title: TP0001651G05_6_10.000000uM_DMEM_12h_TC00283154_I03

description:
TP0001651G05_6_10.000000uM_DMEM_12h
TC00283154_I03

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of Cyproterone acetate

tag: chemical name

value: Cyproterone acetate

tag: chemical sample id

tag: chemical concentration

value: 10 uM


title: TP0001651F04_3_0.300000uM_DMEM_12h_TC00283154_H23

status: Public on Dec 05 2023

type: SRA

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

country: USA

institute: U.S. Environmental Protection Agency

description:
TP0001651F04_3_0.300000uM_DMEM_12h
TC00283154_H23

library_source: transcriptomic

data_processing:
Each FASTQ file was aligned to the probe sequences in the hWTv1 assay using HISAT2 v2.1.0 with spliced alignment disabled.
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.
Assembly: hWTv1
Supplementary files format and content: Processed data provided as a single table of counts for all probes x all samples

molecule: total RNA

organism: Homo sapiens

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: cell line

tag: treatment

value: 12h exposure of 0.3 uM of Fulvestrant

value: Fulvestrant

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate well


title: small EV from BDNF-treated cortical neurons 1 1BExo

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description:
small EV from BDNF-treated cortical neurons 1
smallRNA sequencing
1BExo_mm_smallrnaneb_sr_kauranil_D_4_S46_L004_R1_001

data_processing:
An in-house developed pipeline was used to analyze the small RNAome. Quality check and demultiplexing were performed using the CASAVA 1.8.2 software (Illumina)
smallRNA seq: To quantify small RNAome, reads were first mapped to mature miRNA sequences obtained by miRBase (http://www.mirbase.org/) followed by further mapping to other small non coding RNA sequences (http://www.ensembl.org/info/data/ftp/index.html). Reads were then mapped to the mm10 reference genome.
RNA seq: Demultiplexing was performed using Illumina CASAVA version 1.8. Cutadapt-1.8.1 was used to remove sequencing adapters.
smallRNA seq DESeq2: We used raw counts for DE analysis. We adjusted the raw read counts for library size and log2 transformed them prior to doing DE analysis. Each sample was assigned a quality z-score, and those with a low quality (Z > 2.5 or Z -2.5) were classified as outliers and excluded from further analysis. Further DE analysis was performed on samples with read counts greater than 5 in at least 50% of the analyzed samples. To adjust for hidden batch effects and to remove unwanted variation, the RUVSeq package was used.
RNA seq: We used raw counts for the DE analysis. Prior to performing DE analysis, we normalized the raw read counts for library size and converted them using the log2 transformation. Each sample was assigned a quality z-score, and samples with a low quality (Z > 2.5 or Z -2.5) were identified as outliers and excluded from further analysis. Additionally, read counts 10 in at least 50% of examined samples were used in DE analysis. The RUVSeq package was used to account for and eliminate undesired variance due to hidden batch effects. The data were corrected for batch effect. DESeq22 was used to conduct differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts txt files

organism: Mus musculus

source_name: Primary cortical neurons

growth_protocol: primary neurons were derived from mouse embryos at embryonic day 16 according to Animal Welfare regulations. Neurons were seeded onto poly-D-lysine-coated cell culture dishes in plating medium (Basal medium Eagle’s containing Eagle’s salts, 0.45% glucose, 10% horse serum (Capricorn; HOS-1A), 1mM sodium pyruvate, 100U/ml Penicillin and 0,1mg/ml Streptomycin). Plating medium was replaced with maintenance medium (MEM supplemented with 0.6% glucose, 0,2% sodium bicarbonate, 1mM sodium pyruvate, 2% B27 supplement (Gibco), 2mM Glutamax, 100U/ml Penicillin and 0,1mg/ml Streptomycin) 2-3 hours later and kept in a humidified incubator, 37C, 5% CO2.

extract_protocol:
After washing with cold PBS, cells and EVs were lysed directly in homogenization buffer provided by RNeasy or miRNeasy RNA isolation kits (Qiagen)
smallRNA sequencing: control- or BDNF-treated cortical neurons and corresponding sEVs were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) as per manufacturer’s instructions and sequenced in Illumina HiSeq2000. 150 ng of RNA was used as input material. RNA sequencing: Total RNA was used to prepare the sequencing library according to the manufacturer's protocol using the TrueSeq RNA library prep kit v2 (Illumina, USA). As a starting material, 500ng RNA was used. Multiplexed libraries were directly loaded onto an Ilumina Hiseq2000 using a 50 bp single read setup.
smallRNA sequencing and RNA sequencing

treatment_protocol: Cells were treated with BDNF (50ng/ml, 20min) or control vehicle at 6-7 days in vitro, after which cells were washed three times with maintenance medium.

tag: strain

value: NMRI

value: small EV

tag: batch

value: x


title: NK Pt06 Pop4 [CHIP_S061]

city: Cambridge

first: Ce

last: Gao

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

library_source: genomic

data_processing:
library strategy: CUT&RUN
Raw reads in the FASTQ files were trimmed using trimmomatic (v0.36) and aligned to human reference genome (hg38) using bowtie2 (v2.2.9).
Duplicated reads were marked using Picard (v2.8.0).
Peaks were called using macs2 (v2.1.1.20160309).
Assembly: GRCh38
Supplementary files format and content: peaks

molecule: genomic DNA

source_name: PBMC

extract_protocol:
Briefly, isolated NK cells from ECs, HAARTs and HIVNs were bound to concanavalin A-coated magnetic beads (Bangs Laboratories), followed by cell permeabilization using 0.01% digitonin (Millipore) in wash buffer. Primary antibodies against intracellular H3K27ac, H3K27me3 and H3K4me3 histone marks (Cell Signaling Technology) were added and cells were incubated at 4oC for overnight. Guinea pig anti-rabbit IgG antibody (Antibodies-online) was used as a negative control. The next day, fusion protein CUTANA pA/G-MNase (20x) (Epicypher) was added and cells were incubated at 4oC for 1 hour, followed by chromatin digestion using 100mM CaCl2 (Fisher Scientific). Stop buffer was then added to stop the chromatin digestion. DNA fragments were extracted using phenol chloroform (Invitrogen) and the extracted DNA was eluted in 1mM Tris-HCl pH 8.0 (Fisher Scientific) + 0.1 mM EDTA (Sigma Aldrich).
The DNA library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina Sequencing (New England Biolabs).

tag: tissue

value: PBMC

tag: cell type

value: CD56dim CD16+ NK cells

tag: participant id

tag: participant phenotype

value: HIVN

tag: antibody


title: heart, BL6J, Ctrl, rep 3

city: Boston

first: William

middle: T

last: Pu

address: 300 Longwood Ave

institute: Children's Hospital Boston

data_processing:
HiSat alignment
FeatureCount
DESeq2
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Excel table: read counts, expression values, DESeq2 output

source_name: heart

extract_protocol:
total RNA isolation, polyA RNA isolation
stranded RNA-seq library

value: heart

tag: genotype

value: TAZ WT/Y

tag: age

value: 2 months


title: heart, BL6J, Ctrl, rep 2


title: cell lysate from BDNF-treated cortical neurons 9 9BCL

description:
cell lysate from BDNF-treated cortical neurons 9
smallRNA sequencing
9BCL_mm_smallrnaneb_sr_kauranil_B_10_S66_L005_R1_001

value: Cell lysate

value: z


title: heart, BL6J, Ctrl, rep 1


title: TP0001651F05_3_0.300000uM_DMEM_12h_TC00283154_H22

description:
TP0001651F05_3_0.300000uM_DMEM_12h
TC00283154_H22

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.3 uM of Fenofibrate

tag: chemical name

value: Fenofibrate

tag: chemical sample id


title: cell lysate from Ctrl-treated cortical neurons 9 9CCL

description:
cell lysate from Ctrl-treated cortical neurons 9
smallRNA sequencing
9CCL_mm_smallrnaneb_sr_kauranil_C_9_S63_L005_R1_001

tag: treatment


title: cell lysate from Ctrl-treated cortical neurons 8 8CCL

description:
cell lysate from Ctrl-treated cortical neurons 8
smallRNA sequencing
8CCL_mm_smallrnaneb_sr_kauranil_C_9_S62_L005_R1_001


title: NK Pt06 Pop2 [CHIP_S060]

value: CD56bri CD16- NK cells

value: IgG


title: TP0001651B01_5_3.000000uM_DMEM_12h_TC00283154_H21

description:
TP0001651B01_5_3.000000uM_DMEM_12h
TC00283154_H21

tag: cell line

value: 12h exposure of 3 uM of Cyanazine

value: Cyanazine

tag: chemical concentration

value: 3 uM

tag: dose level


title: TP0001651H04_2_0.100000uM_DMEM_12h_TC00283154_H19

description:
TP0001651H04_2_0.100000uM_DMEM_12h
TC00283154_H19

value: 12h exposure of 0.1 uM of Bisphenol A

value: Bisphenol A

tag: exposure time

tag: assay plate

tag: assay plate well


title: Lysis Buffer_TC00283154_I01

description:
Lysis Buffer
TC00283154_I01

source_name: Lysis Buffer

value: untreated


title: NK Pt06 Pop2 [CHIP_S059]

tag: tissue

value: PBMC

value: HIVN


title: TP0001651D04_7_30.000000uM_DMEM_12h_TC00283154_H18

description:
TP0001651D04_7_30.000000uM_DMEM_12h
TC00283154_H18

value: 12h exposure of 30 uM of Clofibrate

value: Clofibrate

value: 30 uM


title: GEN_DMEM_12h_TC00283154_H20

description:
GEN_DMEM_12h
TC00283154_H20

value: 6h exposure of 10 uM of Genistein

value: Genistein

value: 10 uM


title: NK Pt06 Pop2 [CHIP_S057]

tag: cell type


title: heart, BL6J, KO, rep 4

value: heart

value: TAZ KO/Y

tag: strain

value: 2 months


title: TP0001651H01_2_0.100000uM_DMEM_12h_TC00283154_H24

description:
TP0001651H01_2_0.100000uM_DMEM_12h
TC00283154_H24

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.1 uM of Flutamide

value: Flutamide


title: heart, BL6J, KO, rep 3


title: cell lysate from Ctrl-treated cortical neurons 7 7CCL

description:
cell lysate from Ctrl-treated cortical neurons 7
smallRNA sequencing
7CCL_mm_smallrnaneb_sr_kauranil_C_9_S61_L005_R1_001

value: NMRI

value: Cell lysate

tag: batch

value: z


title: NK Pt10 Pop4 [CHIP_S056]

value: PBMC

value: CD56dim CD16+ NK cells

tag: participant id

tag: participant phenotype

value: EC

tag: antibody

value: IgG


title: cell lysate from BDNF-treated cortical neurons 7 7BCL

description:
cell lysate from BDNF-treated cortical neurons 7
smallRNA sequencing
7BCL_mm_smallrnaneb_sr_kauranil_B_10_S64_L005_R1_001


title: TP0001651D01_5_3.000000uM_DMEM_12h_TC00283154_H17

description:
TP0001651D01_5_3.000000uM_DMEM_12h
TC00283154_H17

tag: media

value: 12h exposure of 3 uM of Lactofen

value: Lactofen

value: 3 uM


title: heart, BL6J, KO, rep 1

tag: genotype

tag: age


title: heart, AJ-F1, Ctrl, rep 4

value: TAZ WT/Y


title: NK Pt10 Pop4 [CHIP_S055]


title: NK Pt06 Pop2 [CHIP_S058]

value: CD56bri CD16- NK cells

value: HIVN


title: TP0001651D04_5_3.000000uM_DMEM_12h_TC00283154_H15

description:
TP0001651D04_5_3.000000uM_DMEM_12h
TC00283154_H15

tag: treatment

value: 12h exposure of 3 uM of Clofibrate

tag: chemical name

value: Clofibrate

tag: chemical sample id


title: cell lysate from BDNF-treated cortical neurons 3 3BCL

description:
cell lysate from BDNF-treated cortical neurons 3
smallRNA sequencing
3BCL_mm_smallrnaneb_sr_kauranil_B_2_S42_L004_R1_001

value: x


title: heart, AJ-F1, Ctrl, rep 3

value: heart

value: 2 months


title: cell lysate from BDNF-treated cortical neurons 8 8BCL

description:
cell lysate from BDNF-treated cortical neurons 8
smallRNA sequencing
8BCL_mm_smallrnaneb_sr_kauranil_B_10_S65_L005_R1_001

