:
TP0001651H03_5_3.000000uM_DMEM_6h
TC00283209_O03

value: 6h exposure of 3 uM of Fomesafen

value: Fomesafen

value: 3 uM


title: TP0001651C03_6_10.000000uM_DMEM_6h_TC00283209_O02

description:
TP0001651C03_6_10.000000uM_DMEM_6h
TC00283209_O02

value: DMEM + 10% HI-FBS

value: 6h exposure of 10 uM of Simazine

value: 10 uM


title: DMSO_DMEM_6h_TC00283209_P03

description:
DMSO_DMEM_6h
TC00283209_P03

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: TP0001651B02_3_0.300000uM_DMEM_6h_TC00283209_N22

description:
TP0001651B02_3_0.300000uM_DMEM_6h
TC00283209_N22

value: 6h exposure of 0.3 uM of 3,5,3'-Triiodothyronine


title: TP0001651H03_1_0.030000uM_DMEM_6h_TC00283209_N24

description:
TP0001651H03_1_0.030000uM_DMEM_6h
TC00283209_N24

value: 6h exposure of 0.03 uM of Fomesafen


title: TP0001651D04_2_0.100000uM_DMEM_6h_TC00283209_N21

description:
TP0001651D04_2_0.100000uM_DMEM_6h
TC00283209_N21

value: 6h exposure of 0.1 uM of Clofibrate

value: Clofibrate


title: TP0001651A01_1_0.030000uM_DMEM_6h_TC00283209_O12

description:
TP0001651A01_1_0.030000uM_DMEM_6h
TC00283209_O12

value: 6h exposure of 0.03 uM of Pyraclostrobin

value: Pyraclostrobin


title: TP0001651E04_4_1.000000uM_DMEM_6h_TC00283209_O17

description:
TP0001651E04_4_1.000000uM_DMEM_6h
TC00283209_O17

value: 6h exposure of 1 uM of Farglitazar

value: Farglitazar

value: 1 uM


title: TP0001651F02_6_10.000000uM_DMEM_6h_TC00283209_N20

description:
TP0001651F02_6_10.000000uM_DMEM_6h
TC00283209_N20

value: 6h exposure of 10 uM of Ziram

value: Ziram


title: TP0001651E05_2_0.100000uM_DMEM_6h_TC00283209_N18

description:
TP0001651E05_2_0.100000uM_DMEM_6h
TC00283209_N18

value: DMEM + 10% HI-FBS

value: 6h exposure of 0.1 uM of Atrazine

value: Atrazine


title: TP0001651D05_7_30.000000uM_DMEM_6h_TC00283209_O23

description:
TP0001651D05_7_30.000000uM_DMEM_6h
TC00283209_O23

value: 6h exposure of 30 uM of Thiram

value: Thiram

value: 30 uM


title: TP0001651A03_5_3.000000uM_DMEM_6h_TC00283209_O10

description:
TP0001651A03_5_3.000000uM_DMEM_6h
TC00283209_O10

value: 6h exposure of 3 uM of Butafenacil

value: Butafenacil

value: 3 uM


title: TP0001651C05_3_0.300000uM_DMEM_6h_TC00283209_O04

description:
TP0001651C05_3_0.300000uM_DMEM_6h
TC00283209_O04

value: 6h exposure of 0.3 uM of Bisphenol B

value: Bisphenol B


title: SIRO_DMEM_6h_TC00283209_O09

description:
SIRO_DMEM_6h
TC00283209_O09

value: 6h exposure of 0.1 uM of Sirolimus

value: Sirolimus


title: TP0001651F03_7_30.000000uM_DMEM_6h_TC00283209_N16

description:
TP0001651F03_7_30.000000uM_DMEM_6h
TC00283209_N16

value: 6h exposure of 30 uM of 4-Cumylphenol


title: TP0001651A06_8_100.000000uM_DMEM_6h_TC00283209_N15

description:
TP0001651A06_8_100.000000uM_DMEM_6h
TC00283209_N15

value: 6h exposure of 100 uM of Cyproconazole

value: Cyproconazole


title: TP0001651A02_3_0.300000uM_DMEM_6h_TC00283209_N13

description:
TP0001651A02_3_0.300000uM_DMEM_6h
TC00283209_N13

value: 6h exposure of 0.3 uM of Imazalil

value: Imazalil


title: TP0001651H04_4_1.000000uM_DMEM_6h_TC00283209_N14

description:
TP0001651H04_4_1.000000uM_DMEM_6h
TC00283209_N14

value: DMEM + 10% HI-FBS

value: 6h exposure of 1 uM of Bisphenol A

value: Bisphenol A

value: 1 uM


title: TP0001651D02_6_10.000000uM_DMEM_6h_TC00283209_N04

description:
TP0001651D02_6_10.000000uM_DMEM_6h
TC00283209_N04

value: 6h exposure of 10 uM of PFOA

value: PFOA

value: 10 uM


title: TP0001651A05_3_0.300000uM_DMEM_6h_TC00283209_N05

description:
TP0001651A05_3_0.300000uM_DMEM_6h
TC00283209_N05

value: 6h exposure of 0.3 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)


title: DMSO_DMEM_6h_TC00283209_N06

description:
DMSO_DMEM_6h
TC00283209_N06

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: TP0001651C04_7_30.000000uM_DMEM_6h_TC00283209_N07

