title: Male ACE L3

description: Gene expression in pooled livers of adult male zebrafish exposed to low dose (0.5 μg L-1) acetaminophen (ACE), replicate 3.

treatment_protocol:
Pooled livers of adult male zebrafish exposed to low dose (0.5 μg L-1) acetaminophen (ACE), dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: RNA_ileal_tissue_Sample153_rep1

status: Public on Dec 23 2019

type: RNA

city: Los Angeles

first: Alka

last: Potdar

state: CA

address: 110 George Burns Rd

department: Medicine/GI

country: USA

institute: Cedars-Sinai Medical Center

description: Gene expression from RNA from ileal tissue of Sample153_rep1

hyb_protocol: Hybridization was performed in duplicate for each sample. Hybridization to Whole Human Genome 4x44k Microarrays (Agilent) was performed by the Genome Technology Access Center (GTAC) at Washington University – St. Louis.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies). The feature extraction file was exported as a .txt file.

molecule: total RNA

organism: Homo sapiens

label_protocol: Cy5 labeling was performed with the ULST Fluorescent Labeling kit (Kreatech). Technical duplicate hybridizations (HYB-A and HYB-B) were performed for each sample.

extract_protocol: Two fresh, unstained 5-µm FFPE tissue sections on glass microscope slides were obtained. Slides were not baked after cutting. For each sample, the two tissue sections were scraped off of the slides using a clean razor and placed in 1.5 mL Eppendorf tubes. The tubes were briefly centrifuged to place the sample towards the bottoms or sides of the tube. RNA extraction and DNase treatment was performed using the RNeasy FFPE kit (Qiagen) according to the manufacturer’s instructions, using the Xylene protocol for the paraffin removal step and 30 µL RNase-free H2O for the elution step. RNA was initially quantified by NanoDrop. Subsequent total RNA quantification and quality assessment was performed by Bioanalyzer 2100 (Agilent Technologies). Samples were excluded from the study if >20% of the RNA fragments were >200 base pairs in length, as determined with the Bioanalyzer software.

treatment_protocol: Whole-thickness ileal tissue was scraped from the FFPE tissue sections followed by RNA extraction using the RNeasy FFPE kit (Qiagen) according to the manufacturer's instructions.

tag: ^sample

tag: batch

tag: tissue

value: uninvolved small bowel (SB) ileal tissue

tag: gender

value: female

tag: age


title: RNA_ileal_tissue_Sample153_rep2

description: Gene expression from RNA from ileal tissue of Sample153_rep2


title: Male ACE L2

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

country: Canada

institute: McMaster University

description: Gene expression in pooled livers of adult male zebrafish exposed to low dose (0.5 μg L-1) acetaminophen (ACE), replicate 2.

hyb_protocol: 1.65 ug Cy3 labeled cDNA hybridized to a customized Agilent zebrafish single-channel 4 x 44K V2 microarray by the University Health Network Microarray Centre (Toronto, Canada).

scan_protocol: Hybridization results were scanned using an Agilent DNA Micorarray Scanner.

data_processing: Raw array data obtained from the University Health Network Microarray Centre were extracted using Agilent's feature extraction software using background detrending (spatial and multiplicative). Prior to normalization, Cy3 values below 5 were set to 5. The data were then normalized using the non-linear scaling method based on rank invariant probes. After normalization but before statistical analyses, probes not significantly above background in all microarrays were removed.

organism: Danio rerio

source_name: pooled livers

label_protocol: 500 ug total RNA was Cy3 labeled using the Agilent Low Input Quick Amp Labeling kit, following the manufacturer's instructions.

growth_protocol: Adult wild-type zebrafish were purchased from DAP International (Toronto, ON) and housed in aquaria at a density of 4 fish per liter in 1:1 sex ratio. All aquaria were maintained at 28°C, pH 7-8, dissolved oxygen ≥87%, and conductivity at 470 µS in a partially re-circulating system.  Fish were fed twice per day with tropical fish flake food and once per day with live, adult brine shrimp.  Zebrafish were kept on a light cycle of 14h day / 10h night.

extract_protocol: After 6 weeks of exposure, zebrafish were sacrificed, weighed and tissues (GI tract with livers) were placed into RNAlater, topped up to 5-10 mL RNAlater per gram tissue.  Tubes were incubated overnight at 4 °C to allow for tissues to be saturated with RNAlater and all tissues were then stored at -80 °C in RNAlater. Prior to RNA extraction, samples were thawed on ice and livers were stripped from the GI tract in RNAlater. Livers from 10-20 fish per gender liver were pooled to a maximum 100 mg of tissue and kept in RNAlater and on ice until RNA extractions.  Immediately prior to extraction, RNAlater was diluted 50% with molecular water and total RNA was then extracted using100 mg of liver tissue in 1 ml of TRIzol reagent. Tissues were homogenized on ice in TRIzol for 10-30 seconds using an OMNI GLH homogenizer, following the manufacturer’s protocol. The RNA was reconstituted in molecular biology grade water, quantified spectrophotometrically, and absorbance at 260 and 280 nm was used as a measure of relative purity and quantity. The RNA samples were further analyzed for structural integrity using an Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Nano Kit.

value: liver

value: male

tag: treatment group

tag: treatment


title: RNA_ileal_tissue_Sample155_rep2

description: Gene expression from RNA from ileal tissue of Sample155_rep2


title: Male ACE H2

description: Gene expression in pooled livers of adult male zebrafish exposed to high dose (10 μg L-1) acetaminophen (ACE), replicate 2.

treatment_protocol:
Pooled livers of adult male zebrafish exposed to high dose (10 μg L-1) acetaminophen (ACE), dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: RNA_ileal_tissue_Sample152_rep2

description: Gene expression from RNA from ileal tissue of Sample152_rep2


title: Male CBZ C1

description: Gene expression in pooled livers of adult male zebrafish exposed to DMSO below 0.004% (to account for solvent use in experimental tanks) as a CONTROL for the CBZ experiment, replicate 1.

treatment_protocol:
Pooled livers of adult male zebrafish exposed to DMSO below 0.004% (to account for solvent use in experimental tanks) as a CONTROL for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: Male ACE H3

description: Gene expression in pooled livers of adult male zebrafish exposed to high dose (10 μg L-1) acetaminophen (ACE), replicate 3.


title: Male CBZ H2

description: Gene expression in pooled livers of adult male zebrafish exposed to high dose (10 μg L-1) carbamazepine (CBZ), replicate 2.

treatment_protocol:
Pooled livers of adult male zebrafish exposed to high dose (10 μg L-1) carbamazepine (CBZ), dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: RNA_ileal_tissue_Sample152_rep1

description: Gene expression from RNA from ileal tissue of Sample152_rep1


title: Female WWE L3

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (5%) of wastewater effluent (WWE), replicate 3.

treatment_protocol:
Pooled livers of adult female zebrafish exposed to low dose (5%) of wastewater effluent (WWE) dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: Male ACE H1

description: Gene expression in pooled livers of adult male zebrafish exposed to high dose (10 μg L-1) acetaminophen (ACE), replicate 1.


title: Male CBZ C2

description: Gene expression in pooled livers of adult male zebrafish exposed to DMSO below 0.004% (to account for solvent use in experimental tanks) as a CONTROL for the CBZ experiment, replicate 2.


title: RNA_ileal_tissue_Sample151_rep2

description: Gene expression from RNA from ileal tissue of Sample151_rep2


title: 226 ADH

city: Boston

first: Lyndsey

middle: A.

last: Emery

state: MA

address: 650 Albany Street - EBRC 4th Floor

department: Medicine - Hematology/Oncology

institute: Boston University Medical Center

description: Gene expression data from case 226 ADH (rehyb)

hyb_protocol: 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)

scan_protocol: The stained arrays were scanned using a G2500 Scanner (Agilent)

data_processing: Images from the scanned chips were quantified and scaled using Affymetrix Microarray Suite 5.0 (Affymetrix), and the unnormalized data were then rescaled to a target of 100 to remove bias.