value: NMRI

value: Cell lysate


title: TP0001651H01_6_10.000000uM_DMEM_12h_TC00283154_H14

description:
TP0001651H01_6_10.000000uM_DMEM_12h
TC00283154_H14

tag: cell line

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of Flutamide

value: Flutamide

tag: chemical concentration

value: 10 uM

tag: dose level


title: cell lysate from Ctrl-treated cortical neurons 2 2CCL

description:
cell lysate from Ctrl-treated cortical neurons 2
smallRNA sequencing
2CCL_mm_smallrnaneb_sr_kauranil_C_1_S38_L004_R1_001


title: NK Pt10 Pop4 [CHIP_S053]

value: PBMC

value: CD56dim CD16+ NK cells

value: EC


title: cell lysate from BDNF-treated cortical neurons 2 2BCL

description:
cell lysate from BDNF-treated cortical neurons 2
smallRNA sequencing
2BCL_mm_smallrnaneb_sr_kauranil_B_2_S41_L004_R1_001


title: heart, AJ-F1, Ctrl, rep 2

value: TAZ WT/Y


title: heart, AJ-F1, Ctrl, rep 1


title: TP0001651E02_4_1.000000uM_DMEM_12h_TC00283154_H13

description:
TP0001651E02_4_1.000000uM_DMEM_12h
TC00283154_H13

value: 12h exposure of 1 uM of 4-Nonylphenol, branched

value: 4-Nonylphenol, branched

value: 1 uM

tag: exposure time

tag: assay plate

tag: assay plate well


title: NK Pt10 Pop2 [CHIP_S052]

tag: tissue

tag: cell type

value: CD56bri CD16- NK cells

value: IgG


title: NK Pt10 Pop2 [CHIP_S051]

tag: participant id


title: heart, BL6J, KO, rep 2

value: heart

value: TAZ KO/Y

tag: strain


title: TP0001651B03_3_0.300000uM_DMEM_12h_TC00283154_H12

description:
TP0001651B03_3_0.300000uM_DMEM_12h
TC00283154_H12

value: 12h exposure of 0.3 uM of Reserpine

value: Reserpine


title: NK Pt10 Pop2 [CHIP_S050]

tag: participant phenotype

tag: antibody


title: TP0001651C02_1_0.030000uM_DMEM_12h_TC00283154_H11

description:
TP0001651C02_1_0.030000uM_DMEM_12h
TC00283154_H11

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of 4-Hydroxytamoxifen


title: cell lysate from BDNF-treated cortical neurons 1 1BCL

description:
cell lysate from BDNF-treated cortical neurons 1
smallRNA sequencing
1BCL_mm_smallrnaneb_sr_kauranil_B_2_S40_L004_R1_001

value: NMRI

value: Cell lysate

tag: batch

value: x


title: cell lysate from Ctrl-treated cortical neurons  1 1CCL

description:
cell lysate from Ctrl-treated cortical neurons  1
smallRNA sequencing
1CCL_mm_smallrnaneb_sr_kauranil_C_1_S37_L004_R1_001

tag: treatment


title: heart, AJ-F1, KO, rep 3

tag: genotype

tag: age

value: 2 months


title: NK Pt10 Pop2 [CHIP_S049]

value: PBMC

value: EC


title: TP0001651E02_8_100.000000uM_DMEM_12h_TC00283154_H16

description:
TP0001651E02_8_100.000000uM_DMEM_12h
TC00283154_H16

tag: cell line

value: 12h exposure of 100 uM of 4-Nonylphenol, branched

tag: chemical name

tag: chemical sample id


title: heart, AJ-F1, KO, rep 2


title: NK Pt10 Pop4 [CHIP_S054]

value: CD56dim CD16+ NK cells


title: TP0001651A06_7_30.000000uM_DMEM_12h_TC00283154_H10

description:
TP0001651A06_7_30.000000uM_DMEM_12h
TC00283154_H10

value: 12h exposure of 30 uM of Cyproconazole

value: Cyproconazole

tag: chemical concentration

value: 30 uM

tag: dose level

tag: exposure time


title: NK Pt14 Pop4 [CHIP_S048]

tag: tissue

value: HAART

value: IgG


title: GF SKN-1GFP with antibody rep2

city: Los Angeles

first: Chris

last: Turner

state: CA

address: 3715 McClintock Ave

institute: University of Southern California

data_processing:
Quality trimming and Adapter sequences were trimmed from raw paired end reads using Trim Galore package v 0.6.4.
Reads were mapped to the C. elegans reference genome using bwa v 0.7.17.
BAM files were sorted with Samtools v 1.10. BAM files were sorted to contain only uniquely mapped reads using Sambamba v 0.6.8.
Peak calls were made using MACS2 v2.2.7.1
Assembly: ce10
Supplementary files format and content: narrowPeak

organism: Caenorhabditis elegans

source_name: Whole Animal

growth_protocol: C. elegans were raised on 6 cm nematode growth media (NGM) plates supplemented with streptomycin and seeded with OP50. All worm strains were grown at 20°C and unstarved for at least three generations before being used.

extract_protocol:
Worm pellets were ground via mortar and pestle and resuspended with 1.1% formaldehyde to crosslink proteins.
Purified DNA fragments were then used as input for sequencing library preparation using the Diagenode MicroPlex Library prep kit V2.

value: Whole Animal

value: Chromotek, Cat. gta , Lot 90513001MA


title: heart, AJ-F1, KO, rep 1

value: heart

value: TAZ KO/Y


title: TP0001651B01_1_0.030000uM_DMEM_12h_TC00283154_H09

description:
TP0001651B01_1_0.030000uM_DMEM_12h
TC00283154_H09

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Cyanazine

value: Cyanazine

tag: assay plate

tag: assay plate well


title: cell lysate from Ctrl-treated cortical neurons 3 3CCL

description:
cell lysate from Ctrl-treated cortical neurons 3
smallRNA sequencing
3CCL_mm_smallrnaneb_sr_kauranil_C_1_S39_L004_R1_001

tag: strain

value: NMRI

value: Cell lysate

value: x


title: NK Pt14 Pop4 [CHIP_S047]

value: PBMC

tag: cell type

tag: participant id

tag: participant phenotype


title: jq_adult_flx_M2

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

data_processing:
Reads were aligned using the Seq2Fun algorithm which translates raw reads to protein orthologs and maps them to a high-resolution protein-ortholog database - EcoOmicsDB available at www.expressanalyst.ca. The filtering parameters are provided below
Filtering: N. of amino acid mismatches was set at 2
Filtering: Minimum matching length was set at 19
Filtering: Minimum matching score was set at 80
Assembly: Mapping was species agnostic. Translated reads were mapped to the Vertebrate database
Raw fastq files were filtered as mentioned above and provided count matrices. These were analyzed for gene expression and pathway enrichment analysis.
Raw files and count files are provided as fastq files and .txt files, respectively.
Supplementary files format and content: Files here are from 49 datasets (datasets column below). Each dataset has a processed file which contains the counts for all samples within that dataset. Hence all samples (with unique title) from a dataset is present in the corresponding processed file. The title of the raw file for each sample is provided below as well. Some exposures were conducted together and hence had a common control exposure. Hence while 776 libraries are listed, they will correspond to fewer fastq files. But all fastq files are present.

organism: Coturnix japonica

source_name: liver

extract_protocol:
RNA was extracted from Japanese quail and Double-crested cormorant samples using the Qiagen RNeasy mini kits; RNA was extracted from the fathead minnow, rainbow trout, African-clawed frog and the northern leopard frog using the Qiagen RNeasy Universal Mini kit.
Library was prepared according to Illumina instructions for NovaSeq 6000 S4 PE100 or HiSeq 4000 PE100 101-bp paired-end reads.

tag: lifestage

value: adult

value: liver

tag: chemical

value: flx

tag: concentration

value: MED


title: TP0001651H04_5_3.000000uM_DMEM_12h_TC00283154_H08

description:
TP0001651H04_5_3.000000uM_DMEM_12h
TC00283154_H08

tag: media

tag: treatment

value: 12h exposure of 3 uM of Bisphenol A

value: Bisphenol A

value: 3 uM


title: GF SKN-1GFP no ab rep2

value: Whole Animal

tag: genotype

tag: antibody

value: Chromotek, Cat. gta , Lot 90513001MA


title: jq_adult_flx_H1

value: HIGH


title: GF SKN-1GFP no ab rep1


title: TP0001651E04_4_1.000000uM_DMEM_12h_TC00283154_H07

description:
TP0001651E04_4_1.000000uM_DMEM_12h
TC00283154_H07

tag: cell line

value: DMEM + 10% HI-FBS

value: 12h exposure of 1 uM of Farglitazar

tag: chemical name

value: Farglitazar

tag: chemical sample id

tag: chemical concentration

value: 1 uM


title: TP0001651E02_5_3.000000uM_DMEM_12h_TC00283154_H06

description:
TP0001651E02_5_3.000000uM_DMEM_12h
TC00283154_H06

value: 12h exposure of 3 uM of 4-Nonylphenol, branched

value: 4-Nonylphenol, branched

tag: dose level

tag: exposure time

tag: assay plate


title: NK Pt14 Pop2 [CHIP_S044]

tag: tissue

value: PBMC

tag: cell type

value: CD56bri CD16- NK cells

value: HAART

value: IgG


title: jq_adult_flx_M5

value: adult

value: liver

value: flx

value: MED


title: WT SKN-1GFP with antibody rep2

value: Whole Animal

value: WT


title: jq_adult_flx_M1


title: TP0001651B01_2_0.100000uM_DMEM_12h_TC00283154_H05

description:
TP0001651B01_2_0.100000uM_DMEM_12h
TC00283154_H05

value: 12h exposure of 0.1 uM of Cyanazine

value: Cyanazine

tag: assay plate well


title: NK Pt14 Pop2 [CHIP_S043]

tag: participant id

tag: participant phenotype


title: NK Pt14 Pop4 [CHIP_S045]

value: CD56dim CD16+ NK cells


title: WT SKN-1GFP no ab rep2

value: Chromotek, Cat. gta , Lot 90513001MA


title: NK Pt14 Pop2 [CHIP_S042]


title: jq_adult_flx_H5

tag: lifestage

tag: chemical

tag: concentration

value: HIGH


title: jq_adult_flx_H4


title: WT SKN-1GFP no ab rep1

tag: genotype


title: TP0001651F01_2_0.100000uM_DMEM_12h_TC00283154_H04

description:
TP0001651F01_2_0.100000uM_DMEM_12h
TC00283154_H04

tag: media

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 0.1 uM of Tetrac

value: Tetrac


title: WT SKN-1GFP with antibody rep1

tag: antibody


title: TP0001651B03_6_10.000000uM_DMEM_12h_TC00283154_H03

description:
TP0001651B03_6_10.000000uM_DMEM_12h
TC00283154_H03

tag: cell line

value: 12h exposure of 10 uM of Reserpine

tag: chemical name

value: Reserpine

tag: chemical sample id

value: 10 uM


title: NK Pt14 Pop2 [CHIP_S041]

value: PBMC

value: CD56bri CD16- NK cells

value: HAART


title: jq_adult_flx_H2

value: adult

value: liver

value: flx


title: GF SKN-1GFP with antibody rep1

value: Whole Animal


title: TP0001651A02_4_1.000000uM_DMEM_12h_TC00283154_H02

description:
TP0001651A02_4_1.000000uM_DMEM_12h
TC00283154_H02

value: 12h exposure of 1 uM of Imazalil

value: Imazalil

tag: chemical concentration

value: 1 uM

tag: dose level

tag: exposure time


title: jq_adult_flx_H3

tag: tissue

value: HIGH


title: omk_els_bap_81UGDP1

organism: Oncorhynchus mykiss

source_name: embryo

value: els

value: embryo

value: bap


title: NK Pt14 Pop4 [CHIP_S046]

tag: cell type

value: CD56dim CD16+ NK cells


title: NK Pt07 Pop4 [CHIP_S040]

tag: participant id

value: EC

value: IgG


title: BL_TSA_TC00283154_H01

description:
BL_TSA
TC00283154_H01

value: 6h exposure of 1 uM of Trichostatin A

value: Trichostatin A

tag: assay plate

tag: assay plate well


title: omk_els_bap_81UGBP2

tag: lifestage

tag: chemical


title: NK Pt07 Pop4 [CHIP_S039]

value: PBMC

tag: participant phenotype


title: jq_adult_flx_M4

value: adult

tag: concentration

value: MED


title: TP0001651D05_8_100.000000uM_DMEM_12h_TC00283154_G22

description:
TP0001651D05_8_100.000000uM_DMEM_12h
TC00283154_G22

tag: media

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 100 uM of Thiram

value: Thiram


title: NK Pt07 Pop2 [CHIP_S036]

