title: AGH121_2 TBP ChIP-seq (no SM) Repl.2

description:
Biological replicate 2
TBP ChIP-seq (no SM) Repl.2

tag: strain

tag: genotype

tag: antibody


title: p-T7R2

status: Public on Dec 24 2019

type: SRA

city: Thuwal

first: Magdalena

last: Julkowska

state: Makkah

address: KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description:
replicate 2
batch1

library_source: transcriptomic

data_processing:
bcl2fastq v1.8.4 for raw data processing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR genome by Tophat, and quantified in samtools htseq-count
Reads were mapped to TAIR10 genome by TopHat (v2.0.14), with Bowtie (2.1.0.0)
Transcripts were quantified using Samtools ht-seq-count
Counts per million (cpm) were calculated and normalized by the size of the library.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Expression values of cpm (log2 transformed) for each sample.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedling leaf tissue

growth_protocol: Plates each containing about 80 Arabidopsis Col-0 seedlings were grown inside growth chamber (Percival) with 22°C under 16h / 8h of light / dark cycle (~100 μmol m−2 s−1) with 60% relative humidity. The acclimation treatment was applied by subjecting plates with Arabidopsis seedlings into the growth chamber (Percival) with the temperature gradually rising from 22C to 45C over the course of 6 hours (starting at the beginning of the photoperiod) in the light and keep at 45C for 90 mins. Subsequently, the plates were transferred back to a growth chamber with standard (22C) temperature. For the heat shock application, the growth chamber (Percival) was pre-heated to 45C with lighting (~100 μmol m−2 s−1) and 60% relative humidity. Each plate containing 80 acclimated or non-acclimated seedlings was transferred from the control growth condition (22C) chamber to a heated growth chamber (45C) for 90 mins from 1:30 pm to 3:00 pm (7.5 - 9h after the beginning of the photoperiod).

extract_protocol:
RNA extraction was performed for each sample using RNeasy Plant Mini Kit (Qiagen)
2μg of RNA for each sample was used to construct mRNA library following the protocol of Illumina’s TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: We collected samples of 11 time-points. 11 plates each containing about 80 germinated Arabidopsis seedlings were divided into the acclimated and non-acclimated group. At each sampling time-point from the experimental design (Figure 2.2 A), all leaf tissue from the designated plate was harvested and divided into two separate Eppendorf tubes, snap-frozen in liquid nitrogen and stored at -80°C. At day 12 after seed germination, T1 samples were taken right after the start of the photoperiod and before acclimation treatment starts. Plates from acclimated group were exposed to the heat acclimation treatment and samples were taken after 3 h (T2), 6 h (T3) and 7.5 h (T4), while other plates were returned to normal growth conditions and samples were collected two days (T5) and four days (T6) after at 1:30 pm. At day 16, the remaining acclimated and all the non-acclimated plants were exposed to heat shock treatment (45°C for 90 min), and samples were taken before the heat treatment (T7 for acclimated seedlings, T9 for non-acclimated seedlings), at the end of the heat shock (T8 for acclimated seedlings, T10 for non-acclimated seedlings) and two days after the application of heat stress at 1:30pm (T9 for the acclimated seedlings, T11 for non-acclimated seedlings).

tag: time point

tag: cultivar

tag: tissue

value: leaf

tag: sampling temperature


title: ASA01053 intermittent 12 weeks

type: RNA

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

country: USA

institute: Boston University School of Medicine

description: Gene expression from nasal epithelium of ASA01053 (intermittent dosing regimen) at 12 weeks.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.48.0), using R version 3.2.3 and the Brainarray hugene10sthsentrezgcdf R package (version 20.0.0).

label: biotin

organism: Homo sapiens

source_name: brushing of nasal epithelium

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

extract_protocol: Total RNA was isolated using Qiagen miRNeasy Mini Kit following manufacturer’s instruction. Integrity of the RNA samples was assessed by Agilent BioAnalyzer, and purity of the RNA was confirmed using a NanoDrop spectrophotometer.

tag: batch

value: batch 3

tag: subject

tag: dosing regimen

value: intermittent

tag: timepoint

value: 12 weeks

tag: Sex

value: female

tag: age


title: ASA01056 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01056 (continuous dosing regimen) at 12 weeks.

value: continuous

value: male


title: ASA01056 continuous baseline

description: Gene expression from nasal epithelium of ASA01056 (continuous dosing regimen) at baseline.

value: baseline


title: p-T7R1

description:
replicate 1
batch1


title: AGH106_14 Rpb3 ChIP-seq (+SM) Repl. 6

city: Bethesda

first: Alan

middle: G.

last: Hinnubusch

state: MD

address: 6 Center Dr. Bldg 6, Rm 230

institute: NICHD

description:
Biological replicate 6
Rpb3 ChIP-seq (+SM) Repl. 6

library_source: genomic

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive, to map sequences up to 1 kb with maximum accuracy.
Histones H3 and H2B, Rpb3, TBP and Ino80-myc occupancies profiles were created using custom R programs.
The processed data were converted to the bigwig files supplied here: different DNA length exclusion limits were used in the processing (listed with Processed Data Files)
Genome_build: SacCer3

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

growth_protocol: All strains were grown to mid-log phase (OD600 about 0.6 to 0.8) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), sulfometuron (SM) was added at 1µg/ml for 25 min to induce Gcn4, or without adding SM (no SM).

extract_protocol:
The procedure of ChIP-seq has been described in Qiu et al., Genome Research 26:211-225, 2016.
Libraries were prepared using DNA Library Prep Kit for llumina (Cat# E7370) from New England Biolabs.

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 htz1delta::natMX4 INO80-FRB-GFP::hphMX4

value: anti-Rpb3 from NeoClone, Cat# W0012

tag: treatment

value: Formaldehyde-fixed and sonicated


title: AGH121_1 TBP ChIP-seq (no SM) Repl.1

description:
Biological replicate 1
TBP ChIP-seq (no SM) Repl.1

value: MATa his3delta1 leu2delta met15delta ura3delta

value: anti-TBP antibody is a generous gift from Joe Reese


title: AGH106_13 Rpb3 ChIP-seq (+SM) Repl. 5

description:
Biological replicate 5
Rpb3 ChIP-seq (+SM) Repl. 5


title: ASA01053 intermittent baseline

description: Gene expression from nasal epithelium of ASA01053 (intermittent dosing regimen) at baseline.


title: p-T6R2

description:
replicate 2
batch1


title: AGH106_12 Rpb3 ChIP-seq (+SM) Repl. 4

description:
Biological replicate 4
Rpb3 ChIP-seq (+SM) Repl. 4


title: dkfz-RIG-ref-pedGBM-MYCN_19

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_19

hyb_protocol: Illumina

scan_protocol: Illumina

data_processing: Normalization was performed by applying the function preprocessIllumina available in Bioconductor package minfi, matrix processed value definition: Average Beta

label: Cy3, Cy5

source_name: Primary brain tumor tissue

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

tag: methylation class

value: MYCN

tag: gender

tag: location

tag: primary malignancy

tag: pdgfra amplified

tag: cdkn2a/b loss


title: p-T5R2

description:
replicate 2
batch1

tag: time point


title: ASA01052 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01052 (continuous dosing regimen) at 13 weeks.

