title: 2D_PROL_PLATE1_REPLICATE1_L01

source_name: RNA-Seq of undifferentiated HepaRG cells in culture


title: 2D_PROL_PLATE1_REPLICATE1_J22

status: Public on Mar 06 2020

type: SRA

city: Durham

first: Scott

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

country: USA

institute: Division of the National Toxicology Program at NIEHS

library_source: transcriptomic

data_processing:
TempO-Seq analysis was performed as described previously, at a targeted sequencing depth of 500 mapped read counts per transcript (Yeakley, et al., 2017).
genome build: A pseudo human transcriptome. Sequences that were included in the pseudo human transcriptome can be found here:  https://ntp.niehs.nih.gov/ntp/research/areas/tox21/human_s1500_manifest_09182018.xlsx
Supplementary_files_format_and_content: read counts per transcript

molecule: total RNA

organism: Homo sapiens

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9.49 nM of aspirin

growth_protocol: Cryopreserved HepaRG cells (Lonza, Catalog:NSHPRG) were thawed, and approximately 20 000 cells per well were seeded onto collagen(I)-coated 384-well plates (Corning, Catalog: 356667) 10 days prior to compound exposures for recovery/differentiation with differentiated cultures (2D-DIFF). For proliferated/non-differentiated cultures (PROLIF), 2000 cells per well were seeded 3 days prior to chemical exposure. Cells were plated using Williams E medium (ThermoFisher, Catalog: A1217601) supplemented with plating additive (Lonza, Catalog: MHTAP), and 24h later exchanged with William’s E medium supplemented with maintenance additive (Lonza, Catalog: MHPIT) for the duration of cultures.

extract_protocol: At the end of the 96-hour compound exposure period, exposure media was removed, and cells were washed once with 50 μL Phosphate-buffered saline (ThermoFisher) followed by addition of 20 μL of 1X TempO-Seq lysis buffer (Biospyder) to culture plates. Plates were then incubated for 15 minutes at room temperature and frozen at -80° C. TempO-Seq analysis was performed as described previously, at a targeted sequencing depth of 500 mapped read counts per transcript (Yeakley, et al., 2017).

treatment_protocol: Compounds were procured from MRI Global (Kansas City, Missouri). Chemicals were blinded to the laboratory personnel involved in compound exposures. Briefly, 500X concentrations of each compound were prepared in DMSO, with the exception of phenobarbital and acetaminophen, which were prepared in exposure medium due to aqueous solubility incompatible with dissolution in DMSO. Stock concentrations (500X) were serial diluted in 96-well plates for a total of 10 concentrations (half-log spacing). From these stocks, 2 ml of each compound was stamped in a separate 96-well plate containing maintenance medium (Lonza, Catalog: MHPIT) using Vialflo semi-automated pipettor (Integra Biosciences, Catalog: 6031). Compound mixtures were subsequently mixed thoroughly, and 50 ml was transferred to the culture plates containing cells. Media from each exposed culture well were exchanged after the initial 48h of treatment, spent culture media were removed for lactate dehydrogenase (LDH) assays, and fresh exposure medium was added to the plates, as described above. The total chemical exposure period was 96 h prior to cell lysis for Tempo-Seq analysis. Three independent technical replicates per treatment group, and 3 independent experimental runs were performed in this study.

tag: cell type

value: HepaRG cells

tag: sample preparation

value: unpurified cell lysates

tag: treatment time

value: 96 hours

tag: dose

tag: chemical

value: aspirin


title: 2D_PROL_PLATE1_REPLICATE1_K08

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30001.15 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_K06

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94871.97 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_K02


title: 2D_PROL_PLATE1_REPLICATE1_J20

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30.00 nM of aspirin

value: 30 nM


title: 2D_PROL_PLATE1_REPLICATE1_J24

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to DMSO

value: DMSO


title: 2D_PROL_PLATE1_REPLICATE1_K04

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 300011.51 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_K12

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 3000.12 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_K05

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 63257.30 nM of CDCA

value: CDCA


title: 2D_PROL_PLATE1_REPLICATE1_K01


title: 2D_PROL_PLATE1_REPLICATE1_J21

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 6.33 nM of CDCA


title: 2D_PROL_PLATE1_REPLICATE1_J19

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 20.00 nM of CDCA

value: 20 nM


title: 2D_PROL_PLATE1_REPLICATE1_J09

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 6325.73 nM of CDCA


title: 2D_PROL_PLATE1_REPLICATE1_J12


title: 2D_PROL_PLATE1_REPLICATE1_J11

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 2000.37 nM of CDCA


title: 2D_PROL_PLATE1_REPLICATE1_J14

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 948.72 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_J16

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 300.01 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_J07

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 20003.71 nM of CDCA


title: 2D_PROL_PLATE1_REPLICATE1_J18

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94.87 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_J10

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9487.20 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_J13

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 632.57 nM of CDCA


title: 2D_PROL_PLATE1_REPLICATE1_J08

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30001.15 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_J06

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94871.97 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_J02

source_name: RNA-Seq of undifferentiated HepaRG cells in culture


title: 2D_PROL_PLATE1_REPLICATE1_J05


title: 2D_PROL_PLATE1_REPLICATE1_J04


title: 2D_PROL_PLATE1_REPLICATE1_J23

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to DMSO


title: 2D_PROL_PLATE1_REPLICATE1_J03

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 200037.13 nM of CDCA


title: 2D_PROL_PLATE1_REPLICATE1_J17

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 63.26 nM of CDCA


title: 2D_PROL_PLATE1_REPLICATE1_I21


title: 2D_PROL_PLATE1_REPLICATE1_J01


title: 2D_PROL_PLATE1_REPLICATE1_I17


title: 2D_PROL_PLATE1_REPLICATE1_I24


title: 2D_PROL_PLATE1_REPLICATE1_I23


title: 2D_PROL_PLATE1_REPLICATE1_I20

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30.00 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_I19


title: 2D_PROL_PLATE1_REPLICATE1_I16


title: 2D_PROL_PLATE1_REPLICATE1_J15

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 200.04 nM of CDCA


title: 2D_PROL_PLATE1_REPLICATE1_I18


title: 2D_PROL_PLATE1_REPLICATE1_I14


title: 2D_PROL_PLATE1_REPLICATE1_I10


title: 2D_PROL_PLATE1_REPLICATE1_I12

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 3000.12 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_I13


title: 2D_PROL_PLATE1_REPLICATE1_I05

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 63257.30 nM of CDCA


title: 2D_PROL_PLATE1_REPLICATE1_I08


title: 2D_PROL_PLATE1_REPLICATE1_I06


title: 2D_PROL_PLATE1_REPLICATE1_I07


title: 2D_PROL_PLATE1_REPLICATE1_I03


title: 2D_PROL_PLATE1_REPLICATE1_I09

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 6325.73 nM of CDCA


title: 2D_PROL_PLATE1_REPLICATE1_I22

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9.49 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_H24


title: 2D_PROL_PLATE1_REPLICATE1_I15


title: 2D_PROL_PLATE1_REPLICATE1_H22

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9.49 nM of rosiglitazone

value: rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_I01


title: 2D_PROL_PLATE1_REPLICATE1_I04

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 300011.51 nM of aspirin


title: 2D_PROL_PLATE1_REPLICATE1_I02


title: 2D_PROL_PLATE1_REPLICATE1_H23


title: 2D_PROL_PLATE1_REPLICATE1_H20

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30.00 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_H18

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94.88 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_H19

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30.00 nM of cyclophosphamide

value: cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_H17

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94.86 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_H16

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 300.05 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_H14

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 948.84 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_H21

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9.49 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_H12

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 3000.50 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_H10

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9488.41 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_H07

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 29998.31 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_H06

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94884.09 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_H08

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30004.98 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_H02

source_name: RNA-Seq of undifferentiated HepaRG cells in culture


title: 2D_PROL_PLATE1_REPLICATE1_I11

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 2000.37 nM of CDCA


title: 2D_PROL_PLATE1_REPLICATE1_H03

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 299983.06 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_G24

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to DMSO


title: 2D_PROL_PLATE1_REPLICATE1_H15

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 299.98 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_H01


title: 2D_PROL_PLATE1_REPLICATE1_G20

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30.00 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_H13

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 948.63 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_H05

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94862.97 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_H11

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 2999.83 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_G11


title: 2D_PROL_PLATE1_REPLICATE1_G22

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9.49 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_H09

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9486.30 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_G08


title: 2D_PROL_PLATE1_REPLICATE1_H04

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 300049.84 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_G23


title: 2D_PROL_PLATE1_REPLICATE1_G19

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30.00 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_G21

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9.49 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_G17

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94.86 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_G14

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 948.84 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_G10

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9488.41 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_G18

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94.88 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_G12

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 3000.50 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_G13


title: 2D_PROL_PLATE1_REPLICATE1_G15


title: 2D_PROL_PLATE1_REPLICATE1_G09


title: 2D_PROL_PLATE1_REPLICATE1_F22


title: 2D_PROL_PLATE1_REPLICATE1_F21


title: 2D_PROL_PLATE1_REPLICATE1_F19


title: 2D_PROL_PLATE1_REPLICATE1_G04


title: 2D_PROL_PLATE1_REPLICATE1_G06

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94884.09 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_G07

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 29998.31 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_F16

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 300.05 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_G05


title: 2D_PROL_PLATE1_REPLICATE1_F17


title: 2D_PROL_PLATE1_REPLICATE1_G03

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 299983.06 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_G02

source_name: RNA-Seq of undifferentiated HepaRG cells in culture


title: 2D_PROL_PLATE1_REPLICATE1_G01


title: 2D_PROL_PLATE1_REPLICATE1_F23

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to DMSO


title: 2D_PROL_PLATE1_REPLICATE1_G16


title: 2D_PROL_PLATE1_REPLICATE1_F10


title: 2D_PROL_PLATE1_REPLICATE1_F09


title: 2D_PROL_PLATE1_REPLICATE1_F20

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30.00 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_F07


title: 2D_PROL_PLATE1_REPLICATE1_F14


title: 2D_PROL_PLATE1_REPLICATE1_F13

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 948.63 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_F12


title: 2D_PROL_PLATE1_REPLICATE1_F24


title: 2D_PROL_PLATE1_REPLICATE1_F01


title: 2D_PROL_PLATE1_REPLICATE1_F18


title: 2D_PROL_PLATE1_REPLICATE1_F08

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30004.98 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_F04