value: CD56bri CD16- NK cells

tag: antibody


title: omk_els_bap_1UGEP1


title: TP0001651D06_2_0.100000uM_DMEM_12h_TC00283154_G23

description:
TP0001651D06_2_0.100000uM_DMEM_12h
TC00283154_G23

tag: cell line

value: 12h exposure of 0.1 uM of PFOS

tag: chemical name

value: PFOS


title: jq_adult_flx_M3

description:
S337, S338, S339, S340, S341
jq_adult_flx_S1, jq_adult_flx_S2, jq_adult_flx_S3, jq_adult_flx_S4, jq_adult_flx_S5
NS.1119.001.NEBNext_dual_i7_D8---NEBNext_dual_i5_D8.QA3-S1-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_E8---NEBNext_dual_i5_E8.QA3-S2-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_F8---NEBNext_dual_i5_F8.QA3-S3-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_G8---NEBNext_dual_i5_G8.QA3-S4-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_H8---NEBNext_dual_i5_H8.QA3-S5-LLT_RNA-seq_R1.fastq.gz
NS.1119.001.NEBNext_dual_i7_D8---NEBNext_dual_i5_D8.QA3-S1-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_E8---NEBNext_dual_i5_E8.QA3-S2-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_F8---NEBNext_dual_i5_F8.QA3-S3-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_G8---NEBNext_dual_i5_G8.QA3-S4-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_H8---NEBNext_dual_i5_H8.QA3-S5-LLT_RNA-seq_R2.fastq.gz
jq_adult_flx.txt

value: liver

value: flx


title: M2_JQA_EE2


title: NK Pt07 Pop2 [CHIP_S035]


title: TP0001651H04_8_100.000000uM_DMEM_12h_TC00283154_G24

description:
TP0001651H04_8_100.000000uM_DMEM_12h
TC00283154_G24

value: 12h exposure of 100 uM of Bisphenol A

value: Bisphenol A

tag: chemical sample id

tag: chemical concentration


title: TP0001651F02_4_1.000000uM_DMEM_12h_TC00283154_G21

description:
TP0001651F02_4_1.000000uM_DMEM_12h
TC00283154_G21

value: 12h exposure of 1 uM of Ziram

value: Ziram

value: 1 uM

tag: dose level

tag: exposure time


title: H6_JQA_EE2

tag: tissue

value: HIGH


title: omk_els_bap_3UGCP1

value: els

value: embryo

value: bap


title: TP0001651G03_6_10.000000uM_DMEM_12h_TC00283154_G20

description:
TP0001651G03_6_10.000000uM_DMEM_12h
TC00283154_G20

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of Nilutamide

value: Nilutamide

value: 10 uM


title: omk_els_bap_1UGAP1


title: H5_JQA_EE2

value: adult


title: M1_JQA_EE2

value: MED


title: omk_els_bap_1UGCP3


title: NK Pt07 Pop4 [CHIP_S037]

value: PBMC

tag: cell type

value: CD56dim CD16+ NK cells

tag: participant id

value: EC


title: omk_els_bap_1UGDP2


title: omk_els_bap_CBP2

value: dmso

value: CTRL


title: H3_JQA_EE2

value: liver


title: omk_els_bap_27UGDP2


title: NK Pt07 Pop2 [CHIP_S033]

value: CD56bri CD16- NK cells


title: TP0001651B04_8_100.000000uM_DMEM_12h_TC00283154_G18

description:
TP0001651B04_8_100.000000uM_DMEM_12h
TC00283154_G18

value: 12h exposure of 100 uM of Propiconazole

value: Propiconazole

tag: assay plate

tag: assay plate well


title: TP0001651B01_8_100.000000uM_DMEM_12h_TC00283154_G19

description:
TP0001651B01_8_100.000000uM_DMEM_12h
TC00283154_G19

value: 12h exposure of 100 uM of Cyanazine

value: Cyanazine


title: NK Pt07 Pop4 [CHIP_S038]


title: NK Pt16 Pop4 [CHIP_S032]

value: HAART

value: IgG


title: S6_JQA_EE2

tag: lifestage

tag: chemical


title: TP0001651A04_6_10.000000uM_DMEM_12h_TC00283154_G17

description:
TP0001651A04_6_10.000000uM_DMEM_12h
TC00283154_G17

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of Rotenone

value: Rotenone


title: omk_els_bap_3UGBP1

value: els

value: embryo

value: bap

tag: concentration


title: H2_JQA_EE2

value: adult

value: HIGH


title: NK Pt16 Pop4 [CHIP_S030]

value: PBMC

value: CD56dim CD16+ NK cells

tag: participant phenotype


title: NK Pt16 Pop4 [CHIP_S031]


title: TP0001651H02_3_0.300000uM_DMEM_12h_TC00283154_G16

description:
TP0001651H02_3_0.300000uM_DMEM_12h
TC00283154_G16

tag: media

tag: treatment

value: 12h exposure of 0.3 uM of Maneb

value: Maneb


title: omk_els_bap_CAP3

value: dmso

value: CTRL


title: NK Pt07 Pop2 [CHIP_S034]

value: CD56bri CD16- NK cells

value: EC

tag: antibody


title: omk_els_bap_27UGCP3


title: TP0001651E02_6_10.000000uM_DMEM_12h_TC00283154_G15

description:
TP0001651E02_6_10.000000uM_DMEM_12h
TC00283154_G15

tag: cell line

value: 12h exposure of 10 uM of 4-Nonylphenol, branched

tag: chemical name

value: 4-Nonylphenol, branched

value: 10 uM


title: S5_JQA_EE2

value: liver


title: NK Pt16 Pop4 [CHIP_S029]

value: HAART


title: S4_JQA_EE2


title: TP0001651B05_1_0.030000uM_DMEM_12h_TC00283154_G14

description:
TP0001651B05_1_0.030000uM_DMEM_12h
TC00283154_G14

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride

tag: chemical sample id

tag: chemical concentration


title: H1_JQA_EE2

value: adult

value: HIGH


title: NK Pt16 Pop2 [CHIP_S028]

value: PBMC

value: IgG


title: omk_els_bap_27UGBP1

value: els

value: embryo

value: bap


title: TP0001651A01_3_0.300000uM_DMEM_12h_TC00283154_G13

description:
TP0001651A01_3_0.300000uM_DMEM_12h
TC00283154_G13

value: 12h exposure of 0.3 uM of Pyraclostrobin

value: Pyraclostrobin

tag: dose level

tag: exposure time


title: NK Pt16 Pop2 [CHIP_S027]

tag: tissue

tag: cell type

value: CD56bri CD16- NK cells


title: omk_els_bap_SEP1

value: dmso

value: CTRL


title: NK Pt16 Pop2 [CHIP_S025]

tag: participant id


title: TP0001651B01_3_0.300000uM_DMEM_12h_TC00283154_G11

description:
TP0001651B01_3_0.300000uM_DMEM_12h
TC00283154_G11

value: 12h exposure of 0.3 uM of Cyanazine

value: Cyanazine

tag: assay plate

tag: assay plate well


title: S3_JQA_EE2

tag: lifestage

value: liver

tag: chemical


title: omk_els_bap_3UGAP2

tag: concentration


title: M5_JQA_EE2

value: MED


title: TP0001651D01_1_0.030000uM_DMEM_12h_TC00283154_G12

description:
TP0001651D01_1_0.030000uM_DMEM_12h
TC00283154_G12

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Lactofen

value: Lactofen


title: NK Pt16 Pop2 [CHIP_S026]

value: PBMC

tag: participant phenotype

value: HAART


title: TP0001651B01_4_1.000000uM_DMEM_12h_TC00283154_G10

description:
TP0001651B01_4_1.000000uM_DMEM_12h
TC00283154_G10

tag: treatment

value: 12h exposure of 1 uM of Cyanazine

value: 1 uM


title: omk_els_bap_9UGDP3

value: els

value: embryo

value: bap


title: omk_els_bap_SDP3


title: TP0001651C04_4_1.000000uM_DMEM_12h_TC00283154_G09

description:
TP0001651C04_4_1.000000uM_DMEM_12h
TC00283154_G09

tag: cell line

value: 12h exposure of 1 uM of Simvastatin

value: Simvastatin


title: omk_els_bap_81UGEP3


title: NK Pt04 Pop4 [CHIP_S024]

value: CD56dim CD16+ NK cells

value: EC

tag: antibody

value: IgG


title: S2_JQA_EE2

value: adult

value: liver

value: dmso

value: CTRL


title: NK Pt04 Pop4 [CHIP_S023]


title: M3_JQA_EE2

value: MED


title: TP0001651G02_8_100.000000uM_DMEM_12h_TC00283154_G08

description:
TP0001651G02_8_100.000000uM_DMEM_12h
TC00283154_G08

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of Lovastatin

tag: chemical name

value: Lovastatin

tag: chemical sample id


title: NK Pt04 Pop4 [CHIP_S022]

value: PBMC


title: S1_JQA_EE2


title: NK Pt04 Pop4 [CHIP_S021]


title: M4_JQA_EE2


title: omk_els_bap_SCP1

value: els


title: TP0001651B02_2_0.100000uM_DMEM_12h_TC00283154_G07

description:
TP0001651B02_2_0.100000uM_DMEM_12h
TC00283154_G07

value: 12h exposure of 0.1 uM of 3,5,3'-Triiodothyronine

tag: chemical concentration

tag: dose level


title: jq_adult_cpf_H3

tag: tissue

value: cpf

value: HIGH


title: omk_els_bap_9UGBP1

value: embryo

value: bap


title: TP0001651C05_7_30.000000uM_DMEM_12h_TC00283154_G06

description:
TP0001651C05_7_30.000000uM_DMEM_12h
TC00283154_G06

value: 12h exposure of 30 uM of Bisphenol B

value: Bisphenol B

value: 30 uM

tag: exposure time


title: TP0001651A02_8_100.000000uM_DMEM_12h_TC00283154_G05

description:
TP0001651A02_8_100.000000uM_DMEM_12h
TC00283154_G05

value: 12h exposure of 100 uM of Imazalil

value: Imazalil


title: NK Pt04 Pop2 [CHIP_S019]

tag: cell type

value: CD56bri CD16- NK cells

tag: participant id

value: EC


title: jq_adult_cpf_H2

value: adult

value: liver


title: omk_els_bap_SBP1

value: dmso

value: CTRL


title: TP0001651F03_4_1.000000uM_DMEM_12h_TC00283154_G04

description:
TP0001651F03_4_1.000000uM_DMEM_12h
TC00283154_G04

value: DMEM + 10% HI-FBS

value: 12h exposure of 1 uM of 4-Cumylphenol

value: 1 uM

tag: assay plate

tag: assay plate well


title: NK Pt04 Pop2 [CHIP_S018]

value: PBMC


title: omk_els_bap_81UGCP2

tag: lifestage

value: els

value: embryo

tag: chemical


title: TP0001651D06_5_3.000000uM_DMEM_12h_TC00283154_G03

description:
TP0001651D06_5_3.000000uM_DMEM_12h
TC00283154_G03

tag: media

value: 12h exposure of 3 uM of PFOS

value: PFOS

value: 3 uM


title: omk_els_bap_9UGAP3

value: bap

tag: concentration


title: NK Pt04 Pop2 [CHIP_S017]

tag: participant phenotype


title: omk_els_bap_9UGCP1


title: jq_adult_cpf_M5

value: cpf

value: MED


title: TP0001651H04_6_10.000000uM_DMEM_12h_TC00283154_G02

description:
TP0001651H04_6_10.000000uM_DMEM_12h
TC00283154_G02

tag: cell line

tag: treatment

value: 12h exposure of 10 uM of Bisphenol A

value: Bisphenol A

value: 10 uM


title: omk_els_bap_CEP2

value: dmso


title: jq_adult_cpf_M4

value: adult

value: liver


title: BL_TSA_TC00283154_G01

description:
BL_TSA
TC00283154_G01

value: 6h exposure of 1 uM of Trichostatin A

tag: chemical name

value: Trichostatin A


title: NK Pt04 Pop2 [CHIP_S020]

value: PBMC

value: CD56bri CD16- NK cells

value: EC

tag: antibody

value: IgG


title: NK Pt08 Pop4 [CHIP_S016]

value: CD56dim CD16+ NK cells

value: HAART


title: omk_els_bap_27UGEP2

value: els

value: embryo

value: bap


title: NK Pt08 Pop4 [CHIP_S015]