description:
TP0001651C04_7_30.000000uM_DMEM_6h
TC00283209_N07

value: 6h exposure of 30 uM of Simvastatin

value: Simvastatin

value: 30 uM


title: TP0001651D03_8_100.000000uM_DMEM_6h_TC00283209_N03

description:
TP0001651D03_8_100.000000uM_DMEM_6h
TC00283209_N03

value: 6h exposure of 100 uM of Cypermethrin

value: Cypermethrin


title: TP0001651A02_2_0.100000uM_DMEM_6h_TC00283209_N11

description:
TP0001651A02_2_0.100000uM_DMEM_6h
TC00283209_N11

value: DMEM + 10% HI-FBS

value: 6h exposure of 0.1 uM of Imazalil

value: Imazalil


title: TP0001651B01_8_100.000000uM_DMEM_6h_TC00283209_N08

description:
TP0001651B01_8_100.000000uM_DMEM_6h
TC00283209_N08

value: 6h exposure of 100 uM of Cyanazine

value: Cyanazine


title: TP0001651H04_5_3.000000uM_DMEM_6h_TC00283209_M23

description:
TP0001651H04_5_3.000000uM_DMEM_6h
TC00283209_M23

value: 6h exposure of 3 uM of Bisphenol A

value: Bisphenol A

value: 3 uM


title: TP0001651C06_3_0.300000uM_DMEM_6h_TC00283209_N19

description:
TP0001651C06_3_0.300000uM_DMEM_6h
TC00283209_N19

value: 6h exposure of 0.3 uM of Cycloheximide

value: Cycloheximide


title: TP0001651E02_6_10.000000uM_DMEM_6h_TC00283209_N12

description:
TP0001651E02_6_10.000000uM_DMEM_6h
TC00283209_N12

value: 6h exposure of 10 uM of 4-Nonylphenol, branched

value: 4-Nonylphenol, branched

value: 10 uM


title: TP0001651G02_2_0.100000uM_DMEM_6h_TC00283209_M22

description:
TP0001651G02_2_0.100000uM_DMEM_6h
TC00283209_M22

value: 6h exposure of 0.1 uM of Lovastatin

value: Lovastatin


title: TP0001651G01_6_10.000000uM_DMEM_6h_TC00283209_N02

description:
TP0001651G01_6_10.000000uM_DMEM_6h
TC00283209_N02

value: 6h exposure of 10 uM of Vinclozolin

value: Vinclozolin


title: TP0001651A06_3_0.300000uM_DMEM_6h_TC00283209_N17

description:
TP0001651A06_3_0.300000uM_DMEM_6h
TC00283209_N17

value: DMEM + 10% HI-FBS

value: 6h exposure of 0.3 uM of Cyproconazole

value: Cyproconazole


title: TP0001651A01_5_3.000000uM_DMEM_6h_TC00283209_M24

description:
TP0001651A01_5_3.000000uM_DMEM_6h
TC00283209_M24

value: 6h exposure of 3 uM of Pyraclostrobin

value: Pyraclostrobin


title: TP0001651B06_3_0.300000uM_DMEM_6h_TC00283209_M19

description:
TP0001651B06_3_0.300000uM_DMEM_6h
TC00283209_M19

value: 6h exposure of 0.3 uM of Troglitazone

value: Troglitazone


title: TP0001651A05_2_0.100000uM_DMEM_6h_TC00283209_M20

description:
TP0001651A05_2_0.100000uM_DMEM_6h
TC00283209_M20

value: 6h exposure of 0.1 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)