value: 13 weeks


title: dkfz-RIG-ref-pedGBM-MYCN_20

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_20


title: ASA01053 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01053 (intermittent dosing regimen) at 13 weeks.


title: AGH93_6 Rpb3 ChIP-seq (+SM) Repl. 3

description:
Biological replicate 3
Rpb3 ChIP-seq (+SM) Repl. 3

tag: strain

tag: genotype

tag: antibody


title: ASA01052 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01052 (continuous dosing regimen) at 12 weeks.

tag: batch


title: dkfz-RIG-ref-pedGBM-RTK1_02

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_02


title: dkfz-RIG-ref-pedGBM-RTK1_01

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_01


title: p-T4R2

description:
replicate 2
batch1

tag: cultivar

tag: tissue

tag: sampling temperature


title: AGH93_5 Rpb3 ChIP-seq (+SM) Repl. 2

description:
Biological replicate 2
Rpb3 ChIP-seq (+SM) Repl. 2


title: dkfz-RIG-ref-pedGBM-MYCN_18

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_18


title: AGH121_8 TBP ChIP-seq (no SM) Repl.2

description:
Biological replicate 2
TBP ChIP-seq (no SM) Repl.2

value: MATa his3delta1 leu2delta met15delta ura3delta ino80delta::kanMX4


title: p-T6R1

description:
replicate 1
batch1


title: dkfz-RIG-ref-pedGBM-MYCN_16

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_16


title: AGH93_4 Rpb3 ChIP-seq (+SM) Repl. 1

description:
Biological replicate 1
Rpb3 ChIP-seq (+SM) Repl. 1


title: ASA01051 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01051 (continuous dosing regimen) at 13 weeks.

tag: subject

tag: dosing regimen

tag: timepoint

tag: Sex


title: p-T3R1

description:
replicate 1
batch1


title: dkfz-RIG-ref-pedGBM-MYCN_15

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_15

tag: methylation class

tag: age

tag: gender


title: dkfz-RIG-ref-pedGBM-MYCN_14

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_14

tag: location

tag: primary malignancy

tag: pdgfra amplified


title: ASA01052 continuous baseline

description: Gene expression from nasal epithelium of ASA01052 (continuous dosing regimen) at baseline.


title: p-T2R2

description:
replicate 2
batch1

tag: time point


title: AGH106_10 Rpb3 ChIP-seq (+SM) Repl. 2

tag: strain

tag: genotype

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 INO80-FRB-GFP::hphMX4

tag: treatment


title: ASA01050 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01050 (continuous dosing regimen) at 13 weeks.

tag: batch

value: batch 1


title: AGH106_9 Rpb3 ChIP-seq (+SM) Repl. 1

tag: antibody


title: dkfz-RIG-ref-pedGBM-MYCN_17

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_17

tag: cdkn2a/b loss


title: ASA01051 continuous baseline

description: Gene expression from nasal epithelium of ASA01051 (continuous dosing regimen) at baseline.

value: batch 3

tag: subject


title: dkfz-RIG-ref-pedGBM-MYCN_13

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_13


title: dkfz-RIG-ref-pedGBM-MYCN_12

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_12


title: p-T2R1

description:
replicate 1
batch1

tag: cultivar

tag: tissue

value: leaf

tag: sampling temperature


title: dkfz-RIG-ref-pedGBM-MYCN_11

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_11

tag: methylation class


title: p-T1R2

description:
replicate 2
batch1


title: p-T1R1

description:
replicate 1
batch1


title: ASA01050 continuous baseline

description: Gene expression from nasal epithelium of ASA01050 (continuous dosing regimen) at baseline.

tag: dosing regimen

tag: timepoint

tag: Sex

tag: age


title: ASA01050 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01050 (continuous dosing regimen) at 12 weeks.

value: 12 weeks


title: AGH106_11 Rpb3 ChIP-seq (+SM) Repl. 3

description:
Biological replicate 3
Rpb3 ChIP-seq (+SM) Repl. 3


title: AGH106_7 Rpb3 ChIP-seq (+SM) Repl. 2

description:
Biological replicate 2
Rpb3 ChIP-seq (+SM) Repl. 2

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 htz1delta::natMX4


title: dkfz-RIG-ref-pedGBM-MYCN_10

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_10

tag: gender

tag: location

tag: primary malignancy

tag: pdgfra amplified


title: dkfz-RIG-ref-pedGBM-MYCN_09

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_09


title: ASA01047 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01047 (intermittent dosing regimen) at 13 weeks.

value: intermittent


title: AGH106_17 Rpb3 ChIP-seq (+SM) Repl. 5

description:
Biological replicate 5
Rpb3 ChIP-seq (+SM) Repl. 5

tag: strain

tag: genotype

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6

tag: treatment


title: ASA01047 intermittent 12 weeks

description: Gene expression from nasal epithelium of ASA01047 (intermittent dosing regimen) at 12 weeks.

tag: batch

value: male


title: ASA01047 intermittent baseline

description: Gene expression from nasal epithelium of ASA01047 (intermittent dosing regimen) at baseline.

tag: subject

value: baseline


title: AGH106_16 Rpb3 ChIP-seq (+SM) Repl. 4

description:
Biological replicate 4
Rpb3 ChIP-seq (+SM) Repl. 4

tag: antibody

value: anti-Rpb3 from NeoClone, Cat# W0012


title: dkfz-RIG-ref-pedGBM-MYCN_08

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_08

tag: cdkn2a/b loss


title: AGH106_8 Rpb3 ChIP-seq (+SM) Repl. 3

value: Formaldehyde-fixed and sonicated


title: dkfz-RIG-ref-pedGBM-MYCN_07

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_07


title: AGH106_15 Rpb3 ChIP-seq (+SM) Repl. 3


title: dkfz-RIG-ref-pedGBM-MYCN_06

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_06


title: AGH106_5 Rpb3 ChIP-seq (+SM) Repl. 2


title: AGH106_6 Rpb3 ChIP-seq (+SM) Repl. 1

description:
Biological replicate 1
Rpb3 ChIP-seq (+SM) Repl. 1


title: AGH106_4 Rpb3 ChIP-seq (+SM) Repl. 1


title: dkfz-RIG-ref-pedGBM-MYCN_05

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_05


title: ASA01046 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01046 (continuous dosing regimen) at 12 weeks.

value: batch 2

value: continuous


title: WT_46C_30min_r1

city: Munich

first: Evi

last: Berchtold

address: Amalienstr. 17

department: Institute for Informatics

institute: Ludwig-Maximilians-University Munich

hyb_protocol: 6 µg of fragmented a-RNA were hybridized for 16hr at 45C in a GeneChip hybridization oven 640.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Summarization using RMA excluding all S. pombe probes was carried out using affy R package. Each temperature was processed separately with the control samples of the corresponding batch.