title: jq_adult_cpf_H4

value: cpf

value: HIGH


title: omk_els_bap_3UGDP3


title: jq_adult_cpf_M3

value: MED


title: TP0001651E05_1_0.030000uM_DMEM_12h_TC00283154_F23

description:
TP0001651E05_1_0.030000uM_DMEM_12h
TC00283154_F23

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Atrazine

value: Atrazine

tag: chemical sample id

tag: chemical concentration


title: omk_els_flx_25C

tag: tissue

value: flx


title: jq_adult_cpf_H1

value: adult

value: liver


title: NK Pt08 Pop2 [CHIP_S012]

value: PBMC

value: CD56bri CD16- NK cells


title: jq_adult_cpf_H5


title: NK Pt08 Pop4 [CHIP_S013]


title: jq_adult_cpf_M1


title: TP0001651B04_7_30.000000uM_DMEM_12h_TC00283154_F24

description:
TP0001651B04_7_30.000000uM_DMEM_12h
TC00283154_F24

value: 12h exposure of 30 uM of Propiconazole

value: Propiconazole

value: 30 uM

tag: dose level

tag: exposure time


title: NK Pt08 Pop4 [CHIP_S014]

tag: cell type

value: CD56dim CD16+ NK cells

tag: participant id

value: HAART


title: omk_els_flx_98C

value: els

value: embryo


title: DMSO_DMEM_12h_TC00283154_F21

description:
DMSO_DMEM_12h
TC00283154_F21

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM

tag: assay plate

tag: assay plate well


title: jq_adult_cpf_M2

description:
S305, S306, S307, S308, S309, S310
jq_adult_cpf_S1, jq_adult_cpf_S2, jq_adult_cpf_S3, jq_adult_cpf_S4, jq_adult_cpf_S5, jq_adult_cpf_S6
NS.1119.001.NEBNext_dual_i7_A1---NEBNext_dual_i5_A1.QA1-S1-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_B1---NEBNext_dual_i5_B1.QA1-S2-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_C1---NEBNext_dual_i5_C1.QA1-S3-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_D1---NEBNext_dual_i5_D1.QA1-S4-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_E1---NEBNext_dual_i5_E1.QA1-S5-LLT_RNA-seq_R1.fastq.gz, NS.1119.001.NEBNext_dual_i7_F1---NEBNext_dual_i5_F1.QA1-S6-LLT_RNA-seq_R1.fastq.gz
NS.1119.001.NEBNext_dual_i7_A1---NEBNext_dual_i5_A1.QA1-S1-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_B1---NEBNext_dual_i5_B1.QA1-S2-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_C1---NEBNext_dual_i5_C1.QA1-S3-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_D1---NEBNext_dual_i5_D1.QA1-S4-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_E1---NEBNext_dual_i5_E1.QA1-S5-LLT_RNA-seq_R2.fastq.gz, NS.1119.001.NEBNext_dual_i7_F1---NEBNext_dual_i5_F1.QA1-S6-LLT_RNA-seq_R2.fastq.gz
jq_adult_cpf.txt

tag: lifestage

tag: chemical

value: cpf

value: MED


title: TP0001651C04_5_3.000000uM_DMEM_12h_TC00283154_F22

description:
TP0001651C04_5_3.000000uM_DMEM_12h
TC00283154_F22

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 3 uM of Simvastatin

value: Simvastatin

value: 3 uM


title: NK Pt08 Pop2 [CHIP_S011]

value: PBMC

value: CD56bri CD16- NK cells

tag: participant phenotype


title: omk_els_flx_5B

value: flx

tag: concentration


title: H3_JQA_BaP

value: adult

value: liver

value: bap

value: HIGH


title: TP0001651E03_7_30.000000uM_DMEM_12h_TC00283154_F20

description:
TP0001651E03_7_30.000000uM_DMEM_12h
TC00283154_F20

tag: cell line

tag: treatment

value: 12h exposure of 30 uM of Prochloraz

value: Prochloraz

value: 30 uM


title: omk_els_flx_125A

value: els

value: embryo


title: S5_JQA_BaP

value: dmso

value: CTRL


title: TP0001651A05_8_100.000000uM_DMEM_12h_TC00283154_F19

description:
TP0001651A05_8_100.000000uM_DMEM_12h
TC00283154_F19

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of Clomiphene citrate (1:1)

tag: chemical name

value: Clomiphene citrate (1:1)


title: NK Pt08 Pop2 [CHIP_S010]

value: PBMC

value: HAART

tag: antibody


title: omk_els_flx_5A

value: flx


title: NK Pt08 Pop2 [CHIP_S009]

value: CD56bri CD16- NK cells


title: TP0001651A04_7_30.000000uM_DMEM_12h_TC00283154_F18

description:
TP0001651A04_7_30.000000uM_DMEM_12h
TC00283154_F18

value: 12h exposure of 30 uM of Rotenone

value: Rotenone

tag: chemical sample id

tag: chemical concentration


title: H2_JQA_BaP

value: adult

tag: tissue

value: liver

value: bap

value: HIGH


title: omk_els_flx_25A

value: els


title: H1_JQA_BaP


title: S4_JQA_BaP


title: omk_els_flx_98A

value: embryo


title: S3_JQA_BaP

value: dmso


title: omk_els_flx_25B


title: NK Pt01 Pop4 [CHIP_S008]

value: CD56dim CD16+ NK cells

value: EC

value: IgG


title: NK Pt01 Pop4 [CHIP_S005]


title: NK Pt01 Pop4 [CHIP_S006]


title: M5_JQA_BaP

value: MED


title: TP0001651C02_6_10.000000uM_DMEM_12h_TC00283154_F16

description:
TP0001651C02_6_10.000000uM_DMEM_12h
TC00283154_F16

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of 4-Hydroxytamoxifen

value: 10 uM

tag: dose level

tag: exposure time


title: NK Pt01 Pop4 [CHIP_S007]

value: PBMC

tag: cell type

tag: participant id


title: TP0001651E04_8_100.000000uM_DMEM_12h_TC00283154_F17

description:
TP0001651E04_8_100.000000uM_DMEM_12h
TC00283154_F17

value: 12h exposure of 100 uM of Farglitazar

value: Farglitazar

tag: assay plate

tag: assay plate well


title: omk_els_flx_81B

tag: lifestage

tag: chemical

value: flx


title: omk_els_flx_CB

value: CTRL


title: TP0001651G02_6_10.000000uM_DMEM_12h_TC00283154_F15

description:
TP0001651G02_6_10.000000uM_DMEM_12h
TC00283154_F15

tag: media

value: 12h exposure of 10 uM of Lovastatin

value: Lovastatin


title: S2_JQA_BaP

value: adult

value: liver

tag: concentration


title: TP0001651C02_2_0.100000uM_DMEM_12h_TC00283154_F14

description:
TP0001651C02_2_0.100000uM_DMEM_12h
TC00283154_F14

tag: cell line

value: 12h exposure of 0.1 uM of 4-Hydroxytamoxifen


title: NK Pt01 Pop2 [CHIP_S003]

value: CD56bri CD16- NK cells

tag: participant phenotype


title: omk_els_flx_81C

value: els

value: embryo


title: NK Pt01 Pop2 [CHIP_S004]

value: EC

value: IgG


title: TP0001651A02_3_0.300000uM_DMEM_12h_TC00283154_F13

description:
TP0001651A02_3_0.300000uM_DMEM_12h
TC00283154_F13

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 0.3 uM of Imazalil

tag: chemical name

value: Imazalil


title: M4_JQA_BaP

value: bap

value: MED


title: omk_els_flx_81A

value: flx


title: S1_JQA_BaP

value: dmso

value: CTRL


title: NK Pt01 Pop2 [CHIP_S002]

value: PBMC

tag: antibody


title: TP0001651E01_4_1.000000uM_DMEM_12h_TC00283154_F11

description:
TP0001651E01_4_1.000000uM_DMEM_12h
TC00283154_F11

value: 12h exposure of 1 uM of Bifenthrin

value: Bifenthrin

tag: chemical sample id

tag: chemical concentration

value: 1 uM


title: NK Pt01 Pop2 [CHIP_S001]

tag: tissue

value: CD56bri CD16- NK cells


title: M3_JQA_BaP

value: adult

value: liver


title: omk_els_flx_CC

value: els

value: embryo


title: TP0001651H01_4_1.000000uM_DMEM_12h_TC00283154_F10

description:
TP0001651H01_4_1.000000uM_DMEM_12h
TC00283154_F10

value: DMEM + 10% HI-FBS

value: 12h exposure of 1 uM of Flutamide

value: Flutamide

tag: dose level

tag: exposure time


title: H5_JQA_BaP

value: bap

value: HIGH


title: omk_els_flx_125C

value: flx


title: NK Pt21 IL15 [RNA_S25]

description:
raw_counts.csv.gz
TPM.csv.gz

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

extract_protocol:
Total RNA was extracted from the NK cell populations using a commercial PicoPure RNA Isolation Kit
RNA-Seq libraries were generated as described in a previous study. Briefly, whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2, followed by sequencing with a 75-cycle kit on a NextSeq 500 instrument (Illumina, CA). The quantification of transcript abundance was conducted using RSEM software (v1.2.22) supported by the STAR aligner software (STAR_2.4.2a). The raw reads were aligned to the Hg38 human genome database.

tag: cell type

value: CD56dim CD16+ NK cells

tag: participant id

tag: paticipant phenotype

value: HIVN


title: NK Pt21 Medium [RNA_S24]

description:
raw_counts.csv.gz
TPM.csv.gz

value: PBMC

value: Medium


title: TP0001651A04_5_3.000000uM_DMEM_12h_TC00283154_F08

description:
TP0001651A04_5_3.000000uM_DMEM_12h
TC00283154_F08

value: 12h exposure of 3 uM of Rotenone

value: Rotenone

value: 3 uM

tag: assay plate

tag: assay plate well


title: DMSO_DMEM_12h_TC00283154_F07

description:
DMSO_DMEM_12h
TC00283154_F07

tag: media

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: TP0001651F05_5_3.000000uM_DMEM_12h_TC00283154_F09

description:
TP0001651F05_5_3.000000uM_DMEM_12h
TC00283154_F09

value: 12h exposure of 3 uM of Fenofibrate

value: Fenofibrate


title: omk_els_flx_CA

tag: lifestage

value: els

value: embryo

tag: chemical

value: dmso

tag: concentration

value: CTRL


title: omk_els_flx_125B

value: flx


title: TP0001651A02_2_0.100000uM_DMEM_12h_TC00283154_F12

description:
TP0001651A02_2_0.100000uM_DMEM_12h
TC00283154_F12

tag: cell line

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 0.1 uM of Imazalil

value: Imazalil


title: M2_JQA_BaP

value: adult

value: liver

value: bap

value: MED


title: TP0001651F05_1_0.030000uM_DMEM_12h_TC00283154_F06

description:
TP0001651F05_1_0.030000uM_DMEM_12h
TC00283154_F06

value: 12h exposure of 0.03 uM of Fenofibrate

tag: chemical name


title: NK Pt19 IL15 [RNA_S21]

description:
raw_counts.csv.gz
TPM.csv.gz

value: PBMC

value: CD56dim CD16+ NK cells

value: HIVN


title: omk_els_flx_98B


title: NK Pt20 Medium [RNA_S22]

description:
raw_counts.csv.gz
TPM.csv.gz

value: Medium


title: H4_JQA_BaP

value: HIGH


title: M1_JQA_BaP


title: kcs1-E834K_biol_rep_3 (kcs1)

city: New York

first: Ana

middle: M

last: Sanchez

state: NY

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description:
kcs1_E834K_3
count_matrix_kcs1_mut.xlsx
ksc1_mut_Deseq.xlsx