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 300049.84 nM of rosiglitazone


title: 2D_PROL_PLATE1_REPLICATE1_F06


title: 2D_PROL_PLATE1_REPLICATE1_E22

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9.49 nM of troglitazone

value: troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_E20

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30.01 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_E18

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94.91 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_E19

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 29.99 nM of KCl

value: KCl


title: 2D_PROL_PLATE1_REPLICATE1_F03


title: 2D_PROL_PLATE1_REPLICATE1_F11

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 2999.83 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_E23


title: 2D_PROL_PLATE1_REPLICATE1_E21

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9.48 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_E17

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94.84 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_E24


title: 2D_PROL_PLATE1_REPLICATE1_E12

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 3001.16 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_F15

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 299.98 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_E16

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 300.12 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_E15

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 299.92 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_E11

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 2999.19 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_E13

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 948.43 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_E07

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 29991.95 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_E14

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 949.05 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_F05

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94862.97 nM of cyclophosphamide


title: 2D_PROL_PLATE1_REPLICATE1_E10

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9490.50 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_E09

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9484.29 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_F02

source_name: RNA-Seq of undifferentiated HepaRG cells in culture


title: 2D_PROL_PLATE1_REPLICATE1_E08

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30011.60 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_E05

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94842.87 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_E03

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 299919.48 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_E06

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94905.00 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_E04

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 300115.97 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_D23

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to DMSO


title: 2D_PROL_PLATE1_REPLICATE1_E02


title: 2D_PROL_PLATE1_REPLICATE1_D24


title: 2D_PROL_PLATE1_REPLICATE1_D19

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 29.99 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_D16

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 300.12 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_D21

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9.48 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_E01


title: 2D_PROL_PLATE1_REPLICATE1_D22

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9.49 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_D14


title: 2D_PROL_PLATE1_REPLICATE1_D11

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 2999.19 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_D20

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30.01 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_D18

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94.91 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_D17

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94.84 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_D15

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 299.92 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_D13

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 948.43 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_D06


title: 2D_PROL_PLATE1_REPLICATE1_D12

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 3001.16 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_D10

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9490.50 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_D08

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30011.60 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_D05

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94842.87 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_D02

source_name: RNA-Seq of undifferentiated HepaRG cells in culture


title: 2D_PROL_PLATE1_REPLICATE1_D09

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9484.29 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_D03

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 299919.48 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_C22


title: 2D_PROL_PLATE1_REPLICATE1_D04

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 300115.97 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_D01


title: 2D_PROL_PLATE1_REPLICATE1_C24

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to DMSO


title: 2D_PROL_PLATE1_REPLICATE1_C17


title: 2D_PROL_PLATE1_REPLICATE1_C19

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 29.99 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_C23


title: 2D_PROL_PLATE1_REPLICATE1_C21

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 9.48 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_C15


title: 2D_PROL_PLATE1_REPLICATE1_C16

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 300.12 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_C13


title: 2D_PROL_PLATE1_REPLICATE1_C14

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 949.05 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_C09


title: 2D_PROL_PLATE1_REPLICATE1_C12


title: 2D_PROL_PLATE1_REPLICATE1_C18

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94.91 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_C06

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 94905.00 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_D07

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 29991.95 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_C07


title: 2D_PROL_PLATE1_REPLICATE1_C11

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 2999.19 nM of KCl


title: 2D_PROL_PLATE1_REPLICATE1_C10


title: 2D_PROL_PLATE1_REPLICATE1_C01


title: 2D_PROL_PLATE1_REPLICATE1_C04


title: 2D_PROL_PLATE1_REPLICATE1_B21


title: 2D_PROL_PLATE1_REPLICATE1_B22


title: 2D_PROL_PLATE1_REPLICATE1_B20


title: 2D_PROL_PLATE1_REPLICATE1_C02


title: 2D_PROL_PLATE1_REPLICATE1_C20

source_name: RNA-Seq of undifferentiated HepaRG cells in culture, after 96 hours of exposure to 30.01 nM of troglitazone


title: 2D_PROL_PLATE1_REPLICATE1_C03


title: 2D_PROL_PLATE1_REPLICATE1_B18


title: 2D_PROL_PLATE1_REPLICATE1_B16


title: 2D_PROL_PLATE1_REPLICATE1_B17


title: 2D_PROL_PLATE1_REPLICATE1_B13


title: 2D_PROL_PLATE1_REPLICATE1_B12


title: 2D_PROL_PLATE1_REPLICATE1_B14


title: 2D_PROL_PLATE1_REPLICATE1_C08


title: 2D_PROL_PLATE1_REPLICATE1_C05


title: 2D_PROL_PLATE1_REPLICATE1_B08


title: 2D_PROL_PLATE1_REPLICATE1_B09


title: 2D_PROL_PLATE1_REPLICATE1_B15


title: 2D_PROL_PLATE1_REPLICATE1_B06


title: 2D_PROL_PLATE1_REPLICATE1_B07


title: 2D_PROL_PLATE1_REPLICATE1_B11


title: 2D_PROL_PLATE1_REPLICATE1_A21


title: 2D_PROL_PLATE1_REPLICATE1_B10


title: 2D_PROL_PLATE1_REPLICATE1_B04


title: 2D_PROL_PLATE1_REPLICATE1_B03


title: 2D_PROL_PLATE1_REPLICATE1_A19


title: 2D_PROL_PLATE1_REPLICATE1_B19


title: 2D_PROL_PLATE1_REPLICATE1_A20


title: 2D_PROL_PLATE1_REPLICATE1_A14


title: 2D_PROL_PLATE1_REPLICATE1_A22


title: 2D_PROL_PLATE1_REPLICATE1_A12


title: 2D_PROL_PLATE1_REPLICATE1_A18


title: 2D_PROL_PLATE1_REPLICATE1_A08


title: 2D_PROL_PLATE1_REPLICATE1_A13


title: 2D_PROL_PLATE1_REPLICATE1_A15


title: 2D_PROL_PLATE1_REPLICATE1_A16


title: 2D_PROL_PLATE1_REPLICATE1_A07


title: 2D_PROL_PLATE1_REPLICATE1_A11


title: 2D_PROL_PLATE1_REPLICATE1_B05


title: 2D_PROL_PLATE1_REPLICATE1_A06


title: miR-30a-5p_rep3

status: Public on Feb 26 2020

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

data_processing:
Sequence mapping and quantification were performed using the methods STAR (V2.5) and HTSeq (V0.6.1), respectively. Standard pipeline of Novogene (https://en.novogene.com/) was used.
For sequence mapping, Human reference genome version hg19 was used.
The read counts were imported into edgeR for differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Ensembl gene ids, read counts, and FPKM values for each sample.

source_name: lung

growth_protocol: A549 lung cell line was cultured in RPMI-1640 media supplemented with 10% FBS and penicillin/streptomycin and with additional L-glutamine. Cells were confirmed to be negative for mycoplasma.

extract_protocol:
RNA was isolated from A549 cell line using Trizol (Invitrogen) according to the manufacturer’s protocol, with one exception. To enhance the isolation of small RNA, the isopropanol precipitation step was performed overnight at −20°C.
Libraries were made and RNA-seq profiles were generated by Novogene (https://en.novogene.com/). Illumina Novaseq 6000 system was used.

treatment_protocol: Lipofectamine 2000 (Invitrogen) was used to transfect A549 lung cancer cell line with 20nM miR-30a-5p, miR-30a-3p, or negative control RNA mimic (Dharmacon), according to the manufacturer’s protocol using the 6-well plate format. Triplicate samples were harvested 72 hours after transfection.

tag: treatment

value: miR-30a-5p mimic transfected


title: 2D_PROL_PLATE1_REPLICATE1_A04


title: 2D_PROL_PLATE1_REPLICATE1_A10


title: 2D_PROL_PLATE1_REPLICATE1_A17


title: miR-30a-3p_rep1

value: miR-30a-3p mimic transfected


title: control_rep3

value: Control RNA transfected


title: 2D_PROL_PLATE1_REPLICATE1_A05


title: Adult-Transverse-Colon2-1

status: Public on Feb 10 2020

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

country: China

institute: Center for Stem Cell and Regenerative Medicine

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the Homo_sapiens. GRCh38 assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cellbarcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Homo_sapiens. GRCh38
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

source_name: Microwell-seq analysis

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

tag: age

tag: Sex

value: Female

tag: tissue

value: Intestine


title: control_rep2


title: Adult-Transverse-Colon2-2


title: miR-30a-5p_rep2


title: Adult-Pancreas1

value: Pancreas


title: Adult-Lung3-4

value: Lung


title: Adult-Lung3-2


title: miR-30a-5p_rep1


title: Adult-Lung3-1


title: Adult-Lung2


title: control_rep1


title: miR-30a-3p_rep3


title: miR-30a-3p_rep2


title: Adult-Lung1

value: Male


title: Adult-Transverse-Colon1


title: 2D_PROL_PLATE1_REPLICATE1_A09

value: HepaRG cells

value: unpurified cell lysates


title: Adult-Liver4-1

value: Liver


title: Adult-Liver2


title: Adult-Liver1-2


title: Adult-Thyroid2

value: Thyroid


title: Adult-Sigmoid-Colon1


title: Adult-Thyroid1


title: 2D_PROL_PLATE1_REPLICATE1_A03


title: Adult-Prostate1

value: Prostate


title: Adult-Bladder2

data_processing:
Base-calls were performed with Illumina bcl2fastq
The cell barcode can be found in read1, the bases 1-6,22-27,43-48 merge (18bp); UMI: In read1, the bases 49-54 (6bp)
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the Homo_sapiens. GRCh38 assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cellbarcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Homo_sapiens. GRCh38
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

value: Bladder


title: Adult-Lung3-3


title: Adult-Bladder1


title: Adult-Jejunum2


title: Adult-Liver1-1


title: Adult-Gall-Bladder1

value: Gall-Bladder


title: Adult-Liver4-2


title: Adult-Rectum1


title: Adult-Ileum2


title: Adult-Gall-Bladder2


title: Adult-Ascending-Colon1


title: Adult-Duodenum1


title: 9 mpf_brain_male_30ppb_Rep3

status: Public on Dec 31 2019

type: RNA

city: West Lafayette

first: Jennifer

last: Freeman

state: IN

address: 550 Stadium Mall Drive

department: School of Health Sciences

institute: Purdue University

description: Gene expression 9 mpf following embryonic exposure (1-72 hpf)