label: biotin

source_name: atypical ductal hyperplasia epithelium

label_protocol:
To convert the RNA to cDNA, the purified total RNA was linearly amplified for two rounds using the MessageAMP aRNA Kit (Ambion, Austin, TX), in which the first round is based on an oligo-dT primer and T7 RNA polymerase.
For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: Following the manufacturer’s protocol, total RNA was extracted and purified using the Picopure RNA Isolation Kit (Arcturus Engineering).

treatment_protocol: Samples were microdissected from lightly H&E stained serial frozen tissue sections.

value: laser capture microdissected human breast

tag: cell type

value: epithelial

tag: disease state

value: atypical ductal hyperplasia

tag: age range

value: 48-92 years old


title: RNA_ileal_tissue_Sample151_rep1

description: Gene expression from RNA from ileal tissue of Sample151_rep1


title: Female WWE L2

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (5%) of wastewater effluent (WWE), replicate 2.


title: Female WWE L1

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (5%) of wastewater effluent (WWE), replicate 1.


title: Female WWE H1

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10%) of wastewater effluent (WWE), replicate 1.

treatment_protocol:
Pooled livers of adult female zebrafish exposed to high dose (10%) of wastewater effluent (WWE) dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: RNA_ileal_tissue_Sample150_rep1

description: Gene expression from RNA from ileal tissue of Sample150_rep1


title: Female WWE C2

description: Gene expression in pooled livers of unexposed adult female zebrafish as a CONTROL for the WWE experiment, replicate 2.

treatment_protocol:
Pooled livers of unexposed adult female zebrafish as a CONTROL for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: RNA_ileal_tissue_Sample150_rep2

description: Gene expression from RNA from ileal tissue of Sample150_rep2


title: RNA_ileal_tissue_Sample149_rep1

description: Gene expression from RNA from ileal tissue of Sample149_rep1


title: RNA_ileal_tissue_Sample149_rep2

description: Gene expression from RNA from ileal tissue of Sample149_rep2


title: Female WWE H2

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10%) of wastewater effluent (WWE), replicate 2.


title: RNA_ileal_tissue_Sample148_rep1

description: Gene expression from RNA from ileal tissue of Sample148_rep1


title: RNA_ileal_tissue_Sample147_rep1

description: Gene expression from RNA from ileal tissue of Sample147_rep1


title: Female VEN L3

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) venlafaxine (VEN), replicate 3.

treatment_protocol:
Pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) venlafaxine (VEN), dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: Female WWE H3

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10%) of wastewater effluent (WWE), replicate 3.


title: Female VEN L2

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) venlafaxine (VEN), replicate 2.


title: RNA_ileal_tissue_Sample146_rep2

description: Gene expression from RNA from ileal tissue of Sample146_rep2


title: Female VEN H3

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) venlafaxine (VEN), replicate 3.

treatment_protocol:
Pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) venlafaxine (VEN), dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: Female WWE C3

description: Gene expression in pooled livers of unexposed adult female zebrafish as a CONTROL for the WWE experiment, replicate 3.


title: Female VEN H2

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) venlafaxine (VEN), replicate 2.


title: Female VEN H1

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) venlafaxine (VEN), replicate 1.


title: RNA_ileal_tissue_Sample146_rep1

description: Gene expression from RNA from ileal tissue of Sample146_rep1


title: Female WWE C1

description: Gene expression in pooled livers of unexposed adult female zebrafish as a CONTROL for the WWE experiment, replicate 1.


title: Female VEN L1

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) venlafaxine (VEN), replicate 1.


title: RNA_ileal_tissue_Sample145_rep2

description: Gene expression from RNA from ileal tissue of Sample145_rep2


title: RNA_ileal_tissue_Sample145_rep1

description: Gene expression from RNA from ileal tissue of Sample145_rep1


title: RNA_ileal_tissue_Sample147_rep2

description: Gene expression from RNA from ileal tissue of Sample147_rep2


title: RNA_ileal_tissue_Sample144_rep2

description: Gene expression from RNA from ileal tissue of Sample144_rep2


title: Female VEN-ACE C3

description: Gene expression in pooled livers of unexposed adult female zebrafish as a CONTROL for the VEN-ACE experiment, replicate 3.


title: Female VEN-ACE C2

description: Gene expression in pooled livers of unexposed adult female zebrafish as a CONTROL for the VEN-ACE experiment, replicate 2.


title: Female MIX L2

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) of acetaminophen (ACE), venlafaxine (VEN), gemfibrozil (GEM), and carbamazepine, replicate 2.

treatment_protocol:
Pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) of acetaminophen (ACE), venlafaxine (VEN), gemfibrozil (GEM), and carbamazepine (CBZ) dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: Female VEN-ACE C1

description: Gene expression in pooled livers of unexposed adult female zebrafish as a CONTROL for the VEN-ACE experiment, replicate 1.


title: RNA_ileal_tissue_Sample144_rep1

description: Gene expression from RNA from ileal tissue of Sample144_rep1


title: Female MIX L3

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) of acetaminophen (ACE), venlafaxine (VEN), gemfibrozil (GEM), and carbamazepine, replicate 3.


title: RNA_ileal_tissue_Sample143_rep2

description: Gene expression from RNA from ileal tissue of Sample143_rep2


title: RNA_ileal_tissue_Sample143_rep1

description: Gene expression from RNA from ileal tissue of Sample143_rep1


title: RNA_ileal_tissue_Sample141_rep1

description: Gene expression from RNA from ileal tissue of Sample141_rep1


title: RNA_ileal_tissue_Sample140_rep2

description: Gene expression from RNA from ileal tissue of Sample140_rep2


title: Female MIX L1

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) of acetaminophen (ACE), venlafaxine (VEN), gemfibrozil (GEM), and carbamazepine, replicate 1.


title: RNA_ileal_tissue_Sample142_rep1

description: Gene expression from RNA from ileal tissue of Sample142_rep1


title: RNA_ileal_tissue_Sample141_rep2

description: Gene expression from RNA from ileal tissue of Sample141_rep2


title: Female MIX H1

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) of acetaminophen (ACE), venlafaxine (VEN), gemfibrozil (GEM), and carbamazepine, replicate 1.

treatment_protocol:
Pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) of acetaminophen (ACE), venlafaxine (VEN), gemfibrozil (GEM), and carbamazepine (CBZ) dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: RNA_ileal_tissue_Sample142_rep2

description: Gene expression from RNA from ileal tissue of Sample142_rep2


title: Female GEM L1

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) gemfibrozil (GEM), replicate 1.

treatment_protocol:
Pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) gemfibrozil (GEM), dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: Female MIX H3

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) of acetaminophen (ACE), venlafaxine (VEN), gemfibrozil (GEM), and carbamazepine, replicate 3.


title: Female MIX H2

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) of acetaminophen (ACE), venlafaxine (VEN), gemfibrozil (GEM), and carbamazepine, replicate 2.


title: Female GEM H1

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) gemfibrozil (GEM), replicate 1.

treatment_protocol:
Pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) gemfibrozil (GEM), dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: RNA_ileal_tissue_Sample139_rep1

description: Gene expression from RNA from ileal tissue of Sample139_rep1


title: Female GEM H3

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) gemfibrozil (GEM), replicate 3.


title: Female GEM L2

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) gemfibrozil (GEM), replicate 2.


title: Female GEM L3

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) gemfibrozil (GEM), replicate 3.


title: RNA_ileal_tissue_Sample138_rep1

description: Gene expression from RNA from ileal tissue of Sample138_rep1


title: RNA_ileal_tissue_Sample137_rep2

description: Gene expression from RNA from ileal tissue of Sample137_rep2


title: Female GEM-MIX C3

description: Gene expression in pooled livers of adult female zebrafish exposed to DMSO below 0.004% (to account for solvent use in experimental tanks) as a CONTROL for the GEM-MIX experiment, replicate 3.