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
Resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: h+ kcs1-E834K::kanMX

growth_protocol: Log phase cultures grown at 30˚C in YES medium or ePMGT medium

extract_protocol:
Hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA seq

tag: lab strain number

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: Vegetative growth

tag: genotype

value: yesat cell


title: omk_seme_highD

value: els

tag: tissue

value: embryo

value: seme


title: NK Pt19 Medium [RNA_S20]

description:
raw_counts.csv.gz
TPM.csv.gz

tag: cell type


title: TP0001651A04_2_0.100000uM_DMEM_12h_TC00283154_F04

description:
TP0001651A04_2_0.100000uM_DMEM_12h
TC00283154_F04

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.1 uM of Rotenone

value: Rotenone

tag: chemical sample id

tag: chemical concentration

tag: dose level

tag: exposure time


title: omk_els_flx_5C

value: flx


title: kcs1-E834K_biol_rep_2 (kcs1)

description:
kcs1_E834K_2
count_matrix_kcs1_mut.xlsx
ksc1_mut_Deseq.xlsx


title: NK Pt18 IL15 [RNA_S19]

description:
raw_counts.csv.gz
TPM.csv.gz

tag: participant id

tag: paticipant phenotype


title: NK Pt20 IL15 [RNA_S23]

description:
raw_counts.csv.gz
TPM.csv.gz


title: kcs1-E834K_biol_rep_1 (kcs1)

description:
kcs1_E834K_1
count_matrix_kcs1_mut.xlsx
ksc1_mut_Deseq.xlsx


title: TP0001651E04_3_0.300000uM_DMEM_12h_TC00283154_F05

description:
TP0001651E04_3_0.300000uM_DMEM_12h
TC00283154_F05

tag: media

value: 12h exposure of 0.3 uM of Farglitazar

value: Farglitazar

tag: assay plate

tag: assay plate well


title: omk_seme_highC

tag: lifestage

tag: chemical

tag: concentration


title: TP0001651D04_2_0.100000uM_DMEM_12h_TC00283154_F03

description:
TP0001651D04_2_0.100000uM_DMEM_12h
TC00283154_F03

tag: cell line

tag: treatment

value: 12h exposure of 0.1 uM of Clofibrate

tag: chemical name

value: Clofibrate


title: omk_seme_highB

tag: tissue


title: TP0001651H02_8_100.000000uM_DMEM_12h_TC00283154_F02

description:
TP0001651H02_8_100.000000uM_DMEM_12h
TC00283154_F02

value: 12h exposure of 100 uM of Maneb

value: Maneb


title: omk_seme_highA

value: HIGH


title: omk_seme_medE

value: MED


title: TP0001651C01_4_1.000000uM_DMEM_12h_TC00283154_E24

description:
TP0001651C01_4_1.000000uM_DMEM_12h
TC00283154_E24

value: 12h exposure of 1 uM of Fenpyroximate (Z,E)

value: Fenpyroximate (Z,E)

value: 1 uM


title: NK Pt17 Ex Vivo [RNA_S17]

description:
raw_counts.csv.gz
TPM.csv.gz

value: PBMC

tag: cell type

value: CD56dim CD16+ NK cells

value: Ex vivo

value: HAART


title: NK Pt16 Ex Vivo [RNA_S16]

description:
raw_counts.csv.gz
TPM.csv.gz

value: EC


title: BL_DMSO_TC00283154_F01

description:
BL_DMSO
TC00283154_F01

value: untreated

tag: chemical sample id

value: 0 uM


title: NK Pt15 Ex Vivo [RNA_S15]

description:
raw_counts.csv.gz
TPM.csv.gz

value: HIVN


title: kcs1-L338R_biol_rep_2 (kcs1)

description:
kcs1_L338R_2
count_matrix_kcs1_mut.xlsx
ksc1_mut_Deseq.xlsx

source_name: h+ kcs1-L338R::kanMX

tag: lab strain number

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: Vegetative growth

tag: genotype

value: yesat cell


title: kcs1-R332T_biol_rep_1 (kcs1)

description:
kcs1_R332T_1
count_matrix_kcs1_mut.xlsx
ksc1_mut_Deseq.xlsx

source_name: h+ kcs1-R332T::kanMX


title: kcs1-L338R_biol_rep_1 (kcs1)

description:
kcs1_L338R_1
count_matrix_kcs1_mut.xlsx
ksc1_mut_Deseq.xlsx


title: TP0001651E05_4_1.000000uM_DMEM_12h_TC00283154_E21

description:
TP0001651E05_4_1.000000uM_DMEM_12h
TC00283154_E21

value: DMEM + 10% HI-FBS

value: 12h exposure of 1 uM of Atrazine

value: Atrazine

tag: chemical concentration

tag: dose level

tag: exposure time


title: NK Pt14 Ex Vivo [RNA_S14]

description:
raw_counts.csv.gz
TPM.csv.gz

tag: participant id

tag: paticipant phenotype


title: omk_seme_medC

tag: lifestage

value: els

value: embryo

tag: chemical

value: seme

value: MED


title: NK Pt12 Ex Vivo [RNA_S12]

description:
raw_counts.csv.gz
TPM.csv.gz

value: PBMC

value: CD56dim CD16+ NK cells


title: WT_biol_rep_3 (kcs1)

description:
kcs1_WT_3
count_matrix_kcs1_mut.xlsx

source_name: h+ kcs1-WT::kanMX


title: kcs1-R332T_biol_rep_2 (kcs1)

description:
kcs1_R332T_2
count_matrix_kcs1_mut.xlsx
ksc1_mut_Deseq.xlsx


title: TP0001651B05_5_3.000000uM_DMEM_12h_TC00283154_E20

description:
TP0001651B05_5_3.000000uM_DMEM_12h
TC00283154_E20

tag: cell line

tag: media

value: 12h exposure of 3 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride

value: 3 uM

tag: assay plate

tag: assay plate well


title: TP0001651H05_3_0.300000uM_DMEM_12h_TC00283154_E22

description:
TP0001651H05_3_0.300000uM_DMEM_12h
TC00283154_E22

tag: treatment

value: 12h exposure of 0.3 uM of Trifloxystrobin

tag: chemical name

value: Trifloxystrobin


title: NK Pt13 Ex Vivo [RNA_S13]

description:
raw_counts.csv.gz
TPM.csv.gz

tag: tissue

tag: cell type

value: Ex vivo

value: EC


title: omk_seme_lowE

tag: concentration

value: LOW


title: TP0001651B02_6_10.000000uM_DMEM_12h_TC00283154_E23

description:
TP0001651B02_6_10.000000uM_DMEM_12h
TC00283154_E23

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of 3,5,3'-Triiodothyronine

tag: chemical sample id

value: 10 uM


title: kcs1-L338R_biol_rep_3 (kcs1)

description:
kcs1_L338R_3
count_matrix_kcs1_mut.xlsx
ksc1_mut_Deseq.xlsx

tag: lab strain number

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: Vegetative growth

tag: genotype

value: yesat cell


title: NK Pt11 Ex Vivo [RNA_S11]

description:
raw_counts.csv.gz
TPM.csv.gz

tag: participant id

tag: paticipant phenotype

value: HAART


title: omk_seme_medA

tag: lifestage

value: els

value: embryo

tag: chemical

value: seme

value: MED


title: NK Pt18 Medium [RNA_S18]

description:
raw_counts.csv.gz
TPM.csv.gz

value: PBMC

value: CD56dim CD16+ NK cells

value: Medium

value: HIVN


title: TP0001651H02_4_1.000000uM_DMEM_12h_TC00283154_E19

description:
TP0001651H02_4_1.000000uM_DMEM_12h
TC00283154_E19

tag: cell line

tag: media

value: 12h exposure of 1 uM of Maneb

value: Maneb

tag: chemical concentration

value: 1 uM

tag: dose level

tag: exposure time


title: omk_seme_medD

tag: tissue


title: kcs1-R332T_biol_rep_3 (kcs1)

description:
kcs1_R332T_3
count_matrix_kcs1_mut.xlsx
ksc1_mut_Deseq.xlsx

tag: cell type


title: omk_seme_lowD

tag: concentration

value: LOW


title: omk_seme_medB


title: NK Pt10 Ex Vivo [RNA_S10]

description:
raw_counts.csv.gz
TPM.csv.gz

tag: treatment

value: Ex vivo

value: EC


title: STF9_biol_rep_3 (asp1)

description:
STF9_3
count_matrix_STF.xlsx
STF6_STF9_DESeq.xlsx

source_name: h+ STF9 [asp1-W493*::hygMX]

tag: lab strain number

value: log phase culture, ePMGT medium

value: Vegetative growth


title: NK Pt09 Ex Vivo [RNA_S09]

description:
raw_counts.csv.gz
TPM.csv.gz


title: omk_seme_lowB


title: TP0001651E01_6_10.000000uM_DMEM_12h_TC00283154_E17

description:
TP0001651E01_6_10.000000uM_DMEM_12h
TC00283154_E17

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of Bifenthrin

tag: chemical name

value: Bifenthrin

tag: chemical sample id

value: 10 uM

tag: assay plate

tag: assay plate well


title: NK Pt08 Ex Vivo [RNA_S08]

description:
raw_counts.csv.gz
TPM.csv.gz

tag: participant id

tag: paticipant phenotype

value: HAART


title: NK Pt07 Ex Vivo [RNA_S07]

description:
raw_counts.csv.gz
TPM.csv.gz

value: PBMC


title: TP0001651D04_8_100.000000uM_DMEM_12h_TC00283154_E15

description:
TP0001651D04_8_100.000000uM_DMEM_12h
TC00283154_E15

value: 12h exposure of 100 uM of Clofibrate

value: Clofibrate


title: STF9_biol_rep_1 (asp1)

description:
STF9_1
count_matrix_STF.xlsx
STF6_STF9_DESeq.xlsx

tag: growth conditions

tag: developmental stage

tag: genotype

value: yesat cell


title: omk_seme_lowA

tag: lifestage

value: els

value: embryo

tag: chemical

value: seme


title: TP0001651H03_6_10.000000uM_DMEM_12h_TC00283154_E16

description:
TP0001651H03_6_10.000000uM_DMEM_12h
TC00283154_E16

tag: cell line

tag: media

value: 12h exposure of 10 uM of Fomesafen

value: Fomesafen

tag: chemical concentration

tag: dose level

tag: exposure time


title: omk_seme_PCE

tag: tissue

value: dmso

tag: concentration

value: CTRL


title: omk_seme_PCD


title: STF6_biol_rep_2 (asp1)

description:
STF6_2
count_matrix_STF.xlsx
STF6_STF9_DESeq.xlsx

source_name: h+ STF6 [asp1-W386*::hygMX]

tag: lab strain number

value: log phase culture, ePMGT medium

value: Vegetative growth

tag: cell type


title: NK Pt05 Ex Vivo [RNA_S05]

description:
raw_counts.csv.gz
TPM.csv.gz

value: CD56dim CD16+ NK cells

tag: treatment

value: Ex vivo


title: TP0001651D05_6_10.000000uM_DMEM_12h_TC00283154_E13

description:
TP0001651D05_6_10.000000uM_DMEM_12h
TC00283154_E13

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of Thiram

tag: chemical name

value: Thiram

tag: chemical sample id

value: 10 uM

tag: assay plate

tag: assay plate well


title: STF6_biol_rep_3 (asp1)

description:
STF6_3
count_matrix_STF.xlsx
STF6_STF9_DESeq.xlsx

tag: growth conditions

tag: developmental stage

tag: genotype


title: TP0001651H05_5_3.000000uM_DMEM_12h_TC00283154_E14

description:
TP0001651H05_5_3.000000uM_DMEM_12h
TC00283154_E14

tag: cell line

value: 12h exposure of 3 uM of Trifloxystrobin

value: Trifloxystrobin

value: 3 uM


title: NK Pt06 Ex Vivo [RNA_S06]

description:
raw_counts.csv.gz
TPM.csv.gz

value: PBMC

tag: participant id

tag: paticipant phenotype

value: HIVN


title: STF6_biol_rep_1 (asp1)

description:
STF6_1
count_matrix_STF.xlsx
STF6_STF9_DESeq.xlsx

value: yesat cell


title: WT_biol_rep_2 (kcs1)

description:
kcs1_WT_2
count_matrix_kcs1_mut.xlsx

value: log phase culture, YES medium


title: omk_seme_PCC

tag: lifestage

value: els

value: embryo

tag: chemical

value: dmso


title: TP0001651C02_5_3.000000uM_DMEM_12h_TC00283154_E12

description:
TP0001651C02_5_3.000000uM_DMEM_12h
TC00283154_E12

tag: media

value: 12h exposure of 3 uM of 4-Hydroxytamoxifen

tag: chemical concentration

tag: dose level

tag: exposure time


title: omk_seme_lowC

tag: tissue

value: seme

tag: concentration

value: LOW


title: TP0001651D02_6_10.000000uM_DMEM_12h_TC00283154_E18

description:
TP0001651D02_6_10.000000uM_DMEM_12h
TC00283154_E18

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 10 uM of PFOA

tag: chemical name

value: PFOA

tag: chemical sample id


title: WT_biol_rep_1 (kcs1)

description:
kcs1_WT_1
count_matrix_kcs1_mut.xlsx

tag: lab strain number

tag: growth conditions

value: Vegetative growth

tag: cell type


title: NK Pt04 Ex Vivo [RNA_S04]

description:
raw_counts.csv.gz
TPM.csv.gz

value: CD56dim CD16+ NK cells

value: Ex vivo

value: EC


title: NK Pt03 Ex Vivo [RNA_S03]

description:
raw_counts.csv.gz
TPM.csv.gz

value: PBMC


title: WT_biol_rep_3 (asp1)