source_name: Yeast wild type cells kept 30min at 46°C

label_protocol: The Affymetrix GeneChip 3' IVT PLUS Reagent Kit Protocol was used for the preparation of biotinylated aRNA from 150 ng of total RNA.

growth_protocol: cells were grown in 50 ml YPD from an OD595 of 0.2 to an OD595 of 0.8

extract_protocol: cells were harvested (1min, 4000 x g, 4°C) and washed one time with 25ml ice cold H2O. The cells were pelleted and the pellets shock frozen in liquid N2. The cells were homogenized using VK05 glass beads (Precellys), and RNA was extracted using Qiagen's RNeasy Mini Kit.

treatment_protocol: cells were submitted to the corresponding thermal stress in a water bath with the corresponding temperature for the corresponding time span

value: cells kept 30min at 46°C

value: MATa; his3D1; leu2D0; met15D0; ura3D0


title: WT_46C_10min_r1

source_name: Yeast wild type cells kept 10min at 46°C

value: cells kept 10min at 46°C


title: WT_46C_10min_r2


title: AGH106_3 Rpb3 ChIP-seq (no SM) Repl. 3

description:
Biological replicate 3
Rpb3 ChIP-seq (no SM) Repl. 3


title: dkfz-RIG-ref-pedGBM-MYCN_04

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_04

value: MYCN


title: ASA01046 continuous baseline

description: Gene expression from nasal epithelium of ASA01046 (continuous dosing regimen) at baseline.


title: AGH106_2 Rpb3 ChIP-seq (no SM) Repl. 2

description:
Biological replicate 2
Rpb3 ChIP-seq (no SM) Repl. 2


title: dkfz-RIG-ref-pedGBM-MYCN_03

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_03


title: WT_46C_30min_r2


title: WT_42C_80min_r2

source_name: Yeast wild type cells kept 80min at 42°C

value: cells kept 80min at 42°C


title: dkfz-RIG-ref-pedGBM-MYCN_02

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_02


title: WT_42C_80min_r1


title: ASA01046 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01046 (continuous dosing regimen) at 13 weeks.

value: 13 weeks


title: ASA01044 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01044 (continuous dosing regimen) at 12 weeks.


title: ASA01044 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01044 (continuous dosing regimen) at 13 weeks.


title: dkfz-RIG-ref-pedGBM-MYCN_01

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-MYCN_01


title: AGH92_12 Rpb3 ChIP-seq (+SM) Repl. 3

description:
Biological replicate 3
Rpb3 ChIP-seq (+SM) Repl. 3

value: MATa his3delta1 leu2delta met15delta ura3delta htz1delta::kanMX4


title: ASA01044 continuous baseline

description: Gene expression from nasal epithelium of ASA01044 (continuous dosing regimen) at baseline.


title: AGH92_11 Rpb3 ChIP-seq (+SM) Repl. 2

description:
Biological replicate 2
Rpb3 ChIP-seq (+SM) Repl. 2


title: dkfz-RIG-ref-DMG_K27_19

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_19


title: WT_42C_1min_r1

source_name: Yeast wild type cells kept 1min at 42°C

value: cells kept 1min at 42°C


title: dkfz-RIG-ref-DMG_K27_20

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_20


title: AGH64_12 Rpb3 ChIP-seq (+SM) Repl. 3

value: MATa his3delta1 leu2delta met15delta ura3delta ino80delta::kanMX4


title: WT_42C_1min_r2


title: WT_42C_40min_r1

source_name: Yeast wild type cells kept 40min at 42°C

value: cells kept 40min at 42°C


title: dkfz-RIG-ref-DMG_K27_18

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_18


title: ASA01042 intermittent 12 weeks

description: Gene expression from nasal epithelium of ASA01042 (intermittent dosing regimen) at 12 weeks.

value: batch 1

value: intermittent

value: 12 weeks


title: WT_42C_10min_r2

source_name: Yeast wild type cells kept 10min at 42°C

value: cells kept 10min at 42°C


title: dkfz-RIG-ref-pedGBM-RTK1_17

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-pedGBM-RTK1_17


title: AGH92_10 Rpb3 ChIP-seq (+SM) Repl. 1

description:
Biological replicate 1
Rpb3 ChIP-seq (+SM) Repl. 1

value: anti-Rpb3 from NeoClone, Cat# W0012

value: Formaldehyde-fixed and sonicated


title: AGH106_1 Rpb3 ChIP-seq (no SM) Repl. 1

description:
Biological replicate 1
Rpb3 ChIP-seq (no SM) Repl. 1

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: WT_42C_40min_r2


title: ASA01041 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01041 (continuous dosing regimen) at 13 weeks.

value: batch 2

value: continuous

value: male


title: dkfz-RIG-ref-DMG_K27_16

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_16


title: ASA01042 intermittent baseline

description: Gene expression from nasal epithelium of ASA01042 (intermittent dosing regimen) at baseline.

value: baseline


title: WT_42C_10min_r1

value: MATa; his3D1; leu2D0; met15D0; ura3D0


title: WT_42C_5min_r2

source_name: Yeast wild type cells kept 5min at 42°C

value: cells kept 5min at 42°C


title: ASA01041 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01041 (continuous dosing regimen) at 12 weeks.


title: AGH64_10 Rpb3 ChIP-seq (+SM) Repl. 1


title: ASA01042 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01042 (intermittent dosing regimen) at 13 weeks.

value: 13 weeks


title: AGH64_11 Rpb3 ChIP-seq (+SM) Repl. 2


title: ASA01039 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01039 (intermittent dosing regimen) at 13 weeks.

value: female


title: dkfz-RIG-ref-DMG_K27_17

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_17


title: ASA01041 continuous baseline

description: Gene expression from nasal epithelium of ASA01041 (continuous dosing regimen) at baseline.


title: WT_42C_5min_r1


title: ASA01039 intermittent 12 weeks

description: Gene expression from nasal epithelium of ASA01039 (intermittent dosing regimen) at 12 weeks.


title: ASA01039 intermittent baseline

description: Gene expression from nasal epithelium of ASA01039 (intermittent dosing regimen) at baseline.


title: dkfz-RIG-ref-DMG_K27_15

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_15


title: AGH48_8 H2B ChIP-seq (+SM) Repl. 2

description:
Biological replicate 2
H2B ChIP-seq (+SM) Repl. 2

value: MATa his3delta1 leu2delta met15delta ura3delta snf2delta::kanMX4

value: anti-histone H2B from abcam, Cat# ab1790


title: ASA01060 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01060 (continuous dosing regimen) at 13 weeks.