treatment_protocol:
Pooled livers of adult female zebrafish exposed to DMSO below 0.004% (to account for solvent use in experimental tanks) as a CONTROL for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: RNA_ileal_tissue_Sample140_rep1

description: Gene expression from RNA from ileal tissue of Sample140_rep1


title: RNA_ileal_tissue_Sample137_rep1

description: Gene expression from RNA from ileal tissue of Sample137_rep1


title: RNA_ileal_tissue_Sample139_rep2

description: Gene expression from RNA from ileal tissue of Sample139_rep2


title: RNA_ileal_tissue_Sample138_rep2

description: Gene expression from RNA from ileal tissue of Sample138_rep2


title: RNA_ileal_tissue_Sample135_rep2

description: Gene expression from RNA from ileal tissue of Sample135_rep2


title: RNA_ileal_tissue_Sample135_rep1

description: Gene expression from RNA from ileal tissue of Sample135_rep1


title: RNA_ileal_tissue_Sample134_rep1

description: Gene expression from RNA from ileal tissue of Sample134_rep1


title: Female GEM-MIX C2

description: Gene expression in pooled livers of adult female zebrafish exposed to DMSO below 0.004% (to account for solvent use in experimental tanks) as a CONTROL for the GEM-MIX experiment, replicate 2.


title: Female GEM H2

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) gemfibrozil (GEM), replicate 2.


title: Female CBZ L1

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) carbamazepine (CBZ), replicate 1.

treatment_protocol:
Pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) carbamazepine (CBZ), dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: Female CBZ L3

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) carbamazepine (CBZ), replicate 3.


title: Female CBZ H1

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) carbamazepine (CBZ), replicate 1.

treatment_protocol:
Pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) carbamazepine (CBZ), dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: Female GEM-MIX C1

description: Gene expression in pooled livers of adult female zebrafish exposed to DMSO below 0.004% (to account for solvent use in experimental tanks) as a CONTROL for the GEM-MIX experiment, replicate 1.


title: RNA_ileal_tissue_Sample133_rep2

description: Gene expression from RNA from ileal tissue of Sample133_rep2

treatment_protocol: Whole-thickness ileal tissue was scraped from the FFPE tissue sections followed by RNA extraction using the RNeasy FFPE kit (Qiagen) according to the manufacturer's instructions.


title: Female CBZ H2

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) carbamazepine (CBZ), replicate 2.


title: RNA_ileal_tissue_Sample148_rep2

description: Gene expression from RNA from ileal tissue of Sample148_rep2


title: Female CBZ C3

description: Gene expression in pooled livers of adult female zebrafish exposed to DMSO below 0.004% (to account for solvent use in experimental tanks) as a CONTROL for the CBZ experiment, replicate 3.


title: Female CBZ L2

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) carbamazepine (CBZ), replicate 2.


title: RNA_ileal_tissue_Sample132_rep2

description: Gene expression from RNA from ileal tissue of Sample132_rep2


title: RNA_ileal_tissue_Sample133_rep1

description: Gene expression from RNA from ileal tissue of Sample133_rep1


title: RNA_ileal_tissue_Sample136_rep1

description: Gene expression from RNA from ileal tissue of Sample136_rep1


title: Male ACE L1

description: Gene expression in pooled livers of adult male zebrafish exposed to low dose (0.5 μg L-1) acetaminophen (ACE), replicate 1.

treatment_protocol:
Pooled livers of adult male zebrafish exposed to low dose (0.5 μg L-1) acetaminophen (ACE), dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: Female CBZ C1

description: Gene expression in pooled livers of adult female zebrafish exposed to DMSO below 0.004% (to account for solvent use in experimental tanks) as a CONTROL for the CBZ experiment, replicate 1.


title: Female ACE L3

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) acetaminophen (ACE), replicate 3.

treatment_protocol:
Pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) acetaminophen (ACE), dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: Female ACE H3

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) acetaminophen (ACE), replicate 3.

treatment_protocol:
Pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) acetaminophen (ACE), dosed every three days for six weeks after a 90% system water change-out. RNA sampled at the end of the six week exposure.
Hepatic transcriptional responses in zebrafish to four common, environmentally relevant pharmaceuticals (ACE, CBZ, GEM, VEN), a mixture of the pharmaceuticals (MIX), and dilutions of wastewater effluent (WWE) were determined after a 6 week chronic exposure to a low (0.5 μg L-1 or 5% effluent) or high (10 μg L-1 or 10% effluent) concentration. The final nominal concentration of each pharmaceutical in exposure tanks was 0 (control), 0.5 µg L-1 (low dose) or 10 µg L-1 (high dose), with the pharmaceutical mixture (MIX) including equal concentrations of each pharmaceutical (ACE, VEN, GEM, CBZ) at the same two doses (0.5 or 10 µg L-1). The control tank for experiments with gemfibrozil (GEM), carbamazepine (CBZ), and mixture (MIX) had a final concentration of DMSO below 0.004% to account for solvent use in experimental tanks.  Waste water effluent (WWE) exposure was conducted using final effluent collected twice per week and diluted to 5% (low dose) or 25% (high dose) using system water.  The wastewater treatment plant used secondary treatment with activated sludge technology, as previously described.  Effluent was stored in a dark, cold room for no more than 3 days after collection and was diluted just prior to water change-outs. Triplicate tanks for each treatment group housed 50 adult zebrafish each.  Tanks were dosed every three days for six weeks after a 90% system water change-out.  Venlafaxine (VEN) and acetaminophen (ACE) exposures were run together with shared controls (water only) while GEM and the MIX exposures were run together with shared controls (DMSO solvent control).  CBZ and WWE effluent exposures were run separately with their own set of controls (DMSO solvent control for CBZ, water control for wastewater effluent).


title: RNA_ileal_tissue_Sample132_rep1

description: Gene expression from RNA from ileal tissue of Sample132_rep1


title: RNA_ileal_tissue_Sample130_rep2

description: Gene expression from RNA from ileal tissue of Sample130_rep2


title: RNA_ileal_tissue_Sample129_rep1

description: Gene expression from RNA from ileal tissue of Sample129_rep1


title: RNA_ileal_tissue_Sample131_rep2

description: Gene expression from RNA from ileal tissue of Sample131_rep2


title: Female ACE L1

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) acetaminophen (ACE), replicate 1.


title: RNA_ileal_tissue_Sample131_rep1

description: Gene expression from RNA from ileal tissue of Sample131_rep1


title: wild-type_E10.5_3

type: SRA

city: Tokyo

first: Yoshiki

last: Higashijima

address: 1-5-45 Yushima, Bunkyo

department: Medical Research Institute

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression data of embryonic trunk

library_source: transcriptomic

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
Reads were trimmed with Trimmomatic.
The trimmed reads were aligned to the mouse reference genome mm10 with HISAT2.
Sequencing tracks normalized by the mapped read counts were generated with deepTools.
Genome_build: Genome Reference Consortium Mouse Build 38 (mm10)
Supplementary_files_format_and_content: bigwig

organism: Mus musculus

source_name: embryonic trunk

extract_protocol:
Total RNA was isolated from embryonic head and trunk by using a miRNeasy micro Kit (Qiagen) with the DNase digestion step, according to the manufacturer’s instructions.
Libraries were prepared according to Illumina's instructions.

tag: genotype

value: wild-type

tag: developmental stage


title: Kdm7a_E10.5_3

description: Gene expression data of embryonic trunk

value: Kdm7a mutant


title: Kdm7a_E10.5_2

description: Gene expression data of embryonic trunk


title: Female ACE H2

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) acetaminophen (ACE), replicate 2.