description:
WT_3
count_matrix_STF.xlsx

source_name: h+ asp1-WT::hygMX

value: log phase culture, ePMGT medium

tag: developmental stage

tag: genotype


title: TP0001651A04_8_100.000000uM_DMEM_12h_TC00283154_E11

description:
TP0001651A04_8_100.000000uM_DMEM_12h
TC00283154_E11

tag: cell line

value: 12h exposure of 100 uM of Rotenone

value: Rotenone

tag: assay plate

tag: assay plate well


title: STF9_biol_rep_2 (asp1)

description:
STF9_2
count_matrix_STF.xlsx
STF6_STF9_DESeq.xlsx

value: yesat cell


title: omk_seme_PCA

tag: lifestage

value: els

value: embryo

tag: chemical

value: CTRL


title: omk_els_ee2_10B

value: MED


title: WT_biol_rep_2 (asp1)

description:
WT_2
count_matrix_STF.xlsx


title: NK Pt02 Ex Vivo [RNA_S02]

description:
raw_counts.csv.gz
TPM.csv.gz

tag: participant id

tag: paticipant phenotype

value: HAART


title: NK Pt01 Ex Vivo [RNA_S01]

description:
raw_counts.csv.gz
TPM.csv.gz

tag: tissue


title: WT_biol_rep_1 (asp1)

description:
WT_1
count_matrix_STF.xlsx


title: TP0001651E05_5_3.000000uM_DMEM_12h_TC00283154_E10

description:
TP0001651E05_5_3.000000uM_DMEM_12h
TC00283154_E10

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 3 uM of Atrazine

value: Atrazine

tag: chemical concentration

value: 3 uM

tag: dose level

tag: exposure time


title: TP0001651A01_6_10.000000uM_DMEM_12h_TC00283154_E08

description:
TP0001651A01_6_10.000000uM_DMEM_12h
TC00283154_E08

tag: treatment

value: 12h exposure of 10 uM of Pyraclostrobin

tag: chemical name

value: Pyraclostrobin

tag: chemical sample id

value: 10 uM


title: omk_els_ee2_SA

value: dmso

tag: concentration


title: omk_els_ee2_SB


title: healthy skin_8

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

data_processing:
The raw reads were processed with Ion Torrent RNASEQAnalysis pipeline (Torrent Suite version 5.0.4)
htseq-count, version 0.6.0, default parameters
DESeq2, version 1.18.1, normalization
Assembly: hg19 AmpliSeq Transcriptome ERCC v1
Supplementary files format and content: htseq normalized count

source_name: skin

extract_protocol:
Skin biopses were frozen in RNAlater (Sigma) and stored at -80C. For total RNA isolation, the samples were homogenized in Fenozol (A&A Biotechnology, Gdansk, Polska) using a tissue homogenizer (OMNI International, Kennesaw, GA, USA).
Library was prepared using Ion AmpliSeq™ Transcriptome Human Gene Expression Kit according to the manufacturer’s protocol (Thermo Fisher Scientific)

value: skin

tag: patient diagnosis

value: healthy

tag: condition


title: TP0001651H05_4_1.000000uM_DMEM_12h_TC00283154_E07

description:
TP0001651H05_4_1.000000uM_DMEM_12h
TC00283154_E07

tag: cell line

value: 12h exposure of 1 uM of Trifloxystrobin

value: Trifloxystrobin

value: 1 uM

tag: assay plate


title: TP0001651E03_6_10.000000uM_DMEM_12h_TC00283154_E09

description:
TP0001651E03_6_10.000000uM_DMEM_12h
TC00283154_E09

value: 12h exposure of 10 uM of Prochloraz

value: Prochloraz

tag: assay plate well


title: healthy skin_6


title: omk_seme_PCB

tag: lifestage

value: els

value: embryo

tag: chemical

value: CTRL


title: jq_els_tb_H4

value: liver

value: tb

value: HIGH


title: TP0001651C04_6_10.000000uM_DMEM_12h_TC00283154_E06

description:
TP0001651C04_6_10.000000uM_DMEM_12h
TC00283154_E06

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of Simvastatin

value: Simvastatin


title: omk_els_ee2_10A

value: MED


title: TP0001651H01_1_0.030000uM_DMEM_12h_TC00283154_E05

description:
TP0001651H01_1_0.030000uM_DMEM_12h
TC00283154_E05

value: 12h exposure of 0.03 uM of Flutamide

value: Flutamide


title: healthy skin_4

value: skin

value: healthy


title: omk_els_ee2_SC

value: dmso


title: jq_els_tb_M2


title: TP0001651F05_8_100.000000uM_DMEM_12h_TC00283154_E04

description:
TP0001651F05_8_100.000000uM_DMEM_12h
TC00283154_E04

value: 12h exposure of 100 uM of Fenofibrate

value: Fenofibrate


title: healthy skin_3


title: jq_els_tb_S5

value: els


title: omk_els_ee2_10C

value: embryo


title: omk_els_ee2_100C


title: jq_els_tb_H1


title: jq_els_tb_M3


title: omk_els_ee2_100B


title: jq_els_tb_H3


title: jq_els_tb_H2


title: HS perilesional skin_6

value: hidradenitis suppurativa

value: perilesional skin


title: omk_els_ee2_100A


title: TP0001651D06_4_1.000000uM_DMEM_12h_TC00283154_E02

description:
TP0001651D06_4_1.000000uM_DMEM_12h
TC00283154_E02

value: 12h exposure of 1 uM of PFOS

value: PFOS

value: 1 uM


title: HS perilesional skin_3


title: BL_DMSO_TC00283154_E01

description:
BL_DMSO
TC00283154_E01

value: untreated

value: 0 uM


title: HS perilesional skin_2


title: TP0001651B04_6_10.000000uM_DMEM_12h_TC00283154_D24

description:
TP0001651B04_6_10.000000uM_DMEM_12h
TC00283154_D24

value: DMEM + 10% HI-FBS

value: 12h exposure of 10 uM of Propiconazole

value: Propiconazole

value: 10 uM


title: jq_els_tb_M4

value: liver

value: tb

value: MED


title: HS perilesional skin_14

value: skin


title: jq_els_tb_H5

value: els

value: HIGH


title: jq_els_tb_S2

value: dmso

value: CTRL


title: TP0001651G04_8_100.000000uM_DMEM_12h_TC00283154_D23

description:
TP0001651G04_8_100.000000uM_DMEM_12h
TC00283154_D23

value: 12h exposure of 100 uM of Cladribine

value: Cladribine


title: PANC-1 GEM4

city: Leuven

first: Vincent

last: de Laat

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads by CASAVA base recognition (Base Calling).
QC control: error rate (Phred score), GC content distribution, removing reads with adaptor contamination and with MAPQ<10  and with >5nt/100nt mismatches
Assembly: Assembly: mm10 using HISAT2
Supplementary files format and content: The files consists of the FPKM reads for all analyzed genes.

source_name: PDAC

extract_protocol:
RNA was isolated using the PureLink™ RNA Mini Kit (12183018A, Invitrogen).
standard library, poly-A enrichment

value: PDAC

tag: cell type

value: Gemcitabine


title: HS perilesional skin_13

tag: tissue

value: hidradenitis suppurativa

value: perilesional skin


title: PANC-1 GEM3


title: PANC-1 GEM2


title: jq_els_tb_M5


title: healthy skin_14

value: healthy


title: TP0001651A01_1_0.030000uM_DMEM_12h_TC00283154_E03

description:
TP0001651A01_1_0.030000uM_DMEM_12h
TC00283154_E03

source_name: MCF7 Cells

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.03 uM of Pyraclostrobin

value: Pyraclostrobin


title: PANC-1 GEM1


title: HS lesion_6

value: lesion


title: jq_els_tb_S1

value: liver


title: TP0001651D05_4_1.000000uM_DMEM_12h_TC00283154_D21

description:
TP0001651D05_4_1.000000uM_DMEM_12h
TC00283154_D21

value: 12h exposure of 1 uM of Thiram

value: Thiram

tag: chemical concentration

value: 1 uM


title: PANC-1 CTRL4


title: jq_els_tb_S3

value: els

value: dmso


title: HS lesion_3

value: skin


title: TP0001651C05_3_0.300000uM_DMEM_12h_TC00283154_D20

description:
TP0001651C05_3_0.300000uM_DMEM_12h
TC00283154_D20

value: 12h exposure of 0.3 uM of Bisphenol B

value: Bisphenol B

tag: dose level


title: PANC-1 CTRL3

value: PDAC


title: jq_els_tb_S4

value: CTRL


title: TP0001651A03_2_0.100000uM_DMEM_12h_TC00283154_D19

description:
TP0001651A03_2_0.100000uM_DMEM_12h
TC00283154_D19

value: 12h exposure of 0.1 uM of Butafenacil

value: Butafenacil

tag: exposure time


title: HS lesion_14

value: hidradenitis suppurativa


title: PANC-1 CTRL2


title: jq_els_tb_M1

value: tb

value: MED


title: TP0001651F03_2_0.100000uM_DMEM_12h_TC00283154_D18

description:
TP0001651F03_2_0.100000uM_DMEM_12h
TC00283154_D18

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 0.1 uM of 4-Cumylphenol


title: HS lesion_13

value: lesion


title: jq.els_seme_H1

value: liver

value: seme

value: HIGH


title: TP0001651D01_7_30.000000uM_DMEM_12h_TC00283154_D17

description:
TP0001651D01_7_30.000000uM_DMEM_12h
TC00283154_D17

value: 12h exposure of 30 uM of Lactofen

tag: chemical name

value: Lactofen

value: 30 uM


title: PANC-1 CTRL1


title: BxPC3 GEM4

value: Gemcitabine


title: BxPC3 GEM3

value: PDAC


title: jq.els_seme_M1

value: els


title: TP0001651G05_4_1.000000uM_DMEM_12h_TC00283154_D16

description:
TP0001651G05_4_1.000000uM_DMEM_12h
TC00283154_D16

value: 12h exposure of 1 uM of Cyproterone acetate

value: Cyproterone acetate

tag: chemical sample id

value: 1 uM


title: TP0001651F03_3_0.300000uM_DMEM_12h_TC00283154_D15

description:
TP0001651F03_3_0.300000uM_DMEM_12h
TC00283154_D15

value: 12h exposure of 0.3 uM of 4-Cumylphenol


title: TP0001651C05_4_1.000000uM_DMEM_12h_TC00283154_D22

description:
TP0001651C05_4_1.000000uM_DMEM_12h
TC00283154_D22

value: 12h exposure of 1 uM of Bisphenol B

value: Bisphenol B


title: jq.els_seme_M4

tag: concentration

value: MED


title: BxPC3 GEM2


title: BxPC3 GEM1


title: HS lesion_2

value: skin

tag: patient diagnosis

value: hidradenitis suppurativa

value: lesion


title: Irf4-/- control

city: HOUSTON

first: Xiaolong

last: Zhang

state: Texas

address: 6670 Bertner Avenue, R7-211

department: Immunobiology & Transplant Research Center

institute: Houston Methodist Research Institute

description: Novogene

data_processing:
The RNA-seq reads were aligned to the mouse reference genome mm10 using TopHat. Prior to differential gene expression analysis, the read counts for each sequenced library were adjusted with the edgeR package with a single scaling factor for normalization. Differential expression analysis was performed using the DEGSeq R package (1.20.0). All p values were adjusted using the Benjamini & Hochberg method. For samples without biological replicates, differentially expressed genes were determined by the criteria |log2(FoldChange)|> 1 and padj (q value) < 0.005.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary NK cells

extract_protocol:
WT and Irf4−/− mice were intravenously injected with 2.5 × 105 B16-F10 cells. Twenty days post-injection, splenic NK cells were isolated using the EasySep Mouse NK Cell Isolation Kit, followed by further purification through flow-sorting the CD3−NK1.1+ cell population. Total RNA was extracted from the sorted NK cells using the RNeasy Plus Mini Kit.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: from spleen

value: NK cells


title: WT treated

description: Novogene


title: Irf4-/- treated

description: Novogene


title: WT control

description: Novogene


title: TP0001651E04_2_0.100000uM_DMEM_12h_TC00283154_D14

description:
TP0001651E04_2_0.100000uM_DMEM_12h
TC00283154_D14

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.1 uM of Farglitazar

value: Farglitazar


title: BxPC3 CTRL4

value: PDAC


title: jq.els_seme_H4

value: els

value: liver

value: seme

value: HIGH


title: Chow Adipose tissue (VAT) WT

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

description: Chow

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were aligned by Hisat2 version 2.0.5 and mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: Novogene DEG analysis: Contract ID H202SC22053202; Batch: X202SC22053202-Z01-F001

source_name: Adipose tissue (VAT)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Primary cells (GFP+)

