title: Bt_B22M_13

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
13_Bt_B22M_564_1

source_name: Bull_untreated control


title: Bt_B22M_16

status: Public on Oct 02 2015

type: RNA

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
16_Bt_B22M_564_4

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing:
Data processed with FeatureExtraction v9.5 and normalized using R2.15.0 statistical software. Data from each matrix were analyzed and filtered separately to avoid any bias.
Normalized with quantile method; 'blank' (no value) corresponds to probes not considered for the normalization step; null corresponds to missing data from analysis and/or probes (genes) that didn't pass the filtering step.

molecule: total RNA

organism: Bos taurus

source_name: Bull_treated TBA(200 mg)+BE2(40 mg)

label_protocol: Amplification and labelling was done according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

extract_protocol: RNA from liver and muscle tissues' aliquots was isolated using Trizol reagent according to manufacturer's instruction and purified according to Qiagen RNeasy Mini Kit protocol for tissue samples.

tag: tissue

value: Muscle

tag: breed

value: Charolais

tag: gender

value: male

tag: age

value: 10-14 months


title: MLL B 34+38-93-

city: Stanford

first: Masayuki

last: Iwasaki

state: CA

address: 265 Campus Drive

department: Pathology

country: USA

institute: Stanford University School of Medicine

hyb_protocol: The array was placed in 45°C hybridization oven, at 60 rpm, and incubated for 17 hours ± 1 hour.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G was used for scanning. It takes approximately 10 minutes to scan each Gene Array.

data_processing: RMA using Custom CDF chip definition files

label: biotin

organism: Homo sapiens

source_name: human MLLr leukemia cells

label_protocol: The Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay is  designed to generate amplified and biotinylated sense-strand DNA targets

extract_protocol: Total RNA was extracted from prospectively isolated cells using Trizol reagent followed by RNeasy MinElute Cleanup Kit

tag: cell type

value: human leukemia cells

tag: cell subtype

value: CD34+CD38-CD93- sorted cells


title: Bt_B22M_22

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
22_Bt_B22M_566_2


title: Bt_B22M_17

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
17_Bt_B22M_565_1


title: Bt_B22M_19

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
19_Bt_B22M_565_3


title: Bt_B22M_20

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
20_Bt_B22M_565_4


title: U87MG_SIRT5KD_rep1

city: shanghai

first: feng

last: li

address: 2005, songhu road

country: China

institute: fudan university

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization

label_protocol: Labeled with Flourolink Cy3

extract_protocol: RNA extraction was performed following the instruction of Trizol RNA Extraction Reagent

tag: cell line


title: Bt_B22M_18

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
18_Bt_B22M_565_2


title: Bt_B22M_15

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
15_Bt_B22M_564_3


title: Bt_B22M_10

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
10_Bt_B22M_563_2


title: Bt_B22M_11

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
11_Bt_B22M_563_3


title: Bt_B22M_8

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
8_Bt_B22M_572_4


title: Bt_B22M_14

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
14_Bt_B22M_564_2


title: Bt_B22M_12

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
12_Bt_B22M_563_4


title: Bt_B22L_30

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
30_Bt_B22L_557_4

value: Liver


title: Bt_B22M_4

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
4_Bt_B22M_571_2


title: Bt_B22L_29

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
29_Bt_B22L_557_3


title: Bt_B22M_1

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
1_Bt_B22M_572_1


title: Bt_B22M_5

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
5_Bt_B22M_571_3


title: Bt_B22M_2

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
2_Bt_B22M_572_2


title: Bt_B22L_28

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
28_Bt_B22L_557_2


title: Bt_B22M_3

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
3_Bt_B22M_571_1


title: Bt_B22L_27

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
27_Bt_B22L_555_4


title: Bt_B22M_6

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
6_Bt_B22M_571_4


title: Bt_B22M_7

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
7_Bt_B22M_572_3


title: Bt_B22M_9

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
9_Bt_B22M_563_1


title: Bt_B22L_26

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
26_Bt_B22L_556_4


title: Bt_B22L_25

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
25_Bt_B22L_556_3


title: Bt_B22L_17

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
17_Bt_B22L_554_3


title: Bt_B22L_23

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
23_Bt_B22L_556_1


title: Bt_B22L_21

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
21_Bt_B22L_555_3


title: Bt_B22L_24

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
24_Bt_B22L_556_2


title: Bt_B22L_19

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
19_Bt_B22L_555_1


title: Bt_B22L_18

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
18_Bt_B22L_554_4


title: Bt_B22L_22

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
22_Bt_B22L_557_1


title: Bt_B22L_16

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
16_Bt_B22L_554_2


title: Bt_B22L_20

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
20_Bt_B22L_555_2


title: Bt_B22L_15

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
15_Bt_B22L_554_1


title: vessel_normotensive_5months_rep2

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

description: total RNA including microRNAs

hyb_protocol: Labeled samples were hybridized on rat 8x15k miRNA microarrays (G4471A-046066, Agilent Technologies), which are based on Sanger miRbase release 19.0.

scan_protocol: After washing, the arrays were scanned in an ozone-free room with an Agilent DNA microarray scanner (G2565CA, Agilent Technologies)

data_processing: Pre-processing and summarization of miRNA probe-level data was done using a modified version of the robust multi-array average (RMA) method with background correction, implemented in version 2.10.0 of the AgiMicroRna Bioconductor package.

organism: Rattus norvegicus

source_name: vessel, normotensive, 5months

label_protocol: 100 ng of total RNA including microRNAs was labeled with Cy3 as described in the “miRNA Microarray System with miRNA Complete Labeling and Hyb Kit Manual” version 2.2 (Agilent Technologies) with the inclusion of spike-ins and the optional desalting step with spin columns (Micro Bio-Spin 6, Bio-Rad)

extract_protocol: Total RNA including microRNAs was isolated using the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. Integrity of the isolated RNA was evaluated using the RNA 6000 Pico kit and Small RNA kit on a BioAnalyzer system (Agilent Technologies).

value: 5 months

tag: condition

value: normotensive

tag: subline

value: WKY/NTac

value: artery


title: vessel_normotensive_6weeks_rep3

description: total RNA including microRNAs

source_name: vessel, normotensive, 6weeks

value: 6 weeks

value: WKY/NCrL


title: vessel_hypertensive_6weeks_rep2

description: total RNA including microRNAs

source_name: vessel, hypertensive, 6weeks

value: hypertensive

value: SHR/NCrL


title: vessel_hypertensive_5months_rep3

description: total RNA including microRNAs

source_name: vessel, hypertensive, 5months

value: SHR/NHsd


title: vessel_normotensive_5months_rep3

description: total RNA including microRNAs


title: vessel_normotensive_5months_rep1

description: total RNA including microRNAs

value: WKY/NHsd


title: vessel_hypertensive_6weeks_rep3

description: total RNA including microRNAs


title: Bt_B22L_14

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
14_Bt_B22L_553_4


title: vessel_hypertensive_6weeks_rep1

description: total RNA including microRNAs

value: SHR/SP


title: vessel_hypertensive_5months_rep2

description: total RNA including microRNAs


title: Bt_B22L_13

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
13_Bt_B22L_553_3

value: Charolais


title: Bt_B22L_11

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
11_Bt_B22L_553_1

value: male


title: Bt_B22L_10

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
10_Bt_B22L_570_4

value: 10-14 months


title: Bt_B22L_9

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
9_Bt_B22L_570_3


title: Bt_B22L_12

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
12_Bt_B22L_553_2


title: vessel_normotensive_6weeks_rep2

description: total RNA including microRNAs


title: vessel_hypertensive_5months_rep1

description: total RNA including microRNAs


title: PANC-1 TVB3166 1.0 µM rep3

city: Menlo Park

first: Timothy

middle: S.

last: Heuer

address: 1050 Hamilton Court

department: Biology

institute: 3-V Biosciences

description: Gene expreession data from PANC-1 tumor cell treated with 1.0 µM TVB-3166 in 0.5% DMSO for 72 hours

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Gene Chip scan files were processed with Expresssion Console to produce probe set analysis results using the MAS5 algorithm

label: Biotin

source_name: PANC-1 tumor cell line, 1.0 µM TVB3166, 72 hours

label_protocol: Affymetrix Enzo Service - 3' Arrays AF720 kits were used for labeling accordign to the manufacture's instructions

growth_protocol: PANC-1 cells were seeded in growth media (DMEM supplemented with 10% FBS, 1% NEAA, 1% L-Glutamine, and 1% Penicillin/Streptomycin). The following day, treatment media with DMSO alone or with TVB-3166 (0.1 or 1.0 µM) was added and cells were incubated for an additional 72 hours.

extract_protocol: Cell were rinsed in PBS, lysed using Qiazol (Qiagen, 79306), and processed using the RNeasy microarray kit (Qiagen ,73304) according to manufacturer’s instructions.

treatment_protocol: One day after cell seeding, growth media was exchanged for treatment media (Advanced MEM (Life technologies, 12492-013) supplemented with 1% charcoal filtered FBS and 1% L-glutamine) with DMSO alone or with TVB-3166 (0.1 or 1.0 µM) was added and cells were incubated for an additional 72 hours.

tag: tumor model

value: Pancreatic adenocarcinoma

tag: kras genotype

tag: treatment

value: 0.1 µM TVB3166, 72 hours


title: Bt_B22L_7

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
7_Bt_B22L_570_1

value: Liver


title: PANC-1 TVB3166 1.0 µM rep2


title: Bt_B22L_5

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
5_Bt_B22L_569_3


title: vessel_normotensive_6weeks_rep2

hyb_protocol: Labeled test samples and common reference were combined and hybridized on SurePrint G3 Rat GE 8x60K microarrays (G4858A-028279, Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: After washing, the arrays were scanned in an ozone-free room with an Agilent DNA microarray scanner (G2565CA, Agilent Technologies). Data was extracted with Feature Extraction software v10.7.3.1 (Agilent Technologies)

data_processing: Data processing was carried out with Bioconductor packages in the statistical software package R (Version 3.0.0). Background correction was performed using the “normexp” method with an offset of 15 to adjust the foreground signal without introducing negative values (limma package). The resulting log ratios were transformed using intensity-dependent loess normalization (limma package). Control probes were down-weighted to zero in the normalization step. Normalized log-ratios for replicate probes were averaged.