title: Female ACE L2

description: Gene expression in pooled livers of adult female zebrafish exposed to low dose (0.5 μg L-1) acetaminophen (ACE), replicate 2.


title: wild-type_E10.5_1

description: Gene expression data of embryonic trunk


title: Female CBZ C2

description: Gene expression in pooled livers of adult female zebrafish exposed to DMSO below 0.004% (to account for solvent use in experimental tanks) as a CONTROL for the CBZ experiment, replicate 2.


title: Kdm7a_E9.5_3

description: Gene expression data of embryonic trunk


title: RNA_ileal_tissue_Sample130_rep1

description: Gene expression from RNA from ileal tissue of Sample130_rep1


title: Kdm7a_E10.5_1

description: Gene expression data of embryonic trunk


title: RNA_ileal_tissue_Sample129_rep2

description: Gene expression from RNA from ileal tissue of Sample129_rep2


title: Female ACE H1

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) acetaminophen (ACE), replicate 1.


title: Kdm7a_E9.5_1

description: Gene expression data of embryonic trunk


title: wild-type_E10.5_2

description: Gene expression data of embryonic trunk


title: RNA_ileal_tissue_Sample126_rep2

description: Gene expression from RNA from ileal tissue of Sample126_rep2


title: RNA_ileal_tissue_Sample128_rep2

description: Gene expression from RNA from ileal tissue of Sample128_rep2


title: RNA_ileal_tissue_Sample127_rep2

description: Gene expression from RNA from ileal tissue of Sample127_rep2


title: RNA_ileal_tissue_Sample128_rep1

description: Gene expression from RNA from ileal tissue of Sample128_rep1


title: Kdm7a_E9.5_2

description: Gene expression data of embryonic trunk


title: RNA_ileal_tissue_Sample127_rep1

description: Gene expression from RNA from ileal tissue of Sample127_rep1


title: wild-type_E9.5_3

description: Gene expression data of embryonic trunk


title: RNA_ileal_tissue_Sample125_rep1

description: Gene expression from RNA from ileal tissue of Sample125_rep1


title: IV2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
BS-Seq sequences were trimmed with Trim Galore (v0.4.4; Cutadapt v1.9.1) in single-end mode with the options --clip_r1 9. Trimmed sequences were mapped to the human GRCm38 genome in single-end --pbat mode using Bismark (Krueger and Andrews, 2011) (v0.19.0); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

molecule: genomic DNA

source_name: In vivo_oocytes

extract_protocol:
Sample lysis: an individual mouse blastocyst was lysed for 1 hr in 1% SDS with proteinase K (1ul, 20 mg/mL) at 37C
Post bisulfite adapter tagging (PBAT) as  described in Muira et al (2012, PMID: 22649061) with few modifications (Canovas et al, 2017) (PMID: 28134613)
Bisulfite-seq; Post bisulfite adapter tagging (PBAT), same as above

tag: strain

value: C57BL/6J X CBA/Ca F1 female

value: 10 weeks old

tag: type

value: In vivo

value: oocytes


title: RNA_ileal_tissue_Sample125_rep2

description: Gene expression from RNA from ileal tissue of Sample125_rep2


title: RNA_ileal_tissue_Sample126_rep1

description: Gene expression from RNA from ileal tissue of Sample126_rep1


title: wild-type_E9.5_2

description: Gene expression data of embryonic trunk


title: wild-type_E9.5_1

description: Gene expression data of embryonic trunk


title: RNA_ileal_tissue_Sample124_rep2

description: Gene expression from RNA from ileal tissue of Sample124_rep2


title: RNA_ileal_tissue_Sample124_rep1

description: Gene expression from RNA from ileal tissue of Sample124_rep1


title: RNA_ileal_tissue_Sample123_rep1

description: Gene expression from RNA from ileal tissue of Sample123_rep1


title: IV1


title: RNA_ileal_tissue_Sample122_rep2

description: Gene expression from RNA from ileal tissue of Sample122_rep2


title: SOA4

source_name: Superovulation Adult_oocytes

value: Superovulation Adult


title: SOA3


title: SOA2


title: RNA_ileal_tissue_Sample121_rep2

description: Gene expression from RNA from ileal tissue of Sample121_rep2


title: RNA_ileal_tissue_Sample121_rep1

description: Gene expression from RNA from ileal tissue of Sample121_rep1


title: SO5

source_name: Superovulation prepubertal_oocytes

value: 23 days-old

value: Superovulation prepubertal


title: RNA_ileal_tissue_Sample120_rep2

description: Gene expression from RNA from ileal tissue of Sample120_rep2

value: uninvolved small bowel (SB) ileal tissue


title: RNA_ileal_tissue_Sample120_rep1

description: Gene expression from RNA from ileal tissue of Sample120_rep1


title: SO4


title: RNA_ileal_tissue_Sample136_rep2

description: Gene expression from RNA from ileal tissue of Sample136_rep2

value: female


title: SO2


title: IV3


title: RNA_ileal_tissue_Sample119_rep2

description: Gene expression from RNA from ileal tissue of Sample119_rep2


title: SO1


title: RNA_ileal_tissue_Sample123_rep2

description: Gene expression from RNA from ileal tissue of Sample123_rep2


title: RNA_ileal_tissue_Sample119_rep1

description: Gene expression from RNA from ileal tissue of Sample119_rep1


title: IFC4

source_name: In vitro follicle culture_oocytes

value: In vitro follicle culture


title: RNA_ileal_tissue_Sample118_rep2

description: Gene expression from RNA from ileal tissue of Sample118_rep2


title: RNA_ileal_tissue_Sample118_rep1

description: Gene expression from RNA from ileal tissue of Sample118_rep1


title: IFC3


title: RNA_ileal_tissue_Sample117_rep2

description: Gene expression from RNA from ileal tissue of Sample117_rep2


title: IFC2


title: IFC1


title: RNA_ileal_tissue_Sample122_rep1

description: Gene expression from RNA from ileal tissue of Sample122_rep1

value: male


title: SOA1


title: HiC_rep2_run3

city: Cincinnati

first: Harinder

last: Singh

state: OH

address: 3333 Burnet Ave

department: Immunobiology

institute: CCHMC

description:
aB Cells
CD43- Splenic B cells cultured in the presence of LPS for 3 days
HiC_Filtered_Enhancer_Promoter_Interactions.txt