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

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

data_processing: Array image data was extracted using Agilent Feature Extraction Software 12.0 (Agilent Technologies, Santa Clara, CA). Array image data was then uploaded to GeneSpring 14.9 (Agilent Technologies, Santa Clara, CA) for statistical analysis. Each gene list was imported into Ingenuity Pathway Analysis (IPA) for gene ontology and molecular pathway analysis.

organism: Danio rerio

source_name: 9 mpf, brain, male, 30 ppb, replicate 3

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

growth_protocol: Zebrafish (wild-type AB strain) were housed in a Z-Mod System (Aquatic Habitats, Apopka, FL) on a 14:10 hour light:dark cycle and maintained at 28ºC ± 1°C with a pH of 7.0-7.2 and conductivity range of 470-550 µS.

extract_protocol: Total RNA was isolated using an RNeasy MinElute Cleanup Kit (Qiagen Sciences, Maryland, USA) following established protocols. RNA concentrations were measured by using a NanoDrop 1000 spectrophotometer and the quality was verified by absorbance ratio 260/280 nm.

treatment_protocol: Zebrafish embryos were exposed to 0, 0.3, 3, or 30 ppb atrazine from approximately 1 hpf through 72 hpf. Zebrafish were rinsed at 72 hpf and reared in normal conditions until 9 mpf. After euthanasia, brains were removed, homogenized in Trizol (Life Technolgies, Carlsbad, CA) and flash frozen in liquid nitrogen and stored at -80°C until RNA extraction. Each replicate represents one zebrafish brain and four biological replicates were completed (n=4).

tag: gender

value: Brain

value: 9 mpf

tag: atz exposue


title: 9 mpf_brain_male_3ppb_Rep4

source_name: 9 mpf, brain, male, 3 ppb, replicate 4


title: 9 mpf_brain_male_0ppb_Rep1

source_name: 9 mpf, brain, male, 0 ppb, replicate 1


title: 9 mpf_brain_male_30ppb_Rep4

source_name: 9 mpf, brain, male, 30 ppb, replicate 4


title: 9 mpf_brain_male_0.3ppb_Rep4

source_name: 9 mpf, brain, male, 0.3 ppb, replicate 4


title: 9 mpf_brain_Female_30ppb_Rep4

source_name: 9 mpf, brain, female, 30 ppb, replicate 4

tag: atz exposure


title: 9 mpf_brain_Female_0.3ppb_Rep3

source_name: 9 mpf, brain, female, 0.3 ppb, replicate 3


title: 9 mpf_brain_male_0ppb_Rep3

source_name: 9 mpf, brain, male, 0 ppb, replicate 3


title: 9 mpf_brain_male_3ppb_Rep3

source_name: 9 mpf, brain, male, 3 ppb, replicate 3


title: 9 mpf_brain_Female_0.3ppb_Rep4

source_name: 9 mpf, brain, female, 0.3 ppb, replicate 4


title: 9 mpf_brain_male_0ppb_Rep4

source_name: 9 mpf, brain, male, 0 ppb, replicate 4


title: 9 mpf_brain_Female_0.3ppb_Rep2

source_name: 9 mpf, brain, female, 0.3 ppb, replicate 2


title: 9 mpf_brain_Female_0ppb_Rep4

source_name: 9 mpf, brain, female, 0 ppb, replicate 4


title: 9 mpf_brain_male_30ppb_Rep2

source_name: 9 mpf, brain, male, 30 ppb, replicate 2


title: 9 mpf_brain_male_3ppb_Rep2

source_name: 9 mpf, brain, male, 3 ppb, replicate 2


title: 9 mpf_brain_male_3ppb_Rep1

source_name: 9 mpf, brain, male, 3 ppb, replicate 1


title: 9 mpf_brain_male_0.3ppb_Rep3

source_name: 9 mpf, brain, male, 0.3 ppb, replicate 3


title: 9 mpf_brain_Female_3ppb_Rep3

source_name: 9 mpf, brain, female, 3 ppb, replicate 3


title: 9 mpf_brain_male_0.3ppb_Rep2

source_name: 9 mpf, brain, male, 0.3 ppb, replicate 2


title: CRISPRi library DNA

status: Public on Nov 25 2019

city: Cleveland

first: Peter

last: Scacheri

state: OH

address: 2109 Adelbert Road

department: Genetics and Genome Sciences

institute: Case Western Reserve University

library_source: genomic

data_processing:
Library strategy: CRISPR interference screen
gRNA sequences were counted from reads using count_spacers.py from Joung et al. Nature Protocols 2017.
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain the raw counts for each gRNA within the sequenced library.  The columns are: gRNA location chromsome, gRNA start nucleotide, gRNA end nucleotide, gRNA strand, and raw count of gRNA in the sequenced file. Non targeting gRNAs have no genome location.

molecule: genomic DNA

organism: synthetic construct

source_name: EGFR CRISPRi plasmid library DNA

growth_protocol: Glioblastoma stem cell cultures were grown as neurospheres as previously described (Bao et al. Nature 2006). Briefly, the incubator is set at 37C, 20% oxygen, and 5% CO2. They are grown in neurobasal media minus phenol red (Thermo) supplemented with 1x B27, 100 U/mL pen/strep, 2 mM glutamine, 20ng/mL FGF, 20 ng/mL EGF, and 1mM sodium pyruvate.

extract_protocol:
Genomic DNA was extracted with standard laboratory tecniques.
Libraries were prepared according previous methods (e.g. Klann et al. Nature Biotechnology 2017). Briefly, the gRNAs were PCR amplified from 5 ug of genomic DNA using custom oligonucleotides custructed with sequencing adapters, custom indices, and a sequence specific gRNA construct. Libraries were purified using PCR Clean Dx beads (Aline Biosciences) before sequencing on an Illumina MiSeq.

treatment_protocol: GBM3565 and GSC23 were infected with lentiviral particules, containing gRNA library cloned into hUbC-dCas9-KRAB-T2a-Puro (Addgene 71236), at an MOI of ~0.3 and 500x coverage. The glioblastoma cells were selected with 750 ng/mL puromycin and cultured under normal conditions and maintained at 500x coverage until 21 days post infection.

tag: time point

tag: egfr amplification status


title: 9 mpf_brain_Female_0ppb_Rep2

source_name: 9 mpf, brain, female, 0 ppb, replicate 2


title: 9 mpf_brain_Female_3ppb_Rep2

source_name: 9 mpf, brain, female, 3 ppb, replicate 2


title: 9 mpf_brain_Female_0.3ppb_Rep1

source_name: 9 mpf, brain, female, 0.3 ppb, replicate 1


title: GSC23 CRISPRi day 21

value: glioblastoma patient-derived cell model

value: Day 21

value: unamplified


title: 9 mpf_brain_Female_0ppb_Rep3

source_name: 9 mpf, brain, female, 0 ppb, replicate 3

value: Female


title: 9 mpf_brain_Female_0ppb_Rep1

source_name: 9 mpf, brain, female, 0 ppb, replicate 1


title: 9 mpf_brain_Female_3ppb_Rep1

source_name: 9 mpf, brain, female, 3 ppb, replicate 1


title: 9 mpf_brain_male_0ppb_Rep2

source_name: 9 mpf, brain, male, 0 ppb, replicate 2


title: 9 mpf_brain_male_0.3ppb_Rep1

source_name: 9 mpf, brain, male, 0.3 ppb, replicate 1


title: 9 mpf_brain_male_30ppb_Rep1

source_name: 9 mpf, brain, male, 30 ppb, replicate 1


title: 9 mpf_brain_Female_30ppb_Rep1

source_name: 9 mpf, brain, female, 30 ppb, replicate 1


title: 9 mpf_brain_Female_30ppb_Rep3

source_name: 9 mpf, brain, female, 30 ppb, replicate 3


title: 9 mpf_brain_Female_3ppb_Rep4

source_name: 9 mpf, brain, female, 3 ppb, replicate 4


title: 031108MS-29; Heart tissue from untreated C57BI/6 male mouse

status: Public on Nov 15 2019

description: replicate 4

hyb_protocol: Labeled cRNA was fragmented and hybridized to the Affymetrix Mouse Genome 430 2.0 Array. Array hybridization, washing, and staining were performed according to the Affymetrix recommended protocol EuKGE_Ws2v5.

scan_protocol: The chips were scanned using an Affymetrix GeneChipScanner 3000.

data_processing: Normalization was performed using the MAS5 algorithm and baseline transformed. Quality control measurements were evaluated to determine whether the data derived from the Affymetrix GeneChips were of sufficient quality prior to comparisons for differential expression. Affymetrix-recommended guidelines for evaluating quality were used to evaluate the output files for each GeneChip using the R/Bioconductor package, Simpleaffy (Wilson and Miller 2005).

label: biotin

organism: Mus musculus

source_name: heart apical tissue

label_protocol: TotalRNA(50 ng) was used to synthesize double-stranded cDNA for each sample using Affymetrix GeneChipExpression 30amplication two-cycle target labeling and control reagents (Affymetrix Inc. Santa Clara, CA). The cDNA served as a template to synthesize biotin-labeled antisense cRNA using an in vitro transcription labeling kit.