label_protocol: 100 ng total RNA per test sample was combined with Spike A and amplified incorporating Cy3 according to the “Agilent Two-Color Microarray-Based Gene Expression  Analysis Guide” version 6.6 using the Quick Amp Labeling Kit (Agilent Technologies). As common reference an equimolar pool of all test samples was made of which 100 ng was amplified as described  above with the exception that Spike B was included and Cy5 was used for labeling. Synthesized cyanine-dye labeled antisense RNA (aRNA) was purified using the RNeasy MinElute Cleanup Kit (Qiagen) before measuring yield and dye incorporation on a NanoDrop ND-1000.

source_name: reference pool

value: reference pool


title: Bt_B22L_8

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
8_Bt_B22L_570_2


title: Bt_B22L_6

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
6_Bt_B22L_569_4


title: PANC-1 TVB3166 0.1 µM rep3

description: Gene expreession data from PANC-1 tumor cell treated with 0.1 µM TVB-3166 in 0.5% DMSO for 72 hours

source_name: PANC-1 tumor cell line, 0.1 µM TVB3166, 72 hours


title: vessel_normotensive_6weeks_rep1

description: total RNA including microRNAs

value: normotensive


title: PANC-1 TVB3166 1.0 µM rep1


title: Bt_B22L_4

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
4_Bt_B22L_568_4


title: PANC-1 TVB3166 0.1 µM rep1

description: Gene expreession data from PANC-1 tumor cell treated with 0.5% DMSO for 72 hours


title: PANC-1 DMSO rep2

source_name: PANC-1 tumor cell line, 0.05% DMSO, 72 hours

value: 0.05% DMSO, 72 hours


title: PANC-1 DMSO rep3


title: Bt_B22L_2

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
2_Bt_B22L_569_2


title: Bt_B22M_26

description:
Tissue aliquots from the muscle biceps brachii were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
26_Bt_B22M_558_4

value: Muscle


title: Chondrocyte_Mock vs Epas1_rep2.

city: Gwangju

first: Jang-Soo

last: Chun

department: School of Life Science

country: South Korea

institute: Gwangju institute of science and technology

description: Biological replicate 2 of 4.

hyb_protocol: 825 ng of Cy3-labelled cRNA and 825 ng of Cy5-labelled cRNA  (specific activity >6.0 pmol Cy3/ug cRNA) were combined and fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) 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: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

organism: Mus musculus

source_name: Mock #2 infected chondrocytes

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Chondrocytes were grown as a monolayer in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and antibiotics

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Chondrocytes at culture day 2 were infected with Ad-Epas1 or mock virus for 2hr at 800 of multiplicity of infection and cultured for 24 hr.

value: day 5

value: Knee articular chndrocytes

tag: strain

source_name: Ad-Eaps1 #2 infected chondrocytes


title: Bt_B22L_1

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
1_Bt_B22L_569_1


title: PANC-1 TVB3166 0.1 µM rep2


title: Chondrocyte_Mock vs Epas1_rep1.

description: Biological replicate 1 of 4.

source_name: Mock #1 infected chondrocytes

source_name: Ad-Eaps1 #1 infected chondrocytes


title: Chondrocyte_Mock vs Epas1_rep4.

description: Biological replicate 4 of 4.

source_name: Mock #4 infected chondrocytes

source_name: Ad-Eaps1 #4 infected chondrocytes


title: Chondrocyte_Mock vs Epas1_rep3.

description: Biological replicate 3 of 4.

source_name: Mock #3 infected chondrocytes

source_name: Ad-Eaps1 #3 infected chondrocytes


title: Mouse_Dienc_Hypoth_E12.5

status: Public on Oct 01 2015

city: Genova

first: Luca

last: Pandolfini

state: Genova

address: Via Enrico Melen 83, Building B

department: Center for Human Technologies

country: Italy

institute: Istituto Italiano di Tecnologia - I

description:
DieHyp
Gene expression of E12.5 mouse Diencephalon/Hypothalamus

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 65Â°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 37Â°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 (G2564C) using one color scan default setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (GE1_107_Sep09 and Grid: 028005_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities. Data were background-corrected and normalized between arrays by means of Bioconductor package limma (Smyth, 2005).

source_name: E12.5 Mouse Diencephalon/Hypothalamus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng of RNA using the LowInput QuickAmp Labeling Kit One-Color (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The protocol of ES neuralization consisted of two steps. In Step-I, dissociated ES cells were washed with DMEM/F12, aggregated in agar-coated culture dishes (65,000 cells per cm2) and cultured as floating aggregates in CDMM for 2 days. The second day, 75% of CDMM was renewed. In Step-II, ES cell aggregates were dissociated and cultured in adhesion (65,000 cells per cm2) on Poly-ornithine and natural mouse Laminin for 4/6 days, changing CDMM daily. CDMM consisted of DMEM/F12 (Invitrogen), 2mM Glutamine, 1mM sodium Pyruvate, 0.1mM non-essential amino acids, 0.05mM β-mercaptoethanol, 100 U/ml Penicillin/Streptomycin supplemented with N2/B27 (no vitamin A; Invitrogen).

extract_protocol: Total RNA was extracted with NucleoSpin RNA II columns (Macherey–Nagel). RNA from three different sets of experiments was pooled. RNA quality was assessed with Agilent Bioanalyzer RNA 6000 Nano kit.

treatment_protocol: Recombinant Human/Mouse/Rat Activin-A (R&D; 10 ng/ml) or SAG (Shh agonist; Santa Cruz Biotechnology; 100 nM) were applied 12hr after the start of Wnt inhibitor treatment (IWR-1-Endo; Calbiochem; 5μM) at 3DIV. Cells were detached by trypsinization, washed and resuspended in PBS, 2% FBS, 2mM EDTA and kept on ice. Rax::GFP+ and Rax::GFP- populations were separated on a S3 Cell sorter (Biorad). Tissues (Cortex, Hypothalamus/Diencephalon and Eye) were dissected from n = 3 mouse embryos (Sv129s6 strain, Taconic) at embryonic day (E)12.5.

value: mixed (male/female)

tag: developmental stage

value: Diencephalon/Hypothalamus

tag: tissue type

value: Tissue


title: E14Tg2A_10DIV_Wi

description:
WiCtrl
Gene expression of control E14Tg2A ES cells at 10 days of in vitro differentiation, after treatment with Wnt Inhibitor

source_name: E14Tg2a at 10DIV, Wi

tag: strain background

value: In vitro


title: K/l-EB5_10DIV_SAGt_RaxN

description:
SAG_RaxN
Gene expression of Rax-negative K/l-EB5 ES cells at 10 days of in vitro differentiation, after treatment with Wnt Inhibitor and Sonic Hedgehog Agonist

source_name: K/l-EB5 at 10DIV, Wi+SAG, RAX-

tag: treated with

value: Wnt inhibitor and Sonic Hedgehog Agonist

value: sorted RAX::GFP-negative ES cells


title: Bt_B22L_3

description:
Tissue aliquots from the liver tissue were aseptically collected after slaughtering the animal, submerged in RNAlater solution and stored at –80 °C until extraction
3_Bt_B22L_568_3

source_name: Bull_untreated control

tag: tissue

value: Charolais

value: male


title: Mouse_Cortex_E12.5

description:
Ctx
Gene expression of E12.5 mouse Cerebral Cortex

source_name: E12.5 Mouse Cortex

value: cortex


title: K/l-EB5_10DIV_WiAct_RaxP

description:
Act_RaxP
Gene expression of Rax-positive  K/l-EB5 ES cells at 10 days of in vitro differentiation, after treatment with Wnt Inhibitor and Activin A

source_name: K/l-EB5 at 10DIV, Wi+Act, RAX+

value: Wnt inhibitor and Activin A

value: sorted RAX::GFP-positive ES cells


title: PANC-1 DMSO rep1

value: Pancreatic adenocarcinoma


title: D3 Mouse 17_forestomach [IP]

city: Ottawa

first: Sarah

last: Labib

state: Ontario

address: 204b-50 Colombine

country: Canada

institute: Health Canada

description: Sample 47

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (300ng) were co-hybridized to Agilent Sureprint G3 Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Microarray slides were scanned using an Agilent DNA Microarray Scanner (G2505B) according to manufacturer's recommendations.  Data was extracted from the scanned images using Feature Extraction Version 10.7.3.1.

data_processing: The log2 of the ratio (sample(Cy5)/reference(Cy3)), using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Male MutaTMMouse, aged ~13 weeks, were individually housed in a plastic film isolator, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine lung, liver, and forestomachs were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (D0 n=4, D1 n=5, D2 n=5, D3 n=5) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.1.

treatment_protocol: Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of indeno(123,cd)pyrene dissolved in olive oil were selected to dose the animals: 12.5 mg/kw-bw/day, 25 mg/kg-bw/day, and 50 mg/kg-bw/day. Control animals were gavaged with olive oil only.   Tissues were collected 72 hours following the final dose.

value: MutaTMMouse

value: ~13 weeks

tag: exposed to

value: D3; 50 mg/kg-bw/day indeno(123,cd)pyrene for 28 days

value: forestomach

tag: tissue collection tiime

value: 72 hrs following the final dose

source_name: Universal Mouse Reference RNA

tag: sample source

value: 11 mouse cell lines

tag: vendor

value: Stratagene, La Jolla, CA, USA

tag: catalog #


title: D1 Mouse 7_forestomach [IP]

description: Sample 45

tag: gender

tag: age

value: D1; 12.5 mg/kg-bw/day indeno(123,cd)pyrene for 28 days


title: D3 Mouse 20_forestomach [IP]

description: Sample 59


title: D0 Mouse 3_forestomach [IP]

description: Sample 56

value: D0; vehicle control


title: K/l-EB5_10DIV_WiAct_RaxN

description:
Act_RaxN
Gene expression of Rax-negative K/l-EB5 ES cells at 10 days of in vitro differentiation, after treatment with Wnt Inhibitor and Activin A

source_name: K/l-EB5 at 10DIV, Wi+Act, RAX-

value: In vitro

tag: cell type


title: Mouse_Eye_E12.5

description:
Eye
Gene expression of E12.5 mouse Eye

source_name: E12.5 Mouse Eye

value: mixed (male/female)

value: eye

value: Tissue


title: D3 Mouse 19_forestomach [IP]

description: Sample 55

value: male


title: D0 Mouse 5_forestomach [IP]

description: Sample 52


title: D2 Mouse 14_forestomach [IP]

description: Sample 54

value: D2; 25 mg/kg-bw/day indeno(123,cd)pyrene for 28 days


title: D2 Mouse 13_forestomach [IP]