title: TP0001651C02_5_3.000000uM_DMEM_6h_TC00283209_M17

description:
TP0001651C02_5_3.000000uM_DMEM_6h
TC00283209_M17

value: 6h exposure of 3 uM of 4-Hydroxytamoxifen

value: 3 uM


title: TP0001651B02_8_100.000000uM_DMEM_6h_TC00283209_M18

description:
TP0001651B02_8_100.000000uM_DMEM_6h
TC00283209_M18

value: 6h exposure of 100 uM of 3,5,3'-Triiodothyronine


title: TP0001651E03_5_3.000000uM_DMEM_6h_TC00283209_M16

description:
TP0001651E03_5_3.000000uM_DMEM_6h
TC00283209_M16

value: 6h exposure of 3 uM of Prochloraz

value: Prochloraz


title: TP0001651H02_8_100.000000uM_DMEM_6h_TC00283209_M13

description:
TP0001651H02_8_100.000000uM_DMEM_6h
TC00283209_M13

value: 6h exposure of 100 uM of Maneb

value: Maneb


title: TP0001651D05_5_3.000000uM_DMEM_6h_TC00283209_M14

description:
TP0001651D05_5_3.000000uM_DMEM_6h
TC00283209_M14

value: 6h exposure of 3 uM of Thiram

value: Thiram


title: GEN_DMEM_6h_TC00283209_N10

description:
GEN_DMEM_6h
TC00283209_N10

value: DMEM + 10% HI-FBS

value: 6h exposure of 10 uM of Genistein

value: Genistein

value: 10 uM


title: TP0001651C02_3_0.300000uM_DMEM_6h_TC00283209_M12

description:
TP0001651C02_3_0.300000uM_DMEM_6h
TC00283209_M12

value: 6h exposure of 0.3 uM of 4-Hydroxytamoxifen


title: TP0001651C06_4_1.000000uM_DMEM_6h_TC00283209_N09

description:
TP0001651C06_4_1.000000uM_DMEM_6h
TC00283209_N09

value: 6h exposure of 1 uM of Cycloheximide

value: Cycloheximide

value: 1 uM


title: TP0001651G05_6_10.000000uM_DMEM_6h_TC00283209_M21

description:
TP0001651G05_6_10.000000uM_DMEM_6h
TC00283209_M21

value: 6h exposure of 10 uM of Cyproterone acetate

value: Cyproterone acetate


title: TP0001651B04_3_0.300000uM_DMEM_6h_TC00283209_M15

description:
TP0001651B04_3_0.300000uM_DMEM_6h
TC00283209_M15

value: 6h exposure of 0.3 uM of Propiconazole

value: Propiconazole


title: TP0001651B04_7_30.000000uM_DMEM_6h_TC00283209_M10

description:
TP0001651B04_7_30.000000uM_DMEM_6h
TC00283209_M10

value: 6h exposure of 30 uM of Propiconazole

value: 30 uM


title: TP0001651C03_8_100.000000uM_DMEM_6h_TC00283209_M09

description:
TP0001651C03_8_100.000000uM_DMEM_6h
TC00283209_M09

value: 6h exposure of 100 uM of Simazine

value: Simazine


title: TP0001651B03_5_3.000000uM_DMEM_6h_TC00283209_M08

description:
TP0001651B03_5_3.000000uM_DMEM_6h
TC00283209_M08

value: 6h exposure of 3 uM of Reserpine

value: Reserpine

value: 3 uM


title: TP0001651A04_6_10.000000uM_DMEM_6h_TC00283209_M04

description:
TP0001651A04_6_10.000000uM_DMEM_6h
TC00283209_M04

value: DMEM + 10% HI-FBS

value: 6h exposure of 10 uM of Rotenone

value: Rotenone


title: TP0001651D06_7_30.000000uM_DMEM_6h_TC00283209_M03

description:
TP0001651D06_7_30.000000uM_DMEM_6h
TC00283209_M03

value: 6h exposure of 30 uM of PFOS

value: PFOS


title: TP0001651C01_6_10.000000uM_DMEM_6h_TC00283209_M02

description:
TP0001651C01_6_10.000000uM_DMEM_6h
TC00283209_M02

value: 6h exposure of 10 uM of Fenpyroximate (Z,E)

value: Fenpyroximate (Z,E)

value: 10 uM


title: TP0001651F02_1_0.030000uM_DMEM_6h_TC00283209_M07

description:
TP0001651F02_1_0.030000uM_DMEM_6h
TC00283209_M07

value: 6h exposure of 0.03 uM of Ziram

value: Ziram


title: TP0001651C02_1_0.030000uM_DMEM_6h_TC00283209_M06

description:
TP0001651C02_1_0.030000uM_DMEM_6h
TC00283209_M06

value: 6h exposure of 0.03 uM of 4-Hydroxytamoxifen


title: TP0001651F04_8_100.000000uM_DMEM_6h_TC00283209_L24

description:
TP0001651F04_8_100.000000uM_DMEM_6h
TC00283209_L24

value: 6h exposure of 100 uM of Fulvestrant

value: Fulvestrant


title: TP0001651B05_8_100.000000uM_DMEM_6h_TC00283209_M11

description:
TP0001651B05_8_100.000000uM_DMEM_6h
TC00283209_M11

value: 6h exposure of 100 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride


title: TP0001651G04_5_3.000000uM_DMEM_6h_TC00283209_L23

description:
TP0001651G04_5_3.000000uM_DMEM_6h
TC00283209_L23

value: 6h exposure of 3 uM of Cladribine

value: Cladribine


title: TP0001651C06_6_10.000000uM_DMEM_6h_TC00283209_M05

description:
TP0001651C06_6_10.000000uM_DMEM_6h
TC00283209_M05

value: DMEM + 10% HI-FBS

value: 6h exposure of 10 uM of Cycloheximide

value: Cycloheximide


title: TP0001651F03_6_10.000000uM_DMEM_6h_TC00283209_L20

description:
TP0001651F03_6_10.000000uM_DMEM_6h
TC00283209_L20

value: 6h exposure of 10 uM of 4-Cumylphenol


title: TP0001651E05_6_10.000000uM_DMEM_6h_TC00283209_L18

description:
TP0001651E05_6_10.000000uM_DMEM_6h
TC00283209_L18

value: 6h exposure of 10 uM of Atrazine

value: Atrazine


title: TP0001651A05_7_30.000000uM_DMEM_6h_TC00283209_L22

description:
TP0001651A05_7_30.000000uM_DMEM_6h
TC00283209_L22

value: 6h exposure of 30 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)