growth_protocol: All mice were housed individually with a twelve-hour light/dark cycle (6:00 AM to 6:00 PM) per day. NTP 2000 diet (Ziegler Bros, Inc., Gardner, PA) was available ad libitum. The experiment was conducted at an AAALAC-accredited facility, and animal handling and husbandry met all NIH guidelines (Institute of Laboratory Animal Resources 1996).

extract_protocol: A section of the heart apex (10–18 mg) was placed into RNAlater (Ambion, Inc., Austin, TX) at necropsy. RNA was extracted from tissue of five control mice from each strain, C3H/HeJ, C57BL/6J, and B6C3F1/J. Total RNA was isolated using the QIAGEN RNeasy kit (QIAGEN, Valencia, CA). TheRNA was analyzed for quantity and purity by ultraviolet analysis using the NanoDrop ND-1000 spetrophotometer (NanoDropTechnologies, Wilmington, DE). Samples were concentrated using Microcon filters (Millipore, Billerica, MA). All samples were evaluated for RNA integrity by gel electrophoresis using the Flash GelRNAcassette system (Lonza, Rockland, ME).

treatment_protocol: Animals received no treatment other than surgical implant of a Data Sciences radiotelemetry transmitter in the abdominal cavity. Mice were anesthetized with tribromoethanol (Avertine) 250 mg/kg IP at seven weeks of age. Two to two and a half weeks post-surgery, animals were euthanized with CO2.

tag: strain

value: male

value: 9-10 weeks

value: heart apical tissue


title: 9 mpf_brain_Female_30ppb_Rep2

source_name: 9 mpf, brain, female, 30 ppb, replicate 2


title: WT choroid plexus

status: Public on Mar 27 2019

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: WT choroid plexus of C57BL/6JRj mice

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger mkfastq
Demultiplexed data was then processed using the Cell Ranger count pipeline
8bp I7 sample barcode
26bp read1 (16bp Chromium barcode and 10bp UMI)
98bp read2 (transcript)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output CellRanger Count) for each sample

source_name: choroid plexus

extract_protocol: All Methods listed in Van Hove et al.  A single-cell atlas of non-parenchymal brain macrophages reveals unique transcriptional identities that are shaped by ontogeny and tissue environment.  Nature Neuroscience. 2019.

tag: genotype/variation

value: WT

value: choroid plexus

tag: platform

value: 10x Genomics

tag: number of cells


title: HNSCC_7_PBMC

status: Public on Nov 13 2019

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

data_processing:
Demultiplexing using CellRanger mkfastq
Alignment and generation of gene/barcode matrices using CellRanger count
Genome_build: GRCh38
Supplementary_files_format_and_content: files containing gene/barcode matrices

molecule: polyA RNA

source_name: peripheral blood

extract_protocol: 10x 3' v2 scRNAseq

treatment_protocol: Ficoll density gradient centrifugation to isolate peripheral blood mononuclear cells from whole blood; mechanical distruption of tissues; live CD45+ single cells were sorted from all samples using a Beckman Coulter MoFlo Astrios.

value: peripheral blood

tag: disease state

value: Head and neck squamous cell carcinoma (HNSCC)


title: 031108MS-22; Heart tissue from untreated C57BI/6 male mouse

description: replicate 1


title: 031108MS-13; Heart tissue from untreated C3H male mouse

description: replicate 2


title: 031108MS-28; Heart tissue from untreated C57BI/6 male mouse

description: replicate 3


title: 031108MS-18; Heart tissue from untreated C3H male mouse

description: replicate 5


title: MRC5 fibroblasts, Ad_2_48hpi_R1

status: Public on Sep 12 2019

city: Rochester

first: Joshua

last: Munger

state: New York

address: 601 Elmwood Ave, Room 3-8828

department: Biochemistry & Biophysics

institute: University of Rochester

data_processing:
Raw read counts were obtained using featurecounts from the subread1.5.0p3 package and gencode 25 human gene annotations using only uniquely aligned reads (default) and including multi-mapping reads (-M)
Sequence reads were cleaned and adapter trimmed using trimmomatic-0.36
Each sample was mapped individually to the human reference genome (GRCh38.p7, primary assembly + gencode 25 annotation) with STAR2.5.2b
DESeq2-1.14.1 within R-3.3.2 was used to perform data normalization and differential expression analysis with a false-discovery rate adjusted p-value threshold of 0.05 on each set of raw expression measures.
Genome_build: GRCh38.p7, primary assembly + gencode 25 annotation
Supplementary_files_format_and_content: predeSeq2_counts.txt containing raw expression measures.  deSeq2_Ad_vs_dUL26.xlsx containing gene names, abundance values, log2 fold changes, and significance scores (p-values).

source_name: Human Lung Fibroblasts

growth_protocol: MRC5 fibroblasts (ATCC CCL-171) were cultured in Dulbecco’s modified Eagle serum (DMEM; Invitrogen) supplemented with 10% (vol/vol) FBS, 4.5 g/liter glucose, and 1% penicillin-streptomycin (Life Technologies) at 37oC in a 5% (vol/vol) CO2 atmosphere.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) according to manufacturer's instructions.
TruSeq Stranded mRNA Sample Preparation Kit (Illumina) was used for next generation sequencing library construction per manufacturer's protocols

treatment_protocol: Cells were infected for 2 hrs with each indicated virus and then allowed to grow in fresh, serum-free DMEM for 48 hrs.

tag: cell type

value: MRC5 fibroblasts

tag: infection

value: HCMV strain AD169


title: MRC5 fibroblasts, Ad_3_48hpi_R1


title: MRC5 fibroblasts, Ad_1_48hpi_R1


title: 031108MS-16; Heart tissue from untreated C3H male mouse

description: replicate 3


title: 031108MS-7; Heart tissue from untreated B6C3F1 male mouse

description: replicate 4


title: 031108MS-30; Heart tissue from untreated C57BI/6 male mouse

description: replicate 5


title: 031108MS-11; Heart tissue from untreated C3H male mouse

description: replicate 1


title: 031108MS-6; Heart tissue from untreated B6C3F1 male mouse

description: replicate 3


title: 031108MS-5; Heart tissue from untreated B6C3F1 male mouse

description: replicate 2


title: 031108MS-4; Heart tissue from untreated B6C3F1 male mouse

description: replicate 1


title: dxo1-2_RNAseq_rep2

status: Public on Feb 08 2019

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

description: Illumina HiSeq; strand specific

data_processing:
RNA-seq: mapping with hisat2
RNA-seq: expression estimation with HTseq-count and DESeq2
miRNA-seq: quality filtering and trimming, adapter removal
miRNA-seq: mapping with bowtie
miRNA-seq: expression estimation with HTseq-count and DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: bigwig files were generated using bedtools genomecov and bedGraphToBigWig; Scores represent reads normalized to 1e7 reads
Supplementary_files_format_and_content: miRNA-seq: bigwig files were generated using bedtools genomecov and bedGraphToBigWig; Scores represent reads normalized to 1e7 reads

organism: Arabidopsis thaliana

growth_protocol: Seeds were stratified for 2 days at 4ºC and grown on soil under a 16 h light/8 h dark (long-day) conditions.

extract_protocol:
trizol
Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant rRNA Removal (Plant Leaf)
Total plant RNA was isolated from 3-week-old plants grown using Trizol reagent (Sigma) according to manufacturer’s instructions.

value: 21 day old seedlings


title: dxo1-2_RNAseq_rep1

description: Illumina HiSeq; strand specific


title: dxo1-2_RNAseq_rep3

description: Illumina HiSeq; strand specific


title: GBM3565 CRISPRi day 21

value: amplified


title: 031108MS-17; Heart tissue from untreated C3H male mouse

description: replicate 4


title: 031108MS-9; Heart tissue from untreated B6C3F1 male mouse

description: replicate 5


title: Liver-881.0 mg/kg-2

status: Public on Oct 23 2018

hyb_protocol: Labeled aRNA was fragmented and subsequently hybridized to the Affymetrix Rat Genome 230 2.0 Array (Cat #: 900505; 31,099 probe sets) using an Affymetrix GeneChip® Hybridization Oven 645.

scan_protocol: After washing and staining, arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G, and the raw microarray data (.CEL files) were acquired using Affymetrix GeneChip® Command Console® Software.

data_processing: Probe set intensities from raw microarray data (CEL files from Affymetrix Rat Genome 230 2.0 Arrays) were normalized by applying the Robust Multi-array Average (RMA) algorithm from the genomics analysis tool, GeneSpring GX 12.6 (Agilent Technology, Foster City, CA).

label: Biotin

organism: Rattus norvegicus

source_name: Liver-881.0 mg/kg

label_protocol: Total RNA (100 ng), isolated from each liver sample, was used to synthesize single-stranded DNA, which was subsequently converted into a double-stranded complementary DNA (cDNA) template for transcription. An in vitro transcription (IVT) reaction, which incorporates biotinylated ribonucleotide analogs, then was used to create labeled amplified RNA (aRNA).

extract_protocol: Three pieces (3-mm cubes) of left liver lobe were dissected and flash frozen. The frozen liver tissues were submerged in 10 volumes of prechilled RNAlater®-ICE (Life Technologies, Carlsbad, CA) and stored at −20°C ± 10°C for a minimum of 16 hours. The tissues were removed from the RNAlater®-ICE and weighed. Each liver tissue sample, weighing between 21 and 30 mg, was added to lysis buffer and homogenized using plastic disposable pestles (Fisher Scientific, Pittsburgh, PA). Following homogenization, samples were stored at −70°C ± 10°C until RNA was isolated. Samples were thawed and centrifuged. RNA was extracted from the supernatant, subjected to DNase digestion, and isolated using the Qiagen RNeasy Mini Kit (Cat #: 74104; Qiagen, Valencia, CA).