description: Sample 50


title: D1 Mouse 10_forestomach [IP]

description: Sample 57


title: D1 Mouse 9_forestomach [IP]

description: Sample 53


title: D1 Mouse 8_forestomach [IP]

description: Sample 49


title: D3 Mouse 18_forestomach [IP]

description: Sample 51


title: D2 Mouse 12_forestomach [IP]

description: Sample 46


title: D2 Mouse 15_forestomach [IP]

description: Sample 58


title: K/l-EB5_10DIV_SAG_RaxP

description:
SAG_RaxP
Gene expression of Rax-positive cells  K/l-EB5 ES at 10 days of in vitro differentiation, after treatment with Wnt Inhibitor and Sonic Hedgehog Agonist

source_name: K/l-EB5 at 10DIV, Wi+SAG, RAX+

value: Wnt inhibitor and Sonic Hedgehog Agonist

value: sorted RAX::GFP-positive ES cells


title: D2 Mouse 11_forestomach [IP]

description: Sample 42

value: MutaTMMouse


title: D3 Mouse 16_forestomach [IP]

description: Sample 43

value: ~13 weeks


title: D0 Mouse 2_forestomach [IP]

description: Sample 44


title: D3 Mouse 17_liver [IP]

description: Sample 39

value: D3; 50 mg/kg-bw/day indeno(123,cd)pyrene for 28 days

value: liver


title: D0 Mouse 1_forestomach [IP]

description: Sample 40

value: forestomach

value: 72 hrs following the final dose


title: D1 Mouse 9_liver [IP]

description: Sample 37

value: 11 mouse cell lines

value: Stratagene, La Jolla, CA, USA


title: D2 Mouse 15_liver [IP]

description: Sample 35


title: D3 Mouse 18_liver [IP]

description: Sample 31


title: D1 Mouse 10_liver [IP]

description: Sample 34

value: D1; 12.5 mg/kg-bw/day indeno(123,cd)pyrene for 28 days


title: D3 Mouse 20_liver [IP]

description: Sample 36


title: D0 Mouse 5_liver [IP]

description: Sample 33

value: D0; vehicle control


title: D1 Mouse 6_forestomach [IP]

description: Sample 41


title: D2 Mouse 14_liver [IP]

description: Sample 38


title: D1 Mouse 6_liver [IP]

description: Sample 22


title: D2 Mouse 12_liver [IP]

description: Sample 27


title: D3 Mouse 19_liver [IP]

description: Sample 32


title: D2 Mouse 13_liver [IP]

description: Sample 30


title: D1 Mouse 7_liver [IP]

description: Sample 26


title: D3 Mouse 16_liver [IP]

description: Sample 24


title: D1 Mouse 8_liver [IP]

description: Sample 29


title: D0 Mouse 2_liver [IP]

description: Sample 25


title: D0 Mouse 1_liver [IP]

description: Sample 21


title: D0 Mouse 3_liver [IP]

description: Sample 28


title: D2 Mouse 15_lung [IP]

description: Sample 19

value: lung


title: D3 Mouse 20_lung [IP]

description: Sample 20


title: D0 Mouse 4_lung [IP]

description: Sample 17


title: D3 Mouse 18_lung [IP]

description: Sample 12


title: D3 Mouse 19_lung [IP]

description: Sample 16


title: D2 Mouse 11_liver [IP]

description: Sample 23


title: D2 Mouse 14_lung [IP]

description: Sample 15


title: D1 Mouse 10_lung [IP]

description: Sample 18


title: D0 Mouse 5_lung [IP]

description: Sample 13


title: D2 Mouse 13_lung [IP]

description: Sample 11


title: D1 Mouse 8_lung [IP]

description: Sample 10


title: D1 Mouse 9_lung [IP]

description: Sample 14


title: D0 Mouse 3_lung [IP]

description: Sample 9


title: D0 Mouse 2_lung [IP]

description: Sample 5


title: D2 Mouse 11_lung [IP]

description: Sample 3


title: D2 Mouse 12_lung [IP]

description: Sample 7


title: D3 Mouse 16_lung [IP]

description: Sample 4


title: D3 Mouse 17_lung [IP]

description: Sample 8


title: D0 Mouse 1_lung [IP]

description: Sample 1


title: D2 Mouse 15_forestomach [DBahA]

description: Sample 33

growth_protocol: Male MutaTMMouse, aged ~10 weeks, were individually housed in a plastic film isolator, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Muring lung and forestomachs were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (D0 n=5, D1 n=5, D2 n=4, D3 n=5) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.

treatment_protocol: Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of dibenz(ah)anthracene dissolved in olive oil were selected to dose the animals: 6.25 mg/kw-bw/day, 12.5 mg/kg-bw/day, and 25 mg/kg-bw/day. Control animals were gavaged with olive oil only.   Tissues were collected 72 hours following the final dose.

value: ~10 weeks

value: D2; 12.5 mg/kg-bw/day dibenz(ah)anthracene for 28 days


title: D1 Mouse 7_lung [IP]

description: Sample 6

value: male


title: D0 Mouse 5_forestomach [DBahA]

description: Sample 35


title: D3 Mouse 19_forestomach [DBahA]

description: Sample 34

value: D3; 25 mg/kg-bw/day dibenz(ah)anthracene for 28 days


title: D0 Mouse 1_forestomach [DBahA]

description: Sample 37


title: D1 Mouse 9_forestomach [DBahA]

description: Sample 32

value: D1; 6.25 mg/kg-bw/day dibenz(ah)anthracene for 28 days


title: D0 Mouse 4_forestomach [DBahA]

description: Sample 31


title: D3 Mouse 18_forestomach rep1 [DBahA]

description: Sample 30


title: D2 Mouse 13_forestomach [DBahA]

description: Sample 29


title: D2 Mouse 12_forestomach [DBahA]

description: Sample 25


title: D3 Mouse 18_forestomach rep2 [DBahA]

description: Sample 38


title: D1 Mouse 8_forestomach [DBahA]

description: Sample 28


title: D1 Mouse 6_lung [IP]

description: Sample 2


title: D0 Mouse 3_forestomach [DBahA]

description: Sample 27


title: D1 Mouse 7_forestomach [DBahA]

description: Sample 24


title: D3 Mouse 16_forestomach [DBahA]

description: Sample 22


title: D3 Mouse 17_forestomach [DBahA]

description: Sample 26


title: D1 Mouse 6_forestomach [DBahA]

description: Sample 20


title: D2 Mouse 11_forestomach [DBahA]

description: Sample 21


title: D0 Mouse 1_lung [DBahA]

description: Sample 18


title: D1 Mouse 10_lung [DBahA]

description: Sample 17


title: D0 Mouse 5_lung [DBahA]

description: Sample 16


title: D2 Mouse 15_lung [DBahA]

description: Sample 14


title: D0 Mouse 2_forestomach [DBahA]

description: Sample 23


title: D3 Mouse 19_lung [DBahA]

description: Sample 15


title: D3 Mouse 18_lung [DBahA]

description: Sample 11


title: D3 Mouse 20_lung [DBahA]

description: Sample 19


title: D2 Mouse 13_lung [DBahA]

description: Sample 10


title: D1 Mouse 6_lung [DBahA]

description: Sample 1


title: D0 Mouse 3_lung [DBahA]

description: Sample 8


title: D3 Mouse 17_lung [DBahA]

description: Sample 7


title: D1 Mouse 8_lung [DBahA]

description: Sample 9


title: D3 Mouse 19_forestomach [Chr]

description: Sample 56

source_name: D3 Mouse 19_forestomach

growth_protocol: Male MutaTMMouse, aged ~14 weeks, were individually housed in a plastic film isolator, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine lung, liver, and forestomachs were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.1.

treatment_protocol: Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of chrysene dissolved in olive oil were selected to dose the animals: 17.5 mg/kw-bw/day, 50 mg/kg-bw/day, and 150 mg/kg-bw/day. Control animals were gavaged with olive oil only.   Tissues were collected 72 hours following the final dose.

value: ~14 weeks; adult

value: D3; 150 mg/kg-bw/day chrysene for 28 days


title: D2 Mouse 11_lung [DBahA]

description: Sample 2

value: MutaTMMouse


title: D1 Mouse 9_lung [DBahA]

description: Sample 13


title: D2 Mouse 12_lung [DBahA]

description: Sample 6


title: D0 Mouse 2_lung [DBahA]

description: Sample 4


title: D2 Mouse 15_forestomach [Chr]

description: Sample 49

source_name: D2 Mouse 15_forestomach

value: D2; 50 mg/kg-bw/day chrysene for 28 days


title: D1 Mouse 7_lung [DBahA]

description: Sample 5


title: D3 Mouse 20_forestomach [Chr]

description: Sample 52

source_name: D3 Mouse 20_forestomach


title: D1 Mouse 10_forestomach [Chr]

description: Sample 51

source_name: D1 Mouse 10_forestomach

value: D1; 17.5 mg/kg-bw/day chrysene for 28 days


title: D2 Mouse 12_forestomach [Chr]

description: Sample 55

source_name: D2 Mouse 12_forestomach

value: forestomach


title: D1 Mouse 9_forestomach [Chr]

description: Sample 48

source_name: D1 Mouse 9_forestomach

value: 72 hrs following the final dose


title: D3 Mouse 16_lung [DBahA]

description: Sample 3

value: 11 mouse cell lines


title: D0 Mouse 2_forestomach [Chr]

description: Sample 53

source_name: D0 Mouse 2_forestomach

value: Stratagene, La Jolla, CA, USA


title: D0 Mouse 5_forestomach [Chr]

description: Sample 50

source_name: D0 Mouse 5_forestomach


title: D1 Mouse 6_forestomach [Chr]

description: Sample 54

source_name: D1 Mouse 6_forestomach


title: D3 Mouse 18_forestomach [Chr]

description: Sample 46

source_name: D3 Mouse 18_forestomach


title: D0 Mouse 4_forestomach [Chr]

description: Sample 47

source_name: D0 Mouse 4_forestomach


title: D1 Mouse 7_forestomach [Chr]

description: Sample 41

source_name: D1 Mouse 7_forestomach


title: D3 Mouse 20_liver [Chr]

description: Sample 34

source_name: D3 Mouse 20_liver

value: liver


title: D0 Mouse 3_forestomach [Chr]

description: Sample 43

source_name: D0 Mouse 3_forestomach

value: D0; vehicle control

source_name: Universal Mouse Reference RNA


title: D2 Mouse 13_forestomach [Chr]