value: 30 uM


title: TP0001651H04_7_30.000000uM_DMEM_6h_TC00283209_L19

description:
TP0001651H04_7_30.000000uM_DMEM_6h
TC00283209_L19

value: 6h exposure of 30 uM of Bisphenol A

value: Bisphenol A


title: TP0001651D04_1_0.030000uM_DMEM_6h_TC00283209_L16

description:
TP0001651D04_1_0.030000uM_DMEM_6h
TC00283209_L16

value: 6h exposure of 0.03 uM of Clofibrate

value: Clofibrate


title: TP0001651G04_8_100.000000uM_DMEM_6h_TC00283209_L14

description:
TP0001651G04_8_100.000000uM_DMEM_6h
TC00283209_L14

value: 6h exposure of 100 uM of Cladribine


title: TP0001651D03_1_0.030000uM_DMEM_6h_TC00283209_L15

description:
TP0001651D03_1_0.030000uM_DMEM_6h
TC00283209_L15

value: 6h exposure of 0.03 uM of Cypermethrin

value: Cypermethrin


title: TP0001651F04_4_1.000000uM_DMEM_6h_TC00283209_L13

description:
TP0001651F04_4_1.000000uM_DMEM_6h
TC00283209_L13

value: 6h exposure of 1 uM of Fulvestrant

value: Fulvestrant

value: 1 uM


title: TP0001651B06_7_30.000000uM_DMEM_6h_TC00283209_N23

description:
TP0001651B06_7_30.000000uM_DMEM_6h
TC00283209_N23

value: DMEM + 10% HI-FBS

value: 6h exposure of 30 uM of Troglitazone

value: Troglitazone


title: TP0001651C06_5_3.000000uM_DMEM_6h_TC00283209_L17

description:
TP0001651C06_5_3.000000uM_DMEM_6h
TC00283209_L17

value: 6h exposure of 3 uM of Cycloheximide

value: Cycloheximide

value: 3 uM


title: TP0001651C03_5_3.000000uM_DMEM_6h_TC00283209_L12

description:
TP0001651C03_5_3.000000uM_DMEM_6h
TC00283209_L12

value: 6h exposure of 3 uM of Simazine

value: Simazine


title: TP0001651E03_4_1.000000uM_DMEM_6h_TC00283209_L11

description:
TP0001651E03_4_1.000000uM_DMEM_6h
TC00283209_L11

value: 6h exposure of 1 uM of Prochloraz

value: Prochloraz


title: TP0001651E03_1_0.030000uM_DMEM_6h_TC00283209_L08

description:
TP0001651E03_1_0.030000uM_DMEM_6h
TC00283209_L08

value: 6h exposure of 0.03 uM of Prochloraz


title: TP0001651E01_8_100.000000uM_DMEM_6h_TC00283209_L10

description:
TP0001651E01_8_100.000000uM_DMEM_6h
TC00283209_L10

value: 6h exposure of 100 uM of Bifenthrin

value: Bifenthrin


title: TP0001651F01_5_3.000000uM_DMEM_6h_TC00283209_L07

description:
TP0001651F01_5_3.000000uM_DMEM_6h
TC00283209_L07

value: 6h exposure of 3 uM of Tetrac

value: Tetrac


title: TP0001651B02_4_1.000000uM_DMEM_6h_TC00283209_L09

description:
TP0001651B02_4_1.000000uM_DMEM_6h
TC00283209_L09

value: 6h exposure of 1 uM of 3,5,3'-Triiodothyronine


title: TP0001651H04_3_0.300000uM_DMEM_6h_TC00283209_L06

description:
TP0001651H04_3_0.300000uM_DMEM_6h
TC00283209_L06

value: 6h exposure of 0.3 uM of Bisphenol A

value: Bisphenol A


title: TP0001651D06_2_0.100000uM_DMEM_6h_TC00283209_L05

description:
TP0001651D06_2_0.100000uM_DMEM_6h
TC00283209_L05

value: DMEM + 10% HI-FBS

value: 6h exposure of 0.1 uM of PFOS

value: PFOS


title: TP0001651F04_6_10.000000uM_DMEM_6h_TC00283209_L21

description:
TP0001651F04_6_10.000000uM_DMEM_6h
TC00283209_L21

value: 6h exposure of 10 uM of Fulvestrant

value: Fulvestrant

value: 10 uM


title: TP0001651G03_7_30.000000uM_DMEM_6h_TC00283209_L04

description:
TP0001651G03_7_30.000000uM_DMEM_6h
TC00283209_L04

value: 6h exposure of 30 uM of Nilutamide

value: Nilutamide

value: 30 uM


title: TP0001651C01_7_30.000000uM_DMEM_6h_TC00283209_K21

description:
TP0001651C01_7_30.000000uM_DMEM_6h
TC00283209_K21

value: 6h exposure of 30 uM of Fenpyroximate (Z,E)

value: Fenpyroximate (Z,E)