value: batch 3


title: dkfz-RIG-ref-DMG_K27_14

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_14


title: WT_42C_3min_r2

source_name: Yeast wild type cells kept 3min at 42°C

value: cells kept 3min at 42°C


title: dkfz-RIG-ref-DMG_K27_13

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_13


title: AGH48_7 H2B ChIP-seq (+SM) Repl. 1

description:
Biological replicate 1
H2B ChIP-seq (+SM) Repl. 1


title: WT_42C_3min_r1


title: dkfz-RIG-ref-DMG_K27_12

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_12


title: AGH61_12 H2B ChIP-seq (+SM) Repl. 3

description:
Biological replicate 3
H2B ChIP-seq (+SM) Repl. 3

value: MATa his3delta1 leu2delta met15delta ura3delta ino80delta::kanMX4


title: AGH48_9 H2B ChIP-seq (+SM) Repl. 3


title: ASA01038 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01038 (continuous dosing regimen) at 13 weeks.

value: batch 1


title: AGH61_11 H2B ChIP-seq (+SM) Repl. 2


title: dkfz-RIG-ref-DMG_K27_10

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_10


title: ASA01037 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01037 (continuous dosing regimen) at 13 weeks.


title: ASA01038 continuous baseline

description: Gene expression from nasal epithelium of ASA01038 (continuous dosing regimen) at baseline.


title: WT_42C_0min_r1

source_name: Yeast wild type cells at 25°C

value: cells at 25°C


title: dkfz-RIG-ref-DMG_K27_09

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_09


title: AGH61_9 H2B ChIP-seq (no SM) Repl. 3

description:
Biological replicate 3
H2B ChIP-seq (no SM) Repl. 3

value: Formaldehyde-fixed and sonicated


title: AGH61_8 H2B ChIP-seq (no SM) Repl. 2

description:
Biological replicate 2
H2B ChIP-seq (no SM) Repl. 2


title: dkfz-RIG-ref-DMG_K27_08

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_08


title: AGH61_10 H2B ChIP-seq (+SM) Repl. 1


title: WT_37C_80min_r2

source_name: Yeast wild type cells kept 80min at 37°C

value: cells kept 80min at 37°C


title: ASA01037 continuous baseline

description: Gene expression from nasal epithelium of ASA01037 (continuous dosing regimen) at baseline.


title: WT_37C_80min_r1


title: dkfz-RIG-ref-DMG_K27_07

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_07


title: AGH61_7 H2B ChIP-seq (no SM) Repl. 1

description:
Biological replicate 1
H2B ChIP-seq (no SM) Repl. 1


title: ASA01037 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01037 (continuous dosing regimen) at 12 weeks.

value: 12 weeks


title: dkfz-RIG-ref-DMG_K27_11

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_11


title: AGH48_6 H2B ChIP-seq (+SM) Repl. 3

value: MATa his3delta1 leu2delta met15delta ura3delta


title: WT_37C_40min_r2

source_name: Yeast wild type cells kept 40min at 37°C

value: cells kept 40min at 37°C


title: ASA01038 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01038 (continuous dosing regimen) at 12 weeks.

value: continuous


title: dkfz-RIG-ref-DMG_K27_06

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_06


title: WT_37C_40min_r3

value: MATa; his3D1; leu2D0; met15D0; ura3D0


title: ASA01036 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01036 (continuous dosing regimen) at 13 weeks.

value: batch 2


title: WT_37C_80min_r3


title: ASA01051 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01051 (continuous dosing regimen) at 12 weeks.


title: WT_37C_40min_r1


title: AGH48_5 H2B ChIP-seq (+SM) Repl. 2

description:
Biological replicate 2
H2B ChIP-seq (+SM) Repl. 2


title: ASA01036 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01036 (continuous dosing regimen) at 12 weeks.


title: ASA01036 continuous baseline

description: Gene expression from nasal epithelium of ASA01036 (continuous dosing regimen) at baseline.

value: baseline


title: dkfz-RIG-ref-DMG_K27_04

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_04


title: AGH48_4 H2B ChIP-seq (+SM) Repl. 1

description:
Biological replicate 1
H2B ChIP-seq (+SM) Repl. 1


title: dkfz-RIG-ref-DMG_K27_03

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_03


title: AGH48_3 H2B ChIP-seq (no SM) Repl. 3

description:
Biological replicate 3
H2B ChIP-seq (no SM) Repl. 3


title: WT_37C_15min_r3

source_name: Yeast wild type cells kept 15min at 37°C

value: cells kept 15min at 37°C


title: WT_37C_15min_r2


title: ASA01031 intermittent 12 weeks

description: Gene expression from nasal epithelium of ASA01031 (intermittent dosing regimen) at 12 weeks.

value: intermittent

value: male


title: WT_37C_15min_r1


title: dkfz-RIG-ref-DMG_K27_01

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_01


title: AGH48_2 H2B ChIP-seq (no SM) Repl. 2

description:
Biological replicate 2
H2B ChIP-seq (no SM) Repl. 2

value: anti-histone H2B from abcam, Cat# ab1790


title: ASA01031 intermittent baseline

description: Gene expression from nasal epithelium of ASA01031 (intermittent dosing regimen) at baseline.


title: dkfz-RIG-ref-DMG_K27_05

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_05


title: AGH100_14 H3 ChIP-seq (+SM) Repl. 6

description:
Biological replicate 6
H3 ChIP-seq (+SM) Repl. 6

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 htz1delta::natMX4 INO80-FRB-GFP::hphMX4

value: anti-histone H3 from abcam, Cat#ab1791


title: dkfz-RIG-ref_G34_20

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_20


title: AGH100_13 H3 ChIP-seq (+SM) Repl. 5

description:
Biological replicate 5
H3 ChIP-seq (+SM) Repl. 5


title: WT_37C_10min_r1

source_name: Yeast wild type cells kept 10min at 37°C

value: cells kept 10min at 37°C


title: WT_37C_10min_r2


title: WT_37C_10min_r3


title: ASA01030 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01030 (intermittent dosing regimen) at 13 weeks.

value: 13 weeks


title: WT_37C_7min_r3

source_name: Yeast wild type cells kept 7min at 37°C

value: cells kept 7min at 37°C


title: ASA01031 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01031 (intermittent dosing regimen) at 13 weeks.

source_name: brushing of nasal epithelium


title: dkfz-RIG-ref_G34_19

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_19


title: ASA01030 intermittent 12 weeks

description: Gene expression from nasal epithelium of ASA01030 (intermittent dosing regimen) at 12 weeks.


title: dkfz-RIG-ref_G34_18

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_18


title: AGH100_12 H3 ChIP-seq (+SM) Repl. 4

description:
Biological replicate 4
H3 ChIP-seq (+SM) Repl. 4

source_name: S. cerevisiae

value: Formaldehyde-fixed and sonicated


title: dkfz-RIG-ref-DMG_K27_02

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref-DMG_K27_02

source_name: Primary brain tumor tissue


title: dkfz-RIG-ref_G34_17

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_17


title: WT_37C_7min_r2


title: AGH82_6 H3 ChIP-seq (+SM) Repl. 3

description:
Biological replicate 3
H3 ChIP-seq (+SM) Repl. 3


title: ASA01029 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01029 (continuous dosing regimen) at 13 weeks.