description: Sample 45

source_name: D2 Mouse 13_forestomach


title: D0 Mouse 1_forestomach [Chr]

description: Sample 38

source_name: D0 Mouse 1_forestomach


title: D2 Mouse 11_forestomach [Chr]

description: Sample 39

source_name: D2 Mouse 11_forestomach


title: D0 Mouse 1_liver [Chr]

description: Sample 35

source_name: D0 Mouse 1_liver


title: D0 Mouse 4_lung [DBahA]

description: Sample 12

value: lung


title: D3 Mouse 16_forestomach [Chr]

description: Sample 40

source_name: D3 Mouse 16_forestomach


title: D1 Mouse 10_liver [Chr]

description: Sample 33

source_name: D1 Mouse 10_liver


title: D1 Mouse 8_forestomach [Chr]

description: Sample 44

source_name: D1 Mouse 8_forestomach


title: D1 Mouse 7_liver [Chr]

description: Sample 36

source_name: D1 Mouse 7_liver


title: D2 Mouse 13_liver [Chr]

description: Sample 37

source_name: D2 Mouse 13_liver


title: D3 Mouse 17_forestomach [Chr]

description: Sample 42

source_name: D3 Mouse 17_forestomach


title: D0 Mouse 5_liver [Chr]

description: Sample 32

source_name: D0 Mouse 5_liver


title: D2 Mouse 15_liver [Chr]

description: Sample 30

source_name: D2 Mouse 15_liver


title: D1 Mouse 9_liver [Chr]

description: Sample 29

source_name: D1 Mouse 9_liver


title: D3 Mouse 19_liver [Chr]

description: Sample 31

source_name: D3 Mouse 19_liver


title: D1 Mouse 10_forestomach [DBahA]

description: Sample 36

value: ~10 weeks


title: D3 Mouse 17_liver [Chr]

description: Sample 24

source_name: D3 Mouse 17_liver


title: D0 Mouse 4_liver [Chr]

description: Sample 28

source_name: D0 Mouse 4_liver


title: D3 Mouse 18_liver [Chr]

description: Sample 27

source_name: D3 Mouse 18_liver

source_name: Universal Mouse Reference RNA


title: D2 Mouse 11_liver [Chr]

description: Sample 20

source_name: D2 Mouse 11_liver


title: D0 Mouse 3_liver [Chr]

description: Sample 25

source_name: D0 Mouse 3_liver


title: D0 Mouse 2_liver [Chr]

description: Sample 22

source_name: D0 Mouse 2_liver


title: D1 Mouse 8_liver [Chr]

description: Sample 26

source_name: D1 Mouse 8_liver


title: D2 Mouse 12_liver [Chr]

description: Sample 23

source_name: D2 Mouse 12_liver


title: D3 Mouse 16_liver [Chr]

description: Sample 21

source_name: D3 Mouse 16_liver


title: D3 Mouse 16_lung [Chr]

description: Sample 15

source_name: D3 Mouse 16_lung


title: D3 Mouse 17_lung [Chr]

description: Sample 5

source_name: D3 Mouse 17_lung


title: D1 Mouse 7_lung [Chr]

description: Sample 4

source_name: D1 Mouse 7_lung


title: D1 Mouse 9_lung [Chr]

description: Sample 10

source_name: D1 Mouse 9_lung


title: D1 Mouse 6_lung [Chr]

description: Sample 2

source_name: D1 Mouse 6_lung


title: D2 Mouse 15_lung [Chr]

description: Sample 11

source_name: D2 Mouse 15_lung


title: D0 Mouse 2_lung [Chr]

description: Sample 3

source_name: D0 Mouse 2_lung


title: D3 Mouse 16_forestomach [BkF]

description: Sample 1

growth_protocol: Male MutaTMMouse, aged ~11 weeks, were individually housed in a plastic film isolator, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine lung, liver, and forestomachs were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (D0 n=4, D1 n=3, D2 n=4, D3 n=4) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.

treatment_protocol: Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of benzo(k)fluoranthene dissolved in olive oil were selected to dose the animals: 25 mg/kw-bw/day, 50 mg/kg-bw/day, and 100 mg/kg-bw/day. Control animals were gavaged with olive oil only.   Tissues were collected 72 hours following the final dose.

value: ~11 weeks

value: D3; 100 mg/kg-bw/day benzo(k)fluoranthene for 28 days


title: D0 Mouse 3_lung [Chr]

description: Sample 17

source_name: D0 Mouse 3_lung

value: male


title: D1 Mouse 10_lung [Chr]

description: Sample 14

source_name: D1 Mouse 10_lung


title: D0 Mouse 5_lung [Chr]

description: Sample 13

source_name: D0 Mouse 5_lung


title: D0 Mouse 4_lung [Chr]

description: Sample 9

source_name: D0 Mouse 4_lung

source_name: Universal Mouse Reference RNA


title: D2 Mouse 12_lung [Chr]

description: Sample 18

source_name: D2 Mouse 12_lung


title: D1 Mouse 8_lung [Chr]

description: Sample 6

source_name: D1 Mouse 8_lung


title: D3 Mouse 19_lung [Chr]

description: Sample 12

source_name: D3 Mouse 19_lung


title: D3 Mouse 20_lung [Chr]

description: Sample 16

source_name: D3 Mouse 20_lung


title: D1 Mouse 6_liver [Chr]

description: Sample 19

source_name: D1 Mouse 6_liver


title: D2 Mouse 13_lung [Chr]

description: Sample 7

source_name: D2 Mouse 13_lung


title: D0 Mouse 1_lung [Chr]

description: Sample 1

source_name: D0 Mouse 1_lung


title: D3 Mouse 18_lung [Chr]

description: Sample 8

source_name: D3 Mouse 18_lung


title: D0 Mouse 2_forestomach [BkF]

description: Sample 1


title: D0 Mouse 3_forestomach [BkF]

description: Sample 1


title: D0 Mouse 4_forestomach [BkF]

description: Sample 1


title: D3 Mouse 17_forestomach [BkF]

description: Sample 1


title: D2 Mouse 13_forestomach [BkF]

description: Sample 1

value: D2; 50 mg/kg-bw/day benzo(k)fluoranthene for 28 days


title: D2 Mouse 15_forestomach [BkF]

description: Sample 1


title: D1 Mouse 8_forestomach [BkF]

description: Sample 1

value: D1; 25 mg/kg-bw/day benzo(k)fluoranthene for 28 days


title: D2 Mouse 12_forestomach [BkF]

description: Sample 1


title: D1 Mouse 7_forestomach [BkF]

description: Sample 1


title: D3 Mouse 20_forestomach [BkF]

description: Sample 1


title: D2 Mouse 11_forestomach [BkF]

description: Sample 1


title: D1 Mouse 9_forestomach [BkF]

description: Sample 1


title: D2 Mouse 13_liver [BkF]

description: Sample 1


title: D0 Mouse 1_forestomach [BkF]

description: Sample 1


title: D3 Mouse 20_liver [BkF]

description: Sample 1


title: D3 Mouse 19_liver [BkF]

description: Sample 1


title: D3 Mouse 17_liver [BkF]

description: Sample 1


title: D1 Mouse 8_liver [BkF]

description: Sample 1


title: D3 Mouse 20_lung [BkF]

description: Sample 1


title: D0 Mouse 1_liver [BkF]

description: Sample 1


title: D2 Mouse 13_lung [BkF]

description: Sample 1


title: D3 Mouse 16_liver [BkF]

description: Sample 1


title: D0 Mouse 3_liver [BkF]

description: Sample 1


title: D1 Mouse 9_lung [BkF]

description: Sample 1


title: D1 Mouse 8_lung [BkF]

description: Sample 1


title: D0 Mouse 2_liver [BkF]

description: Sample 1


title: D0 Mouse 2_lung [BkF]

description: Sample 1


title: D1 Mouse 9_liver [BkF]

description: Sample 1


title: D2 Mouse 12_lung [BkF]

description: Sample 1


title: D2 Mouse 11_lung [BkF]

description: Sample 1


title: D2 Mouse 11_liver [BkF]

description: Sample 1


title: D3 Mouse 19_lung [BkF]

description: Sample 1


title: D2 Mouse 12_liver [BkF]

description: Sample 1


title: D3 Mouse 17_lung [BkF]

description: Sample 1


title: D0 Mouse 4_lung [BkF]

description: Sample 1


title: D0 Mouse 3_lung [BkF]

description: Sample 1


title: D3 Mouse 20_forestomach [BghiP]

description: Sample 60

extract_protocol: Mice were anaesthetized under isofluorane followed by exsanguination.  Murine lung, liver, and forestomachs were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from random sections (n=5 per group) using Trizol reagent (Invitrogen) and further purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 2.0 and RINs > 7.0.

treatment_protocol: Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of benzo(ghi)perylene dissolved in olive oil were selected to dose the animals: 6.25 mg/kw-bw/day, 12.5 mg/kg-bw/day, and 25 mg/kg-bw/day. Control animals were gavaged with olive oil only.   Tissues were collected 72 hours following the final dose.