value: Adipose tissue (VAT)

tag: strain

value: Tie2e-cre; TERT+/+; mTmG

tag: age

value: 8 months

value: Chow


title: BxPC3 CTRL3

tag: cell line


title: DMSO_DMEM_12h_TC00283154_D12

description:
DMSO_DMEM_12h
TC00283154_D12

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM

tag: assay plate

tag: assay plate well


title: jq.els_seme_M5

tag: lifestage

tag: chemical

value: MED


title: Chow Adipose tissue (VAT) KO

description: Chow

tag: cell type

tag: tissue

value: Tie2e-cre; TERTfl/fl; mTmG


title: jq.els_seme_S1

value: dmso

value: CTRL


title: TP0001651G04_2_0.100000uM_DMEM_12h_TC00283154_D11

description:
TP0001651G04_2_0.100000uM_DMEM_12h
TC00283154_D11

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.1 uM of Cladribine

value: Cladribine

tag: chemical concentration


title: BxPC3 CTRL2

value: PDAC


title: jq.els_seme_M2

value: els

value: liver

value: seme


title: Chow Adipose tissue (SAT) WT

description: Chow

source_name: Adipose tissue (SAT)

value: Primary cells (GFP+)

value: Adipose tissue (SAT)

value: Tie2e-cre; TERT+/+; mTmG


title: jq.els_seme_S5


title: TP0001651E03_4_1.000000uM_DMEM_12h_TC00283154_D10

description:
TP0001651E03_4_1.000000uM_DMEM_12h
TC00283154_D10

value: 12h exposure of 1 uM of Prochloraz

value: Prochloraz

value: 1 uM

tag: dose level

tag: exposure time


title: BxPC3 CTRL1


title: Chow Adipose tissue (SAT) KO

description: Chow

value: 8 months

tag: treatment

value: Chow


title: jq.els_seme_H2

value: HIGH


title: TP0001651H05_8_100.000000uM_DMEM_12h_TC00283154_D09

description:
TP0001651H05_8_100.000000uM_DMEM_12h
TC00283154_D09

value: 12h exposure of 100 uM of Trifloxystrobin

tag: chemical name

value: Trifloxystrobin

tag: chemical sample id


title: Chow skeletal muscle WT

description: Chow

source_name: skeletal muscle

value: skeletal muscle


title: TP0001651B05_4_1.000000uM_DMEM_12h_TC00283154_D13

description:
TP0001651B05_4_1.000000uM_DMEM_12h
TC00283154_D13

value: DMEM + 10% HI-FBS

value: 12h exposure of 1 uM of Amiodarone hydrochloride

value: Amiodarone hydrochloride


title: TP0001651D01_3_0.300000uM_DMEM_12h_TC00283154_D08

description:
TP0001651D01_3_0.300000uM_DMEM_12h
TC00283154_D08

value: 12h exposure of 0.3 uM of Lactofen

value: Lactofen


title: P9

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

data_processing:
For the gene expression, we mapped the sequencing data to reference genome (hg38) using STAR, and defined transcript coordinates according to the gene annotation format file (GTF file) from GENCODE (Release 27, GRCh38).
The Gene abundances are given as Reads Per Kilobase per Million mapped reads (RPKM) with “cuffnorm” command using the Cufflinks package.
Assembly: hg38
Supplementary files format and content: Excel file includes RPKM values for each Sample

source_name: Bone Marrow

extract_protocol:
Total RNA were extracted using the QIAamp AllPrep RNA Mini Kit (Cat# 80204, QIAGEN), according to the manufacturer's specifications.
Libraries were constructed using the TruSeq RNA Sample Preparation Kits (Illumina), and the quality of the library was assessed using Bioanalyzer 2100 (Agilent Technologies).

value: Bone Marrow

value: Mononuclear cell

tag: disease state

value: AML

tag: Sex

value: Male

tag: ethnicity

value: Asian

tag: fab

tag: outcome

value: Alive

tag: osimertinib sensitivity

value: Sensitive

value: High


title: jq.els_seme_H5

source_name: liver

tag: lifestage

value: els

value: liver

value: seme

tag: concentration

value: HIGH


title: P10

tag: cell type

tag: age


title: TP0001651A06_4_1.000000uM_DMEM_12h_TC00283154_D07

description:
TP0001651A06_4_1.000000uM_DMEM_12h
TC00283154_D07

tag: cell line

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 1 uM of Cyproconazole

value: Cyproconazole

value: 1 uM

tag: assay plate

tag: assay plate well


title: P8

tag: tissue

value: Female

value: Dead

value: Non-Sensitive

value: Low


title: High fat diet Adipose tissue (SAT) WT

description: High fat diet

value: Primary cells (GFP+)

value: Adipose tissue (SAT)

tag: strain

value: Tie2e-cre; TERT+/+; mTmG

value: 8 months

tag: treatment

value: High fat diet


title: TP0001651F02_8_100.000000uM_DMEM_12h_TC00283154_D06

description:
TP0001651F02_8_100.000000uM_DMEM_12h
TC00283154_D06

value: 12h exposure of 100 uM of Ziram

tag: chemical name

value: Ziram

tag: chemical sample id

tag: chemical concentration

tag: dose level

tag: exposure time


title: jq.els_seme_S3

value: els

value: liver

tag: chemical

value: dmso

value: CTRL


title: jq.els_seme_M3

tag: lifestage

value: seme

value: MED


title: Chow skeletal muscle KO

description: Chow

value: skeletal muscle

value: Tie2e-cre; TERTfl/fl; mTmG

value: Chow


title: P7

value: Bone Marrow

value: Mononuclear cell

tag: disease state

value: AML

tag: Sex

value: Female

tag: ethnicity

value: Asian

tag: fab

tag: outcome

value: Alive

tag: osimertinib sensitivity

value: Sensitive

value: High


title: High fat diet Adipose tissue (SAT) KO

description: High fat diet

tag: cell type

value: Primary cells (GFP+)

value: Adipose tissue (SAT)

tag: age

value: 8 months

value: High fat diet


title: P6

tag: tissue

value: Dead

value: Non-Sensitive

value: Low


title: TP0001651C06_1_0.030000uM_DMEM_12h_TC00283154_D05

description:
TP0001651C06_1_0.030000uM_DMEM_12h
TC00283154_D05

tag: cell line

tag: media

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 0.03 uM of Cycloheximide

value: Cycloheximide

tag: assay plate

tag: assay plate well


title: Muscle tissue, KO3

city: New Haven

first: Haining

last: Lyu

state: Connecticut

address: 1145 chapel street, 401

institute: Yale

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: tissue

extract_protocol:
Total RNA was extracted using RNeasy Fibrous Tissue Mini Kit (74704, Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: tissue

tag: genotype

value: mKD

tag: time


title: jq.els_seme_S2

tag: lifestage

value: els

value: liver

tag: chemical

value: dmso

tag: concentration

value: CTRL


title: jq.els_seme_S4


title: P5

value: Bone Marrow

value: Mononuclear cell

tag: disease state

value: AML

tag: Sex

value: Female

tag: ethnicity

value: Asian


title: Muscle tissue, KO2


title: TP0001651E04_7_30.000000uM_DMEM_12h_TC00283154_D04

description:
TP0001651E04_7_30.000000uM_DMEM_12h
TC00283154_D04

value: 12h exposure of 30 uM of Farglitazar

tag: chemical name

value: Farglitazar

tag: chemical sample id

tag: chemical concentration

value: 30 uM

tag: dose level

tag: exposure time


title: jq.els_seme_H3

tag: tissue

value: seme

value: HIGH


title: P4

tag: cell type

tag: age

value: Male

tag: fab

tag: outcome

value: Alive

tag: osimertinib sensitivity

value: Sensitive

value: High


title: Muscle tissue, KO1

tag: cell line

value: tissue

tag: genotype

value: mKD

tag: treatment

tag: time


title: TP0001651A06_3_0.300000uM_DMEM_12h_TC00283154_D03

description:
TP0001651A06_3_0.300000uM_DMEM_12h
TC00283154_D03

tag: media

value: DMEM + 10% HI-FBS

value: 12h exposure of 0.3 uM of Cyproconazole

value: Cyproconazole

tag: assay plate

tag: assay plate well


title: TP0001651F02_6_10.000000uM_DMEM_12h_TC00283154_D02

description:
TP0001651F02_6_10.000000uM_DMEM_12h
TC00283154_D02

value: 12h exposure of 10 uM of Ziram

tag: chemical name

value: Ziram

tag: chemical sample id

value: 10 uM


title: jq.els.pb.H3

tag: lifestage

value: els

value: liver

tag: chemical

value: pb

tag: concentration


title: P3

tag: tissue

value: Bone Marrow

tag: cell type

value: Mononuclear cell

tag: disease state

value: AML

tag: Sex

value: Female

tag: ethnicity

value: Asian

value: Dead

value: Non-Sensitive

value: Low


title: Muscle tissue, WT2

tag: cell line

value: tissue

value: WT

value: WT littermate


title: Muscle tissue, WT3

tag: genotype


title: jq.els.pb.H2

value: HIGH


title: jq.els.pb.H5


title: P2

tag: age

value: Male

tag: fab

tag: outcome

value: Alive

tag: osimertinib sensitivity

value: Sensitive

value: High


title: HBRR_TC00283154_D01

description:
HBRR
TC00283154_D01

source_name: Human Brain Reference RNA

tag: media

tag: treatment

value: untreated

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate well


title: TP0001651E05_8_100.000000uM_DMEM_12h_TC00283154_C24

description:
TP0001651E05_8_100.000000uM_DMEM_12h
TC00283154_C24

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of Atrazine

tag: chemical name

value: Atrazine

tag: chemical sample id


title: P1

tag: tissue

value: Bone Marrow

tag: cell type

value: Mononuclear cell

tag: disease state

value: AML

tag: Sex

value: Female


title: TP0001651G03_1_0.030000uM_DMEM_12h_TC00283154_C23

description:
TP0001651G03_1_0.030000uM_DMEM_12h
TC00283154_C23

tag: cell line

value: 12h exposure of 0.03 uM of Nilutamide

value: Nilutamide


title: jq.els.pb.H4

tag: lifestage

value: els

value: liver

tag: chemical

value: pb

tag: concentration


title: Muscle tissue, WT1

value: tissue

tag: genotype

value: WT

value: WT littermate

tag: time


title: A549-RIP-seq-HNRNPC-input

city: Guiyang

first: Chuyu

last: Li

state: Guizhou

address: 28 Guiyi Street, Yunyan District

department: Department of Respiratory and Critical Care Medicine

institute: Affiliated Hospital of Guizhou Medical University

data_processing:
The reads after quality control were de-jointed using trim-galory, and after de-jointing, the reads were quality checked again, mainly to detect whether the joints were removed cleanly. The reads with joints removed were mapped to the genome using HISAT2 software to get the information of the reads on the genome, i.e. the .bam file.
The commonly used reads enrichment peak identification software MACS2 was used to perform peak scanning in the whole gene range to get the information of Peak's position on the genome, peak enrichment and other information. The .bam file of input and the .bam file of IP were peak called by MASC2, and the peak file was obtained, which is the .narrowPeak file.
The obtained peaks were annotated and functionally analyzed. Use bedtools to take the intersection of enriched peaks with protein coding to get the gene where the peak is located, annotate the gene, and perform subsequent enrichment analysis.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak(except for Input sample)

growth_protocol: Ham’s F-12K supplemented with 10% of fetal bovine serum, 1% of penicillin/streptomycin solution. Cells were cultured at a humidified incubator containing 5% CO2 at 37 °C.

extract_protocol:
Cells were harvested by RIP lysis buffer, and then the lysates were immunoprecipitated by 5μg anti-HNRNPC antibody. The purified input and HNRNPC-IP RNA samples were then collected for RNA-seq analysis.
RIP Sequencing library construction process, firstly, use qubit and 2100 to quantify the RIP fragments and detect the fragment length, then add appropriate Mg2+, heat to interrupt the RNA fragments, add reverse transcriptase, reverse transcription into cDNA, break the RNA strand and form double-stranded DNA by using the broken RNA as the primer and the cDNA as the template, make up the ends of the fragments and add A-tail at the 3' end of the fragment, add Adapter. Add A tail at the 3' end, add Adapter, use 0.8X AMPure beads to remove the excess Adapter, amplify by library PCR, XAMPure beads to remove the excess primer, qPCR to determine the concentration of library, Agilent 2100 to determine the size of the library fragments.