data_processing:
H3K27ac ChIP-seq: ChIP-seq reads were aligned to mm9 genome with default bowtie2 options. Unique reads were used for peak calling with Homer function findPeaks with a 500 bp sliding window using option “-style histone”. For calling super-enhancers we used option “-style super” with default settings.
H3K4me3 ChIP-seq: ChIP-seq reads were aligned to mm9 genome with default bowtie2 options. Unique reads were used for peak calling with Homer function findPeaks with a 500 bp sliding window using option “-style histone”.
FAIRE-seq: Paired end reads were aligned using bowtie options “—very-sensitive –k 1 –m 500” and output sam files were converted to bam files. Then bamToBed tools were used to convert bam files into paired end bed files in “bedpe” format. A custom R script was used to filter out spurious alignments such as reads aligned to random scaffold, reads mapping to mitochondrial DNA, or paired reads with ends mapping to different chromosomes. Tags were generated using start and end coordinates derived from paired alignment of forward and reverse reads, and only unique tags were considered in the following analysis. Tags longer than 1kb were discarded. Bed files containing tag information were analysed with Homer suite of tools. Peak calling was done using function “findPeaks” with options “-size 300 –minDist 300 –L 0 –center -fdr 0.05”. Peaks were 300bp in size and centered on maximum tag density. Peaks were separated by at least 300bp.Peaks from blacklisted regions in mm9 genome were discarded.
STARR-seq: Paired end reads were aligned using bowtie options “—very-sensitive –k 1 –m 500” and output sam files were converted to bam files. Then bamToBed tools were used to convert bam files into paired end bed files in “bedpe” format. A custom R script was used to filter out spurious alignments such as reads aligned to random scaffold, reads mapping to mitochondrial DNA, or paired reads with ends mapping to different chromosomes. Tags were generated using start and end coordinates derived from paired alignment of forward and reverse reads, and only unique tags were considered in the following analysis. Tags longer than 1kb were discarded. Bed files containing tag information were analysed with Homer suite of tools. Peak calling was done using function “findPeaks” with options “-size 300 –minDist 300 –L 0 –center -fdr 0.05”. Peaks were 300bp in size and centered on maximum tag density. For peak calling in STARR-seq the tags from replicate experiments were combined. Peaks from blacklisted regions in mm9 genome were discarded.
Hi-C: Hi-C paired end reads were aligned separately with default bowtie options to mm9 and up to 2 best alignments were kept considering that a chimeric junction can reside in one of the paired ends. Alignment output was used as input data for Homer functions (makeTagDirectory) to generate primary Hi-C tag directory. Tags which were result of self-ligation, ends close to a “GATC” site in mm9 genome, were discarded. Tags where read ends were closer than 900 bp, were eliminated. Background models were generated for each bin size using function “analyzeHiC –bgonly”. Next Homer function “findHiCInteractionsByChr” was used to selectively analyze cis-regulatory interactions only, for bin sizes of 1kb, 2kb, 5kb and 10kb with overlapping regions of varying sizes to avoid penalizing elements at the boundaries of bins. For bin resolution of 5 kb, sliding windows of 1 kb and 2.5 kb were used and for bin resolution of 10 kb, sliding windows of 2.5 kb and 5 kb were used. 1kb and 2kb bin resolutions used 500bp and 1kb sliding windows, respectively. Interactions with at least 5 interaction read pairs with p-values less than 0.0001 were used in assembly of cis-regulome. Interactions were further filtered containing enahncers and promoter containing interactions.
Software used: Bowtie2 (DNA reads aligner) version 2.2.3, Tophat2 (RNA reads aligner) version 2.0.13, Homer (analysis suite for mapped read data) version 4.9, STAR (RNA reads aligner) version 2.5
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing reported peak coordinates for mm9 genome assembly. RNA-seq data as cufflink reported FPKM values. Interaction file for Hi-C data with Hi-C interacting bins with associated interaction read counts, modified z-score and logP values. All these Hi-C interactions represent active-promoter and active-enhancer interactions based on each interaction having overlap of its each of two bins such that interactions represent enhancer-promoter pairs.

source_name: Hi-C in activated B Cells

growth_protocol: Splenic B cells isolated for CD43- fraction using magentice labeling, culture in coplete RPMI for 3 days in presence of 10ug/ul LPS.

extract_protocol:
Crosslinked with 1% formaldehyde
Illumina single and paired end libraries, RNA-seq and DNA-seq
Adapter ligation to fragements followed by pcr amplification using indexed primers for Illumnia HiSeq-2500

treatment_protocol: Cultured in complete RPMI with 10 ug/ml LPS for 3 days

value: LPS activated splenic B cells CD43-


title: RNA_ileal_tissue_Sample117_rep1

description: Gene expression from RNA from ileal tissue of Sample117_rep1


title: RNA_ileal_tissue_Sample116_rep2

description: Gene expression from RNA from ileal tissue of Sample116_rep2


title: RNA_ileal_tissue_Sample116_rep1

description: Gene expression from RNA from ileal tissue of Sample116_rep1


title: HiC_rep1_run4


title: SO3


title: RNA_ileal_tissue_Sample115_rep2

description: Gene expression from RNA from ileal tissue of Sample115_rep2


title: rB_RNA-seq_rep2

description:
rB Cells
CD43- Splenic B cells
CD43Neg_BCells_RNAseq.txt

source_name: RNA-seq in resting B Cells

value: Splenic B cells CD43-


title: rB_RNA-seq_rep1


title: RNA_ileal_tissue_Sample114_rep2

description: Gene expression from RNA from ileal tissue of Sample114_rep2


title: RNA_ileal_tissue_Sample115_rep1

description: Gene expression from RNA from ileal tissue of Sample115_rep1


title: RNA_ileal_tissue_Sample114_rep1

description: Gene expression from RNA from ileal tissue of Sample114_rep1


title: rB_H3K27ac

description:
rB Cells
CD43- Splenic B cells

source_name: H3K27ac ChIP-Seq in resting B Cells

tag: antibody

value: rabbit polyclonal anti-H3K27ac antibody (Cat. No. C15410196, Diagenode Inc.)


title: RNA_ileal_tissue_Sample113_rep2

description: Gene expression from RNA from ileal tissue of Sample113_rep2


title: RNA_ileal_tissue_Sample113_rep1

description: Gene expression from RNA from ileal tissue of Sample113_rep1


title: rB_H3K4me1

description:
rB Cells
CD43- Splenic B cells

source_name: H3K4me1 ChIP-Seq in resting B Cells

value: rabbit polyclonal anti-H3K4me1 antibody (Cat. No. C15410194, Diagenode Inc.)


title: H3K4Me1_rep2

description:
aB Cells
CD43- Splenic B cells cultured in the presence of LPS for 3 days

source_name: H3K4me1 ChIP-Seq in activated B Cells


title: Female CBZ H3

description: Gene expression in pooled livers of adult female zebrafish exposed to high dose (10 μg L-1) carbamazepine (CBZ), replicate 3.