value: D3; 25 mg/kg-bw/day benzo(ghi)perylene for 28 days


title: D2 Mouse 15_lung [BkF]

description: Sample 1

value: MutaTMMouse


title: D1 Mouse 7_lung [BkF]

description: Sample 1


title: D0 Mouse 1_lung [BkF]

description: Sample 1


title: D3 Mouse 16_lung [BkF]

description: Sample 1


title: D1 Mouse 10_forestomach [BghiP]

description: Sample 58

value: D1; 6.25 mg/kg-bw/day benzo(ghi)perylene for 28 days


title: D0 Mouse 5_forestomach [BghiP]

description: Sample 57


title: D2 Mouse 15_forestomach [BghiP]

description: Sample 59

value: D2; 12.5 mg/kg-bw/day benzo(ghi)perylene for 28 days


title: D3 Mouse 19_forestomach [BghiP]

description: Sample 56

value: forestomach


title: D1 Mouse 9_forestomach [BghiP]

description: Sample 54

value: 72 hrs following the final dose


title: D0 Mouse 4_forestomach [BghiP]

description: Sample 53

value: 11 mouse cell lines


title: D3 Mouse 18_forestomach [BghiP]

description: Sample 52

value: Stratagene, La Jolla, CA, USA


title: D0 Mouse 3_forestomach [BghiP]

description: Sample 49


title: D0 Mouse 4_liver [BkF]

description: Sample 1

value: liver


title: D2 Mouse 14_forestomach [BghiP]

description: Sample 55


title: D2 Mouse 14_liver [BghiP]

description: Sample 39


title: D3 Mouse 17_forestomach [BghiP]

description: Sample 48


title: D3 Mouse 20_liver [BghiP]

description: Sample 37


title: D3 Mouse 16_forestomach [BghiP]

description: Sample 44


title: D1 Mouse 7_forestomach [BghiP]

description: Sample 46


title: D2 Mouse 11_forestomach [BghiP]

description: Sample 43


title: D0 Mouse 1_forestomach [BghiP]

description: Sample 41

value: D0; vehicle control


title: D1 Mouse 6_forestomach [BghiP]

description: Sample 42


title: D1 Mouse 8_forestomach [BghiP]

description: Sample 50


title: D2 Mouse 12_forestomach [BghiP]

description: Sample 47


title: D1 Mouse 10_liver [BghiP]

description: Sample 35


title: D0 Mouse 2_liver [BghiP]

description: Sample 38


title: D0 Mouse 3_liver [BghiP]

description: Sample 28


title: D3 Mouse 19_liver [BghiP]

description: Sample 40


title: D2 Mouse 13_forestomach [BghiP]

description: Sample 51


title: D0 Mouse 2_forestomach [BghiP]

description: Sample 45


title: D1 Mouse 9_liver [BghiP]

description: Sample 33


title: D2 Mouse 15_liver [BghiP]

description: Sample 36


title: D0 Mouse 5_liver [BghiP]

description: Sample 34


title: D3 Mouse 17_liver [BghiP]

description: Sample 27


title: D3 Mouse 18_liver [BghiP]

description: Sample 31


title: D2 Mouse 13_liver [BghiP]

description: Sample 30


title: D0 Mouse 4_liver [BghiP]

description: Sample 32


title: D1 Mouse 7_liver [BghiP]

description: Sample 25


title: D2 Mouse 12_liver [BghiP]

description: Sample 26


title: D2 Mouse 11_liver [BghiP]

description: Sample 23


title: D3 Mouse 16_liver [BghiP]

description: Sample 24


title: D1 Mouse 8_liver [BghiP]

description: Sample 29


title: D1 Mouse 6_liver [BghiP]

description: Sample 22


title: D2 Mouse 15_lung [BghiP]

description: Sample 19

value: lung


title: D3 Mouse 18_lung [BghiP]

description: Sample 12

value: ~10 weeks


title: D1 Mouse 9_lung [BghiP]

description: Sample 14


title: D2 Mouse 12_lung [BghiP]

description: Sample 7


title: D1 Mouse 10_lung [BghiP]

description: Sample 18


title: D3 Mouse 20_lung [BghiP]

description: Sample 20


title: D3 Mouse 17_lung [BghiP]

description: Sample 8


title: D3 Mouse 19_lung [BghiP]

description: Sample 16


title: D0 Mouse 5_lung [BghiP]

description: Sample 17


title: D1 Mouse 8_lung [BghiP]

description: Sample 10


title: D3 Mouse 20_forestomach [BbF]

description: Sample 57

growth_protocol: Male MutaTMMouse, aged ~16 weeks, were individually housed in a plastic film isolator, provided with water and food (2012 Teklad Global standard rodent diet) ad libitum, and were subjected to a 12 hour light/dark cycle. All animal procedures were in accordance with the guidelines of the Canadian Council for Animal Care and approved by the Health Canada Animal Care Committee.

treatment_protocol: Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of benzo(b)fluoranthene dissolved in olive oil were selected to dose the animals: 25 mg/kw-bw/day, 50 mg/kg-bw/day, and 100 mg/kg-bw/day. Control animals were gavaged with olive oil only.   Tissues were collected 72 hours following the final dose.

value: ~16 weeks

value: D3; 100 mg/kg-bw/day benz(a)anthracene for 28 days


title: D0 Mouse 1_liver [BghiP]

description: Sample 21

value: male


title: D0 Mouse 4_lung [BghiP]

description: Sample 13


title: D3 Mouse 16_lung [BghiP]

description: Sample 4


title: D1 Mouse 7_lung [BghiP]

description: Sample 6


title: D1 Mouse 6_lung [BghiP]

description: Sample 2


title: D0 Mouse 3_lung [BghiP]

description: Sample 9


title: D2 Mouse 12_forestomach [BbF]

description: Sample 59

value: D2; 50 mg/kg-bw/day benz(a)anthracene for 28 days


title: D2 Mouse 11_lung [BghiP]

description: Sample 3


title: D1 Mouse 9_forestomach [BbF]

description: Sample 58

value: D1; 25 mg/kg-bw/day benz(a)anthracene for 28 days


title: D2 Mouse 14_lung [BghiP]

description: Sample 15


title: D0 Mouse 1_lung [BghiP]

description: Sample 1


title: D1 Mouse 10_forestomach [BbF]

description: Sample 55


title: D0 Mouse 3_forestomach [BbF]

description: Sample 54


title: D0 Mouse 2_lung [BghiP]

description: Sample 5


title: D3 Mouse 17_forestomach [BbF]

description: Sample 53


title: D1 Mouse 7_forestomach [BbF]

description: Sample 52


title: D2 Mouse 15_forestomach [BbF]

description: Sample 56


title: D2 Mouse 13_lung [BghiP]

description: Sample 11


title: D3 Mouse 18_forestomach [BbF]

description: Sample 43


title: D3 Mouse 16_forestomach [BbF]

description: Sample 50


title: D2 Mouse 15_liver [BbF]

description: Sample 34


title: D0 Mouse 2_forestomach [BbF]

description: Sample 51


title: D3 Mouse 19_forestomach [BbF]

description: Sample 46


title: D2 Mouse 11_liver [BbF]

description: Sample 37


title: D1 Mouse 8_forestomach [BbF]

description: Sample 41


title: D0 Mouse 1_forestomach [BbF]

description: Sample 47


title: D3 Mouse 19_liver [BbF]

description: Sample 39


title: D2 Mouse 13_forestomach [BbF]

description: Sample 42


title: D1 Mouse 6_forestomach [BbF]

description: Sample 48


title: D3 Mouse 20_liver [BbF]

description: Sample 35


title: D1 Mouse 10_liver [BbF]

description: Sample 33


title: D2 Mouse 11_forestomach [BbF]

description: Sample 49


title: D0 Mouse 5_forestomach [BbF]

description: Sample 44


title: D0 Mouse 5_liver [BbF]

description: Sample 32


title: D0 Mouse 4_forestomach [BbF]

description: Sample 40


title: D1 Mouse 6_liver [BbF]

description: Sample 36


title: D0 Mouse 2_liver [BbF]

description: Sample 28


title: D2 Mouse 12_liver [BbF]

description: Sample 30


title: D3 Mouse 18_liver [BbF]

description: Sample 38


title: D3 Mouse 17_liver [BbF]

description: Sample 31


title: D1 Mouse 7_liver [BbF]

description: Sample 29


title: D3 Mouse 16_liver [BbF]

description: Sample 27


title: D1 Mouse 9_liver [BbF]

description: Sample 24


title: D2 Mouse 14_lung [BbF]

description: Sample 18


title: D0 Mouse 1_liver [BbF]

description: Sample 26


title: D1 Mouse 8_liver [BbF]

description: Sample 21


title: D2 Mouse 15_lung [BbF]

description: Sample 15


title: D0 Mouse 4_liver [BbF]

description: Sample 23


title: D3 Mouse 19_lung [BbF]

description: Sample 19


title: D3 Mouse 20_lung [BbF]

description: Sample 16


title: D2 Mouse 14_liver [BbF]

description: Sample 25


title: D3 Mouse 18_lung [BbF]

description: Sample 10


title: D0 Mouse 3_lung [BbF]

description: Sample 7


title: D2 Mouse 12_lung [BbF]

description: Sample 5


title: D0 Mouse 2_lung [BbF]

description: Sample 4


title: D0 Mouse 3_liver [BbF]

description: Sample 20


title: D2 Mouse 13_liver [BbF]

description: Sample 22


title: D1 Mouse 6_lung [BbF]

description: Sample 2


title: D0 Mouse 4_lung [BbF]

description: Sample 11


title: D1 Mouse 9_lung [BbF]

description: Sample 12


title: D2 Mouse 11_lung [BbF]

description: Sample 17


title: D0 Mouse 5_lung [BbF]

description: Sample 13


title: D2 Mouse 13_lung [BbF]

description: Sample 9


title: D1 Mouse 8_lung [BbF]

description: Sample 8


title: D1 Mouse 10_lung [BbF]

description: Sample 14


title: D1 Mouse 7_forestomach [BaA]

description: Sample 57

treatment_protocol: Mice were dosed via oral gavage daily for 28 consecutive days. Three different doses of benz(a)anthracene dissolved in olive oil were selected to dose the animals: 20 mg/kw-bw/day, 40 mg/kg-bw/day, and 80 mg/kg-bw/day. Control animals were gavaged with olive oil only.   Tissues were collected 72 hours following the final dose.