value: Human non-small cell lung cancer cells

tag: rip antibody


title: TP0001651G05_8_100.000000uM_DMEM_12h_TC00283154_C21

description:
TP0001651G05_8_100.000000uM_DMEM_12h
TC00283154_C21

tag: media

tag: treatment

value: 12h exposure of 100 uM of Cyproterone acetate

value: Cyproterone acetate

tag: chemical concentration

tag: dose level


title: A549-RIP-seq-HNRNPC-IP

value: anti-HNRNPC antibody


title: jq.els.pb.M3

value: MED


title: A4galt KO mouse naive B cells BCR-seq rep3

first: Frederick

last: Alt

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital / Harvard Medical School

data_processing:
Rep-SHM-Seq was performed as described previously using our established bioinformatics pipeline (18).
In addition, to minimize the potential cross-contamination due to FACS sorting, we further filtered reads by assigning mutated sequences to GC B cell samples and non-mutated sequences to naive B cell samples.
V segment usage analysis: For each sample, the ratio of each functional V segment was calculated as % usage among total productive and non-productive V(D)J junctions.
Assembly: mm9
Supplementary files format and content: xls (tab-delimited)
Supplementary files format and content: *.db.xls: VDJ annotation for each read (R1 & R2 joined read)
Supplementary files format and content: *.stat.*.xls: V segment usage for each sample
Library strategy: BCR-Seq

source_name: spleen

growth_protocol: WT (C57BL/6), and Gla-KO (B6;129-Glatm1Kul/J) mice were acquired from The Jackson Laboratory. A4galt-deficient mice were generated by Koichi Furukawa (50).

extract_protocol:
Splenic naive and germinal-center (GC) B cells were enriched using a B cell isolation kit followed by FACS-sorting. Mice were immunized with NP-OVA and leukocytes were harvested from spleen by passage through a 40-μm mesh and incubated for 10 min with 1 μg/mL of anti-CD16/32 Fc-block in FACS buffer (PBS supplemented with 1 mM EDTA, 2% heat-inactivated FBS, and 0.02% sodium azide). Cells were further labeled using fluorochrome-coupled antibodies directed against the respective antigens: CD45R, GL-7, CD95, CD38 and CD138.  Cells were surface-stained at 4°C for 30 minutes, and subsequently, GC B cells (CD45R+, GL7+, CD95+) and naïve B cells (IgD+, CD45R+, GL7-, CD38-) were sorted either using a FACS Aria II (Becton Dickinson) or SH-800 cell sorter (Sony).
Libraries for sequencing were prepared as described (17). Briefly, genomic DNA was sonicated and subjected to linear amplification-mediated PCR using biotinylated bait primers. Linear amplification-mediated PCR products were purified using Dynabeads MyOne streptavidin C1 magnetic beads (Thermo Fisher Scientific, MA, USA) and ligated to bridge adaptors. Adaptor-ligated products were amplified by nested PCR with indexed JH1/JH3 primers as well as primers annealed to the adaptor. PCR products were further tagged with Illumina sequencing adaptor sequences and size-selected via gel extraction. Libraries were sequenced by paired-end 300-bp sequencing on MiSeq, an Illumina sequencing platform (San Diego, CA, USA).
Rep-SHM-Seq was performed as described previously using our established bioinformatics pipeline (18). We used bait primers close to the coding ends of JHs to capture full-length V(D)J sequences for SHM analysis and used Illumina MiSeq 2 × 300-bp paired-end sequencing (19, 53). As described before, mixed JH primers were designed based on a highly degenerate region to minimize the amplification bias caused by different primers. 400 ng genomic DNA from FACS-sorted naive or GC B cells was used as starting material to keep the level of PCR amplification comparable among different samples. In addition, to minimize the potential cross-contamination due to FACS sorting, we further filtered reads by assigning mutated sequences to GC B cell samples and non-mutated sequences to naive B cell samples.

value: spleen

value: naive B cells

value: A4galt KO


title: TP0001651D04_4_1.000000uM_DMEM_12h_TC00283154_C20

description:
TP0001651D04_4_1.000000uM_DMEM_12h
TC00283154_C20

value: DMEM + 10% HI-FBS

value: 12h exposure of 1 uM of Clofibrate

tag: chemical name

value: Clofibrate

value: 1 uM

tag: exposure time

tag: assay plate

tag: assay plate well


title: Female_LumbarDH_GrayMatter_SingleNuclei

city: Stanford

first: Vivianne

middle: L

last: Tawfik

state: California

address: 1291 Welch Road, Grant Building S007

department: Anesthesiology, Perioperative and Pain Medicine

institute: Stanford University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (version 6.0.0) was used for barcode processing, unique molecular identifiers filtering, gene counting, and sample mapping to the reference transcriptome.
The filtered UMI count matrix was provided from Cell Ranger as an input in the Seurat workflow (version 4.0).
Nuclei with less than 200 and greater than 6,000 (for the male sample) or 8,000 (for the female sample) detected genes based on read depth were filtered out to eliminate low quality nuclei and multiplets. Nuclei with more than 5% mitochondrial genes detected were further removed.
The samples were merged via multiple Seurat functions, keeping only the top 2,000 highly variable genes shared between the samples. Integration anchors were identified using canonical correlation analysis and then the datasets were integrated based on the anchors.
Principal component analysis (PCA) was performed on the integrated dataset. Based on the first 30 principal components (PC), the uniform manifold approximation and projection (UMAP) was used for dimension reduction.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files

molecule: nuclear RNA

source_name: Lumbar Dorsal Horn Gray Matter

extract_protocol:
Human lumbar spinal cords were collected from donors and immediately frozen on dry ice. The spinal cords were then embedded in OCT, sliced via cryostat, and the dorsal horn gray matter was collected. Neuclei were isolated via FANS by DAPI and enriched for microglia by sorting out NeuN+, Sox10+, and Sox9+ nuclei.
Nuclei were loaded onto a 10X Genomic Chromium single cell chip. Reverse transcription and subsequent library preparations were performed using the Chromium Next GEM Single Cell 3' Kit v3 by the Stanford Functional Genomics Facility.
snRNA-seq

tag: tissue

value: Lumbar Dorsal Horn Gray Matter

tag: cell type

value: Enriched for Microglia

tag: age

value: 49 years

value: female


title: jq.els.pb.M2

tag: lifestage

value: els

value: liver

value: pb


title: A4galt KO mouse naive B cells BCR-seq rep1


title: Male_LumbarDH_GrayMatter_SingleNuclei

description: 10X Genomics

value: 43 years

tag: Sex

value: male


title: TP0001651G01_1_0.030000uM_DMEM_12h_TC00283154_C19

description:
TP0001651G01_1_0.030000uM_DMEM_12h
TC00283154_C19

data_processing:
Each FASTQ file was aligned to the probe sequences in the hWTv1 assay using HISAT2 v2.1.0 with spliced alignment disabled.
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.
Assembly: hWTv1
Supplementary files format and content: Processed data provided as a single table of counts for all probes x all samples

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).

tag: cell line

value: 12h exposure of 0.03 uM of Vinclozolin

value: Vinclozolin

tag: chemical sample id


title: jq.els.pb.M1

tag: chemical

tag: concentration

value: MED


title: Gla KO mouse naive B cells BCR-seq rep3

value: spleen

value: naive B cells

tag: genotype

value: Gla KO


title: TP0001651D01_2_0.100000uM_DMEM_12h_TC00283154_C17

description:
TP0001651D01_2_0.100000uM_DMEM_12h
TC00283154_C17

tag: media

value: DMEM + 10% HI-FBS

tag: treatment

value: 12h exposure of 0.1 uM of Lactofen

value: Lactofen


title: Gla KO mouse naive B cells BCR-seq rep1


title: jq.els.pb.M4

description:
S488, S489, S490, S491, S492
jq.els.pb.S1, jq.els.pb.S2, jq.els.pb.S3, jq.els.pb.S4, jq.els.pb.S5
NS.1100.003.NEBNext_dual_i7_E1---NEBNext_dual_i5_E1.QE2-S1-LT_R1.fastq.gz, NS.1100.003.NEBNext_dual_i7_D12---NEBNext_dual_i5_D12.QE2-S2-LT_R1.fastq.gz, NS.1100.003.NEBNext_dual_i7_E7---NEBNext_dual_i5_E7.QE2-S3-LT_R1.fastq.gz, NS.1100.003.NEBNext_dual_i7_F9---NEBNext_dual_i5_F9.QE2-S4-LT_R1.fastq.gz, NS.1100.004.NEBNext_dual_i7_E5---NEBNext_dual_i5_E5.QE2-S5-LT_R1.fastq.gz
NS.1100.003.NEBNext_dual_i7_E1---NEBNext_dual_i5_E1.QE2-S1-LT_R2.fastq.gz, NS.1100.003.NEBNext_dual_i7_D12---NEBNext_dual_i5_D12.QE2-S2-LT_R2.fastq.gz, NS.1100.003.NEBNext_dual_i7_E7---NEBNext_dual_i5_E7.QE2-S3-LT_R2.fastq.gz, NS.1100.003.NEBNext_dual_i7_F9---NEBNext_dual_i5_F9.QE2-S4-LT_R2.fastq.gz, NS.1100.004.NEBNext_dual_i7_E5---NEBNext_dual_i5_E5.QE2-S5-LT_R2.fastq.gz
jq_els_pb.txt


title: TP0001651E02_3_0.300000uM_DMEM_12h_TC00283154_C18

description:
TP0001651E02_3_0.300000uM_DMEM_12h
TC00283154_C18

value: 12h exposure of 0.3 uM of 4-Nonylphenol, branched

value: 4-Nonylphenol, branched

tag: chemical concentration

tag: dose level


title: A4galt KO mouse naive B cells BCR-seq rep4

value: A4galt KO


title: HePG2 cells,zhimasu1

city: Weifang

first: mengyun

last: dong

state: Shandong Province

address: No. 7166, West Baotong Street

department: Public health

institute: Weifang Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38
Supplementary files format and content: tab-delimited text files contain the count number and expression level of the gene in each sample.
Supplementary files format and content: tab-delimited text files contain the FPKM expression of all genes in each sample.

source_name: sesamin treated

growth_protocol: HePG2 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and 1% non-essential amino acids in an incubator at 37 ° C, constant humidity, and 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

treatment_protocol: The experiment was divided into control, model, and treat  groups, respectively.After 24 h after cell adhesion, a high-fat cell model was constructed by 400  M oleic acid (Sigma) treatment for 24 h, and the treat group was subjected to 16   M sesamin treatment for another 36 h.

value: Human hepatocellular carcinoma cells


title: A4galt KO mouse naive B cells BCR-seq rep2


title: HePG2 cells,zhimasu2


title: HePG2 cells,zhimasu3


title: TP0001651B06_6_10.000000uM_DMEM_12h_TC00283154_C16

first: Logan

last: Everett

address: 109 T.W. Alexander Dr

institute: U.S. Environmental Protection Agency

description:
TP0001651B06_6_10.000000uM_DMEM_12h
TC00283154_C16

value: 12h exposure of 10 uM of Troglitazone

tag: chemical name

value: Troglitazone

value: 10 uM

tag: exposure time


title: jq.els.pb.H1

value: els

value: liver

value: pb

value: HIGH


title: TP0001651H02_6_10.000000uM_DMEM_12h_TC00283154_C22

description:
TP0001651H02_6_10.000000uM_DMEM_12h
TC00283154_C22

value: 12h exposure of 10 uM of Maneb

value: Maneb

tag: assay plate

tag: assay plate well


title: H2_JQE_HBCD

tag: tissue

value: hbcd


title: HePG2 cells,zhengchang3

source_name: Control

tag: cell type


title: jq.els.pb.M5

tag: lifestage

value: MED


title: HePG2 cells,zhengchang2


title: H3_JQE_HBCD


title: TP0001651B03_8_100.000000uM_DMEM_12h_TC00283154_C15

description:
TP0001651B03_8_100.000000uM_DMEM_12h
TC00283154_C15

value: DMEM + 10% HI-FBS

value: 12h exposure of 100 uM of Reserpine

value: Reserpine


title: WT mouse naive B cells BCR-seq rep3

value: spleen

value: naive B cells

value: WT


title: WT mouse naive B cells BCR-seq rep2


title: M1_JQE_HBCD


title: TP0001651A02_1_0.030000uM_DMEM_12h_TC00283154_C14

description:
TP0001651A02_1_0.030000uM_DMEM_12h
TC00283154_C14

value: 12h exposure of 0.03 uM of Imazalil

value: Imazalil


title: healthy skin_9

value: skin

tag: patient diagnosis

value: healthy

tag: condition


title: WT mouse naive B cells BCR-seq rep1


title: HePG2 cells,zhengchang1

tag: cell line

value: Human hepatocellular carcinoma cells