value: batch 1


title: AGH48_1 H2B ChIP-seq (no SM) Repl. 1

description:
Biological replicate 1
H2B ChIP-seq (no SM) Repl. 1

value: MATa his3delta1 leu2delta met15delta ura3delta


title: WT_42C_0min_r2

value: cells at 25°C


title: ASA01029 continuous baseline

description: Gene expression from nasal epithelium of ASA01029 (continuous dosing regimen) at baseline.

value: continuous


title: WT_37C_7min_r1

value: MATa; his3D1; leu2D0; met15D0; ura3D0


title: ASA01030 intermittent baseline

description: Gene expression from nasal epithelium of ASA01030 (intermittent dosing regimen) at baseline.

value: batch 2


title: AGH82_4 H3 ChIP-seq (+SM) Repl. 1

description:
Biological replicate 1
H3 ChIP-seq (+SM) Repl. 1


title: WT_37C_5min_r3

source_name: Yeast wild type cells kept 5min at 37°C

value: cells kept 5min at 37°C


title: AGH100_11 H3 ChIP-seq (+SM) Repl. 6

description:
Biological replicate 6
H3 ChIP-seq (+SM) Repl. 6

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 INO80-FRB-GFP::hphMX4


title: ASA01027 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01027 (continuous dosing regimen) at 13 weeks.

value: female


title: ASA01027 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01027 (continuous dosing regimen) at 12 weeks.

value: 12 weeks


title: AGH100_10 H3 ChIP-seq (+SM) Repl. 5

description:
Biological replicate 5
H3 ChIP-seq (+SM) Repl. 5


title: ASA01029 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01029 (continuous dosing regimen) at 12 weeks.

value: male


title: dkfz-RIG-ref_G34_12

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_12


title: WT_37C_5min_r1


title: WT_37C_5min_r2


title: ASA01027 continuous baseline

description: Gene expression from nasal epithelium of ASA01027 (continuous dosing regimen) at baseline.

value: baseline


title: ASA01019 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01019 (continuous dosing regimen) at 13 weeks.


title: dkfz-RIG-ref_G34_11

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_11


title: WT_37C_3min_r3

source_name: Yeast wild type cells kept 3min at 37°C

value: cells kept 3min at 37°C


title: dkfz-RIG-ref_G34_16

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_16


title: AGH80_6 H3 ChIP-seq (+SM) Repl. 3

value: anti-histone H3 from abcam, Cat#ab1791


title: AGH82_5 H3 ChIP-seq (+SM) Repl. 2

description:
Biological replicate 2
H3 ChIP-seq (+SM) Repl. 2

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 htz1delta::natMX4 INO80-FRB-GFP::hphMX4


title: WT_37C_3min_r2


title: dkfz-RIG-ref_G34_10

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_10


title: dkfz-RIG-ref_G34_15

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_15


title: WT_37C_3min_r1


title: AGH80_5 H3 ChIP-seq (+SM) Repl. 2


title: dkfz-RIG-ref_G34_14

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_14


title: ASA01018 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01018 (continuous dosing regimen) at 13 weeks.

value: 13 weeks


title: dkfz-RIG-ref_G34_13

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_13


title: WT_37C_1min_r3

source_name: Yeast wild type cells kept 1min at 37°C

value: cells kept 1min at 37°C


title: dkfz-RIG-ref_G34_09

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_09


title: AGH100_9 H3 ChIP-seq (+SM) Repl. 4

description:
Biological replicate 4
H3 ChIP-seq (+SM) Repl. 4

value: Formaldehyde-fixed and sonicated


title: AGH80_4 H3 ChIP-seq (+SM) Repl. 1

description:
Biological replicate 1
H3 ChIP-seq (+SM) Repl. 1


title: AGH100_8 H3 ChIP-seq (+SM) Repl. 6

description:
Biological replicate 6
H3 ChIP-seq (+SM) Repl. 6

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 htz1delta::natMX4


title: dkfz-RIG-ref_G34_08

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_08


title: WT_37C_1min_r2


title: ASA01018 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01018 (continuous dosing regimen) at 12 weeks.

value: batch 1


title: WT_37C_1min_r1


title: dkfz-RIG-ref_G34_07

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_07


title: ASA01019 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01019 (continuous dosing regimen) at 12 weeks.

value: continuous


title: AGH100_7 H3 ChIP-seq (+SM) Repl. 5

description:
Biological replicate 5
H3 ChIP-seq (+SM) Repl. 5


title: ASA01018 continuous baseline

description: Gene expression from nasal epithelium of ASA01018 (continuous dosing regimen) at baseline.


title: AGH98_12 H3 ChIP-seq (+SM) Repl. 3

description:
Biological replicate 3
H3 ChIP-seq (+SM) Repl. 3


title: AGH98_11 H3 ChIP-seq (+SM) Repl. 2

description:
Biological replicate 2
H3 ChIP-seq (+SM) Repl. 2


title: dkfz-RIG-ref_G34_04

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_04


title: ASA01019 continuous baseline

description: Gene expression from nasal epithelium of ASA01019 (continuous dosing regimen) at baseline.


title: WT_25C_r3

value: cells at 25°C

value: MATa; his3D1; leu2D0; met15D0; ura3D0


title: WT_25C_r2


title: ASA01015 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01015 (intermittent dosing regimen) at 13 weeks.

value: intermittent


title: dkfz-RIG-ref_G34_03

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_03


title: AGH98_10 H3 ChIP-seq (+SM) Repl. 1


title: LG-A

city: Utrecht

first: Hessel

last: Honkoop

state: Zuid-Holland

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. (2014) Cell.
(Sample 1,2) Mapped reads were assigned to cells based on barcodes according to the CEL-seq2 protocol (Hashimshony et al., 2016)) In brief, read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier (UMI) and followed by a 24 nt PolyA stretch and a number (<40) of transcript derived bases. Cell specific barcodes are specified in the file "cel-seq2_barcodes.csv", well numbers refer to the 384-well plate in the following ordre: A1 to A24 - B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2, containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded.
(Sample 3,4) Mapped reads were assigned to cells based on barcodes according to the CEL-seq2 protocol (Hashimshony et al., 2016)) In brief, read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier (UMI) and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file "cel-seq2_barcodes.csv".  Read 1 was not used for quantification. Read 2, containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded.
Genome_build: zv9 (with improved 3' annotation, see Junker et al (2014) Cell)
Supplementary_files_format_and_content: text files: read count matrices in which rows correspond to genes and  columns to single cells.

organism: Danio rerio

source_name: Tg(myl7:GFP) 2dpf embryo

extract_protocol:
Live cells were sorted into 384-well plates with Vapor-Lock oil containing a droplet with barcoded primers, spike-in RNA and dNTPs, followed by heat-induced cell lysis and cDNA syntheses using a robotic liquid handler. After cell lysis for 5 minutes at 65C, RT and second strand mixes were distributed with the Nanodrop II liquid handling platform.
Primers consisted of a 24bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific 8bp barcode, the 5' Illumina Truseq small RNA kit adapter and a T7 promoter. After all cells were pooled in one library, the CEL-seq2 protocol was used for librabry prep (Hashimony et al., 2016)

treatment_protocol: Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  (Samples 1,2) Transgenic tg(myl7:GFP) 2dpf embryos (n=200) were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase, followed by TrypLE express treatement. (Samples 3,4) Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates, each well containing 1 cell.