treatment_protocol: Sprague Dawley SD rats were assigned to one of five dose groups, each containing three rats. The rats in each dose group then were administered TPHP by gavage in corn oil at a dose level of 0, 55, 110, 220, 441, or 881 mg/kg body weight. These doses correspond to molar equivalencies of 0, 0.169, 0.338, 0.675, 1.35, and 2.7 mmol/kg. Dosing of the test article occurred on 4 consecutive days.

value: Harlan Sprague-Dawley

value: Male

tag: chemical

value: Triphenyl phosphate

tag: vehicle

value: Corn oil

tag: dose

tag: route

value: Oral Gavage

tag: number of doses

value: Liver


title: Liver-881.0 mg/kg-3

tag: Sex

tag: tissue


title: Liver-55.0 mg/kg-2

source_name: Liver-55.0 mg/kg


title: Liver-55.0 mg/kg-3


title: Liver-55.0 mg/kg-1


title: Liver-881.0 mg/kg-1


title: Liver-440.0 mg/kg-3

source_name: Liver-440.0 mg/kg


title: Liver-220.0 mg/kg-1

source_name: Liver-220.0 mg/kg


title: Liver-110.0 mg/kg-3

source_name: Liver-110.0 mg/kg


title: Liver-220.0 mg/kg-2


title: Liver-110.0 mg/kg-2


title: Liver-440.0 mg/kg-1


title: Liver-0.0 mg/kg-4

source_name: Liver-0.0 mg/kg

value: 0.0 mg/kg


title: Liver-440.0 mg/kg-2


title: Liver-110.0 mg/kg-1


title: 031108MS-23; Heart tissue from untreated C57BI/6 male mouse

description: replicate 2

tag: gender

value: male

tag: age

value: 9-10 weeks

value: heart apical tissue


title: Liver-0.0 mg/kg-3


title: Rats-Kidney-Group_3-10_mg/kg_PPH-215

status: Public on Oct 15 2018

hyb_protocol: Amplified RNA (aRNA) was fragmented and hybridized to Affymetrix Rat Genome 230 2.0 Array.

scan_protocol: Each array was scanned using an Affymetrix GeneChip Scanner, model 3000 7G to generate microarray image data and raw expression level data files.

data_processing: The raw microarray data (.CEL files) was normalized by applying the Robust Multi-array Average (RMA) algorithm from the genomics analysis tool, GeneSpring GX 12.6 (Agilent Technology,Foster City,CA). Normalized data were examined by visual inspection using a Principal Component Analysis (PCA) plot and standard quality control metrics describing the technical accuracy of the sample processing.

source_name: PPH_Group 3:  10 mg/kg

label_protocol: Standard Affymetrix Procedures

extract_protocol: At termination, within 5 minutes subsequent to blood collection, liver and kidneys were removed.RNA was isolated from tissue samples preservered in RNAlater using the Qiagen Rneasy Mini Kit (Qiagen Inc.,Valencia, CA) with a deoxyribonucleic acid (DNA) digestion step. Concentration and purity was determined from absorbance readings taken at 260 and 280 nm using a NanoDrop ND-1000 Specrophotometer (NanoDrop Technolgies, Wilmington, DE)

treatment_protocol: At each of six dosages for MCHM,crude MCHM and PPH together with vehicle control (MCHM,crude MCHM, PPH 0 mg/kg body weight; corn oil), 6-8 week old,male Harlan Sprague-Dawley rats received the test article via gavage on each of 5 consecutive days. Dosing was carried out in the morning with completion by approximately noon each day.