value: liver


title: H3K4me1_rep1


title: RNA_ileal_tissue_Sample112_rep2

description: Gene expression from RNA from ileal tissue of Sample112_rep2


title: RNA_ileal_tissue_Sample111_rep2

description: Gene expression from RNA from ileal tissue of Sample111_rep2


title: RNA_ileal_tissue_Sample112_rep1

description: Gene expression from RNA from ileal tissue of Sample112_rep1


title: STARR-Seq_24hrs_rep2_run_LibReplicate

data_processing:
Library strategy: STARR-Seq
H3K27ac ChIP-seq: ChIP-seq reads were aligned to mm9 genome with default bowtie2 options. Unique reads were used for peak calling with Homer function findPeaks with a 500 bp sliding window using option “-style histone”. For calling super-enhancers we used option “-style super” with default settings.
H3K4me3 ChIP-seq: ChIP-seq reads were aligned to mm9 genome with default bowtie2 options. Unique reads were used for peak calling with Homer function findPeaks with a 500 bp sliding window using option “-style histone”.
FAIRE-seq: Paired end reads were aligned using bowtie options “—very-sensitive –k 1 –m 500” and output sam files were converted to bam files. Then bamToBed tools were used to convert bam files into paired end bed files in “bedpe” format. A custom R script was used to filter out spurious alignments such as reads aligned to random scaffold, reads mapping to mitochondrial DNA, or paired reads with ends mapping to different chromosomes. Tags were generated using start and end coordinates derived from paired alignment of forward and reverse reads, and only unique tags were considered in the following analysis. Tags longer than 1kb were discarded. Bed files containing tag information were analysed with Homer suite of tools. Peak calling was done using function “findPeaks” with options “-size 300 –minDist 300 –L 0 –center -fdr 0.05”. Peaks were 300bp in size and centered on maximum tag density. Peaks were separated by at least 300bp.Peaks from blacklisted regions in mm9 genome were discarded.
STARR-seq: Paired end reads were aligned using bowtie options “—very-sensitive –k 1 –m 500” and output sam files were converted to bam files. Then bamToBed tools were used to convert bam files into paired end bed files in “bedpe” format. A custom R script was used to filter out spurious alignments such as reads aligned to random scaffold, reads mapping to mitochondrial DNA, or paired reads with ends mapping to different chromosomes. Tags were generated using start and end coordinates derived from paired alignment of forward and reverse reads, and only unique tags were considered in the following analysis. Tags longer than 1kb were discarded. Bed files containing tag information were analysed with Homer suite of tools. Peak calling was done using function “findPeaks” with options “-size 300 –minDist 300 –L 0 –center -fdr 0.05”. Peaks were 300bp in size and centered on maximum tag density. For peak calling in STARR-seq the tags from replicate experiments were combined. Peaks from blacklisted regions in mm9 genome were discarded.
Hi-C: Hi-C paired end reads were aligned separately with default bowtie options to mm9 and up to 2 best alignments were kept considering that a chimeric junction can reside in one of the paired ends. Alignment output was used as input data for Homer functions (makeTagDirectory) to generate primary Hi-C tag directory. Tags which were result of self-ligation, ends close to a “GATC” site in mm9 genome, were discarded. Tags where read ends were closer than 900 bp, were eliminated. Background models were generated for each bin size using function “analyzeHiC –bgonly”. Next Homer function “findHiCInteractionsByChr” was used to selectively analyze cis-regulatory interactions only, for bin sizes of 1kb, 2kb, 5kb and 10kb with overlapping regions of varying sizes to avoid penalizing elements at the boundaries of bins. For bin resolution of 5 kb, sliding windows of 1 kb and 2.5 kb were used and for bin resolution of 10 kb, sliding windows of 2.5 kb and 5 kb were used. 1kb and 2kb bin resolutions used 500bp and 1kb sliding windows, respectively. Interactions with at least 5 interaction read pairs with p-values less than 0.0001 were used in assembly of cis-regulome. Interactions were further filtered containing enahncers and promoter containing interactions.
Software used: Bowtie2 (DNA reads aligner) version 2.2.3, Tophat2 (RNA reads aligner) version 2.0.13, Homer (analysis suite for mapped read data) version 4.9, STAR (RNA reads aligner) version 2.5
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing reported peak coordinates for mm9 genome assembly. RNA-seq data as cufflink reported FPKM values. Interaction file for Hi-C data with Hi-C interacting bins with associated interaction read counts, modified z-score and logP values. All these Hi-C interactions represent active-promoter and active-enhancer interactions based on each interaction having overlap of its each of two bins such that interactions represent enhancer-promoter pairs.

source_name: STARR-Seq in activated B Cells


title: STARR-Seq_12hrs_rep2_run_LibReplicate


title: STARR-Seq_24hrs_rep1_run_LibReplicate


title: RNA_ileal_tissue_Sample110_rep2

description: Gene expression from RNA from ileal tissue of Sample110_rep2


title: RNA_ileal_tissue_Sample111_rep1

description: Gene expression from RNA from ileal tissue of Sample111_rep1


title: STARR-Seq_12hrs_rep1_run_LibReplicate


title: RNA_ileal_tissue_Sample110_rep1

description: Gene expression from RNA from ileal tissue of Sample110_rep1


title: STARR_plasmid_library_run2


title: H3K4me3_rep2

source_name: H3K4me3 ChIP-Seq in activated B Cells

value: rabbit monoclonal anti-H3K4me3 antibody (Cat. No. 17-614, Millipore)


title: RNA_ileal_tissue_Sample109_rep1

description: Gene expression from RNA from ileal tissue of Sample109_rep1


title: STARR_plasmid_library_run1


title: H3K4me3_rep1

description:
aB Cells
CD43- Splenic B cells cultured in the presence of LPS for 3 days
H3K4me3_aB_peaks.bed


title: RNA_ileal_tissue_Sample108_rep1

description: Gene expression from RNA from ileal tissue of Sample108_rep1


title: Nascent RNA

molecule: nuclear RNA

source_name: Nascent RNA-seq in activated B Cells


title: RNA_ileal_tissue_Sample109_rep2

description: Gene expression from RNA from ileal tissue of Sample109_rep2


title: RNA_ileal_tissue_Sample106_rep2

description: Gene expression from RNA from ileal tissue of Sample106_rep2


title: FAIRE-Seq_rep2_run1

source_name: FAIRE-Seq in activated B Cells


title: FAIRE-Seq_rep1_run1

description:
aB Cells
CD43- Splenic B cells cultured in the presence of LPS for 3 days
FAIREseq_aB_peaks.bed


title: RNA_ileal_tissue_Sample105_rep2

description: Gene expression from RNA from ileal tissue of Sample105_rep2


title: RNA_ileal_tissue_Sample108_rep2

description: Gene expression from RNA from ileal tissue of Sample108_rep2


title: RNA_ileal_tissue_Sample107_rep1

description: Gene expression from RNA from ileal tissue of Sample107_rep1


title: RNA_ileal_tissue_Sample106_rep1

description: Gene expression from RNA from ileal tissue of Sample106_rep1


title: H3K27ac_rep2

description:
aB Cells
CD43- Splenic B cells cultured in the presence of LPS for 3 days

source_name: H3K27ac ChIP-Seq in activated B Cells


title: H3K27ac_rep1

description:
aB Cells
CD43- Splenic B cells cultured in the presence of LPS for 3 days
H3K27ac_aB_peaks.bed


title: FAIRE-Seq_rep2_run2


title: STARR-Seq_24hrs_rep2_run1

description:
aB Cells
CD43- Splenic B cells cultured in the presence of LPS for 3 days
STARRseq_aB_peaks.bed


title: RNA_ileal_tissue_Sample104_rep2

description: Gene expression from RNA from ileal tissue of Sample104_rep2


title: RNA_ileal_tissue_Sample104_rep1

description: Gene expression from RNA from ileal tissue of Sample104_rep1


title: STARR-Seq_24hrs_rep1_run1


title: RNA_ileal_tissue_Sample105_rep1

description: Gene expression from RNA from ileal tissue of Sample105_rep1


title: RNA_ileal_tissue_Sample103_rep2

description: Gene expression from RNA from ileal tissue of Sample103_rep2


title: RNA_ileal_tissue_Sample134_rep2

description: Gene expression from RNA from ileal tissue of Sample134_rep2


title: RNA_ileal_tissue_Sample103_rep1

description: Gene expression from RNA from ileal tissue of Sample103_rep1


title: STARR-Seq_12hrs_rep2_run1


title: STARR-Seq_12hrs_rep1_run1


title: RNA-seq_rep2

description:
aB Cells
CD43- Splenic B cells cultured in the presence of LPS for 3 days
CD43Neg_BCells_RNAseq.txt

source_name: RNA-Seq in activated B Cells


title: STARR-Seq_12hrs_rep2_run2


title: HiC_rep1_run3

description:
aB Cells
CD43- Splenic B cells cultured in the presence of LPS for 3 days
HiC_Filtered_Enhancer_Promoter_Interactions.txt


title: RNA_ileal_tissue_Sample107_rep2

description: Gene expression from RNA from ileal tissue of Sample107_rep2


title: HiC_rep2_run2


title: RNA_ileal_tissue_Sample102_rep2

description: Gene expression from RNA from ileal tissue of Sample102_rep2


title: RNA-seq_rep1


title: HiC_rep2_run1


title: RNA_ileal_tissue_Sample102_rep1

description: Gene expression from RNA from ileal tissue of Sample102_rep1


title: RNA_ileal_tissue_Sample100_rep2

description: Gene expression from RNA from ileal tissue of Sample100_rep2


title: RNA_ileal_tissue_Sample101_rep2

description: Gene expression from RNA from ileal tissue of Sample101_rep2


title: RNA_ileal_tissue_Sample100_rep1

description: Gene expression from RNA from ileal tissue of Sample100_rep1


title: RNA_ileal_tissue_Sample99_rep2

description: Gene expression from RNA from ileal tissue of Sample99_rep2


title: HiC_rep1_run2


title: C57BL/6J-mtBPL/J  4

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

data_processing:
Raw sequence reads were pseudo aligned to the mouse transcriptome mm10 (Ensembl Build 84) using Kallisto (Version 0.44.0, Bray et al. Nat. Biotechnology 2016) runing 30 bootstrap rounds.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files per sample include effectice read counts and transcript per million (TPM) values for each transcript

source_name: Liver obtained from C57BL/6J-mtBPL/J mouse

extract_protocol:
Total RNAs were extracted from liver samples obtained from conplastic mouse strains (C57BL/6J and C57BL/6J-mtAKR/J), using innuPREP RNA Mini Kit (Analytik Jena) according to the manufacturer’s protocol. RNAs quality was checked using a Bioanalyzer system (Agilent Genomics).
RNA sequencing of primary samples was carried out by using oligo-dT beads to enrich molecules with poly-A tails. Libraries were sequenced on a Illumina HiSeq 2500 as 75bp single ended.