tag: Stage

tag: line

tag: tissue

value: 2dpf zebrafish embryo


title: ASA01015 intermittent 12 weeks

description: Gene expression from nasal epithelium of ASA01015 (intermittent dosing regimen) at 12 weeks.

tag: dosing regimen

tag: timepoint

value: female


title: AGH100_6 H3 ChIP-seq (+SM) Repl. 4


title: dkfz-RIG-ref_G34_06

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_06

tag: methylation class

tag: age


title: WT_25C_r1


title: AGH100_5 H3 ChIP-seq (+SM) Repl. 5

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: ASA01015 intermittent baseline

description: Gene expression from nasal epithelium of ASA01015 (intermittent dosing regimen) at baseline.

tag: Sex


title: dkfz-RIG-ref_G34_02

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_02

tag: gender

tag: location

tag: primary malignancy


title: dkfz-RIG-ref_G34_05

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_05

tag: pdgfra amplified


title: FK2

source_name: Tg(nppa:mCitrine) ventricle 7dpi

value: Adult zebrafish ventricle


title: ASA01011 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01011 (continuous dosing regimen) at 12 weeks.

value: batch 2

value: 12 weeks

value: male


title: LG-B


title: FK1


title: dkfz-RIG-ref_G34_01

description:
Methylation data from radiation-induced glioma and reference cohort
RIG-ref_G34_01


title: HYNYAtx_mms7701+liver

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

data_processing:
Assembled RNA-seq reads with Velvet and Oases.
Mapped on Treefam9 Reference Proteins for protein annotations
Genome_build: Primary transcripts assembled in this study (also uploaded)
Supplementary_files_format_and_content: FASTA file with annotation info; mapped reads with BWA MEM, and count the reads with samtools.

molecule: polyA RNA

organism: Hynobius yangi

source_name: Liver

growth_protocol: Captured in nature

extract_protocol:
The extraction of total RNA was done by lysing the embryos in Trizol reagent (Invitrogen), and purified with Direct-Zol RNA purification kit (Zymo)
RNA sequencing library was constructed according to manufacturer’s instructions (Illumina, San Diego, CA, USA) after polyA enrichment.

treatment_protocol: No additional treatment

tag: developmental stage

value: adult tissue

value: Liver


title: AGH100_4 H3 ChIP-seq (+SM) Repl. 4

description:
Biological replicate 4
H3 ChIP-seq (+SM) Repl. 4

tag: strain

tag: genotype

value: anti-histone H3 from abcam, Cat#ab1791

tag: treatment


title: AGH98_6 H3 ChIP-seq (+SM) Repl. 3

tag: antibody

value: Formaldehyde-fixed and sonicated


title: ASA01010 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01010 (continuous dosing regimen) at 13 weeks.

tag: batch

tag: subject

value: 13 weeks


title: dkfz_RIG_33

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_33

value: m

value: cerebellum

value: MB Group4

value: yes

tag: cdkn2a/b loss


title: ASA01011 continuous baseline

description: Gene expression from nasal epithelium of ASA01011 (continuous dosing regimen) at baseline.

tag: dosing regimen

value: continuous

value: baseline


title: dkfz_RIG_27

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_27

value: MB Group3


title: AGH98_5 H3 ChIP-seq (+SM) Repl. 2

description:
Biological replicate 2
H3 ChIP-seq (+SM) Repl. 2

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: HYNYAtx_mms7701+intestinte

source_name: Intestine

tag: tissue

value: Intestine


title: dkfz_RIG_22

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_22

tag: methylation class

value: f

value: MB

value: no


title: HYNYAtx_mms7700+liver

value: adult tissue


title: HYNUNtx_mms7714+liver

organism: Hynobius unisacculus

value: Liver


title: AGH98_4 H3 ChIP-seq (+SM) Repl. 1

description:
Biological replicate 1
H3 ChIP-seq (+SM) Repl. 1

value: anti-histone H3 from abcam, Cat#ab1791


title: ASA01010 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01010 (continuous dosing regimen) at 12 weeks.

value: batch 1

tag: timepoint

value: 12 weeks

value: male

tag: age


title: AGH100_3 H3 ChIP-seq (no SM) Repl. 3

description:
Biological replicate 3
H3 ChIP-seq (no SM) Repl. 3

value: Formaldehyde-fixed and sonicated


title: dkfz_RIG_21

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_21

value: PXA

tag: gender

value: cerebellum


title: HYNUNtx_mms7712+skin

source_name: Skin

value: Skin


title: AGH100_2 H3 ChIP-seq (no SM) Repl. 2

description:
Biological replicate 2
H3 ChIP-seq (no SM) Repl. 2


title: HYNUNtx_mms7712+liver


title: dkfz_RIG_20

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_20

value: m

tag: location

value: yes


title: dkfz_RIG_19

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_19

tag: primary malignancy


title: AGH100_1 H3 ChIP-seq (no SM) Repl. 1

description:
Biological replicate 1
H3 ChIP-seq (no SM) Repl. 1

value: MATa his3delta1 leu2delta met15delta ura3delta fpr1delta::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: HYNUNtx_mms7712+intestine

value: Intestine


title: ASA01008 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01008 (intermittent dosing regimen) at 13 weeks.

value: intermittent

value: 13 weeks

tag: Sex

value: female


title: dkfz_RIG_18

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_18

value: f

value: parieto-occipital

value: MB

tag: pdgfra amplified


title: HYNQUtx_mmsX002+liver

organism: Hynobius quelpaertensis

tag: developmental stage

value: adult tissue

value: Liver


title: AGH90_12 H3 ChIP-seq (+SM) Repl. 3

description:
Biological replicate 3
H3 ChIP-seq (+SM) Repl. 3

tag: strain

tag: genotype

value: MATa his3delta1 leu2delta met15delta ura3delta htz1delta::kanMX4

value: anti-histone H3 from abcam, Cat#ab1791


title: ASA01008 intermittent 12 weeks

description: Gene expression from nasal epithelium of ASA01008 (intermittent dosing regimen) at 12 weeks.

value: batch 1

value: 12 weeks


title: ASA01007 intermittent 13 weeks

description: Gene expression from nasal epithelium of ASA01007 (intermittent dosing regimen) at 13 weeks.

value: batch 2

value: male


title: dkfz_RIG_17

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_17

value: cerebellum

value: no

value: yes


title: AGH90_11 H3 ChIP-seq (+SM) Repl. 2

tag: antibody

tag: treatment

value: Formaldehyde-fixed and sonicated


title: ASA01010 continuous baseline

description: Gene expression from nasal epithelium of ASA01010 (continuous dosing regimen) at baseline.