value: 10 weeks

value: D1; 20 mg/kg-bw/day benz(a)anthracene for 28 days


title: D3 Mouse 19_forestomach [BaA]

description: Sample 58

value: MutaTMMouse

value: D3; 80 mg/kg-bw/day benz(a)anthracene for 28 days


title: D3 Mouse 17_lung [BbF]

description: Sample 6


title: D3 Mouse 16_lung [BbF]

description: Sample 3


title: D0 Mouse 2_forestomach [BaA]

description: Sample 56

value: forestomach


title: D3 Mouse 18_forestomach [BaA]

description: Sample 49

value: 72 hrs following the final dose


title: D3 Mouse 20_forestomach [BaA]

description: Sample 55

value: 11 mouse cell lines


title: D0 Mouse 1_lung [BbF]

description: Sample 1

value: Stratagene, La Jolla, CA, USA


title: D0 Mouse 4_forestomach [BaA]

description: Sample 50


title: D1 Mouse 9_forestomach [BaA]

description: Sample 51


title: D1 Mouse 10_forestomach [BaA]

description: Sample 53


title: D2 Mouse 13_forestomach [BaA]

description: Sample 48

value: D2; 40 mg/kg-bw/day benz(a)anthracene for 28 days


title: D2 Mouse 15_forestomach [BaA]

description: Sample 54


title: D3 Mouse 17_forestomach [BaA]

description: Sample 45


title: D1 Mouse 8_forestomach [BaA]

description: Sample 47


title: D2 Mouse 14_forestomach [BaA]

description: Sample 52


title: D3 Mouse 16_forestomach [BaA]

description: Sample 43


title: D0 Mouse 1_forestomach [BaA]

description: Sample 40

value: D0; vehicle control


title: D3 Mouse 16_liver [BaA]

description: Sample 39

value: liver


title: D0 Mouse 3_forestomach [BaA]

description: Sample 46


title: D2 Mouse 15_liver [BaA]

description: Sample 36


title: D0 Mouse 5_liver [BaA]

description: Sample 34


title: D2 Mouse 11_forestomach [BaA]

description: Sample 42


title: D0 Mouse 2_liver [BaA]

description: Sample 37


title: D1 Mouse 10_liver [BaA]

description: Sample 35


title: D2 Mouse 12_forestomach [BaA]

description: Sample 44


title: D3 Mouse 17_liver [BaA]

description: Sample 33


title: D1 Mouse 7_liver [BaA]

description: Sample 31


title: D2 Mouse 11_liver [BaA]

description: Sample 30


title: D1 Mouse 6_forestomach [BaA]

description: Sample 41


title: D1 Mouse 8_liver [BaA]

description: Sample 38


title: D2 Mouse 12_liver [BaA]

description: Sample 32


title: D0 Mouse 1_liver [BaA]

description: Sample 28


title: D1 Mouse 6_liver [BaA]

description: Sample 29


title: D2 Mouse 14_forestomach [BbF]

description: Sample 45


title: D3 Mouse 19_liver [BaA]

description: Sample 27


title: D1 Mouse 9_lung [BaA]

description: Sample 11

value: lung


title: D0 Mouse 4_liver [BaA]

description: Sample 24


title: D0 Mouse 4_lung [BaA]

description: Sample 18


title: D2 Mouse 15_lung [BaA]

description: Sample 16


title: D1 Mouse 10_lung [BaA]

description: Sample 15


title: D3 Mouse 16_lung [BaA]

description: Sample 4


title: D2 Mouse 14_liver [BaA]

description: Sample 26


title: D1 Mouse 9_liver [BaA]

description: Sample 25


title: D1 Mouse 7_lung [BaA]

description: Sample 19


title: D0 Mouse 3_liver [BaA]

description: Sample 21


title: D0 Mouse 2_lung [BaA]

description: Sample 5


title: D0 Mouse 3_lung [BaA]

description: Sample 8


title: D3 Mouse 17_lung [BaA]

description: Sample 7


title: D2 Mouse 13_liver [BaA]

description: Sample 22


title: D2 Mouse 14_lung [BaA]

description: Sample 12


title: D1 Mouse 6_lung [BaA]

description: Sample 2


title: D2 Mouse 12_lung [BaA]

description: Sample 6


title: D0 Mouse 5_lung [BaA]

description: Sample 14


title: D2 Mouse 11_lung [BaA]

description: Sample 3


title: Epidermis_control_vs_transgenic_rep1

city: College Station

first: Penny

middle: K

last: Riggs

state: TX

address: 2471 TAMU

department: Animal Science

institute: Texas A&M University

description: Sample name: NT_TG_untr1

hyb_protocol: Agilent hybridization protocol

scan_protocol: Axon GenePix Pro 4200A

data_processing: GeneSpring GX13 Baseline to Median Normalization

label_protocol: Agilent low input linear amp kit

extract_protocol: epidermal RNA, tri-reagent extraction

treatment_protocol: no treatment

value: female

value: FVB

tag: genotype/variation

value: control

value: epidermis


title: D2 Mouse 13_lung [BaA]

description: Sample 10

value: male


title: D3 Mouse 18_lung [BaA]

description: Sample 20

value: 10 weeks


title: D1 Mouse 8_lung [BaA]

description: Sample 9

value: D1; 20 mg/kg-bw/day benz(a)anthracene for 28 days


title: D3 Mouse 19_lung [BaA]

description: Sample 13

value: MutaTMMouse


title: D0 Mouse 1_lung  [BaA]

description: Sample 1


title: D3 Mouse 18_liver [BaA]

description: Sample 23

value: D3; 80 mg/kg-bw/day benz(a)anthracene for 28 days


title: D3 Mouse 20_lung [BaA]

description: Sample 17


title: IC1766

type: genomic

city: Raleigh

first: Ignazio

last: Carbone

state: NC

address: 851 Main Campus Drive, Suite 233

department: Plant Pathology

institute: North Carolina State University - Center for Integrated Fungal Research

description:
NRRL:  62358
IC1766
processed data: dendrogram_data_log_transformed_unnormalized.txt

hyb_protocol: Each sample was analyzed by the Microarray Laboratories of Expression Analysis (Raleigh-Durham NC).  Briefly, 300-350 ng of fragmented genomic DNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix).  The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm.  GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with streptavidin-phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.

scan_protocol: Fluorescent images were detected in a GeneChip® Scanner 3000 and array data was extracted using the GeneChip Operating System v 1.1 (Affymetrix). Arrays images were further inspected for defects or debris. Quality control was based on a comparison of the conformity of hybridization controls, scaling factor, and noise; percent detection metrics were analyzed to determine if any outliers were present.

data_processing: For the parent-offspring trio heat maps (figure5_heatmap_data_log_transformed_loess_normalized.txt), array data for all strains examined using aCGH were imported into JMP genomics (SAS, Cary, NC, USA) for further transformation and normalization.  Data were log2 transformed and normalized using Loess normalization.  Because we are interested in detecting differences in hybridization intensities no background correction was applied.  For the genome-wide dendrogram (dendrogram_data_log_transformed_unnormalized.txt), the A. flavus probe data were log2 transformed, but not normalized.

molecule: genomic DNA

organism: Aspergillus flavus

source_name: mycelia

label_protocol: Genomic DNA was labeled using the BioPrime DNA labeling System (Invitrogen Catalogue No. 18094-011) as follows: (1) fungal DNA in the amount of 300-350 ng was mixed with 60 μl of 2.5X random primers (BioPrime kit) and 132 μl of dH2O, (2) the reaction mixture was denatured in an Eppendorf thermocycler at 99°C for 10 min, and then cooled at 4°C for 15 min, (3) 15 μl of 10X dNTPs containing biotin dCTP and 3 μl Klenow polymerase were added and incubated at 25°C in a thermocycler for 18 h, (4) the reaction mixture was precipitated by adding 15 μl of 3M NaOAc and 400 μl of cold 95% ethanol, followed by incubation at 20°C for 15 min, (5) samples were centrifuged at high speed in a refrigerated microcentrifuge for 20 min, and (6) the pellets were washed with 500 μl ice-cold 70% ethanol, centrifuged, and then vacuum dried with heating for 10 min.  DNA was resuspended in 100 μl of dH2O and 5 μl was used to check the quality of the labeled DNA on a gel.

growth_protocol: Isolates were grown in Potato Dextrose Broth (DifcoTM) for up to 5 days before the mycelia was harvested and lyophilized.

extract_protocol: Total genomic DNA was extracted from freeze-dried mycelia using either the Qiagen maxiprep kit (Qiagen, Valencia, CA) or the MasterPure Yeast DNA Purification Kit (Epicentre Technologies, Madison, WI) following the manufacturer’s protocol.

value: mycelia


title: IC2171

description:
NRRL:  62374
IC2171
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: Chromosomal distribution of Sgo2 in WT

city: Kami

first: Kojiro

last: Ishii

state: Kochi

address: 185 Miyanokuchi, Tosayamada

country: Japan

institute: Kochi University of Technology

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Sgo2-Flag (Cy5) from the Schizosaccharomyces pombe wild-type strain

hyb_protocol: Hybridisation was carried out at 65 °C for 40 h against the KU-LSI Schizosaccharomyces pombe genome tiling array 4x44K_v1.0 (Agilent Technologies) according to the manufacturer’s instructions. The slide was then washed with Wash Buffer 1 for 5 min at room temperature and with Wash Buffer 2 for 5 min at 31 ºC, according to the manufacturer’s instructions (Agilent Technologies), in ozone-depleted surroundings.

scan_protocol: Microarray slide was scanned using the Agilent Microarray Scanner G2505B and Scan Control Software G2565BA, followed by extraction of information from the probe features using Agilent Feature Extraction Software 9.5.1.1.

data_processing: For each data set, intra-array Lowess (intensity-dependent) normalization was performed using the Agilent ChIP Analytics Software 1.3.1, and the enrichment ratios were calculated by dividing the normalised ChIP (Cy5) signals over corresponding WCE (Cy3) signals.

organism: Schizosaccharomyces pombe

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Sgo2-Flag

label_protocol: ChIP-purified DNA was treated with RNase A, flush-ended using T4 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy5-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS. WCE DNA was treated with RNase A, flush-ended using T4 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy3-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS.

growth_protocol: Cells were exponentially grown in YES medium at 32˚C

extract_protocol: Cells were broken by vigorous vortex for 9 min. at 0˚C. Genomic DNA in the cell lysates were sonicated to < 0.5 kb long. After centrifugation (14,000 rpm, 15 min.), cell lysates were collected, and the Sgo2-Flag protein-genomic DNA complex was immunoprecipitated using anti-Flag antibody and Dynabeads M-280 Sheep anti-mouse (Life Technologies). Immunoprecipitates were washed by ChIP-1 buffer twice, by ChIP-1' buffer (50 mM HEPES/KOH(pH7.5), 500 mM NaCl, 1 mM EDTA, 1% Triton, 0.1 % Deoxycholeic acid) twice, by ChIP-2 buffer (10 mM Tris-HCl(pH8.0), 0.25 M LiCl, 1 mM EDTA, 0.5 % NP-40, 0.5 % Deoxycholeic acid) twice, and TE buffer twice. After treatment with RNase and Proteinase K, genomic DNA was purified by phenol-chroloform extraction and ethanol precipitation.

treatment_protocol: Cells were fixed with 3% para-formaldehyde for 30 min. at 32˚C, and the fixation was stopped by 150 mM glycine. Cells were washed for 4 times by ChIP-1 buffer (50 mM HEPES/KOH(pH7.5), 140 mM NaCl, 1 mM EDTA(pH8), 1% TritonX-100, 0.1% Deoxycholeic acid).