value: 6-8 weeks

value: PPH

value: Group 3: 10 mg/kg

value: Kidney


title: Rats-Kidney-Group_6-1000_mg/kg_PPH-234

source_name: PPH_Group 6:  1000 mg/kg

value: Group 6: 1000 mg/kg


title: Rats-Kidney-Group_2-1_mg/kg_PPH-214

source_name: PPH_Group 2:  1 mg/kg

value: Group 2: 1 mg/kg


title: Liver-0.0 mg/kg-2


title: Liver-0.0 mg/kg-1


title: Rats-Kidney-Group_4-100_mg/kg_PPH-223

source_name: PPH_Group 4:  100 mg/kg

value: Group 4: 100 mg/kg


title: Liver-220.0 mg/kg-3

value: Harlan Sprague-Dawley


title: Rats-Kidney-Group_6-1000_mg/kg_PPH-233

value: Male


title: Rats-Kidney-Group_4-100_mg/kg_PPH-221


title: Rats-Kidney-Group_3-10_mg/kg_PPH-217


title: Rats-Kidney-Group_5-500_mg/kg_PPH-232

source_name: PPH_Group 5:  500 mg/kg

value: Group 5: 500 mg/kg


title: Rats-Kidney-Group_1-0_mg/kg_PPH-208

source_name: PPH_Group 1:  0 mg/kg

value: Group 1: 0 mg/kg


title: Rats-Kidney-Group_6-1000_mg/kg_PPH-236

value: Oral Gavage


title: Rats-Kidney-Group_2-1_mg/kg_PPH-210


title: Rats-Kidney-Group_1-0_mg/kg_PPH-206


title: Rats-Kidney-Group_5-500_mg/kg_PPH-230


title: Rats-Kidney-Group_1-0_mg/kg_PPH-205


title: Rats-Kidney-Group_3-10_mg/kg_PPH-218


title: Rats-Kidney-Group_3-10_mg/kg_PPH-219


title: Rats-Kidney-Group_4-100_mg/kg_PPH-225


title: Rats-Kidney-Group_2-1_mg/kg_PPH-212


title: Rats-Kidney-Group_4-100_mg/kg_PPH-222


title: Rats-Kidney-Group_2-1_mg/kg_PPH-213


title: Rats-Kidney-Group_1-0_mg/kg_PPH-202


title: Rats-Liver-Group_6-1000_mg/kg_PPH-233

value: Liver


title: Rats-Kidney-Group_1-0_mg/kg_PPH-203


title: Rats-Kidney-Group_6-1000_mg/kg_PPH-237


title: Rats-Kidney-Group_5-500_mg/kg_PPH-229


title: Rats-Liver-Group_3-10_mg/kg_PPH-216


title: Rats-Liver-Group_5-500_mg/kg_PPH-232


title: Rats-Liver-Group_4-100_mg/kg_PPH-221


title: Rats-Liver-Group_5-500_mg/kg_PPH-231


title: Rats-Liver-Group_2-1_mg/kg_PPH-210


title: Rats-Liver-Group_2-1_mg/kg_PPH-214


title: Rats-Liver-Group_1-0_mg/kg_PPH-208


title: Rats-Liver-Group_4-100_mg/kg_PPH-223


title: Rats-Liver-Group_6-1000_mg/kg_PPH-236


title: Rats-Liver-Group_3-10_mg/kg_PPH-217


title: Rats-Liver-Group_3-10_mg/kg_PPH-219


title: Rats-Liver-Group_1-0_mg/kg_PPH-203


title: Rats-Liver-Group_6-1000_mg/kg_PPH-235


title: Rats-Liver-Group_1-0_mg/kg_PPH-206


title: Rats-Liver-Group_3-10_mg/kg_PPH-218


title: Rats-Liver-Group_6-1000_mg/kg_PPH-237


title: Rats-Liver-Group_5-500_mg/kg_PPH-230


title: Rats-Kidney-Group_4-10_mg/kg_Crude_MCHM-126

source_name: Crude MCHM_Group 4:  10 mg/kg

value: Crude MCHM

value: Group 4: 10 mg/kg


title: Rats-Kidney-Group_3-1_mg/kg_Crude_MCHM-120

source_name: Crude MCHM_Group 3:  1 mg/kg

value: Group 3: 1 mg/kg


title: Liver-0.0 mg/kg-5

value: Triphenyl phosphate

value: Corn oil

value: 0.0 mg/kg


title: Rats-Liver-Group_2-1_mg/kg_PPH-212

value: 6-8 weeks

value: PPH


title: Rats-Liver-Group_1-0_mg/kg_PPH-205


title: Rats-Liver-Group_4-100_mg/kg_PPH-222


title: Rats-Liver-Group_2-1_mg/kg_PPH-213


title: Rats-Kidney-Group_7-500_mg/kg_Crude_MCHM-139

source_name: Crude MCHM_Group 7:  500 mg/kg

value: Group 7: 500 mg/kg

value: Kidney


title: Rats-Liver-Group_1-0_mg/kg_PPH-202


title: Rats-Kidney-Group_6-300_mg/kg_Crude_MCHM-133

source_name: Crude MCHM_Group 6:  300 mg/kg

value: Group 6: 300 mg/kg


title: Rats-Kidney-Group_2-0.1_mg/kg_Crude_MCHM-110

source_name: Crude MCHM_Group 2:  0.1 mg/kg

value: Harlan Sprague-Dawley

value: Group 2: 0.1 mg/kg


title: Rats-Kidney-Group_4-10_mg/kg_Crude_MCHM-123

value: Male


title: Rats-Kidney-Group_5-100_mg/kg_Crude_MCHM-129

source_name: Crude MCHM_Group 5:  100 mg/kg

value: Group 5: 100 mg/kg


title: Rats-Liver-Group_6-300_mg/kg_Crude_MCHM-137

value: Oral Gavage


title: Rats-Kidney-Group_2-0.1_mg/kg_Crude_MCHM-114


title: Rats-Kidney-Group_6-300_mg/kg_Crude_MCHM-134


title: Rats-Kidney-Group_1-0_mg/kg_Crude_MCHM-104

source_name: Crude MCHM_Group 1:  0 mg/kg

value: Group 1: 0 mg/kg


title: Rats-Liver-Group_4-10_mg/kg_Crude_MCHM-126

value: Crude MCHM

value: Liver


title: Rats-Liver-Group_5-100_mg/kg_Crude_MCHM-132


title: Rats-Liver-Group_6-300_mg/kg_Crude_MCHM-135


title: Rats-Kidney-Group_1-0_mg/kg_Crude_MCHM-106


title: Rats-Liver-Group_5-500_mg/kg_PPH-229

value: Group 5: 500 mg/kg


title: Rats-Liver-Group_7-500_mg/kg_Crude_MCHM-139


title: Rats-Liver-Group_4-100_mg/kg_PPH-225

value: Group 4: 100 mg/kg


title: Rats-Kidney-Group_6-300_mg/kg_Crude_MCHM-135


title: Rats-Kidney-Group_3-1_mg/kg_Crude_MCHM-119

value: Group 3: 1 mg/kg


title: Rats-Kidney-Group_7-500_mg/kg_Crude_MCHM-143


title: Rats-Kidney-Group_7-500_mg/kg_Crude_MCHM-144


title: Rats-Liver-Group_3-1_mg/kg_Crude_MCHM-119


title: Rats-Liver-Group_4-10_mg/kg_Crude_MCHM-123

value: Group 4: 10 mg/kg


title: Rats-Liver-Group_1-0_mg/kg_Crude_MCHM-104

value: 6-8 weeks


title: Rats-Kidney-Group_1-0_mg/kg_Crude_MCHM-105


title: Rats-Liver-Group_6-300_mg/kg_Crude_MCHM-134


title: Rats-Liver-Group_3-1_mg/kg_Crude_MCHM-120


title: Rats-Liver-Group_5-100_mg/kg_Crude_MCHM-129


title: Rats-Liver-Group_5-100_mg/kg_Crude_MCHM-131


title: Rats-Liver-Group_2-0.1_mg/kg_Crude_MCHM-114


title: Rats-Liver-Group_3-1_mg/kg_Crude_MCHM-117


title: Rats-Kidney-Group_7-500_mg/kg_MCHM-42

source_name: MCHM_Group 7:  500 mg/kg

value: MCHM


title: Rats-Kidney-Group_5-100_mg/kg_Crude_MCHM-132


title: Rats-Liver-Group_1-0_mg/kg_Crude_MCHM-106


title: Rats-Liver-Group_1-0_mg/kg_Crude_MCHM-108


title: Rats-Liver-Group_4-10_mg/kg_Crude_MCHM-125


title: Rats-Liver-Group_1-0_mg/kg_Crude_MCHM-105


title: Rats-Liver-Group_4-10_mg/kg_Crude_MCHM-122


title: Rats-Kidney-Group_6-300_mg/kg_MCHM-33

source_name: MCHM_Group 6:  300 mg/kg


title: Rats-Liver-Group_7-500_mg/kg_Crude_MCHM-143

value: Group 7: 500 mg/kg


title: Rats-Liver-Group_6-300_mg/kg_Crude_MCHM-138


title: Rats-Liver-Group_2-0.1_mg/kg_Crude_MCHM-110


title: Rats-Liver-Group_3-1_mg/kg_Crude_MCHM-116


title: Rats-Kidney-Group_3-1_mg/kg_MCHM-16

source_name: MCHM_Group 3:  1 mg/kg

value: Kidney


title: Rats-Kidney-Group_6-300_mg/kg_MCHM-36

value: Group 6: 300 mg/kg


title: Rats-Kidney-Group_2-0.1_mg/kg_MCHM-13

source_name: MCHM_Group 2:  0.1 mg/kg

value: Harlan Sprague-Dawley


title: Rats-Kidney-Group_7-500_mg/kg_MCHM-43


title: Rats-Liver-Group_5-100_mg/kg_Crude_MCHM-130


title: Rats-Kidney-Group_5-100_mg/kg_MCHM-29

source_name: MCHM_Group 5:  100 mg/kg


title: Rats-Liver-Group_2-0.1_mg/kg_Crude_MCHM-113

value: Group 2: 0.1 mg/kg


title: Rats-Kidney-Group_4-10_mg/kg_MCHM-23

source_name: MCHM_Group 4:  10 mg/kg

value: Male


title: Rats-Kidney-Group_3-1_mg/kg_MCHM-15


title: Rats-Kidney-Group_5-100_mg/kg_MCHM-27

value: Group 5: 100 mg/kg


title: Rats-Liver-Group_7-500_mg/kg_Crude_MCHM-140

value: Oral Gavage


title: Rats-Kidney-Group_1-0_mg/kg_MCHM-3

source_name: MCHM_Group 1:  0 mg/kg

value: Group 1: 0 mg/kg


title: Rats-Kidney-Group_6-300_mg/kg_MCHM-35


title: Rats-Kidney-Group_1-0_mg/kg_MCHM-8


title: Rats-Kidney-Group_5-100_mg/kg_MCHM-28


title: Rats-Kidney-Group_2-0.1_mg/kg_MCHM-10


title: Rats-Kidney-Group_3-1_mg/kg_MCHM-20


title: Rats-Kidney-Group_4-10_mg/kg_MCHM-26


title: Rats-Kidney-Group_1-0_mg/kg_MCHM-6


title: Rats-Kidney-Group_1-0_mg/kg_MCHM-5


title: Rats-Kidney-Group_4-10_mg/kg_MCHM-25


title: Rats-Kidney-Group_7-500_mg/kg_MCHM-41


title: Rats-Kidney-Group_6-300_mg/kg_MCHM-37


title: Rats-Kidney-Group_2-0.1_mg/kg_MCHM-14


title: Rats-Kidney-Group_2-0.1_mg/kg_MCHM-12


title: Rats-Kidney-Group_4-10_mg/kg_MCHM-22


title: Rats-Kidney-Group_3-1_mg/kg_MCHM-19


title: Rats-Liver-Group_7-500_mg/kg_MCHM-42


title: Rats-Liver-Group_3-1_mg/kg_MCHM-16


title: Rats-Liver-Group_2-0.1_mg/kg_MCHM-13


title: Rats-Liver-Group_5-100_mg/kg_MCHM-27


title: Rats-Liver-Group_1-0_mg/kg_MCHM-7


title: Rats-Liver-Group_6-300_mg/kg_MCHM-33


title: Rats-Liver-Group_4-10_mg/kg_MCHM-23


title: Rats-Kidney-Group_5-100_mg/kg_MCHM-31


title: Rats-Liver-Group_5-100_mg/kg_MCHM-29


title: Rats-Liver-Group_4-10_mg/kg_MCHM-25


title: Rats-Liver-Group_6-300_mg/kg_MCHM-36


title: Rats-Liver-Group_7-500_mg/kg_MCHM-43


title: Rats-Liver-Group_1-0_mg/kg_MCHM-3


title: Rats-Liver-Group_7-500_mg/kg_MCHM-41


title: Rats-Liver-Group_2-0.1_mg/kg_MCHM-10


title: Rats-Liver-Group_6-300_mg/kg_MCHM-35


title: Rats-Liver-Group_6-300_mg/kg_MCHM-37


title: Rats-Liver-Group_4-10_mg/kg_MCHM-26


title: Rats-Liver-Group_5-100_mg/kg_MCHM-31


title: Rats-Liver-Group_1-0_mg/kg_MCHM-6


title: Rats-Liver-Group_3-1_mg/kg_MCHM-20


title: Rats-Liver-Group_1-0_mg/kg_MCHM-8


title: Rats-Kidney-Group_7-500_mg/kg_MCHM-40


title: Rats-Liver-Group_3-1_mg/kg_MCHM-19


title: Rats-Liver-Group_3-1_mg/kg_MCHM-15


title: Rats-Liver-Group_5-100_mg/kg_MCHM-28


title: Rats-Liver-Group_7-500_mg/kg_MCHM-40


title: Rats-Liver-Group_1-0_mg/kg_MCHM-4


title: Rats-Liver-Group_4-10_mg/kg_MCHM-22


title: Rats-Liver-Group_2-0.1_mg/kg_MCHM-12


title: Rats-Liver-Group_7-500_mg/kg_Crude_MCHM-144

value: Crude MCHM


title: Rats-Liver-Group_2-0.1_mg/kg_MCHM-14

value: Liver


title: Rats-Kidney-Group_1-0_mg/kg_MCHM-4


title: 72 hpf_0ppbPb_Rep2

status: Public on Jul 20 2018

description: Gene expression 72 hpf following embryonic exposure (1-72 hpf)

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

scan_protocol: Array slides were scanned on a GenePix 4000B microarray scanner with one-color scan setting at 5 microns.

data_processing: Array images were extracted with NimbleScan software (Roche NimbleGen, Madison, WI) in which fluorescence signal intensity values were normalized using quantile normalization and gene calls were generated using the Robust Multichip Average (RMA) algorithm following manufacturer recommendations.

source_name: 72 hpf, 0 ppb, replicate 2

label_protocol: cDNA was labeled using the NimbleGen One-Color DNA Labeling Kit, following the manufacturer's instructions (Roche NimbleGen, Madison, WI). Quality (Yield and specificity) of Cy3 labeled cRNA was measured on Drop® ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE).

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

extract_protocol: Total RNA was isolated using an RNeasy Mini Kit (Qiagen Sciences, Maryland, USA) following established protocols. RNA concentrations were measured by using a NanoDrop 1000 spectrophotometer and the quality was verified by absorbance ratio 260/280 nm. Total RNA was converted to cDNA following established laboratory protocols.

treatment_protocol: Zebrafish embryos/larvae were exposed to 0 or 100 ppb lead acetate from approximately 1 hpf through 72 hpf or 120 hpf. 50 embryos were pooled per sample (considered as one biological replicate). Three biological replicates were completed (n=3) at each time point. Larvae were homogenized in Trizol (Life Technolgies, Carlsbad, CA) and flash frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: 72 hpf

value: whole larvae


title: 120 hpf_0Gy_Rep2

description: Gene expression 120 hpf following irradiation at 26 hpf

source_name: 120 hpf, 0 Gy, replicate 2

treatment_protocol: Zebrafish embryos were irradiated in a Co-60 irradiator with a dose of 5 Gy at 26 hpf. Embryos were placed back in the incubator until 120 hpf. 50 embryos were pooled per sample (considered as one biological replicate). Three biological replicates were completed (n=3) . Larvae were homogenized in Trizol (Life Technolgies, Carlsbad, CA) and flash frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: 120 hpf


title: 120 hpf_0ppbPb_Rep3

description: Gene expression 120 hpf following developmental exposure (1-120 hpf)

source_name: 120 hpf, 0 ppb, replicate 3


title: 120 hpf_0Gy_Rep3

source_name: 120 hpf, 0 Gy, replicate 3


title: 120 hpf_100ppbPb_Rep2

source_name: 120 hpf, 100 ppb, replicate 2


title: 120 hpf_5Gy_Rep3

source_name: 120 hpf, 5 Gy, replicate 3


title: 120 hpf_0Gy_Rep1

source_name: 120 hpf, 0 Gy, replicate 1


title: 120 hpf_5Gy_Rep1

source_name: 120 hpf, 5 Gy, replicate 1


title: 120 hpf_5Gy_Rep2

source_name: 120 hpf, 5 Gy, replicate 2


title: 120 hpf_0ppbPb_Rep1

source_name: 120 hpf, 0 ppb, replicate 1


title: 120 hpf_100ppbPb_Rep1

source_name: 120 hpf, 100 ppb, replicate 1


title: 72 hpf_0ppbPb_Rep3

source_name: 72 hpf, 0 ppb, replicate 3


title: 72 hpf_0ppbPb_Rep1

source_name: 72 hpf, 0 ppb, replicate 1


title: 72 hpf_0.3ppbATZ_Rep3

source_name: 72 hpf, 0.3 ppb, replicate 3

treatment_protocol: Zebrafish embryos were exposed to 0, 0.3, 3, or 30 ppb atrazine from approximately 1 hpf through 72 hpf. 50 embryos were pooled per sample (considered as one biological replicate). Three biological replicates completed (n=3). Larvae were homogenized in Trizol (Life Technolgies, Carlsbad, CA) and flash frozen in liquid nitrogen and stored at -80°C until RNA extraction.


title: 72 hpf_100ppbPb_Rep1

source_name: 72 hpf, 100 ppb, replicate 1


title: 72 hpf_100ppbPb_Rep3

source_name: 72 hpf, 100 ppb, replicate 3


title: 120 hpf_100ppbPb_Rep3

source_name: 120 hpf, 100 ppb, replicate 3


title: 120 hpf_0ppbPb_Rep2

source_name: 120 hpf, 0 ppb, replicate 2


title: 72 hpf_0ppbATZ_Rep3


title: 72 hpf_30ppbATZ_Rep1

source_name: 72 hpf, 30 ppb, replicate 1


title: 72 hpf_0ppbATZ_Rep2

source_name: 72 hpf, 0 ppb, replicate 2


title: 72 hpf_3ppbATZ_Rep1

source_name: 72 hpf, 3 ppb, replicate 1


title: 72 hpf_30ppbATZ_Rep3

source_name: 72 hpf, 30 ppb, replicate 3


title: 72 hpf_30ppbATZ_Rep2

source_name: 72 hpf, 30 ppb, replicate 2


title: 72 hpf_3ppbATZ_Rep2

source_name: 72 hpf, 3 ppb, replicate 2


title: 72 hpf_100ppbPb_Rep2

source_name: 72 hpf, 100 ppb, replicate 2


title: 72 hpf_0.3ppbATZ_Rep2

source_name: 72 hpf, 0.3 ppb, replicate 2


title: 72 hpf_3ppbATZ_Rep3

source_name: 72 hpf, 3 ppb, replicate 3


title: 5002_C1D1-2

status: Public on Jun 05 2018

city: Bloomington

first: Kenneth

last: Nephew

institute: Indiana University

data_processing:
CASAVA VERSION 1.8.2
Sequenced reads were trimmed for adaptor sequence and low-quality using Trimmomatic version 0.32
Trimmed reads were mapped to hg19 using Tophat2 version 2.0.10 with the parameters -p 8 --b2-very-sensitive --read-edit-dist 2 --max-multihits 100 --library-type fr-secondstrand
Custom perl scripts were used to count mapped reads using Gencode v19 as the reference annotation
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: human ovarian cancer tissue

extract_protocol:
flash frozen on dry ice, and RNA was harvested using QIAGEN AllPrep DNA/RNA/Protein kit. Sequencing libraries were constructed by 0.5-1 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: organ

value: ovary

value: human ovarian cancer tissue

tag: treatment

value: pre-guadecitabine


title: 5002_C1D1-1


title: 5001_C1D1


title: 5105_C1D1-1


title: 5105_C1D1-2


title: 2517_C1D1-2


title: 2516_C1D1-2


title: 2515-C1D1-1


title: 2516_C1D1-1


title: 2515-C2D8-1

value: post-guadecitabine


title: 2513_C1D1-1


title: 2512_C1D1-2


title: 2513_C1D1-2


title: 2512_C1D1-1


title: Brain_female_0ppb_rep3

status: Public on Jul 18 2018

description: Gene expression in 5-6 months aged female brain after a developmental exposure to 0ppb atrazine

scan_protocol: Array slides were scanned on Nimblegen MS 200 microarray scanner with one-color scan setting (Scan region, 61 x 21.6 mm; Scan resolution, 2um; Tiff file dyamic range, 20 bit; Dye channel, Green; Green PMT gain, 100%).

source_name: Brain, 5-6months old female zebrafish, 0ppb atrazine, replicate 3

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

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

extract_protocol: Zebrafish brains dissected at 5-6 months of age were homogenized in Trizol Reagent (Life Technologies, Carlsbad, CA) and stored at -80ºC until RNA isolation. Total RNA was extracted according to established protocols as descrived in Peterson and Freeman (2009) and then purified using the RNeay Mini Kit (Qiagen, Valencia, CA) following manufacturer’s recommendation. Quality and quantity of purified RNA samples were checked on the NanoDrop® ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE).

treatment_protocol: Zebrafish embryos at <2 hours post fertilization (hpf) were developmentally treated with 0, 0.3, 3, or 30 ppb atrazine until 72 hpf. Following the atrazine exposure, the embryos were washed and transferred to clean aquaria water with no atrazine treatment. Fish were grown until 5-6 months of age at which brains were subjected to RNA extraction and then cDNA synthesis for further microarray analysis.

value: 5-6 months old

value: female

value: brain


title: Brain_female_30ppb_rep2

description: Gene expression in 5-6 months aged female brain after a developmental exposure to 30ppb atrazine

source_name: Brain, 5-6months old female zebrafish, 30ppb atrazine, replicate 2


title: 2511_C1D1-2


title: 2517_C1D1-1


title: Brain_female_0.3ppb_rep2

description: Gene expression in 5-6 months aged female brain after a developmental exposure to 0.3ppb atrazine

source_name: Brain, 5-6months old female zebrafish, 0.3ppb atrazine, replicate 2


title: Brain_female_3ppb_rep2

description: Gene expression in 5-6 months aged female brain after a developmental exposure to 3ppb atrazine

source_name: Brain, 5-6months old female zebrafish, 3ppb atrazine, replicate 2


title: 2510_C1D1-1


title: Brain_female_0.3ppb_rep1

source_name: Brain, 5-6months old female zebrafish, 0.3ppb atrazine, replicate 1


title: Brain_female_30ppb_rep1

source_name: Brain, 5-6months old female zebrafish, 30ppb atrazine, replicate 1


title: 2511_C1D1-1


title: Brain_female_3ppb_rep1

source_name: Brain, 5-6months old female zebrafish, 3ppb atrazine, replicate 1


title: 2510_C1D1-2


title: 2509_C1D1-2


title: 2501_C1D1-2


title: 2504_C1D1-2


title: 2508_C1D1-1


title: 2509_C1D1-1


title: 2508_C1D1-2


title: Brain_female_0ppb_rep1

source_name: Brain, 5-6months old female zebrafish, 0ppb atrazine, replicate 1


title: 2506_C1D1-2


title: 2506_C1D1-1


title: Brain_female_30ppb_rep3

source_name: Brain, 5-6months old female zebrafish, 30ppb atrazine, replicate 3


title: Brain_female_3ppb_rep3

source_name: Brain, 5-6months old female zebrafish, 3ppb atrazine, replicate 3


title: 2504_C1D1-1


title: Brain_female_0ppb_rep2

source_name: Brain, 5-6months old female zebrafish, 0ppb atrazine, replicate 2


title: 2501_C1D1-1


title: 2302_C2D8-1


title: 2302_C1D1-2


title: 2301_C2D8-2


title: 2302_C1D1-1


title: Brain_female_0.3ppb_rep3

source_name: Brain, 5-6months old female zebrafish, 0.3ppb atrazine, replicate 3


title: 2301_C1D1-2


title: 2301_C2D8-1


title: 2302_C2D8-2


title: 17501_C1D1-2


title: 2301_C1D1-1


title: 72 hpf_0.3ppbATZ_Rep1

source_name: 72 hpf, 0.3 ppb, replicate 1


title: 1603_C2D8-1


title: 72 hpf_0ppbATZ_Rep1

source_name: 72 hpf, 0 ppb, replicate 1


title: 1603_C1D1-2


title: 1403_C1D1-2


title: 1401_C1D1-2


title: 1405_C1D1-1


title: 1603_C1D1-1


title: 1603_C2D8-2


title: 17501_C1D1-1


title: 1405_C1D1-2


title: 1104_C1D1-1


title: 1109_C1D1-1


title: 1401_C1D1-1


title: 1403_C1D1-1


title: 1102_C1D1-2


title: 1001_C1D1-2


title: 1109_C1D1-2


title: 1102_C1D1-1


title: 0903_C2D8-2


title: 1001_C1D1-1


title: 0903_C1D1-1


title: 0903_C1D1-2


title: 0506_C2D8-2


title: 0903_C2D8-1


title: 0802_C1D1-2


title: 0801_C1D1-1


title: 0801_C1D1-2


title: 0802_C1D1-1


title: 0506_C1D1-1


title: 0304_C1D1-1


title: 0309_C2D8-1


title: 0207_C2D8-1


title: 0309_C1D1-1


title: 0305_C1D1-1


title: 0305_C1D1-2


title: 0309_C1D1-2


title: 0303_C1D1-1


title: 0309_C2D8-2


title: 0506_C1D1-2


title: 0304_C1D1-2


title: 0206_C1D1-1


title: 0207_C2D8-2


title: 0204_C1D1-2


title: 0204_C1D1-1


title: 0207_C1D1-2


title: 0205_C1D1-1


title: 0203_C1D1-1


title: 0203_C2D8-2


title: 0205_C1D1-2


title: 0506_C2D8-1


title: NT_rep3

status: Public on Feb 13 2018

data_processing:
RNA-sequencing data were analyzed by Kallisto v0.43.0.
Human transcript definitions (Ensembl release 84) were used for transcriptome quantification.
Kallisto was run in strand specific mode with the option --fr-stranded.
The tool Tximport was used to summarize transcript-level estimates for gene level analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include transcript ids, length, effective length, estiimated counts, and Transcript Per Million (TPM) values for each sample.