tag: batch

tag: subject

value: continuous

value: baseline


title: HYNQUtx_mms7722+liver


title: ASA01007 intermittent 12 weeks

description: Gene expression from nasal epithelium of ASA01007 (intermittent dosing regimen) at 12 weeks.

tag: dosing regimen

value: intermittent


title: AGH90_10 H3 ChIP-seq (+SM) Repl. 1


title: HYNQUtx_mms7722+intestine

tag: tissue

value: Intestine


title: dkfz_RIG_16

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_16

tag: methylation class

value: m

value: MB

tag: cdkn2a/b loss


title: dkfz_RIG_15

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_15

tag: age


title: ASA01007 intermittent baseline

description: Gene expression from nasal epithelium of ASA01007 (intermittent dosing regimen) at baseline.

tag: timepoint


title: HYNLEtx_mms7730+liver

organism: Hynobius leechii

value: adult tissue

value: Liver


title: ASA01003 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01003 (continuous dosing regimen) at 13 weeks.

value: 13 weeks

value: female


title: ASA01008 intermittent baseline

description: Gene expression from nasal epithelium of ASA01008 (intermittent dosing regimen) at baseline.

value: batch 1


title: AGH88_1 H3 ChIP-seq (+SM) Repl. 1

description:
Biological replicate 1
H3 ChIP-seq (+SM) Repl. 1

value: MATa his3delta1 leu2delta met15delta ura3delta ino80delta::kanMX4 pINO80

value: anti-histone H3 from abcam, Cat#ab1791


title: ASA01003 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01003 (continuous dosing regimen) at 12 weeks.

value: batch 2

value: 12 weeks


title: AGH88_12 H3 ChIP-seq (+SM) Repl. 2

description:
Biological replicate 2
H3 ChIP-seq (+SM) Repl. 2

value: MATa his3delta1 leu2delta met15delta ura3delta ino80delta::kanMX4 empty vector


title: AGH88_2 H3 ChIP-seq (+SM) Repl. 2

value: Formaldehyde-fixed and sonicated


title: dkfz_RIG_14

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_14

tag: gender

tag: location

value: cerebellum

value: yes

value: no


title: HYNLEtx_mms7729+liver


title: dkfz_RIG_13

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_13

tag: primary malignancy

value: MB SHH-AD


title: HYNLEtx_mms7730+intestine

value: Intestine


title: AGH88_4 H3 ChIP-seq (+SM) Repl. 1


title: dkfz_RIG_12

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_12

value: PXA

value: m

value: temporal

value: MB

tag: pdgfra amplified


title: ASA01002 continuous 12 weeks

description: Gene expression from nasal epithelium of ASA01002 (continuous dosing regimen) at 12 weeks.

value: continuous

tag: Sex

value: female


title: HYNLEtx_mms7728+liver

tag: developmental stage

value: adult tissue

value: Liver


title: ASA01003 continuous baseline

description: Gene expression from nasal epithelium of ASA01003 (continuous dosing regimen) at baseline.

value: batch 2

value: baseline


title: ASA01002 continuous 13 weeks

description: Gene expression from nasal epithelium of ASA01002 (continuous dosing regimen) at 13 weeks.

value: batch 1

value: 13 weeks


title: HYNLE+HC3tx_mms7662+liver


title: AGH88_10 H3 ChIP-seq (+SM) Repl. 2

tag: strain

tag: genotype

value: MATa his3delta1 leu2delta met15delta ura3delta empty vector

value: anti-histone H3 from abcam, Cat#ab1791

value: Formaldehyde-fixed and sonicated


title: dkfz_RIG_11

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_11

value: cerebellum

value: MB Group4

value: no

value: yes


title: dkfz_RIG_10

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_10

value: m

value: MB Group3


title: ASA01002 continuous baseline

description: Gene expression from nasal epithelium of ASA01002 (continuous dosing regimen) at baseline.

value: continuous


title: AGH88_8 H3 ChIP-seq (+SM) Repl. 1

tag: antibody

tag: treatment


title: Type 2 Diabetes 5

city: Milan

first: Francesco

last: Prattichizzo

address: via Milanese

country: Italy

institute: IRCCS MultiMedica

description:
Test
miRNA

data_processing: Given the lack of a normalizing gene for circulating miRNAs, the 2-Ct expression of the expressed miRNAs was compared to observe the most abundant miRNA in the two groups.

label: FAM

source_name: Plasma

label_protocol: Array: TaqMan Card A mIRNAs  (Applied Biosystem) ;    Instrument: 7900HT Fast Thermocycler (Applied Biosystems).

extract_protocol: RNA extracted with Norgen kit from CD31 positive Extracellular Vescicles isolated from 1 mL of Plasma

tag: sample type

value: CD31+ Extracellular Vescicles


title: dkfz_RIG_09

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_09

value: f

value: cerebellar


title: HYNLE+HC3tx_mms7661+skin

value: adult tissue

value: Skin


title: HYNLE+HC3tx_mms7661+liver

value: Liver


title: AGH88_6 H3 ChIP-seq (no SM) Repl. 2

description:
Biological replicate 2
H3 ChIP-seq (no SM) Repl. 2


title: Type 2 Diabetes 4

description:
Test
miRNA


title: dkfz_RIG_07

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_07

value: ALL


title: Type 2 Diabetes 2

description:
Test
miRNA


title: Type 2 Diabetes 3

description:
Test
miRNA


title: AGH88_5 H3 ChIP-seq (no SM) Repl. 1

description:
Biological replicate 1
H3 ChIP-seq (no SM) Repl. 1

value: MATa his3delta1 leu2delta met15delta ura3delta empty vector


title: dkfz_RIG_06

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_06

value: frontal lobe


title: HYNLE+HC3tx_mms7660+liver


title: dkfz_RIG_05

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_05

value: left frontal


title: Type 2 Diabetes 1

description:
Test
miRNA


title: Healthy Control 5

description:
Control
miRNA


title: AGH61_6 H3 ChIP-seq (+SM) Repl. 3

description:
Biological replicate 3
H3 ChIP-seq (+SM) Repl. 3

value: MATa his3delta1 leu2delta met15delta ura3delta ino80delta::kanMX4

value: anti-histone H3 from abcam, Cat#ab1791

value: Formaldehyde-fixed and sonicated


title: AGH61_5 H3 ChIP-seq (+SM) Repl. 2

description:
Biological replicate 2
H3 ChIP-seq (+SM) Repl. 2


title: HYNLE+HC1tx_mms7666+liver


title: AGH61_4 H3 ChIP-seq (+SM) Repl. 1

description:
Biological replicate 1
H3 ChIP-seq (+SM) Repl. 1


title: dkfz_RIG_04

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_04

value: parietal lobe

value: no


title: AGH61_3 H3 ChIP-seq (no SM) Repl. 3

description:
Biological replicate 3
H3 ChIP-seq (no SM) Repl. 3


title: HYNLE+HC1tx_mms7665+liver


title: Healthy Control 4

description:
Control
miRNA


title: HYNLE+HC1tx_mms7664+liver


title: dkfz_RIG_02

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_02

value: m

value: left parietal

value: yes


title: AGH61_2 H3 ChIP-seq (no SM) Repl. 2


title: dkfz_RIG_03

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_03

value: f


title: HYNLE+HC1tx_mms7665+intestine

value: Intestine


title: Healthy Control 3

description:
Control
miRNA

value: CD31+ Extracellular Vescicles


title: AGH61_1 H3 ChIP-seq (no SM) Repl. 1


title: Healthy Control 2

description:
Control
miRNA


title: dkfz_RIG_01

description:
Methylation data from radiation-induced glioma and reference cohort
RIG_01


title: HYNLE+HC1tx_mms7665+skin

value: adult tissue

value: Skin


title: siBCLAF1_3

status: Public on Dec 23 2019

city: Tianjin

first: Zhenyi

last: Ma

address: 22 Qixiangtai Road

department: Biochemistry and Molecular Biology

country: China

institute: Tianjin Medical University

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 20 -p 16 --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01 Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each sample

growth_protocol: A549 cells were obtained from American Type Culture Collection and were cultured according to the recommended protocols.