title: TP0001651F02_2_0.100000uM_DMEM_6h_TC00283209_K23

description:
TP0001651F02_2_0.100000uM_DMEM_6h
TC00283209_K23

value: 6h exposure of 0.1 uM of Ziram

value: Ziram


title: TP0001651B02_1_0.030000uM_DMEM_6h_TC00283209_K24

description:
TP0001651B02_1_0.030000uM_DMEM_6h
TC00283209_K24

value: 6h exposure of 0.03 uM of 3,5,3'-Triiodothyronine


title: SIRO_DMEM_6h_TC00283209_L02

description:
SIRO_DMEM_6h
TC00283209_L02

value: 6h exposure of 0.1 uM of Sirolimus

value: Sirolimus


title: TP0001651C06_7_30.000000uM_DMEM_6h_TC00283209_K22

description:
TP0001651C06_7_30.000000uM_DMEM_6h
TC00283209_K22

value: 6h exposure of 30 uM of Cycloheximide

value: Cycloheximide


title: TP0001651F05_6_10.000000uM_DMEM_6h_TC00283209_L03

description:
TP0001651F05_6_10.000000uM_DMEM_6h
TC00283209_L03

value: DMEM + 10% HI-FBS

value: 6h exposure of 10 uM of Fenofibrate

value: Fenofibrate


title: TP0001651G04_7_30.000000uM_DMEM_6h_TC00283209_K20

description:
TP0001651G04_7_30.000000uM_DMEM_6h
TC00283209_K20

value: 6h exposure of 30 uM of Cladribine

value: Cladribine


title: TP0001651D01_7_30.000000uM_DMEM_6h_TC00283209_K19

description:
TP0001651D01_7_30.000000uM_DMEM_6h
TC00283209_K19

value: 6h exposure of 30 uM of Lactofen

value: Lactofen


title: TP0001651G03_6_10.000000uM_DMEM_6h_TC00283209_K13

description:
TP0001651G03_6_10.000000uM_DMEM_6h
TC00283209_K13

value: 6h exposure of 10 uM of Nilutamide

value: Nilutamide

value: 10 uM


title: TP0001651E01_3_0.300000uM_DMEM_6h_TC00283209_K17

description:
TP0001651E01_3_0.300000uM_DMEM_6h
TC00283209_K17

value: 6h exposure of 0.3 uM of Bifenthrin

value: Bifenthrin


title: TP0001651B04_2_0.100000uM_DMEM_6h_TC00283209_K14

description:
TP0001651B04_2_0.100000uM_DMEM_6h
TC00283209_K14

value: 6h exposure of 0.1 uM of Propiconazole

value: Propiconazole


title: TP0001651G01_8_100.000000uM_DMEM_6h_TC00283209_K15

description:
TP0001651G01_8_100.000000uM_DMEM_6h
TC00283209_K15

value: 6h exposure of 100 uM of Vinclozolin

value: Vinclozolin


title: TP0001651D04_4_1.000000uM_DMEM_6h_TC00283209_K18

description:
TP0001651D04_4_1.000000uM_DMEM_6h
TC00283209_K18

value: 6h exposure of 1 uM of Clofibrate

value: Clofibrate

value: 1 uM


title: TP0001651B01_4_1.000000uM_DMEM_6h_TC00283209_K09

description:
TP0001651B01_4_1.000000uM_DMEM_6h
TC00283209_K09

value: DMEM + 10% HI-FBS

value: 6h exposure of 1 uM of Cyanazine

value: Cyanazine


title: TP0001651C04_5_3.000000uM_DMEM_6h_TC00283209_K10

description:
TP0001651C04_5_3.000000uM_DMEM_6h
TC00283209_K10

value: 6h exposure of 3 uM of Simvastatin

value: Simvastatin

value: 3 uM


title: TP0001651A06_6_10.000000uM_DMEM_6h_TC00283209_K12

description:
TP0001651A06_6_10.000000uM_DMEM_6h
TC00283209_K12

value: 6h exposure of 10 uM of Cyproconazole

value: Cyproconazole


title: TP0001651E04_3_0.300000uM_DMEM_6h_TC00283209_K11

description:
TP0001651E04_3_0.300000uM_DMEM_6h
TC00283209_K11

value: 6h exposure of 0.3 uM of Farglitazar

value: Farglitazar


title: TP0001651A06_4_1.000000uM_DMEM_6h_TC00283209_K08

description:
TP0001651A06_4_1.000000uM_DMEM_6h
TC00283209_K08

value: 6h exposure of 1 uM of Cyproconazole


title: TP0001651F04_1_0.030000uM_DMEM_6h_TC00283209_K07

description:
TP0001651F04_1_0.030000uM_DMEM_6h
TC00283209_K07

value: 6h exposure of 0.03 uM of Fulvestrant

value: Fulvestrant


title: TP0001651A02_1_0.030000uM_DMEM_6h_TC00283209_K05

description:
TP0001651A02_1_0.030000uM_DMEM_6h
TC00283209_K05

value: 6h exposure of 0.03 uM of Imazalil

value: Imazalil


title: TP0001651A05_4_1.000000uM_DMEM_6h_TC00283209_K06

description:
TP0001651A05_4_1.000000uM_DMEM_6h
TC00283209_K06

value: 6h exposure of 1 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)