value: Liver

tag: mutation

tag: Sex

value: 4 months

tag: replicate

value: replicate 4


title: C57BL/6J-mtBPL/J  3

value: replicate 3


title: C57BL/6J-mtBPL/J  2

value: 3 months

value: replicate 2


title: RNA_ileal_tissue_Sample97_rep2

description: Gene expression from RNA from ileal tissue of Sample97_rep2

tag: ^sample

tag: batch


title: RNA_ileal_tissue_Sample98_rep2

description: Gene expression from RNA from ileal tissue of Sample98_rep2

tag: tissue

tag: gender


title: HiC_rep1_run1


title: RNA_ileal_tissue_Sample99_rep1

description: Gene expression from RNA from ileal tissue of Sample99_rep1

tag: age


title: RNA_ileal_tissue_Sample98_rep1

description: Gene expression from RNA from ileal tissue of Sample98_rep1


title: C57BL/6J-mtALR/J  6

source_name: Liver obtained from C57BL/6J-mtALR/J mouse

value: replicate 6


title: C57BL/6J-mtALR/J  5

value: replicate 5


title: C57BL/6J-mtALR/J  7

value: female

value: replicate 7


title: C57BL/6J-mtALR/J  3

value: 5 months


title: RNA_ileal_tissue_Sample95_rep2

description: Gene expression from RNA from ileal tissue of Sample95_rep2

value: uninvolved small bowel (SB) ileal tissue

value: male


title: RNA_ileal_tissue_Sample96_rep2

description: Gene expression from RNA from ileal tissue of Sample96_rep2


title: RNA_ileal_tissue_Sample96_rep1

description: Gene expression from RNA from ileal tissue of Sample96_rep1


title: RNA_ileal_tissue_Sample95_rep1

description: Gene expression from RNA from ileal tissue of Sample95_rep1


title: C57BL/6J-mtBPL/J  1

value: replicate 1


title: RNA_ileal_tissue_Sample94_rep2

description: Gene expression from RNA from ileal tissue of Sample94_rep2


title: C57BL/6J-mtALR/J  4


title: C57BL/6J-mtALR/J  1


title: RNA_ileal_tissue_Sample93_rep2

description: Gene expression from RNA from ileal tissue of Sample93_rep2


title: RNA_ileal_tissue_Sample94_rep1

description: Gene expression from RNA from ileal tissue of Sample94_rep1


title: RNA_ileal_tissue_Sample92_rep2

description: Gene expression from RNA from ileal tissue of Sample92_rep2


title: RNA_ileal_tissue_Sample93_rep1

description: Gene expression from RNA from ileal tissue of Sample93_rep1


title: C57BL/6J-mtALR/J  2


title: RNA_ileal_tissue_Sample91_rep1

description: Gene expression from RNA from ileal tissue of Sample91_rep1


title: RNA_ileal_tissue_Sample90_rep2

description: Gene expression from RNA from ileal tissue of Sample90_rep2


title: RNA_ileal_tissue_Sample89_rep2

description: Gene expression from RNA from ileal tissue of Sample89_rep2


title: RNA_ileal_tissue_Sample89_rep1

description: Gene expression from RNA from ileal tissue of Sample89_rep1


title: RNA_ileal_tissue_Sample97_rep1

description: Gene expression from RNA from ileal tissue of Sample97_rep1


title: RNA_ileal_tissue_Sample88_rep2

description: Gene expression from RNA from ileal tissue of Sample88_rep2


title: RNA_ileal_tissue_Sample91_rep2

description: Gene expression from RNA from ileal tissue of Sample91_rep2


title: RNA_ileal_tissue_Sample88_rep1

description: Gene expression from RNA from ileal tissue of Sample88_rep1


title: SC_swarm_TOB_5

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

institute: Simon Fraser University

description: ribosomally depleted RNA

data_processing:
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
Fastq file quality control was performed using FastQC v0.11.7 and MultiQC v1.6.dev0
Fastq files were aligned to the PA14 genome using STAR v2.6.1.a
BAM files were sorted as part of read alignment with STAR
Read count tables were generated using htseq-count v0.11.2
Genome_build: UCBPP-PA14 (GenBank gene annotations) from Pseudomonas Genome Database
Supplementary_files_format_and_content: Tab delimited files containing uniquely mapped reads per gene for each sample

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: Bacteria

growth_protocol: Bacteria were grown on BM2 (0.5% agar) for 16hrs before harvesting

extract_protocol:
RNA stabilized using RNAprotect Bacteria (Qiagen), extracted using Rneasy Mini Kit (Qiagen), DNAase treated using TURBO DNA-free kit (Thermo Fisher), rRNA depletion conducted with Ribozero Bacteria kit (Illumina - USA)
cDNA libraries were constructed for sequencing using a KAPA Stranded Total RNA Kit (Kapa Biosystems)

treatment_protocol: Indicated samples were innoculated into media containing subinhibitory levels of the antibiotic tobramycin, at 0.5ug/mL

tag: growth condition

value: Swarming

tag: treatment

value: Tobramycin

tag: concentration


title: SC_swarm_TOB_4

description: ribosomally depleted RNA


title: RNA_ileal_tissue_Sample87_rep2

description: Gene expression from RNA from ileal tissue of Sample87_rep2


title: RNA_ileal_tissue_Sample87_rep1

description: Gene expression from RNA from ileal tissue of Sample87_rep1


title: SC_swarm_TOB_2

description: ribosomally depleted RNA


title: SC_swarm_5

description: ribosomally depleted RNA

value: Untreated


title: SC_swarm_2

description: ribosomally depleted RNA


title: RNA_ileal_tissue_Sample86_rep2

description: Gene expression from RNA from ileal tissue of Sample86_rep2


title: RNA_ileal_tissue_Sample86_rep1

description: Gene expression from RNA from ileal tissue of Sample86_rep1


title: RNA_ileal_tissue_Sample101_rep1

description: Gene expression from RNA from ileal tissue of Sample101_rep1


title: RNA_ileal_tissue_Sample84_rep2

description: Gene expression from RNA from ileal tissue of Sample84_rep2


title: RNA_ileal_tissue_Sample85_rep2

description: Gene expression from RNA from ileal tissue of Sample85_rep2


title: SC_swarm_4

description: ribosomally depleted RNA


title: RNA_ileal_tissue_Sample85_rep1

description: Gene expression from RNA from ileal tissue of Sample85_rep1


title: RNA_ileal_tissue_Sample92_rep1

description: Gene expression from RNA from ileal tissue of Sample92_rep1


title: KO_25_KO_YF

city: Trondheim

first: Reidar

last: Fossmark

address: Prinsesse Kristinas gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

data_processing:
Base calling were done on the NextSeq 500 instrument by RTA 2.4.6. FASTQ files were generated using bcl2fastq2 Conversion Software v2.17 (Illumina, Inc. San Diego, CA, USA).
Transcript counts were estimated from unfiltered fastq files using Kallisto version 0.42.4 with an index built on the Ensembl GRCm38 cdna sequences. The Kallisto results were imported into the sleuth R-package for further statistical analysis and raw transcript counts were exported to a tab separated file by the command sleuth_to_matrix and options which_df=”obs_raw” and which_units=”est_counts” .
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab separated file with estimated transcript counts from Kallisto/Sleuth. Transcripts in rows and samples in columns.