tag: genotype

value: h- Sgo2-Flag leu1-32 ura4-D18

tag: chip antibody

value: Flag (mouse monoclonal, clone M2,SIGMA, cat.# F3165, lot# 087K60021)

source_name: Chromatin-input DNA (WCE) for Sgo2-Flag


title: IC301

description:
NRRL:  29530
IC301
processed data: dendrogram_data_log_transformed_unnormalized.txt

tag: strain


title: IC4047

description:
NRRL:  35743
IC4047
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC3655

description:
NRRL:  30797
IC3655
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC3656

description:
NRRL:  58987
IC3656
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC903

description:
ATCC 27788
IC903
processed data: dendrogram_data_log_transformed_unnormalized.txt

organism: Aspergillus oryzae


title: IC902

description:
ATCC 22786
IC902
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC904

description:
NRRL:  5590
IC904
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC2205

description:
NRRL:  62407
IC2205
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC2207

description:
NRRL:  62409
IC2207
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC310

description:
NRRL:  35736
IC310
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1719

description:
NRRL:  62347
IC1719
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1722

description:
NRRL:  62350
IC1722
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC311

description:
NRRL:  35737
IC311
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC201

description:
NRRL:  21882 (=IC201, IC316, afla-guard)
IC201
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1775

description:
NRRL:  62367
IC1775
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC277

description:
NRRL:  29506
IC277
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC313

description:
NRRL:  35739
IC313
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC244

description:
NRRL:  29473
IC244
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1650

description:
NRRL:  62315
IC1650
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC3657

description:
NRRL:  30796
IC3657
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC308

description:
NRRL:  29537
IC308
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC278

description:
NRRL:  29507
IC278
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1179

description:
NRRL:  18543 (=IC1179, AF36)
IC1179
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC640

description:
NRRL:  62727
IC640
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1751

description:
NRRL:  62390
IC1751
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC158

description:
NRRL:  1957
IC158
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC307

description:
NRRL:  29536
IC307
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC899

description:
NRRL:  3357
IC899
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1112

description:
NRRL:  62730
IC1112
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1142

description:
NRRL:  62731
IC1142
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC2209

description:
NRRL:  62411
IC2209
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC796

description:
NRRL:  62729
IC796
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1516

description:
NRRL:  26886
IC1516
processed data: dendrogram_data_log_transformed_unnormalized.txt

organism: Aspergillus nomiae


title: IC1630

description:
NRRL:  NULL
IC1630
processed data: dendrogram_data_log_transformed_unnormalized.txt

organism: Aspergillus parasiticus x Aspergillus flavus


title: IC1169

description:
NRRL:  62732
IC1169
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC720

description:
NRRL:  62728
IC720
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1533

description:
NRRL:  26078
IC1533
processed data: dendrogram_data_log_transformed_unnormalized.txt

organism: Aspergillus tamarii


title: IC1566

description:
NRRL:  26111
IC1566
processed data: dendrogram_data_log_transformed_unnormalized.txt

organism: Aspergillus caelatus


title: IC1616

description:
NRRL:  NULL
IC1616
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1637

description:
NRRL:  NULL
IC1637
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1603

description:
NRRL:  NULL
IC1603
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1612

description:
NRRL:  NULL
IC1612
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC36

description:
NRRL:  29573
IC36
processed data: dendrogram_data_log_transformed_unnormalized.txt

organism: Aspergillus parasiticus


title: IC34

description:
NRRL:  29571
IC34
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC327

description:
NRRL:  35782
IC327
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC31

description:
NRRL:  29568
IC31
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC324

description:
NRRL:  35779
IC324
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC35

description:
NRRL:  29572
IC35
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC65

description:
NRRL:  29602
IC65
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1

description:
NRRL:  29538
IC1
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC33

description:
NRRL:  29570
IC33
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1410

description:
NRRL:  62733
IC1410
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC75

description:
NRRL:  29612
IC75
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: IC1622

description:
NRRL:  NULL
IC1622
processed data: dendrogram_data_log_transformed_unnormalized.txt


title: Hep2_anti-PARN-shRNA_rep1

city: Larissa

first: Nikolaos

last: Balatsos

state: Thessaly

address: Ploutonos 26 & Aiolou str

department: Biochemistry and Biotechnology

country: Greece

institute: University of Thessaly

hyb_protocol: 1.5 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays 44k (014850) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565C) using one color (Cy3) scan setting for expression array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Hep2 cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Hep2 cell line was routinely maintained in MEM (Biosera), supplemented with 10% fetal bovine serum (FBS, Biosera) in a humidified atmosphere of 5% CO2 at 37ºC

extract_protocol: Total RNA was extracted using the TRI Reagent® Protocol (Sigma), following the manufacturer's recommendations

treatment_protocol: Hep2 cells grown into 6-well plates, were transfected with 6μg plasmid DNA containing shRNAs sequences (pLKO.1) designed to silence the selected deadenylase, using cationic liposomes (X-fect, Clontech) according to manufacturer’s instructions. Wild type cells, cells transfected with empty vector or shRNA with no homology to known gene sequences were used as controls. The following shDNA plasmids (MISSION® shRNA, SIGMA) were used to silence the respective deadenylases: PARN (NM_002582), CNOT6 (NM_15455), CNOT7 (NM_013354), CNOT8 (NM_004779), Nocturnin (NM_012118), and non-targeting controls (SHC001 and SHC016). Puromycin selection (6μg/mL) was performed 12h after transfection according to the manufacturer. Cells were harvested 72h upon transfection.

tag: cell line

tag: transfection

value: anti-PARN shRNA


title: Hep2_anti-CNOT7-shRNA_rep1

value: anti-CNOT7 shRNA


title: shRNA-mediated BCAT1 knockdown clone B1 vs control (mock-transfected) SKOV3 clone

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

institute: CHU-Q, Centre de recherche-HDQ

description: Cy3 label sample being the reference

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: control (mock-transfected) SKOV3 clone

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 µg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes.

growth_protocol: SKOV3 cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 (HyClone Europe Ltd, Cramlington, UK) supplemented with 10% heat-inactivated fetal calf serum, 2 mM l-glutamine, 1 mM sodium pyruvate, 100 units/ml penicillin and 100 μg/ml streptomycin (all reagents were from HyClone Europe). Cells were grown as adherent cells in a humidified atmosphere at 37°C in 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

treatment_protocol: The human ovarian adenocarcinoma SKOV3 cell line was stably transfected with BCAT1 shRNA cloned into the pSilencer 4.1 puro vector (Ambion). Viral supernatants were generated by transfecting 293T cells with the shRNA construct and the packaging vectors psPAX2 and pMD2.G (Addgene, Cambridge, MA). SKOV3 cells were stably transfected with the shRNA-BCAT1 plasmid using the ExGen 500 transfection reagent (Fermentas Canada Inc., Burlington ON), according to the manufacturer’s instructions. Cells were consecutively grown for 2 weeks in selection medium containing  0,5 μg/mL puromycin (Wisent, Canada) to isolate stable clones. Cells were also mock-transfected with the pSilencer 4.1 puro vector, and stably transfected clones were isolated as controls.

value: ovarian adenocarcinoma  cell line

source_name: shRNA-BCAT1 knockdown SKOV3 clone B1


title: shRNA-mediated BCAT1 knockdown clone B1 vs control (mock-transfected) SKOV3 clone - dye-swap replica

description: Cy5 label sample being the reference


title: Hep2_empty-vector_rep1

value: empty vector


title: Hep2_anti-NOC-shRNA_rep1

value: anti-NOC shRNA


title: B9_DMSO, biological rep1

city: Berkeley

first: Chao

last: Zhang

address: 91 Bolivar Dr.

institute: Plexxikon Inc.

description:
B9_DMSO_050611
Gene expression data from B9 cells incubated with 0.2% DMSO vehicle control for 17 hours

hyb_protocol: 200ul hybridization solution per GeneChip using GeneChip Hybridization, Wash and Stain Kit. 45˚C, 16hr, 60 rpm rotation in GeneChip hybridization trays using GeneChip Hybridization oven 640. Post Hyb Wash #1: 10 cycles of 2 mixes/cycle with wash buffer A (6x SSPE, 0.01% Tween 20) at 30˚C. Post Hyb Wash #2: 6 cycles of 15 mixes/cycle with wash buffer B ( 100mM MES, 0.1M [Na+], 0.01% Tween 20) at 50˚C. First stain: stain the probe array 5 min in Streptavidin Phycoerytherin (SAPE) solution (Stain Cocktail 1, GeneChip Hybridization, Wash and Stain kit) 30˚C. Second Stain: stain probe array 5 min. in Antibody solution (Stain Cocktail 2, GeneChip Hybridization, Wash and Stain Kit). Third Stain: stain probe array for 5 min. in SAPE solution (Stain Cocktail 1) at 35˚C. Final Wash: 15 cycles of 4 mixes/cycle with wash buffer A at 35˚C. Probe array is filled with Array Holding Buffer (GeneChip Hybridization, Wash and Stain kit).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G with Autoloader. Software: Affymetrix GeneChip Command Console (AGCC) ver. 1.1.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: B9 cells

label_protocol: In-vitro Transcription using the GeneChip 3` IVT Express Kit.

growth_protocol: B9 Cells were plated on 10-cm dishes (x10) at 5 x 106 cells/dish in 12 mL growth media (DMEM+1% L-Glutamine) in the morning, and allowed to adhere. In the afternoon, 2.4 µL of compound (5 mM stocks) was added to the cells for a final concentration of 1 µM. The compounds were incubated with the cells for 17 hours at 37˚C. For harvest, the cells were washed once with PBS, and harvested into 300 µL RLT buffer. The lysates were transferred to microfuge tubes for RNA extraction.

extract_protocol: RNA extraction was performed using Qiagen kit according to the manufacturer's instructions.

treatment_protocol: B9 cells were plated in 1 µM vemurafenib, 1 µM PLX7904 or 0.2% DMSO vehicle control and incubated for 17 hours.