title: TP0001651C05_1_0.030000uM_DMEM_6h_TC00283209_J24

description:
TP0001651C05_1_0.030000uM_DMEM_6h
TC00283209_J24

value: DMEM + 10% HI-FBS

value: 6h exposure of 0.03 uM of Bisphenol B

value: Bisphenol B


title: TP0001651F03_8_100.000000uM_DMEM_6h_TC00283209_K03

description:
TP0001651F03_8_100.000000uM_DMEM_6h
TC00283209_K03

value: 6h exposure of 100 uM of 4-Cumylphenol


title: TP0001651B04_4_1.000000uM_DMEM_6h_TC00283209_K04

description:
TP0001651B04_4_1.000000uM_DMEM_6h
TC00283209_K04

value: 6h exposure of 1 uM of Propiconazole

value: Propiconazole

value: 1 uM


title: TP0001651G03_4_1.000000uM_DMEM_6h_TC00283209_K02

description:
TP0001651G03_4_1.000000uM_DMEM_6h
TC00283209_K02

value: 6h exposure of 1 uM of Nilutamide

value: Nilutamide


title: TP0001651E03_6_10.000000uM_DMEM_6h_TC00283209_J23

description:
TP0001651E03_6_10.000000uM_DMEM_6h
TC00283209_J23

value: 6h exposure of 10 uM of Prochloraz

value: Prochloraz

value: 10 uM


title: TP0001651B03_6_10.000000uM_DMEM_6h_TC00283209_K16

description:
TP0001651B03_6_10.000000uM_DMEM_6h
TC00283209_K16

value: 6h exposure of 10 uM of Reserpine

value: Reserpine


title: TP0001651C04_1_0.030000uM_DMEM_6h_TC00283209_J19

description:
TP0001651C04_1_0.030000uM_DMEM_6h
TC00283209_J19

value: 6h exposure of 0.03 uM of Simvastatin

value: Simvastatin


title: TP0001651F03_3_0.300000uM_DMEM_6h_TC00283209_J22

description:
TP0001651F03_3_0.300000uM_DMEM_6h
TC00283209_J22

value: 6h exposure of 0.3 uM of 4-Cumylphenol


title: TP0001651H02_3_0.300000uM_DMEM_6h_TC00283209_J15

description:
TP0001651H02_3_0.300000uM_DMEM_6h
TC00283209_J15

value: DMEM + 10% HI-FBS

value: 6h exposure of 0.3 uM of Maneb

value: Maneb


title: TP0001651A03_2_0.100000uM_DMEM_6h_TC00283209_J18

description:
TP0001651A03_2_0.100000uM_DMEM_6h
TC00283209_J18

value: 6h exposure of 0.1 uM of Butafenacil

value: Butafenacil


title: TP0001651A04_4_1.000000uM_DMEM_6h_TC00283209_J14

description:
TP0001651A04_4_1.000000uM_DMEM_6h
TC00283209_J14

value: 6h exposure of 1 uM of Rotenone

value: Rotenone


title: TP0001651F05_3_0.300000uM_DMEM_6h_TC00283209_J16

description:
TP0001651F05_3_0.300000uM_DMEM_6h
TC00283209_J16

value: 6h exposure of 0.3 uM of Fenofibrate

value: Fenofibrate


title: TP0001651D04_8_100.000000uM_DMEM_6h_TC00283209_J21

description:
TP0001651D04_8_100.000000uM_DMEM_6h
TC00283209_J21

value: 6h exposure of 100 uM of Clofibrate

value: Clofibrate


title: TP0001651B01_5_3.000000uM_DMEM_6h_TC00283209_J13

description:
TP0001651B01_5_3.000000uM_DMEM_6h
TC00283209_J13

value: 6h exposure of 3 uM of Cyanazine

value: Cyanazine

value: 3 uM


title: TP0001651H02_2_0.100000uM_DMEM_6h_TC00283209_J11

description:
TP0001651H02_2_0.100000uM_DMEM_6h
TC00283209_J11

value: 6h exposure of 0.1 uM of Maneb


title: TP0001651H04_8_100.000000uM_DMEM_6h_TC00283209_J08

description:
TP0001651H04_8_100.000000uM_DMEM_6h
TC00283209_J08

value: 6h exposure of 100 uM of Bisphenol A

value: Bisphenol A


title: TP0001651E01_6_10.000000uM_DMEM_6h_TC00283209_J09

description:
TP0001651E01_6_10.000000uM_DMEM_6h
TC00283209_J09

value: DMEM + 10% HI-FBS

value: 6h exposure of 10 uM of Bifenthrin

value: Bifenthrin

value: 10 uM


title: TP0001651D03_4_1.000000uM_DMEM_6h_TC00283209_J12

description:
TP0001651D03_4_1.000000uM_DMEM_6h
TC00283209_J12

value: 6h exposure of 1 uM of Cypermethrin

value: Cypermethrin

value: 1 uM


title: TP0001651F02_3_0.300000uM_DMEM_6h_TC00283209_J17

description:
TP0001651F02_3_0.300000uM_DMEM_6h
TC00283209_J17

value: 6h exposure of 0.3 uM of Ziram

value: Ziram


title: TP0001651F02_8_100.000000uM_DMEM_6h_TC00283209_J10

description:
TP0001651F02_8_100.000000uM_DMEM_6h
TC00283209_J10

value: 6h exposure of 100 uM of Ziram


title: TP0001651A05_8_100.000000uM_DMEM_6h_TC00283209_J06

description:
TP0001651A05_8_100.000000uM_DMEM_6h
TC00283209_J06

value: 6h exposure of 100 uM of Clomiphene citrate (1:1)

value: Clomiphene citrate (1:1)