source_name: SKOV3 ovarian cancer cell line

growth_protocol: SKOV3 cells were cultured in RPMI1640 media with FBS and penicillin/streptomycin. Cells were confirmed to be mycoplasma negative.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) as per manufacturer’s protocol.
Libraries were made using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero Gold.

treatment_protocol: SKOV3 cells were transfected with 50nM smartpool siRNA targeting at human DNM3OS and pool of nontargeting control from Dharmacon using lipofectamine 2000 (Thermo Fisher Scientific) following manufacturer’s protocol.

tag: genotype/variation

value: Non-targeting control

tag: cell line

value: ovarian cancer cell line


title: 0203_C1D1-2


title: NT_rep2


title: 0203_C2D8-1


title: 0303_C1D1-2


title: DNM3OS_KD_rep3

value: DNM3OS knockdown


title: NT_rep1


title: 0206_C1D1-2


title: 0207_C1D1-1


title: DNM3OS_KD_rep1


title: DNM3OS_KD_rep2


title: Col0_RNAseq_rep1

status: Public on Jan 24 2018

description: Illumina HiSeq; strand specific

data_processing:
mapping with hisat2
expression estimation with HTseq-count and DESeq2
bigwig files were generated using bedtools genomecov and bedGraphToBigWig; Scores represent reads normalized to 1e7 reads
Genome_build: TAIR10

source_name: 21 day old seedlings

extract_protocol:
trizol
Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant rRNA Removal (Plant Leaf)

tag: genotype

value: wild type

tag: media

value: grown on soil


title: Col0_RNAseq_rep3

description: Illumina HiSeq; strand specific


title: xrn3-8_RNAseq_rep2

description: Illumina HiSeq; strand specific


title: xrn3-8_RNAseq_rep1

description: Illumina HiSeq; strand specific


title: Col0_RNAseq_rep2

description: Illumina HiSeq; strand specific


title: xrn3-8_RNAseq_rep3

description: Illumina HiSeq; strand specific


title: Brain_12months_female_100ppb_rep3

status: Public on Nov 30 2017

description: Gene expression in 12 months aged brain after a developmental exposure to 100ppb lead

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

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

source_name: Brain, 12months old female zebrafish, 100ppb lead, replicate 3

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

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

tag: strain

value: AB

value: 12 months old


title: Brain_12months_female_100ppb_rep1

source_name: Brain, 12months old female zebrafish, 100ppb lead, replicate 1


title: Brain_12months_female_0ppb_rep1

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

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


title: Brain_12months_male_0ppb_rep3

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

value: male


title: fibroblasts_4OHT

status: Public on Sep 06 2017

data_processing:
RNA-sequencing data were analyzed by Kallisto v0.43.0 (29).
Murine transcript definitions (Ensembl release 85) were used for transcriptome quantification.
Kallisto was run in strand specific mode with the option --rf-stranded.
The tool Tximport was used to summarize transcript-level estimates for gene level analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include transcript ids, length, effective length, estiimated counts, and Transcript Per Million (TPM) values for each sample.

source_name: fibroblasts, Mdm2 deleted

growth_protocol: Tumors (T-cell lymphoma and sarcoma) that developed in Mdm2fl/flp53-/- mice were harvested and placed in short-term culture. Mdm2fl/flp53-/- lymphoma was grown in RPMI 1640 with 10% FBS, 1% L-glutamine, and penicillin/streptomycin. Mdm2fl/flp53-/- sarcoma was grown in DMEM with 10% FBS, 1% L-glutamine, penicillin/streptomycin, and MEM non-essential amino acids. Adult mouse fibroblasts were isolated from ear punches of Mdm2fl/flp53-/- mice and expanded in culture using the same media in which the sarcoma was grown. Cells were confirmed to be negative for mycoplasma.

treatment_protocol: Malignant cells and fibroblasts were infected with a bicistronic retrovirus expressing CreERT2 and GFP or GFP alone. To activate CreERT2, Mdm2fl/flp53-/- cells received 1mM 4-hydroxytamoxifen (4-OHT) or vehicle control (EtOH) for 6hr (lymphoma) or 48hr (sarcoma and fibroblasts).

tag: cell type

value: p53-null fibroblasts

value: Mdm2 deletion


title: fibroblasts_EtOH

source_name: fibroblasts, Vehicle control

value: control


title: sarcoma_EtOH

source_name: sarcoma, Vehicle control

value: p53-null sarcoma


title: 72 hpf_100ppm_Rep3

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

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

source_name: 72 hpf_100ppm

extract_protocol: Total RNA was isolated using an RNeasy Mini Kit (Qiagen Sciences, Maryland, USA) following established protocols. RNA concentrations were measured by using a NanoDrop 1000 spectrophotometer and the quality was verified by absorbance ratio 260/280 nm.

treatment_protocol: Zebrafish embryos were exposed to 0, 1, 10, or 100 ppm coal dust extract from approximately 1 hpf through 72 hpf. 50 embryos were pooled per sample (considered as one biological replicate). Three biological replicates completed (n=3). Larvae were homogenized in Trizol (Life Technolgies, Carlsbad, CA) and flash frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: Whole larvae

tag: exposed to

value: 100 ppm coal dust extract (1-72 hpf)

value: 72 hpf


title: lymphoma_4OHT

source_name: lymphoma, Mdm2 deleted

value: p53-null T cell lymphoma


title: sarcoma_4OHT

source_name: sarcoma, Mdm2 deleted


title: 72 hpf_1ppm_Rep3

source_name: 72 hpf_1ppm

value: 1 ppm coal dust extract (1-72 hpf)


title: Brain_12months_male_0ppb_rep1

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

value: brain


title: 72 hpf_10ppm_Rep1

source_name: 72 hpf_10ppm

value: 10 ppm coal dust extract (1-72 hpf)


title: 72 hpf_1ppm_Rep1


title: Brain_12months_male_100ppb_rep3

source_name: Brain, 12months old male zebrafish, 100ppb lead, replicate 3


title: Brain_12months_male_100ppb_rep2

source_name: Brain, 12months old male zebrafish, 100ppb lead, replicate 2


title: 72 hpf_100ppm_Rep2


title: 72 hpf_10ppm_Rep3


title: 72 hpf_0ppm_Rep2

source_name: 72 hpf_0ppm

value: 0 ppm coal dust extract (1-72 hpf)


title: Brain_12months_female_0ppb_rep2

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

value: female


title: 72 hpf_0ppm_Rep3

value: wild type


title: 72 hpf_100ppm_Rep1

value: AB


title: Brain_12months_male_0ppb_rep2

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

value: 12 months old


title: 72 hpf_1ppm_Rep2


title: Brain_12months_female_100ppb_rep2

source_name: Brain, 12months old female zebrafish, 100ppb lead, replicate 2


title: 72 hpf_0ppm_Rep1


title: Brain_12months_male_100ppb_rep1

source_name: Brain, 12months old male zebrafish, 100ppb lead, replicate 1

value: male


title: BSseq_RIL495_rep2

status: Public on Mar 29 2017

city: Cambridge

first: Mary

last: Gehring

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Bisulfite-treated genomic DNA
Read length: 40x40, 100x100
Processed data file: RIL495_genotypes.bed

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

source_name: rosette leaves, Col/Cvi RIL495

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

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

treatment_protocol: No treatment.

tag: strain/background

value: Col/Cvi RIL495

tag: generation

value: 3 weeks

value: rosette leaves


title: BSseq_RIL495_rep1

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


title: BSseq_RIL363_rep1

description:
Bisulfite-treated genomic DNA
Read length: 40x40
Processed data file: RIL363_genotypes.bed

source_name: rosette leaves, Col/Cvi RIL363

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

value: Col/Cvi RIL363


title: BSseq_RIL303_rep2

description:
Bisulfite-treated genomic DNA
Read length: 40x40, 100x100, 50x50
Processed data file: RIL303_genotypes.bed

source_name: rosette leaves, Col/Cvi RIL303

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

value: Col/Cvi RIL303


title: BSseq_RIL363_rep2

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


title: 72 hpf_10ppm_Rep2

value: Whole larvae


title: BSseq_RIL258_rep2

description:
Bisulfite-treated genomic DNA
Read length: 40x40
Processed data file: RIL258_genotypes.bed

source_name: rosette leaves, Col/Cvi RIL258

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

value: Col/Cvi RIL258


title: BSseq_RIL258_rep1

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


title: BSseq_RIL303_rep1

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


title: BSseq_RIL332_rep1

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

source_name: rosette leaves, Col/Cvi RIL332

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

value: Col/Cvi RIL332


title: lymphoma_EtOH

source_name: lymphoma, Vehicle control

value: p53-null T cell lymphoma

value: control