extract_protocol:
For A549 cells, total RNA was extracted with TRIZOL (Ambion) The RNA was further purified with two phenol chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260 /A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95 ℃ followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomizedhexamer.

treatment_protocol: A549 cells were stably transduced with lentiviral particles encoding small hairpin RNA (shRNA) targeting BCLAF1 or an irrelevant firefly luciferase shRNA.

tag: cell line

tag: cell type

value: lung carcinoma epithelial cell line

tag: genotype/variation


title: siBCLAF1_2


title: Ctrl_2

value: control


title: M-MDSCs_normal_8mon_rep2

city: shanghai

first: yujuan

last: shen

address: Rui jin Er road

institute: National Institute of Parasitic Diseases

description:
Microarray Analysis of miRNA Expression Profiles after 8 months in normal mice splenic monocytic MDSCs
Control2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-v1_91) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: M-MDSCs, 8mon, normal

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted and purified with a RNeasy Mini Kit (Qiagen, p/n 74104) and quantified using NanoDrop ND-2000 (Thermo Fisher Scientific). RNA integrity was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Splenic M-MDSCs were isolated immediately after the BALB/c mice sacrificed under sterile conditions at 8 months after Echinococcus granulosus protoscoleces infection. Single-cell suspensions were enriched with magnetic cell sorting (MACS; Miltenyi Biotec) according to the manufacturer’s protocol.

value: BALB/c

tag: tissue

value: spleen

value: M-MDSCs

tag: infection

tag: time


title: M-MDSCs_normal_8mon_rep3

description:
Microarray Analysis of miRNA Expression Profiles after 8 months in normal mice splenic monocytic MDSCs
Control3


title: Ctrl_3


title: M-MDSCs_Eg-infected_8mon_rep3

description:
Microarray Analysis of miRNA Expression Profiles after 8 months in Echinococcus granulosus protoscoleces-infected mice splenic monocytic MDSCs
Case3

source_name: M-MDSCs, 8mon, Eg-infected

value: Echinococcus granulosus

value: 8 months after infection


title: Healthy Control 1

description:
Control
miRNA


title: Ctrl_1


title: M-MDSCs_Eg-infected_8mon_rep2

description:
Microarray Analysis of miRNA Expression Profiles after 8 months in Echinococcus granulosus protoscoleces-infected mice splenic monocytic MDSCs
Case2


title: M-MDSCs_normal_8mon_rep1

description:
Microarray Analysis of miRNA Expression Profiles after 8 months in normal mice splenic monocytic MDSCs
Control1


title: M-MDSCs_Eg-infected_8mon_rep1

description:
Microarray Analysis of miRNA Expression Profiles after 8 months in Echinococcus granulosus protoscoleces-infected mice splenic monocytic MDSCs
Case1


title: siBCLAF1_1


title: Male WWE C3

city: Hamilton

first: Andrew

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 unexposed adult male zebrafish as a CONTROL for the WWE experiment, replicate 3.

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.

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.

treatment_protocol:
Pooled livers of unexposed adult male 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).

value: liver

tag: gender

value: male

tag: treatment group


title: Male WWE L3

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

treatment_protocol:
Pooled livers of adult male 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 WWE L1

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


title: Male WWE H3

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

treatment_protocol:
Pooled livers of adult male 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: Male VEN L3

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

treatment_protocol:
Pooled livers of adult male 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: Male VEN H3

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

treatment_protocol:
Pooled livers of adult male 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: Male WWE H1

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


title: Male VEN-ACE C1

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


title: Male WWE C1

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


title: Male WWE L2

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


title: Male MIX L3

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

treatment_protocol:
Pooled livers of adult male 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: Male WWE H2

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


title: Male MIX H1

description: Gene expression in pooled livers of adult male 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 male 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: Male VEN-ACE C3

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


title: Male VEN L2

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


title: Male VEN L1

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


title: Male WWE C2

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


title: Male GEM L2

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

treatment_protocol:
Pooled livers of adult male 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: Male GEM L3

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


title: Male MIX L2

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


title: Male VEN-ACE C2

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


title: Male MIX H3

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


title: Male VEN H2

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


title: Male MIX H2

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


title: Male GEM H2

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

treatment_protocol:
Pooled livers of adult male 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: Male GEM L1

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


title: Male VEN H1

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


title: Male GEM H1

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


title: Male GEM-MIX 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 GEM-MIX 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: RNA_ileal_tissue_Sample157_rep2

city: Los Angeles

first: Alka

last: Potdar

state: CA

address: 110 George Burns Rd

department: Medicine/GI

institute: Cedars-Sinai Medical Center

description: Gene expression from RNA from ileal tissue of Sample157_rep2

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.

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

value: uninvolved small bowel (SB) ileal tissue

tag: age


title: Male CBZ L2

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

treatment_protocol:
Pooled livers of adult male 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: Male GEM-MIX 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 GEM-MIX experiment, replicate 2.


title: Male CBZ H1

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

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: Male CBZ L1

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


title: Male CBZ L3

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


title: RNA_ileal_tissue_Sample156_rep2

description: Gene expression from RNA from ileal tissue of Sample156_rep2


title: Male CBZ C3

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 3.


title: RNA_ileal_tissue_Sample155_rep1

description: Gene expression from RNA from ileal tissue of Sample155_rep1

value: female


title: Male GEM H3

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


title: Male GEM-MIX C3

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 GEM-MIX experiment, replicate 3.


title: RNA_ileal_tissue_Sample157_rep1

description: Gene expression from RNA from ileal tissue of Sample157_rep1


title: RNA_ileal_tissue_Sample156_rep1

description: Gene expression from RNA from ileal tissue of Sample156_rep1


title: RNA_ileal_tissue_Sample154_rep2

description: Gene expression from RNA from ileal tissue of Sample154_rep2


title: Male CBZ H3

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


title: Male MIX L1

description: Gene expression in pooled livers of adult male 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_Sample154_rep1

description: Gene expression from RNA from ileal tissue of Sample154_rep1