value: cutaneous squamous cell carcinomas

value: B9 cells

tag: treatment

value: DMSO


title: B9_4032, biological rep2

description:
B9_4032B_050611
Gene expression data from B9 cells incubated with PLX4032 (vemurafenib) for 17 hours

value: PLX4032 (vemurafenib)


title: B9_7904, biological rep2

description:
B9_7904B_050611
Gene expression data from B9 cells incubated with PLX7904 for 17 hours


title: shRNA-mediated BCAT1 knockdown clone B2 vs control (mock-transfected) SKOV3 clone - dye-swap replica

description: Cy5 label sample being the reference

source_name: shRNA-BCAT1 knockdown SKOV3 clone B2


title: Hep2_anti-CNOT6-shRNA_rep1

value: anti-CNOT6 shRNA


title: Hep2_non-target-vector_rep1

value: non-target vector


title: Ssbp3 OE-rep2

city: Shanghai

first: Hui

last: Li

address: 320 Yue Yang Road

institute: Shanghai Jiao Tong University School of Medicine

description: SSbp3-2 24/7

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: E14T_Ssbp3 OE

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Mouse E14T ES cells were cultured under feeder-free condition in GMEM (Glasgow's Minimum Essential Medium, Invitrogen) supplemented with 10% FBS (Fetal Bovine Serum, Hyclone), 1 mM sodium pyruvate (Sigma), 0.1 mM NEAA (Non-Essential Amino Acids, Invitrogen), 2 mM L-glutamine (Invitrogen), 100 μM β-mercaptoethanol (Invitrogen), 100 U/mL penicillin and 100 μg/mL streptomycin (Hyclone), 1000 U/mL recombinant LIF (Leukemia Inhibitory Factor, Chemicon).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Duplicated biological mouse ES cell samples transfected with Vector or Ssbp3 plasmid respectively for 96 hours were collected for gene expression profiling.

value: mouse embryonic stem cells

value: overexpression of Ssbp3 for 96 hrs


title: Hep2_anti-CNOT8-shRNA_rep1

value: anti-CNOT8 shRNA


title: shRNA-mediated BCAT1 knockdown clone B2 vs control (mock-transfected) SKOV3 clone

description: Cy3 label sample being the reference


title: B9_4032, biological rep1

description:
B9_4032A_050611
Gene expression data from B9 cells incubated with PLX4032 (vemurafenib) for 17 hours


title: Ssbp3 OE-rep1

description: SSbp3-1 22/7


title: Vector OE-rep2

description: PPY-2 24/7

source_name: E14T_Vector OE

value: overexpression of Vector for 96 hrs


title: Fetal liver, Rb1;p107 DKO, 48h, rep1

city: New York

first: Paul

middle: A

last: Ney

state: NY

address: 310 E 67th St

institute: New York Blood Center

description: Rb1;p107 DKO-4

hyb_protocol: Biotin-labeled cRNA (15ug) was hybridized overnight at 45C to the Mouse Genome 430 2.0 GeneChip array

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Expression values were summarized using the MAS5 algorithm as implemented in the GCOS v1.4 software. Signals were normalized for each array by scaling to a 2% trimmed mean of 500.

source_name: Fetal liver, Rb1;p107 DKO, 48 hour

label_protocol: Total RNA (1-10ug) was processed in the Hartwell Center microarray core according to the Affymetrix eukaryote one-cycle target labeling protocol (P/N 701025 Rev.6).

growth_protocol: Fetal liver cells grown in culture in complete medium (30% fetal bovine serum, 1% deionized bovine serum albumin, 0.001% monothioglycerol, 2 mM glutamine, and penicillin-streptomycin in Iscove’s modified Dulbecco medium) at 37C for 0, 24, and 48 hours.

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

treatment_protocol: The samples were untreated.

value: liver

tag: developmental stage

value: E14.5 fetal

value: Rb1;p107 DKO

tag: culture time

value: 48 hour


title: B9_7904, biological rep1

description:
B9_7904A_050611
Gene expression data from B9 cells incubated with PLX7904 for 17 hours

tag: tissue


title: Fetal liver, Rb1 KO, 24h, rep1

description: Rb1 KO-6

source_name: Fetal liver, Rb1 KO, 24 hour

value: Rb1 KO

value: 24 hour


title: Fetal liver, Rb1 KO, 24h, rep3

description: Rb1 KO-8


title: Fetal liver, Rb1 KO, 24h, rep2

description: Rb1 KO-7


title: Hep2_no-vector_rep1

value: no vector


title: Fetal liver, Rb1;p107 DKO, 24h, rep1

description: Rb1;p107 DKO-3

source_name: Fetal liver, Rb1;p107 DKO, 24 hour


title: Fetal liver, Rb1 KO, 48h, rep1

description: Rb1 KO-10

source_name: Fetal liver, Rb1 KO, 48 hour


title: Fetal liver, Rb1 KO, 48h, rep2

description: Rb1 KO-11


title: Vector OE-rep1

description: PPY-1 22/7


title: Fetal liver, Rb1;p107 DKO, 0h, rep2

description: Rb1;p107 DKO-2

source_name: Fetal liver, Rb1;p107 DKO, 0 hour

value: 0 hour


title: Fetal liver, Rb1 KO, 24h, rep4

description: Rb1 KO-9


title: Fetal liver, p107 KO, 48h, rep1

description: p107 KO-5

source_name: Fetal liver, p107 KO, 48 hour

value: p107 KO


title: Fetal liver, p107 KO, 24h, rep2

description: p107 KO-4

source_name: Fetal liver, p107 KO, 24 hour


title: Fetal liver, wild type, 24h, rep2

description: wild type-5

source_name: Fetal liver, wild type, 24 hour

value: wild type


title: Fetal liver, Rb1 KO, 0h, rep3

description: Rb1 KO-3

source_name: Fetal liver, Rb1 KO, 0 hour


title: Fetal liver, wild type, 48h, rep1

description: wild type-6

source_name: Fetal liver, wild type, 48 hour


title: Fetal liver, Rb1 KO, 0h, rep5

description: Rb1 KO-5


title: Fetal liver, Rb1 KO, 0h, rep4

description: Rb1 KO-4


title: Fetal liver, Rb1;p107 DKO, 0h, rep1

description: Rb1;p107 DKO-1


title: Fetal liver, Rb1 KO, 0h, rep1

description: Rb1 KO-1


title: Fetal liver, Rb1 KO, 0h, rep2

description: Rb1 KO-2


title: Fetal liver, Rb1;p107;p130 TKO, rep6

description: Rb1;p107;p130 TKO-6

source_name: Freshly isolated, unfractionated fetal liver, Rb1;p107;p130 TKO

growth_protocol: Freshly isolated fetal liver cells.


title: Fetal liver, p107 KO, 0h, rep2

description: p107 KO-2

source_name: Fetal liver, p107 KO, 0 hour


title: Fetal liver, wild type, 48h, rep2

description: wild type-7


title: Fetal liver, Rb1;p107;p130 TKO, rep1

description: Rb1;p107;p130 TKO-1


title: Fetal liver, Rb1;p107;p130 TKO, rep4

description: Rb1;p107;p130 TKO-4


title: Fetal liver, p107 KO, 0h, rep1

description: p107 KO-1


title: Fetal liver, Rb1;p130 DKO, rep7

description: Rb1;p130 DKO-7

source_name: Freshly isolated, unfractionated fetal liver, Rb1;p130 DKO

value: Rb1;p130 DKO


title: Fetal liver, wild type, 0h, rep3

description: wild type-3

source_name: Fetal liver, wild type, 0 hour


title: Fetal liver, wild type, 24h, rep1

description: wild type-4


title: Fetal liver, Rb1;p107;p130 TKO, rep5

description: Rb1;p107;p130 TKO-5


title: Fetal liver, p107 KO, 24h, rep1

description: p107 KO-3


title: Fetal liver, wild type, 0h, rep2

description: wild type-2


title: Fetal liver, Rb1;p107;p130 TKO, rep3

description: Rb1;p107;p130 TKO-3


title: Fetal liver, Rb1;p107;p130 TKO, rep2

description: Rb1;p107;p130 TKO-2


title: Fetal liver, Rb1;p130 DKO, rep5

description: Rb1;p130 DKO-5


title: Fetal liver, wild type, 0h, rep1

description: wild type-1


title: Fetal liver, Rb1;p130 DKO, rep6

description: Rb1;p130 DKO-6


title: Fetal liver, Rb1;p130 DKO, rep2

description: Rb1;p130 DKO-2


title: Fetal liver, Rb1;p107 DKO, rep3

description: Rb1;p107 DKO-3

source_name: Freshly isolated, unfractionated fetal liver, Rb1;p107 DKO


title: Fetal liver, Rb1;p130 DKO, rep8

description: Rb1;p130 DKO-8


title: Fetal liver, Rb1;p107 DKO, rep1

description: Rb1;p107 DKO-1


title: Fetal liver, Rb1;p130 DKO, rep1

description: Rb1;p130 DKO-1


title: Fetal liver, Rb1;p107 DKO, rep4

description: Rb1;p107 DKO-4


title: Fetal liver, Rb1;p130 DKO, rep9

description: Rb1;p130 DKO-9


title: Fetal liver, Rb1 KO, rep1

description: Rb1 KO-1

source_name: Freshly isolated, unfractionated fetal liver, Rb1 KO


title: Fetal liver, Rb1;p130 DKO, rep3

description: Rb1;p130 DKO-3


title: Fetal liver, p107;p130 DKO, rep4

description: p107;p130 DKO-4

source_name: Freshly isolated, unfractionated fetal liver, p107;p130 DKO


title: Fetal liver, p107;p130 DKO, rep3

description: p107;p130 DKO-3


title: Fetal liver, Rb1 KO, rep2

description: Rb1 KO-2


title: Fetal liver, p107;p130 DKO, rep6

description: p107;p130 DKO-6


title: Fetal liver, p107 KO, rep1

description: p107 KO-1

source_name: Freshly isolated, unfractionated fetal liver, p107 KO


title: Fetal liver, p107;p130 DKO, rep2

description: p107;p130 DKO-2


title: Fetal liver, Rb1;p130 DKO, rep4

description: Rb1;p130 DKO-4


title: Fetal liver, p130 KO, rep3

description: p130 KO-3

source_name: Freshly isolated, unfractionated fetal liver, p130 KO

value: p130 KO


title: Fetal liver, Rb1;p107 DKO, rep5

description: Rb1;p107 DKO-5


title: Fetal liver, wild type, rep1

description: wild type-1

source_name: Freshly isolated, unfractionated fetal liver, wild type


title: Fetal liver, Rb1;p107 DKO, rep2

description: Rb1;p107 DKO-2


title: Spc1-OP--biological replicate -1

city: Kolkata

first: Geetanjali

last: Sundaram

address: 35 Ballugunje circular road

department: Biochemistry

country: India

institute: University of Calcutta

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit

scan_protocol: Affymetrix Scanner G 300 7G

data_processing: GeneSpring GX12.6

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: total RNA extraction using Epicentre yeast RNA extraction kit


title: control (empty vector OP)-biological replicate -2

value: empty vector


title: Spc1-OP-biological replicate -2


title: Spc1K49R-OP--biological replicate -1


title: Fetal liver, wild type, rep2

description: wild type-2