source_name: HKATPase KO_yf_gastric corpus

extract_protocol:
A sample of the gastric corpus was colleceted, and RNA was extracted using RNeasy Mini kit (Qiagen).
RNA sequencing libraries were prepared using TruSeq Stranded mRNA kit (Illumina).
Libraries were normalized and pooled to 2.0 pM and subjected to clustering on two NextSeq 500 high output flowcells. Finally single read sequencing was performed for 75 cycles on a NextSeq 500 instrument

tag: strain background

value: BalbC

tag: genotype/variation

value: HKATPase KO

value: 13 months

value: yf

value: gastric corpus


title: RNA_ileal_tissue_Sample84_rep1

description: Gene expression from RNA from ileal tissue of Sample84_rep1


title: RNA_ileal_tissue_Sample90_rep1

description: Gene expression from RNA from ileal tissue of Sample90_rep1


title: RNA_ileal_tissue_Sample83_rep1

description: Gene expression from RNA from ileal tissue of Sample83_rep1


title: RNA_ileal_tissue_Sample83_rep2

description: Gene expression from RNA from ileal tissue of Sample83_rep2


title: WT_130_WT_PEG

source_name: wild type_peg_gastric corpus

value: wild type

value: peg


title: RNA_ileal_tissue_Sample82_rep1

description: Gene expression from RNA from ileal tissue of Sample82_rep1


title: KO_144_KO_PEG

source_name: HKATPase KO_peg_gastric corpus


title: WT_150_WT_PEG


title: RNA_ileal_tissue_Sample82_rep2

description: Gene expression from RNA from ileal tissue of Sample82_rep2


title: KO_24_KO_YF


title: RNA_ileal_tissue_Sample81_rep2

description: Gene expression from RNA from ileal tissue of Sample81_rep2


title: WT_99_WT_YF

source_name: wild type_yf_gastric corpus


title: WT_98_WT_YF


title: RNA_ileal_tissue_Sample81_rep1

description: Gene expression from RNA from ileal tissue of Sample81_rep1


title: RNA_ileal_tissue_Sample80_rep2

description: Gene expression from RNA from ileal tissue of Sample80_rep2


title: KO_26_KO_YF


title: KO_29_KO_YF


title: WT121_WT_PEG


title: WT_118_WT_YF


title: RNA_ileal_tissue_Sample80_rep1

description: Gene expression from RNA from ileal tissue of Sample80_rep1


title: RNA_ileal_tissue_Sample79_rep2

description: Gene expression from RNA from ileal tissue of Sample79_rep2


title: KO_36_KO_YF


title: KO_53_KO_PEG


title: WT_172_WT_PEG_2


title: RNA_ileal_tissue_Sample78_rep2

description: Gene expression from RNA from ileal tissue of Sample78_rep2


title: RNA_ileal_tissue_Sample78_rep1

description: Gene expression from RNA from ileal tissue of Sample78_rep1


title: RNA_ileal_tissue_Sample77_rep2

description: Gene expression from RNA from ileal tissue of Sample77_rep2


title: KO_46_KO_PEG


title: KO_143_KO_PEG


title: RNA_ileal_tissue_Sample77_rep1

description: Gene expression from RNA from ileal tissue of Sample77_rep1


title: KO_45_KO_PEG


title: RNA_ileal_tissue_Sample76_rep2

description: Gene expression from RNA from ileal tissue of Sample76_rep2


title: RNA_ileal_tissue_Sample75_rep2

description: Gene expression from RNA from ileal tissue of Sample75_rep2


title: RNA_ileal_tissue_Sample75_rep1

description: Gene expression from RNA from ileal tissue of Sample75_rep1


title: KO_110_KO_PEG


title: RNA_ileal_tissue_Sample76_rep1

description: Gene expression from RNA from ileal tissue of Sample76_rep1


title: KO_37_KO_YF


title: WT_147_WT_PEG


title: KO_27_KO_YF


title: RNA_ileal_tissue_Sample74_rep2

description: Gene expression from RNA from ileal tissue of Sample74_rep2


title: RNA_ileal_tissue_Sample73_rep2

description: Gene expression from RNA from ileal tissue of Sample73_rep2


title: RNA_ileal_tissue_Sample74_rep1

description: Gene expression from RNA from ileal tissue of Sample74_rep1


title: KO_111_KO_PEG


title: RNA_ileal_tissue_Sample79_rep1

description: Gene expression from RNA from ileal tissue of Sample79_rep1


title: WT_129_WT_PEG


title: RNA_ileal_tissue_Sample73_rep1

description: Gene expression from RNA from ileal tissue of Sample73_rep1


title: KO_51_KO_YF


title: RNA_ileal_tissue_Sample72_rep2

description: Gene expression from RNA from ileal tissue of Sample72_rep2


title: RNA_ileal_tissue_Sample72_rep1

description: Gene expression from RNA from ileal tissue of Sample72_rep1


title: WT_92_WT_YF


title: WT_171_WT_YF


title: RNA_ileal_tissue_Sample71_rep1

description: Gene expression from RNA from ileal tissue of Sample71_rep1

value: Male


title: KO_52_KO_PEG


title: RNA_ileal_tissue_Sample70_rep1

description: Gene expression from RNA from ileal tissue of Sample70_rep1

value: female


title: RNA_ileal_tissue_Sample70_rep2

description: Gene expression from RNA from ileal tissue of Sample70_rep2


title: KO_126_KO_PEG


title: RNA_ileal_tissue_Sample69_rep2

description: Gene expression from RNA from ileal tissue of Sample69_rep2


title: KO_32_KO_PEG


title: KO_31_KO_PEG


title: WT_172_WT_PEG_1


title: RNA_ileal_tissue_Sample69_rep1

description: Gene expression from RNA from ileal tissue of Sample69_rep1


title: RNA_ileal_tissue_Sample68_rep1

description: Gene expression from RNA from ileal tissue of Sample68_rep1


title: KO_110_KO_YF


title: RNA_ileal_tissue_Sample67_rep2

description: Gene expression from RNA from ileal tissue of Sample67_rep2


title: WT_149_WT_PEG


title: WT_103_WT_YF


title: KO_109_KO_PEG


title: WT_117_WT_YF


title: WT_128_WT_PEG


title: RNA_ileal_tissue_Sample66_rep2

description: Gene expression from RNA from ileal tissue of Sample66_rep2


title: KO_30_KO_YF


title: RNA_ileal_tissue_Sample65_rep2

description: Gene expression from RNA from ileal tissue of Sample65_rep2


title: RNA_ileal_tissue_Sample67_rep1

description: Gene expression from RNA from ileal tissue of Sample67_rep1


title: RNA_ileal_tissue_Sample71_rep2

description: Gene expression from RNA from ileal tissue of Sample71_rep2


title: WT_93_WT_YF


title: WT_173_WT_PEG


title: RNA_ileal_tissue_Sample65_rep1

description: Gene expression from RNA from ileal tissue of Sample65_rep1


title: RNA_ileal_tissue_Sample64_rep2

description: Gene expression from RNA from ileal tissue of Sample64_rep2


title: WT_86_WT_YF


title: RNA_ileal_tissue_Sample64_rep1

description: Gene expression from RNA from ileal tissue of Sample64_rep1


title: KO_23_KO_YF


title: RNA_ileal_tissue_Sample62_rep2

description: Gene expression from RNA from ileal tissue of Sample62_rep2


title: RNA_ileal_tissue_Sample63_rep1

description: Gene expression from RNA from ileal tissue of Sample63_rep1


title: RNA_ileal_tissue_Sample61_rep2

description: Gene expression from RNA from ileal tissue of Sample61_rep2