title: TP0001651E01_4_1.000000uM_DMEM_6h_TC00283209_J02

description:
TP0001651E01_4_1.000000uM_DMEM_6h
TC00283209_J02

value: 6h exposure of 1 uM of Bifenthrin


title: TP0001651E04_8_100.000000uM_DMEM_6h_TC00283209_J07

description:
TP0001651E04_8_100.000000uM_DMEM_6h
TC00283209_J07

value: 6h exposure of 100 uM of Farglitazar

value: Farglitazar


title: TP0001651B02_5_3.000000uM_DMEM_6h_TC00283209_J03

description:
TP0001651B02_5_3.000000uM_DMEM_6h
TC00283209_J03

value: 6h exposure of 3 uM of 3,5,3'-Triiodothyronine

value: 3 uM


title: TP0001651D05_6_10.000000uM_DMEM_6h_TC00283209_J04

description:
TP0001651D05_6_10.000000uM_DMEM_6h
TC00283209_J04

value: DMEM + 10% HI-FBS

value: 6h exposure of 10 uM of Thiram

value: Thiram


title: Lysis Buffer_TC00283209_J01

description:
Lysis Buffer
TC00283209_J01

source_name: Lysis Buffer

tag: sample type

value: Lysis Buffer

value: untreated


title: TP0001651H01_3_0.300000uM_DMEM_6h_TC00283209_J20

description:
TP0001651H01_3_0.300000uM_DMEM_6h
TC00283209_J20

value: 6h exposure of 0.3 uM of Flutamide

value: Flutamide


title: TP0001651G04_6_10.000000uM_DMEM_6h_TC00283209_I24

description:
TP0001651G04_6_10.000000uM_DMEM_6h
TC00283209_I24

value: 6h exposure of 10 uM of Cladribine

value: Cladribine

value: 10 uM


title: TP0001651F03_2_0.100000uM_DMEM_6h_TC00283209_I22

description:
TP0001651F03_2_0.100000uM_DMEM_6h
TC00283209_I22

value: 6h exposure of 0.1 uM of 4-Cumylphenol


title: SIRO_DMEM_6h_TC00283209_I23

description:
SIRO_DMEM_6h
TC00283209_I23

value: 6h exposure of 0.1 uM of Sirolimus

value: Sirolimus


title: TP0001651H02_5_3.000000uM_DMEM_6h_TC00283209_I20

description:
TP0001651H02_5_3.000000uM_DMEM_6h
TC00283209_I20

value: 6h exposure of 3 uM of Maneb

value: Maneb


title: TP0001651C03_7_30.000000uM_DMEM_6h_TC00283209_I21

description:
TP0001651C03_7_30.000000uM_DMEM_6h
TC00283209_I21

value: 6h exposure of 30 uM of Simazine

value: Simazine

value: 30 uM


title: TP0001651D03_5_3.000000uM_DMEM_6h_TC00283209_I19

description:
TP0001651D03_5_3.000000uM_DMEM_6h
TC00283209_I19

value: DMEM + 10% HI-FBS

value: 6h exposure of 3 uM of Cypermethrin

value: Cypermethrin

value: 3 uM


title: TP0001651G02_1_0.030000uM_DMEM_6h_TC00283209_J05

description:
TP0001651G02_1_0.030000uM_DMEM_6h
TC00283209_J05

value: 6h exposure of 0.03 uM of Lovastatin

value: Lovastatin


title: TP0001651E02_4_1.000000uM_DMEM_6h_TC00283209_I17

description:
TP0001651E02_4_1.000000uM_DMEM_6h
TC00283209_I17

value: 6h exposure of 1 uM of 4-Nonylphenol, branched

value: 4-Nonylphenol, branched

value: 1 uM


title: TP0001651A04_1_0.030000uM_DMEM_6h_TC00283209_I18

description:
TP0001651A04_1_0.030000uM_DMEM_6h
TC00283209_I18

value: 6h exposure of 0.03 uM of Rotenone

value: Rotenone


title: TP0001651A02_7_30.000000uM_DMEM_6h_TC00283209_I13

description:
TP0001651A02_7_30.000000uM_DMEM_6h
TC00283209_I13

value: 6h exposure of 30 uM of Imazalil

value: Imazalil


title: TP0001651B04_1_0.030000uM_DMEM_6h_TC00283209_I15

description:
TP0001651B04_1_0.030000uM_DMEM_6h
TC00283209_I15

value: 6h exposure of 0.03 uM of Propiconazole

value: Propiconazole


title: TP0001651F03_4_1.000000uM_DMEM_6h_TC00283209_I16

description:
TP0001651F03_4_1.000000uM_DMEM_6h
TC00283209_I16

value: 6h exposure of 1 uM of 4-Cumylphenol


title: TP0001651H01_2_0.100000uM_DMEM_6h_TC00283209_I14

description:
TP0001651H01_2_0.100000uM_DMEM_6h
TC00283209_I14

value: 6h exposure of 0.1 uM of Flutamide

value: Flutamide


title: TP0001651C05_2_0.100000uM_DMEM_6h_TC00283209_I12

description:
TP0001651C05_2_0.100000uM_DMEM_6h
TC00283209_I12

value: DMEM + 10% HI-FBS

value: 6h exposure of 0.1 uM of Bisphenol B

value: Bisphenol B


title: Lysis Buffer_TC00283209_I01

description:
Lysis Buffer
TC00283209_I01

value: Lysis Buffer

value: untreated


title: TP0001651E05_3_0.300000uM_DMEM_6h_TC00283209_I10

description:
TP0001651E05_3_0.300000uM_DMEM_6h
TC00283209_I10

value: 6h exposure of 0.3 uM of Atrazine

value: Atrazine


title: TP0001651E03_2_0.100000uM_DMEM_6h_TC00283209_I07

description:
TP0001651E03_2_0.100000uM_DMEM_6h
TC00283209_I07

value: 6h exposure of 0.1 uM of Prochloraz

value: Prochloraz


title: TP0001651B05_7_30.000000uM_DMEM_6h_TC00283209_H23

description:
TP0001651B05_7_30.000000uM_DMEM_6h
TC00283209_H23

value: 6h exposure of 30 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride

value: 30 uM


title: DMSO_DMEM_6h_TC00283209_I11

description:
DMSO_DMEM_6h
TC00283209_I11

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: TP0001651H01_6_10.000000uM_DMEM_6h_TC00283209_I05

description:
TP0001651H01_6_10.000000uM_DMEM_6h
TC00283209_I05

value: 6h exposure of 10 uM of Flutamide

value: 10 uM


title: TP0001651D05_4_1.000000uM_DMEM_6h_TC00283209_I03

description:
TP0001651D05_4_1.000000uM_DMEM_6h
TC00283209_I03

value: DMEM + 10% HI-FBS

value: 6h exposure of 1 uM of Thiram

value: Thiram

value: 1 uM


title: TP0001651A02_4_1.000000uM_DMEM_6h_TC00283209_H22

description:
TP0001651A02_4_1.000000uM_DMEM_6h
TC00283209_H22

value: 6h exposure of 1 uM of Imazalil

value: Imazalil


title: TP0001651E04_5_3.000000uM_DMEM_6h_TC00283209_H21

description:
TP0001651E04_5_3.000000uM_DMEM_6h
TC00283209_H21

value: 6h exposure of 3 uM of Farglitazar

value: Farglitazar

value: 3 uM


title: TP0001651A03_1_0.030000uM_DMEM_6h_TC00283209_H19

description:
TP0001651A03_1_0.030000uM_DMEM_6h
TC00283209_H19

value: 6h exposure of 0.03 uM of Butafenacil

value: Butafenacil


title: TP0001651A03_7_30.000000uM_DMEM_6h_TC00283209_H20

description:
TP0001651A03_7_30.000000uM_DMEM_6h
TC00283209_H20

value: 6h exposure of 30 uM of Butafenacil

value: 30 uM


title: TP0001651F05_8_100.000000uM_DMEM_6h_TC00283209_H17

description:
TP0001651F05_8_100.000000uM_DMEM_6h
TC00283209_H17

value: 6h exposure of 100 uM of Fenofibrate

value: Fenofibrate


title: TP0001651B05_6_10.000000uM_DMEM_6h_TC00283209_H15

description:
TP0001651B05_6_10.000000uM_DMEM_6h
TC00283209_H15

value: 6h exposure of 10 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride


title: TP0001651F05_2_0.100000uM_DMEM_6h_TC00283209_H16

description:
TP0001651F05_2_0.100000uM_DMEM_6h
TC00283209_H16

value: DMEM + 10% HI-FBS

value: 6h exposure of 0.1 uM of Fenofibrate


title: TP0001651D02_3_0.300000uM_DMEM_6h_TC00283209_I08

description:
TP0001651D02_3_0.300000uM_DMEM_6h
TC00283209_I08

value: 6h exposure of 0.3 uM of PFOA

value: PFOA


title: TP0001651D01_3_0.300000uM_DMEM_6h_TC00283209_I02

description:
TP0001651D01_3_0.300000uM_DMEM_6h
TC00283209_I02

value: 6h exposure of 0.3 uM of Lactofen

value: Lactofen


title: TP0001651B03_4_1.000000uM_DMEM_6h_TC00283209_I06

description:
TP0001651B03_4_1.000000uM_DMEM_6h
TC00283209_I06

value: 6h exposure of 1 uM of Reserpine

value: Reserpine

value: 1 uM


title: TP0001651D01_2_0.100000uM_DMEM_6h_TC00283209_I04

description:
TP0001651D01_2_0.100000uM_DMEM_6h
TC00283209_I04

value: 6h exposure of 0.1 uM of Lactofen


title: TP0001651B01_7_30.000000uM_DMEM_6h_TC00283209_H13

description:
TP0001651B01_7_30.000000uM_DMEM_6h
TC00283209_H13

value: 6h exposure of 30 uM of Cyanazine

value: Cyanazine


title: TP0001651D06_1_0.030000uM_DMEM_6h_TC00283209_H12

description:
TP0001651D06_1_0.030000uM_DMEM_6h
TC00283209_H12

value: 6h exposure of 0.03 uM of PFOS

value: PFOS


title: TP0001651G01_1_0.030000uM_DMEM_6h_TC00283209_H10

description:
TP0001651G01_1_0.030000uM_DMEM_6h
TC00283209_H10

value: 6h exposure of 0.03 uM of Vinclozolin

value: Vinclozolin


title: TP0001651G02_8_100.000000uM_DMEM_6h_TC00283209_H08

description:
TP0001651G02_8_100.000000uM_DMEM_6h
TC00283209_H08

value: 6h exposure of 100 uM of Lovastatin

value: Lovastatin


title: TP0001651B01_6_10.000000uM_DMEM_6h_TC00283209_H11

description:
TP0001651B01_6_10.000000uM_DMEM_6h
TC00283209_H11

value: DMEM + 10% HI-FBS

value: 6h exposure of 10 uM of Cyanazine

value: 10 uM


title: TP0001651D02_5_3.000000uM_DMEM_6h_TC00283209_H06

description:
TP0001651D02_5_3.000000uM_DMEM_6h
TC00283209_H06

value: 6h exposure of 3 uM of PFOA

value: PFOA

value: 3 uM


title: TP0001651F02_4_1.000000uM_DMEM_6h_TC00283209_H04

description:
TP0001651F02_4_1.000000uM_DMEM_6h
TC00283209_H04

value: 6h exposure of 1 uM of Ziram

value: Ziram


title: TP0001651F04_7_30.000000uM_DMEM_6h_TC00283209_H07

description:
TP0001651F04_7_30.000000uM_DMEM_6h
TC00283209_H07

value: 6h exposure of 30 uM of Fulvestrant

value: Fulvestrant

value: 30 uM


title: TP0001651B03_2_0.100000uM_DMEM_6h_TC00283209_H03

description:
TP0001651B03_2_0.100000uM_DMEM_6h
TC00283209_H03

value: 6h exposure of 0.1 uM of Reserpine

value: Reserpine


title: BL_TSA_TC00283209_H01

description:
BL_TSA
TC00283209_H01

value: 6h exposure of 1 uM of Trichostatin A

value: Trichostatin A

value: 1 uM


title: TP0001651H01_1_0.030000uM_DMEM_6h_TC00283209_G24

description:
TP0001651H01_1_0.030000uM_DMEM_6h
TC00283209_G24

value: 6h exposure of 0.03 uM of Flutamide

value: Flutamide


title: TP0001651G03_5_3.000000uM_DMEM_6h_TC00283209_G23

description:
TP0001651G03_5_3.000000uM_DMEM_6h
TC00283209_G23

value: DMEM + 10% HI-FBS

value: 6h exposure of 3 uM of Nilutamide

value: Nilutamide


title: TP0001651E05_1_0.030000uM_DMEM_6h_TC00283209_H02

description:
TP0001651E05_1_0.030000uM_DMEM_6h
TC00283209_H02

value: 6h exposure of 0.03 uM of Atrazine

value: Atrazine


title: TP0001651A02_6_10.000000uM_DMEM_6h_TC00283209_H18

description:
TP0001651A02_6_10.000000uM_DMEM_6h
TC00283209_H18

value: 6h exposure of 10 uM of Imazalil

value: Imazalil

value: 10 uM


title: TP0001651A06_7_30.000000uM_DMEM_6h_TC00283209_G22

description:
TP0001651A06_7_30.000000uM_DMEM_6h
TC00283209_G22

value: 6h exposure of 30 uM of Cyproconazole

value: Cyproconazole


title: TP0001651F01_8_100.000000uM_DMEM_6h_TC00283209_H05

description:
TP0001651F01_8_100.000000uM_DMEM_6h
TC00283209_H05

value: 6h exposure of 100 uM of Tetrac

value: Tetrac


title: TP0001651C06_1_0.030000uM_DMEM_6h_TC00283209_G20

description:
TP0001651C06_1_0.030000uM_DMEM_6h
TC00283209_G20

value: 6h exposure of 0.03 uM of Cycloheximide

value: Cycloheximide


title: TP0001651E05_7_30.000000uM_DMEM_6h_TC00283209_G19

description:
TP0001651E05_7_30.000000uM_DMEM_6h
TC00283209_G19

value: 6h exposure of 30 uM of Atrazine

value: 30 uM


title: TSA_DMEM_6h_TC00283209_G17

description:
TSA_DMEM_6h
TC00283209_G17

value: 6h exposure of 1 uM of Trichostatin A

value: Trichostatin A

value: 1 uM


title: TP0001651C01_4_1.000000uM_DMEM_6h_TC00283209_G14

description:
TP0001651C01_4_1.000000uM_DMEM_6h
TC00283209_G14

value: DMEM + 10% HI-FBS

value: 6h exposure of 1 uM of Fenpyroximate (Z,E)

value: Fenpyroximate (Z,E)


title: TP0001651G02_3_0.300000uM_DMEM_6h_TC00283209_G15

description:
TP0001651G02_3_0.300000uM_DMEM_6h
TC00283209_G15

value: 6h exposure of 0.3 uM of Lovastatin

value: Lovastatin


title: TP0001651B01_2_0.100000uM_DMEM_6h_TC00283209_G16

description:
TP0001651B01_2_0.100000uM_DMEM_6h
TC00283209_G16

value: 6h exposure of 0.1 uM of Cyanazine

value: Cyanazine


title: TP0001651B05_1_0.030000uM_DMEM_6h_TC00283209_H09

description:
TP0001651B05_1_0.030000uM_DMEM_6h
TC00283209_H09

value: 6h exposure of 0.03 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride