title: 2-HeLa control b

value: epithelial

value: HeLa


title: 7-HeLa 52 a

status: Public on Jul 03 2013

type: RNA

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix HG U133 Plus 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450  (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HeLa cells cidofovir resistant (#52), 72h growth

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES

extract_protocol: 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)

treatment_protocol: attached cells (24 h after passaging), grown for 72 h in renewed medium

tag: organ

value: cervix

tag: disease

value: adenocarcinoma

tag: cell type

tag: cell line


title: 30180621_liver_wt_rep1

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: strain

tag: gender

value: male

tag: genotype/variation

value: wild type

tag: age

value: 17 weeks

tag: mouse id

tag: tissue

value: liver


title: 30180622_brain_wt_rep3

description: replicate 3

value: brain


title: 30180626_brain_wt_rep4

description: replicate 4


title: 1-HeLa control a

source_name: HeLa cells, 72h growth


title: 595spVR-24.AVG_Signal

status: Public on Jul 02 2013

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

country: USA

institute: University of Minnesota

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized using gene data analyst (v.7.5)

label_protocol: cDNA was prepared and labeled with the Illumina TotalPrep- 96 RNA Amplification Kit

extract_protocol: total RNA was extracted using QIAshredder and RNeasy RNA purification columns

tag: strain background

value: FVBN crossed with BL/6

value: Bcl-XL/Myc double transgenic

value: Multiple Myeloma derived cell

tag: bortezomib sensitivity

value: resistant

tag: timepoint


title: HRP4

city: Dallas

first: Qiuyue

last: Chen

state: TX

address: 5323 Harry Hines Blvd.

department: Molecular Genetics

institute: UT Southwestern Medical Center

description: Gene expression data from permissive HRP4 cells induced by interferon

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Genechips were scaned on the GeneArray® Scanner or the GeneChip® Scanner 3000

data_processing: MAS5.0 (Algorithm: ExpressionStat 5.0)

source_name: HRP4 cells treated with interferon

label_protocol: First and second strand cDNA was prepared using Superscirpt Choice System (invitrogen). Biotinylated cRNA were prepared using RNA Transcript Labeling Kit (T7) (Enzo)  according to the manufacturer's protocol.

extract_protocol: RNeasy Mini Kit  (Qiagen) was used to extract RNA according to the manufacturer's protocol

treatment_protocol: Cells were treated with 40U/ml of inteferon for 6h.


title: 595spP-24.AVG_Signal

value: sensitive

tag: treated with

value: 33nM bortezomib


title: 595spP-0.AVG_Signal


title: 595spVR-0.AVG_Signal


title: 595spP-16.AVG_Signal


title: 589bmVR-24.AVG_Signal


title: Huh7

description: Gene expression data from nonpermissive Huh7 cells induced by interferon

source_name: Huh7 cells treated with interferon


title: 595spP-8.AVG_Signal


title: 589bmP-8.AVG_Signal


title: 589bmVR-8.AVG_Signal


title: 30180621_brain_wt_rep2

description: replicate 2


title: 22-PHK HPMPC a

source_name: PHK cells, 72h growth + 50µg/ml cidofovir

growth_protocol: cultured at 37°C, 5% CO2 in Keratinocyte Serum Free medium

treatment_protocol: attached cells (24 h after passaging), grown for 72 h in renewed medium + 50 µg/ml cidofovir

value: primary human keratinocytes

value: neonatal foreskin


title: 589bmVR-16.AVG_Signal


title: 595spP-2.AVG_Signal


title: 589bmP-24.AVG_Signal


title: 589bmP-2.AVG_Signal


title: T0_Control.rep1

city: London

first: MARC

last: MARTINEZ-LLORDELLA

address: 3rd Floor Cheyne Wing, Denmark Hill

department: Liver Science Department

country: United Kingdom

institute: King's College London

hyb_protocol: Hybridization protocol was performed by the Genome Core of the J. David Gladstone Institutes according to the manufacturer's instructions.

scan_protocol: Scanning protocol was performed by the Genome Core of the J. David Gladstone Institutes according to the manufacturer's instructions.

data_processing: RMA normalization

source_name: naïve T cells from blood

label_protocol: Labeling protocol was performed by the Genome Core of the J. David Gladstone Institutes according to the manufacturer's instructions.

growth_protocol: Human naïve CD4+ T cells were isolated by FACS sorter and seeded into a 12-well plates at a density of 1x10^6 cells per ml of RMPI-1640 supplemented with 5% human heat-inactivated pooled AB serum.

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

treatment_protocol: The cells were activated with latex beads conjugates to control antibody or antibodies specific for anti-CD3 or to both anti-CD3 and anti-CD28.

value: blood

value: CD4+CD45RA+ T cells

tag: treatment

value: Control

tag: treatment time

value: 0 hours


title: 30180624_brain_wt_rep1

description: replicate 1

value: male


title: 589bmVR-2.AVG_Signal


title: 595spVR-2.AVG_Signal


title: 589bmVR-0.AVG_Signal


title: 595spVR-8.AVG_Signal


title: 589bmP-16.AVG_Signal


title: 589bmP-0.AVG_Signal


title: Huh7

type: genomic

description: wild type Huh7 cells

hyb_protocol: Labeled samples were hybridized at 42˚C for 16-20h.

scan_protocol: Arrays were scaned using the MS 200 Microarray Scanner and the MS 200 Data Collection Software

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan DNA methylation data extraction.

molecule: genomic DNA

source_name: MeDIP DNA from Huh7

label_protocol: 1 µg IP DNA was directly labeled by Klenow random priming with Cy5 and input DNA was labeled with Cy3 using a NimbleGen Dual-Color DNA Labeling Kit.

growth_protocol: cells were maintained in DMEM(HG) with 10% FCS and penicillin and streptomycin

extract_protocol: Genomic DNA was purified using the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer's protocol

treatment_protocol: Huh7 cells are established cell line

tag: medip antibody

tag: medip antibody vendor

value: Diagenode

tag: medip antibody lot#

tag: medip antibody catalog#

source_name: input DNA from Huh7

tag: antibody

value: none (input DNA)


title: 638bm VR 24h.AVG_Signal

description: 638bm VR 24h

source_name: 638bm VR 24h.AVG_Signal

tag: cell line

tag: cell type

value: 33 nM bortezomib


title: 638bm 16h.AVG_Signal

description: 638bm 16h

source_name: 638bm 16h.AVG_Signal

tag: genotype/variation


title: 30180623_brain_Hmgn1_rep1

description: replicate 1

tag: strain

tag: gender

value: Hmgn1 mutant

tag: age

value: 17 weeks

value: brain


title: 595sp 8h.AVG_Signal

description: 595sp 8h

source_name: 595sp 8h.AVG_Signal

tag: strain background

value: FVBN crossed with BL/6

value: Bcl-XL/Myc double transgenic

value: Multiple Myeloma derived cell


title: 638bm 0h.AVG_Signal

description: 638bm 0h

source_name: 638bm 0h.AVG_Signal

tag: bortezomib sensitivity

value: sensitive


title: 638bm 8h.AVG_Signal

description: 638bm 8h

source_name: 638bm 8h.AVG_Signal

tag: timepoint


title: 638bm VR16h.AVG_Signal

description: 638bm VR16h

source_name: 638bm VR16h.AVG_Signal

value: resistant

tag: treated with


title: 595sp VR 0h.AVG_Signal

description: 595sp VR 0h

source_name: 595sp VR 0h.AVG_Signal


title: 595sp VR 24h.AVG_Signal

description: 595sp VR 24h

source_name: 595sp VR 24h.AVG_Signal


title: 4-HeLa HPMPC a

source_name: HeLa cells, 72h growth + 50µg/ml cidofovir

tag: organ

value: cervix

tag: disease

value: adenocarcinoma

value: epithelial

value: HeLa


title: 638bm 2h.AVG_Signal

description: 638bm 2h

source_name: 638bm 2h.AVG_Signal


title: 638bm VR 0h.AVG_Signal

description: 638bm VR 0h

source_name: 638bm VR 0h.AVG_Signal


title: 595spVR-16.AVG_Signal

value: 33nM bortezomib


title: 638bm VR 24h_2.AVG_Signal

description: 638bm VR 24h_2

source_name: 638bm VR 24h_2.AVG_Signal


title: 595sp VR 8h.AVG_Signal

description: 595sp VR 8h

source_name: 595sp VR 8h.AVG_Signal


title: 595sp 2h.AVG_Signal

description: 595sp 2h

source_name: 595sp 2h.AVG_Signal


title: 595sp 24h_2.AVG_Signal

description: 595sp 24h_2

source_name: 595sp 24h_2.AVG_Signal


title: 595sp 24h.AVG_Signal

description: 595sp 24h

source_name: 595sp 24h.AVG_Signal


title: 638bm 24h.AVG_Signal

description: 638bm 24h

source_name: 638bm 24h.AVG_Signal


title: 595sp VR 2h.AVG_Signal

description: 595sp VR 2h

source_name: 595sp VR 2h.AVG_Signal


title: 595sp VR 24h_2.AVG_Signal

description: 595sp VR 24h_2

source_name: 595sp VR 24h_2.AVG_Signal


title: 595sp 16h.AVG_Signal

description: 595sp 16h

source_name: 595sp 16h.AVG_Signal


title: 211At_kidney_medulla_0.64_kBq_#3

city: Gothenburg

first: Britta

last: Langen

address: Gula stråket 2B

department: Department of Radiation Physics

country: Sweden

institute: Sahlgrenska Academy at University of Gothenburg

data_processing: The data were normalized using quantile normalization with BASE.

source_name: Mouse kidney medulla, 0.64 kBq, 24h

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

value: Balb/c

tag: tissue

value: Mouse kidney medulla

tag: injected activity

tag: nuclide


title: PML003

city: Memphis

first: Shann-Ching

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

description:
JD0138-AMD-v5-U133A
t(15:17)-#12  (identifier used in PMID:15226186)

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

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. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microgram of total RNA (Expression Analysis Technical Manual 701025 rev1, 2001, Affymetrix)

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from AML cases

extract_protocol: Trizol

tag: disease state

value: AML

tag: subtype

value: PML-RARalpha

tag: cytogenetics

tag: fab

tag: kras status

value: KRAS wild type

tag: nras status

value: NRAS wild type


title: 638bm 24h_2.AVG_Signal

description: 638bm 24h_2

source_name: 638bm 24h_2.AVG_Signal

tag: genotype/variation

tag: cell line

tag: cell type

value: 33 nM bortezomib


title: 638bm VR 2h.AVG_Signal

description: 638bm VR 2h

source_name: 638bm VR 2h.AVG_Signal

tag: strain background

value: FVBN crossed with BL/6

tag: bortezomib sensitivity


title: 595sp VR 16h.AVG_Signal

description: 595sp VR 16h

source_name: 595sp VR 16h.AVG_Signal

value: Bcl-XL/Myc double transgenic

tag: treated with

tag: timepoint


title: PML002

description:
JD0136-AMD-v5-U133A
t(15:17)-#11  (identifier used in PMID:15226186)


title: 211At_kidney_medulla_0.64_kBq_#2

tag: strain


title: 638bm VR 8h.AVG_Signal

description: 638bm VR 8h

source_name: 638bm VR 8h.AVG_Signal

value: Multiple Myeloma derived cell


title: 211At_kidney_medulla_0.064_kBq_#2

source_name: Mouse kidney medulla, 0.064 kBq, 24h

tag: tissue


title: 595sp 0h.AVG_Signal

description: 595sp 0h

source_name: 595sp 0h.AVG_Signal

value: sensitive


title: 211At_kidney_medulla_0.064_kBq_#3

tag: injected activity


title: 211At_kidney_medulla_42_kBq_#1

source_name: Mouse kidney medulla, 42 kBq, 24h

value: 42 kBq

tag: nuclide


title: 211At_kidney_medulla_0.64_kBq_#1


title: 211At_kidney_medulla_0_kBq_#1

source_name: Mouse kidney medulla, 0 kBq, 24h

value: 0 kBq


title: 211At_kidney_medulla_0_kBq_#3


title: 211At_kidney_medulla_42_kBq_#3


title: 211At_kidney_medulla_0_kBq_#2


title: 211At_kidney_medulla_42_kBq_#2


title: human_E44_HL_Digits_2-5_rep2_RNA-Seq

type: SRA

city: Philadelphia

first: Justin

last: Cotney

state: PA

address: 3501 Civic Center Blvd

department: Surgery

institute: Children's Hospital of Philadelphia

description: processed data file (Anonymized alignments): E44_HL_Digits_2to5_Rep2.bed

library_source: transcriptomic

data_processing:
Basecalls with CASAVA-1.8.2
ChIP-seq and RNA-Seq reads were aligned to the hg19, rheMac2, or mm9 genome assembly using Bowtie (0.12.7) with the -m1 flag.
Aligned ChIP-Seq reads in each sample were scanned along the genome in 500bp windows at 25bp step-size. For each window, the total number of reads from H3K27ac and control experiment were counted respectively. Raw read number in control experiment was then scaled to match the sequencing depth of H3K27ac experiment. The number of expected reads in a window based on uniform distribution of total mapped reads along a specific chromosome was also calculated. Then the significance of enrichment was calculated using a Poisson model where the null model is the larger number of control or expected read counts in the window. Significantly enriched windows (p-value≤10-5) within 1kb of each other were then merged.
Signal plots were generated by extending reads to 300bp and counting number of reads at each position in wiggle format.  Wiggle tracks were then converted to bigwig using wigToBigWig from the Kent utilities.
Genome_build: hg19, rheMac2, or mm9
Supplementary_files_format_and_content: No raw data are provided for human samples.  Human alignments were anonymized by removing sequence information and converting to bed format
Supplementary_files_format_and_content: Enriched Region files are in bed format.
Supplementary_files_format_and_content: Bigwig files were generated with wigToBigWig with the -clip flag.

molecule: polyA RNA

growth_protocol: Normal Gestatation

extract_protocol:
For each ChIP-Seq, limb bud tissue was crosslinked with 1% formaldehyde at room temperature and stored at -80°C. Chromatin was extracted and sheared by sonication. Soluble chromatin was combined with Protein G Dynabeads prebound with appropriate antibodies at 4C overnight. Beads were collected with magnet and washed 5x. Chromatin was eluted with TE+1%SDS at 65C for 10 minutes. Crosslinks were reversed at 65C overnight, and then chromatin was purified with the PCR cleanup kit (Qiagen).
Standard Paired End Illumina Multiplexing protocols

treatment_protocol: Human samples were obtained from the Human Developmental Biological Resource (HDBR).

tag: developmental stage

value: gestational day E51

value: hindlimb digits 2 through 5


title: human_E44_HL_Digit_1_rep2_RNA-Seq

description: processed data file (Anonymized alignments): E44_HL_Digits_2to5_Rep1.bed

value: gestational day E50

value: hindlimb digit 1


title: 211At_kidney_medulla_0.064_kBq_#1

value: Balb/c


title: 211At_kidney_medulla_14_kBq_#3

source_name: Mouse kidney medulla, 14 kBq, 24h

value: Mouse kidney medulla

value: 14 kBq


title: human_E44_FL_Digits_2-5_rep2_RNA-Seq

description: processed data file (Anonymized alignments): E44_HL_Digit_1_Rep2.bed

value: gestational day E49

value: forelimb digits 2 through 5


title: human_E44_FL_Digit_1_rep2_RNA-Seq

description: processed data file (Anonymized alignments): E44_HL_Digit_1_Rep1.bed

value: gestational day E48

value: forelimb digit 1


title: 211At_kidney_medulla_1.8_kBq_#2

source_name: Mouse kidney medulla, 1.8 kBq, 24h

value: 1.8 kBq


title: 211At_kidney_cortex_0_kBq_#3

source_name: Mouse kidney cortex, 0 kBq, 24h

value: Mouse kidney cortex


title: 211At_kidney_cortex_0.64_kBq_#2

source_name: Mouse kidney cortex, 0.64 kBq, 24h


title: 211At_kidney_cortex_0.064_kBq_#2

source_name: Mouse kidney cortex, 0.064 kBq, 24h


title: M7005

description:
JD0293-AML-v5-U133A
Additional Array

tag: disease state

value: AML

tag: subtype

value: KRAS wild type

value: NRAS wild type


title: 211At_kidney_cortex_0.064_kBq_#1


title: 211At_kidney_medulla_1.8_kBq_#1


title: 211At_kidney_medulla_14_kBq_#2


title: 211At_kidney_cortex_0_kBq_#1

value: 0 kBq


title: 211At_kidney_cortex_0.64_kBq_#3


title: 211At_kidney_cortex_0.64_kBq_#1


title: 211At_kidney_cortex_0.064_kBq_#3


title: M7003

description:
JD0295-AML-v5-U133A
Additional Array

tag: cytogenetics

tag: fab


title: 211At_kidney_medulla_1.8_kBq_#3


title: 211At_kidney_cortex_0_kBq_#2


title: 211At_kidney_cortex_42_kBq_#3

source_name: Mouse kidney cortex, 42 kBq, 24h

value: 42 kBq


title: 211At_kidney_cortex_42_kBq_#2


title: 211At_kidney_cortex_14_kBq_#3

source_name: Mouse kidney cortex, 14 kBq, 24h


title: 211At_kidney_medulla_14_kBq_#1


title: human_E44_HL_Digits_2-5_rep1_RNA-Seq

description: processed data file (Anonymized alignments): E44_FL_Digits_2to5_Rep2.bed

value: gestational day E47

value: hindlimb digits 2 through 5


title: human_E44_FL_Digits_2-5_rep1_RNA-Seq

description: processed data file (Anonymized alignments): E44_FL_Digit_1_Rep2.bed

value: gestational day E45


title: human_E44_FL_Digit_1_rep1_RNA-Seq

description: processed data file (Anonymized alignments): E44_FL_Digit_1_Rep1.bed

value: gestational day E44


title: 211At_kidney_cortex_14_kBq_#2

value: Balb/c


title: 211At_kidney_cortex_42_kBq_#1


title: 211At_kidney_cortex_1.8_kBq_#3

source_name: Mouse kidney cortex, 1.8 kBq, 24h


title: human_E47_rep2_H3K27ac_ChIP-Seq

description:
processed data file (Anonymized alignments): E47_rep2_h3k27ac_300_uniq.bed
processed data file (ChIP Enriched Regions): E47_rep2_h3k27ac_1EnrichedRegions0.00001.bed
processed data file (Signal Track): E47_rep2_h3k27ac_300_uniq.bw

library_source: genomic

value: forelimb and hindlimb autopod

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: 211At_kidney_cortex_14_kBq_#1

value: 14 kBq


title: human_E44_rep2_H3K27ac_ChIP-Seq

description:
processed data file (Anonymized alignments): E44_rep2_h3k27ac_300_uniq.bed
processed data file (ChIP Enriched Regions): E44_rep2_h3k27ac_1EnrichedRegions0.00001.bed
processed data file (Signal Track): E44_rep2_h3k27ac_300_uniq.bw


title: human_E44_rep1_H3K27ac_ChIP-Seq

description:
processed data file (Anonymized alignments): E44_rep1_h3k27ac_300_uniq.bed
processed data file (ChIP Enriched Regions): E44_rep1_h3k27acEnrichedRegions0.00001.bed
processed data file (Signal Track): E44_rep1_h3k27ac_300_uniq.bw


title: human_E44_HL_Digit_1_rep1_RNA-Seq

description: processed data file (Anonymized alignments): E44_FL_Digits_2to5_Rep1.bed

value: gestational day E46

value: hindlimb digit 1


title: 211At_kidney_cortex_1.8_kBq_#2

value: 1.8 kBq


title: human_E41_rep1_H3K27ac_ChIP-Seq

description:
processed data file (Anonymized alignments): E41_rep1_h3k27ac_300_uniq.bed
processed data file (ChIP Enriched Regions): E41_rep1_h3k27acEnrichedRegions0.00001.bed
processed data file (Signal Track): E41_rep1_h3k27ac_300_uniq.bw

value: gestational day E41


title: human_E41_rep2_H3K27ac_ChIP-Seq

description:
processed data file (Anonymized alignments): E41_rep2_h3k27ac_300_uniq.bed
processed data file (ChIP Enriched Regions): E41_rep2_h3k27acEnrichedRegions0.00001.bed
processed data file (Signal Track): E41_rep2_h3k27ac_300_uniq.bw


title: 211At_kidney_cortex_1.8_kBq_#1

value: Mouse kidney cortex


title: human_E33_rep1_H3K27ac_ChIP-Seq

description:
processed data file (Anonymized alignments): E33_rep1_h3k27ac_300_uniq.bed
processed data file (ChIP Enriched Regions): E33_rep1_h3k27acEnrichedRegions0.00001.bed
processed data file (Signal Track): E33_rep1_h3k27ac_300_uniq.bw

value: gestational day E33

value: forelimb and hindlimb


title: human_E47_rep2_input

description: processed data file (Anonymized alignments): E47_rep2_input_300_uniq.bed


title: human_E33_rep2_H3K27ac_ChIP-Seq

description:
processed data file (Anonymized alignments): E33_rep2_h3k27ac_300_uniq.bed
processed data file (ChIP Enriched Regions): E33_rep2_h3k27acEnrichedRegions0.00001.bed
processed data file (Signal Track): E33_rep2_h3k27ac_300_uniq.bw


title: human_E47_rep1_H3K27ac_ChIP-Seq

description:
processed data file (Anonymized alignments): E47_rep1_h3k27ac_300_uniq.bed
processed data file (ChIP Enriched Regions): E47_rep1_h3k27acEnrichedRegions0.00001.bed
processed data file (Signal Track): E47_rep1_h3k27ac_300_uniq.bw


title: human_E44_rep2_input

description: processed data file (Anonymized alignments): E44_rep2_input_300_uniq.bed


title: human_E47_rep1_input

description: processed data file (Anonymized alignments): E47_rep1_input_300_uniq.bed


title: human_E44_rep1_input

description: processed data file (Anonymized alignments): E44_rep1_input_300_uniq.bed


title: human_E41_rep2_input

description: processed data file (Anonymized alignments): E41_rep2_input_300_uniq.bed


title: human_E33_rep2_input

description: processed data file (Anonymized alignments): E33_rep2_input_300_uniq.bed


title: human_E33_rep1_input

description: processed data file (Anonymized alignments): E33_rep1_input_300_uniq.bed


title: human_E41_rep1_input

description: processed data file (Anonymized alignments): E41_rep1_input_300_uniq.bed


title: 211At_spleen_0_kBq_#3

source_name: Mouse spleen, 0 kBq, 24h

value: Mouse spleen

value: 0 kBq


title: 211At_spleen_0.64_kBq_#2

source_name: Mouse spleen, 0.64 kBq, 24h


title: 211At_spleen_0.64_kBq_#1


title: 211At_spleen_0.064_kBq_#3

source_name: Mouse spleen, 0.064 kBq, 24h


title: 211At_spleen_0.64_kBq_#3


title: 211At_spleen_0_kBq_#2


title: 211At_spleen_0.064_kBq_#1


title: sample.20 0 mg/kg DB[a,h]A

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

hyb_protocol: Agilent Mouse G4852A  Microarrays (containing approximately 60,000 probes) were hybridized with 300 ng Cy5-labelled liver RNA and 300 ng Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays.  Arrays were incubated for 17 hours at 65 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.

scan_protocol: Arrays were scanned scanned on an Agilent G2505B scanner. Data were acquired using Agilent Feature Extraction software 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.

source_name: Total RNA from mouse livers labeled with Cyanine-5 (red)

label_protocol: Individual 200 ng aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent, (5184-3523)).

extract_protocol: RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON, Canada), and further purified using RNeasy Mini Kits (Qiagen Inc., Mississauga, ON, Canada).  RNA was quantified using UV spectrophotometer, and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).

value: part of liver

tag: gender

value: male

tag: age

value: 10 weeks

tag: genotype/variation

value: transgenic mouse strain 40.6

tag: date of exposure

value: March 2-30

tag: dose

value: 0 mg/kg DB[a,h]A

tag: time post exposure

value: 3 days

source_name: universal mouse reference total RNA

extract_protocol: purchased from Stratagene

tag: vendor

value: Stratagene, La Jolla, CA, USA

tag: catalog #

tag: sample type

value: Total RNA derived from 11 mouse cell lines


title: sample.21 12.50 mg/kg DB[a,h]A

tag: tissue

value: 12.50 mg/kg DB[a,h]A


title: sample.16 6.25 mg/kg DB[a,h]A

value: 6.25 mg/kg DB[a,h]A


title: sample.15 25 mg/kg DB[a,h]A

value: 25 mg/kg DB[a,h]A


title: 211At_spleen_14_kBq_#3

source_name: Mouse spleen, 14 kBq, 24h

tag: strain

value: Balb/c

tag: injected activity

value: 14 kBq

tag: nuclide


title: 211At_spleen_14_kBq_#2


title: sample.13 12.50 mg/kg DB[a,h]A


title: 211At_spleen_42_kBq_#3

source_name: Mouse spleen, 42 kBq, 24h

value: 42 kBq


title: sample.11 6.25 mg/kg DB[a,h]A


title: 211At_spleen_0_kBq_#1

value: Mouse spleen


title: 211At_spleen_0.064_kBq_#2


title: sample.17 0 mg/kg DB[a,h]A


title: sample.19 25 mg/kg DB[a,h]A


title: 211At_spleen_42_kBq_#2


title: 211At_spleen_42_kBq_#1


title: sample.18 6.25 mg/kg DB[a,h]A


title: sample.12 25 mg/kg DB[a,h]A


title: sample.10 12.50 mg/kg DB[a,h]A


title: sample.14 0 mg/kg DB[a,h]A


title: sample.9 0 mg/kg DB[a,h]A


title: sample.7 25 mg/kg DB[a,h]A


title: sample.6 0 mg/kg DB[a,h]A


title: sample.8 6.25 mg/kg DB[a,h]A


title: nasopharyngeal carcinoma patient 199_t

city: Guangzhou

first: juan

last: lu

address: guangzhou da dao bei No. 1838

department: Department of ENT

country: China

institute: Nanfang hospital

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal.

scan_protocol: Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.8, TIGR).

label: Hy3TM fluorescent label

source_name: nasopharyngeal carcinoma

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

value: nasopharyngeal carcinoma

tag: tnm stage

tag: age (years)


title: nasopharyngeal carcinoma patient 200_t


title: nasopharyngeal carcinoma patient 183_t

value: female


title: 211At_spleen_1.8_kBq_#2

source_name: Mouse spleen, 1.8 kBq, 24h

value: 1.8 kBq


title: srr1 null_8mM H2O2_1hr_rep 1

first: Katherine

middle: S

last: Barker

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

hyb_protocol: The cRNA pellet was suspended in 10 μl of RNase-free water and 10 μg was fragmented by ion-mediated hydrolysis at 95 °C for 35 min in 200 mM Tris-acetate (pH 8.1), 500 mM potassium acetate, 150 mM magnesium acetate. The fragmented cRNA was hybridized for 16 h at 45 °C to the C. albicansNimbleExpress GeneChip arrays. Arrays were washed at 25 °C with 6 × SSPE, 0.01% Tween 20 followed by a stringent wash at 50 °C with 100 mM MES, 0.1 M NaCl, 0.01% Tween 20. Hybridizations and washes employed the Affymetrix Fluidics Station 450 using their standard EukGE-WS2v5 protocol. The arrays were then stained with phycoerythrein-conjugated streptavidin (Molecular Probes).

scan_protocol: The fluorescence intensities were determined using the GCS 3000 high-resolution confocal laser scanner (Affymetrix).

data_processing:
The scanned images were analysed using software resident in GeneChip Operating System v2.0 (Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity (250). The signal intensity for each gene was calculated as the average intensity difference, represented by [Σ(PM − MM)/(number of probe pairs)], where PM and MM denote perfect-match and mismatch probes.
The scaled gene expression values from GeneChip Operating System v2.0 software were imported into GeneSpring 7.2 software (Agilent Technologies) for preprocessing and data analysis. Probe sets were deleted from subsequent analysis if they were called absent by the Affymetrix criterion and displayed an absolute value below 20 in all experiments. The expression value of each gene was normalized to the median expression of all genes in each chip as well as the median expression for that gene across all chips in the study. Pairwise comparison of gene expression was performed for each matched experiment. Among direct comparisons between matched clinical isolates, genes were considered to be differentially expressed if their change in expression was ≥ 1.5-fold in three independent experiments.

organism: Candida albicans

source_name: srr1 null, H2O2 treated, 1hr

label_protocol: First and second strand cDNA was synthesized from 15 μg total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and oligo-dT24-T7 primer (PrOligo) according to the manufacturer's instructions. cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double-stranded cDNA as template and the Bioarray HighYield RNA Transcript Labeling Kit (ENZO Diagnostics). Double-stranded cDNA synthesized from the previous steps was washed twice with 70% ethanol and suspended in 22 μl of RNase-free water. The cDNA was incubated as recommended with reaction buffer, biotin-labeled ribonucleotides, dithtiothreitol, RNase inhibitor mix, and T7 RNA polymerase for 5 h at 37 °C. The labeled cRNA was separated from unincorporated ribonucleotides by passing through a CHROMA SPIN-100 column (Clontech) and ethanol precipitated at −20 °C overnight.

growth_protocol: Overnight cultures of C. albicans strains WT (SRR1/SRR1), srr1Δ/Δ (srr1/srr1), and gene reconstituted strain (srr1Δ/Δ+SRR1) were grown in YPD broth at 30 degrees C.

extract_protocol: RNA was extracted from cells by the hot phenol method.

treatment_protocol: These overnight cultures were then diluted to an initial optical density (OD600) of 0.1 in YPD broth (50 ml) and then grown at 30°C until logarithmic growth phase and then treated with H2O2.

tag: treatment

value: peroxide-treated

tag: incubation time

value: 1 hour

tag: genotype

value: srr1 null


title: sample.5 12.50 mg/kg DB[a,h]A

value: part of liver

tag: gender

value: male

tag: age

value: 10 weeks

value: transgenic mouse strain 40.6

value: March 2-30


title: 211At_spleen_1.8_kBq_#3


title: nasopharyngeal carcinoma patient 186_t


title: srr1 null_untreated_0hr_rep2

source_name: srr1 null, untreated, 0hr

value: untreated

value: 0 hours


title: 211At_liver_0.64_kBq_#1

source_name: Mouse liver, 0.64 kBq, 24h

value: Balb/c

value: Mouse liver


title: WT_8mM H2O2_1hr_rep2

source_name: WT, H2O2 treated, 1hr

value: WT


title: 211At_spleen_14_kBq_#1

value: Mouse spleen

value: 14 kBq


title: 211At_spleen_1.8_kBq_#1


title: srr1 null_8mM H2O2_1hr_rep 2


title: 211At_liver_0.064_kBq_#2

source_name: Mouse liver, 0.064 kBq, 24h


title: 211At_liver_0.64_kBq_#3


title: Normal_adrenal_medulla_rep4

city: Madrid

first: Mercedes

last: Robledo

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description:
Normal_4
Normal Adrenal Medulla

hyb_protocol: For each tissue sample, 100 ng total RNA was hybridized and processed in accordance with the manufacturer’s instructions. See the Agilent Technologies website for miRNA microarray hybridization and wash protocols: http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50500

scan_protocol: The arrays were scanned with the G2565C DNA microarray scanner (Agilent) using default parameters. The images were processed using the Agilent Feature Extraction (AFE) software package version 10.1.1 (Agilent Technology), and data were exported as text files.

data_processing: The exported data files were read into R using the limma package, and the processed microRNA signal was obtained with the AgiMicroRNA package applying the RMA algorithm to obtain the normalized dataset. Normalized signal intensity is in Log2 scale.

source_name: Normal, adrenal medulla

label_protocol: Agilent miRNA labeling reagent and Hybridization Kit (Cat # 5190-0408).

growth_protocol: None.

extract_protocol: Frozen tissue specimens were sectioned, and total RNA was obtained using the TriReagent Kit (MRC, Cincinnati, OH, USA). RNA purity and integrity were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Ca, USA). All samples used for hybridization experiments had an RNA Integrity Number of at least 7.

treatment_protocol: Fresh-frozen specimens were evaluated by two pathologists, and only samples containing at least 85% tumor cells were included in this study.

value: normal adrenal medulla

tag: primary mutation


title: Normal_adrenal_medulla_rep5

description:
Normal_5
Normal Adrenal Medulla


title: Normal_adrenal_medulla_rep6

description:
Normal_6
Normal Adrenal Medulla


title: WT_untreated_0hr_rep2

source_name: WT, untreated, 0hr


title: WT_untreated_0hr_rep1


title: HepG2 CAP rep3

city: Sapporo

first: Hiroe

last: Hara-Yamamura

state: Hokkaido

address: Kita 13-jo, Nishi 8-chome

department: Graduate School of Engineering

country: Japan

institute: Hokkaido University

hyb_protocol: Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.

scan_protocol: After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).

data_processing: Probe-level data in CEL files were processed and analyzed using the Avadis 4.3 prophetic (Strand Genomics, Redwood City, CA). Data were normalized using MAS5 algorithm, and the features which were NOT flagged “Present” in all three replicates were rejected.

source_name: human hepatoma cell line, HepG2

label_protocol: Target preparation were carried out as described in the manufacturer’s instruction.

growth_protocol: Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.

extract_protocol: Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: Chemical treatment was done by replacing the culture medium with normal medium (as a control) and that containing arsenic trioxide (As2O3)  at five different concentrations (i.e., 0.005 µM, 0.07 µM, 0.5 µM, 6 µM, and 40 µM).

tag: cell bank no

tag: Sex

tag: age of sampling

value: 15 years

tag: tissue derived

value: liver

tag: case history

value: hepatocyte carcinoma

tag: life span

value: infinite

tag: classification

value: transformed

value: exposed to  15 mM ε-caprolactam


title: srr1 null_untreated_0hr_rep1

value: srr1 null


title: 211At_liver_0.064_kBq_#3

tag: strain

tag: tissue

tag: injected activity


title: 211At_liver_0.64_kBq_#2

tag: nuclide


title: sample.3 6.25 mg/kg DB[a,h]A

value: part of liver

value: male

value: 10 weeks

tag: genotype/variation

value: transgenic mouse strain 40.6

tag: date of exposure

tag: dose

value: 6.25 mg/kg DB[a,h]A

tag: time post exposure

value: 3 days

tag: vendor

value: Stratagene, La Jolla, CA, USA

tag: catalog #

tag: sample type

value: Total RNA derived from 11 mouse cell lines


title: WT_8mM H2O2_1hr_rep1

tag: treatment

value: peroxide-treated

tag: incubation time

value: 1 hour

tag: genotype

value: WT


title: sample.4 25 mg/kg DB[a,h]A

tag: gender

tag: age

value: March 2-30

value: 25 mg/kg DB[a,h]A


title: HepG2 CAP rep2

tag: cell bank no

tag: Sex

tag: age of sampling

value: 15 years

tag: tissue derived

value: liver

tag: case history

value: hepatocyte carcinoma

tag: life span

value: infinite

tag: classification


title: nasopharyngeal carcinoma patient 140_t

tag: tissue

value: nasopharyngeal carcinoma

tag: tnm stage

tag: age (years)


title: nasopharyngeal carcinoma patient 182_t

value: male


title: nasopharyngeal carcinoma patient 178_t


title: Normal_adrenal_medulla_rep2

description:
Normal_2
Normal Adrenal Medulla

value: normal adrenal medulla

tag: primary mutation


title: nasopharyngeal carcinoma patient 161_t


title: HepG2 CAP rep1

value: transformed

value: exposed to  15 mM ε-caprolactam


title: nasopharyngeal carcinoma patient 193_t


title: nasopharyngeal carcinoma patient 181_t


title: Normal_adrenal_medulla_rep1

description:
Normal_1
Normal Adrenal Medulla


title: Pheochromocytoma_adrenal_rep36

description:
FPCC_2
Familial pheochromocytoma (FPCC)

source_name: Pheochromocytoma, adrenal, FPCC

value: adrenal pheochromocytoma

value: FPCC

value: female


title: Pheochromocytoma_adrenal_rep37

description:
FPCC_3
Familial pheochromocytoma (FPCC)


title: HepG2 40 microM rep2

value: exposed to  40 µM arsenic trioxide


title: HepG2 40 microM rep1


title: HepG2 40 microM rep3


title: 211At_liver_0_kBq_#1

source_name: Mouse liver, 0 kBq, 24h

tag: strain

value: Balb/c

value: Mouse liver

tag: injected activity

value: 0 kBq

tag: nuclide


title: 211At_liver_42_kBq_#2

source_name: Mouse liver, 42 kBq, 24h

value: 42 kBq


title: 211At_liver_0_kBq_#3


title: nasopharyngeal carcinoma patient 173_t


title: nasopharyngeal carcinoma patient 171_t


title: nasopharyngeal carcinoma patient 170_t


title: nasopharyngeal carcinoma patient 169_t


title: nasopharyngeal carcinoma patient 163_t


title: Pheochromocytoma_adrenal_rep32

description:
TMEM127_1
Tumor with TMEM127 mutation.

source_name: Pheochromocytoma, adrenal, TMEM127


title: Pheochromocytoma_adrenal_rep33

description:
TMEM127_2
Tumor with TMEM127 mutation.


title: Pheochromocytoma_adrenal_rep34

description:
TMEM127_3
Tumor with TMEM127 mutation.


title: Pheochromocytoma_adrenal_rep31

description:
NF1_4
Tumor with NF1 mutation.

source_name: Pheochromocytoma, adrenal, NF1


title: Pheochromocytoma_adrenal_rep35

description:
FPCC_1
Familial pheochromocytoma (FPCC)


title: nasopharyngeal carcinoma patient 144_t


title: 211At_liver_42_kBq_#1


title: Pheochromocytoma_adrenal_rep29

description:
NF1_2
Tumor with NF1 mutation.


title: Pheochromocytoma_adrenal_rep30

description:
NF1_3
Tumor with NF1 mutation.


title: HepG2 6 microM rep3

value: 15 years

tag: treatment

value: exposed to  6 µM arsenic trioxide


title: nasopharyngeal carcinoma patient 132_t

tag: gender


title: Pheochromocytoma_adrenal_rep28

description:
NF1_1
Tumor with NF1 mutation.

tag: age


title: HepG2 6 microM rep2

tag: cell bank no

value: liver

value: hepatocyte carcinoma


title: 211At_liver_14_kBq_#3

source_name: Mouse liver, 14 kBq, 24h

value: 14 kBq


title: Normal_adrenal_medulla_rep3

description:
Normal_3
Normal Adrenal Medulla


title: nasopharyngeal carcinoma patient 128_t

value: nasopharyngeal carcinoma

value: male


title: 211At_liver_0.064_kBq_#1


title: 211At_liver_1.8_kBq_#3

source_name: Mouse liver, 1.8 kBq, 24h

value: 1.8 kBq


title: HepG2 0.07 microM rep1

tag: Sex

value: infinite

value: transformed

value: exposed to  0.07 µM arsenic trioxide


title: 211At_liver_1.8_kBq_#2


title: nasopharyngeal carcinoma patient 123_t

source_name: nasopharyngeal carcinoma


title: Pheochromocytoma_adrenal_rep27

description:
VHL_12
Tumor with VHL mutation.

source_name: Pheochromocytoma, adrenal, VHL

value: adrenal pheochromocytoma

value: VHL


title: 211At_liver_14_kBq_#1

value: Balb/c


title: 211At_lung_0.64_kBq_#2

source_name: Mouse lung, 0.64 kBq, 24h

value: Mouse lung


title: 211At_liver_1.8_kBq_#1

value: Mouse liver


title: HepG2 6 microM rep1

tag: age of sampling


title: HepG2 0.005 microM rep2

tag: tissue derived

value: exposed to  0.005 µM arsenic trioxide


title: HepG2 0.07 microM rep3

value: 15 years

tag: case history


title: HepG2 0.07 microM rep2

tag: life span


title: HepG2 0.005 microM rep3

tag: classification


title: HepG2 0.5 microM rep1

value: exposed to  0.5 µM arsenic trioxide


title: Pheochromocytoma_adrenal_rep26

description:
VHL_11
Tumor with VHL mutation.

tag: tissue

value: female


title: 211At_liver_14_kBq_#2


title: normal control subject 182_c

source_name: normal control subject

value: non-cancer nasopharyngitis biopsy samples

tag: tnm stage


title: HepG2 0.005 microM rep1

value: liver

value: hepatocyte carcinoma


title: 211At_liver_42_kBq_#3

value: 42 kBq


title: Pheochromocytoma_adrenal_rep25

description:
VHL_10
Tumor with VHL mutation.

value: male


title: normal control subject 151_c

tag: age (years)


title: HepG2 0.5 microM rep2

value: infinite


title: Pheochromocytoma_adrenal_rep24

description:
VHL_9
Tumor with VHL mutation.

tag: primary mutation


title: HepG2 0.5 microM rep3

value: transformed


title: 211At_lung_0.64_kBq_#1

tag: strain


title: normal control subject 133_c


title: normal control subject 127_c


title: Pheochromocytoma_adrenal_rep22

description:
VHL_7
Tumor with VHL mutation.


title: normal control subject 121_c


title: 211At_lung_0.64_kBq_#3

tag: injected activity


title: HepG2 control rep2

value: control


title: Pheochromocytoma_adrenal_rep23

description:
VHL_8
Tumor with VHL mutation.

value: adrenal pheochromocytoma


title: normal control subject 120_c


title: Pheochromocytoma_adrenal_rep21

description:
VHL_6
Tumor with VHL mutation.

value: VHL


title: Pheochromocytoma_adrenal_rep20

description:
VHL_5
Tumor with VHL mutation.


title: 211At_lung_0.064_kBq_#2

source_name: Mouse lung, 0.064 kBq, 24h

value: Balb/c

tag: nuclide


title: nasopharyngeal carcinoma patient 176_t

value: nasopharyngeal carcinoma


title: normal control subject 111_c


title: 211At_lung_0.064_kBq_#3

value: Mouse lung


title: normal control subject 102_c


title: normal control subject 113_c


title: normal control subject 59_c


title: 211At_lung_0.064_kBq_#1


title: HepG2 control rep3

tag: treatment


title: Pheochromocytoma_adrenal_rep15

description:
RET_14
Tumor with RET mutation.

source_name: Pheochromocytoma, adrenal, RET

value: RET

tag: gender


title: HepG2 control rep1

value: 15 years


title: Pheochromocytoma_adrenal_rep16

description:
VHL_1
Tumor with VHL mutation.

tag: age


title: Pheochromocytoma_adrenal_rep14

description:
RET_13
Tumor with RET mutation.


title: 211At_lung_0_kBq_#2

source_name: Mouse lung, 0 kBq, 24h

value: 0 kBq


title: 211At_lung_0_kBq_#1


title: Pheochromocytoma_adrenal_rep11

description:
RET_10
Tumor with RET mutation.


title: 211At_lung_42_kBq_#1

source_name: Mouse lung, 42 kBq, 24h


title: 211At_lung_14_kBq_#3

source_name: Mouse lung, 14 kBq, 24h

value: 14 kBq


title: 211At_lung_42_kBq_#2


title: Pheochromocytoma_adrenal_rep13

description:
RET_12
Tumor with RET mutation.


title: 211At_lung_42_kBq_#3


title: Pheochromocytoma_adrenal_rep12

description:
RET_11
Tumor with RET mutation.

value: female


title: 211At_lung_1.8_kBq_#3

source_name: Mouse lung, 1.8 kBq, 24h

value: 1.8 kBq


title: 211At_lung_14_kBq_#2


title: 211At_lung_14_kBq_#1


title: Pheochromocytoma_adrenal_rep10

description:
RET_9
Tumor with RET mutation.


title: Pheochromocytoma_adrenal_rep8

description:
RET_7
Tumor with RET mutation.


title: Pheochromocytoma_adrenal_rep18

description:
VHL_3
Tumor with VHL mutation.


title: Pheochromocytoma_adrenal_rep19

description:
VHL_4
Tumor with VHL mutation.


title: Pheochromocytoma_adrenal_rep17

description:
VHL_2
Tumor with VHL mutation.


title: 211At_liver_0_kBq_#2

value: Mouse liver


title: 211At_lung_1.8_kBq_#2


title: krt18+/-_lung tissue_Tu_M5251

city: Graz

first: Vendula

last: Svendova

address: Auenbruggerplatz 2

country: Austria

institute: Medical University Graz

description: untreated tumor lung tissue from 18 month-old krt18+/- mouse

hyb_protocol: samples were hybridized on a 8x60k CGH Array according to the Agilents protocol; hybridization buffer (Agilent in situ Hybridization kit plus) were added, samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers

scan_protocol: The slides were scanned with Agilent´s DNA Microarray Scanner (Scan Control Software version 3.0)

data_processing: The datasets were extracted with FeatureExtraction software 10.0.1.1 and subsequently analyzed by AGW 6.5

source_name: lung tissue, aged 18 month, untreated

label_protocol: 500 ng gDNA were primed with BioPrimeLabeling Kit according to the manufacturer`s protocol; samples were incubated at 37°C, 2 h for amplifing and labeling

extract_protocol: gDNA was isolated using the Qiagen DNeasy Blood and Tissue kit following manufacturer's instructions; instead of washing buffer 2, 80% EtOH was used

tag: genotype/variation

value: tumor lung tissue

value: 18 month old

value: lung


title: Pheochromocytoma_adrenal_rep9

description:
RET_8
Tumor with RET mutation.


title: krt18+/-_liver tissue_Tu1_M5251

description: untreated tumor liver tissue from 18 month-old krt18+/- mouse

source_name: liver tissue, aged 18 month, untreated

value: tumor liver tissue

value: liver


title: 211At_lung_1.8_kBq_#1


title: krt18+/-_liver tissue_M5251

description: untreated tumorous liver tissue from 18 month-old krt18+/- mouse


title: Pheochromocytoma_adrenal_rep7

description:
RET_6
Tumor with RET mutation.

value: adrenal pheochromocytoma


title: 211At_lung_0_kBq_#3


title: krt18+/-_lung tissue_Tu_M5246


title: Pheochromocytoma_adrenal_rep3

description:
RET_2
Tumor with RET mutation.


title: Pheochromocytoma_adrenal_rep4

description:
RET_3
Tumor with RET mutation.


title: Pheochromocytoma_adrenal_rep6

description:
RET_5
Tumor with RET mutation.

value: male


title: Pheochromocytoma_adrenal_rep2

description:
RET_1
Tumor with RET mutation.


title: Pheochromocytoma_adrenal_rep5

description:
RET_4
Tumor with RET mutation.


title: Paraganglioma_carotid_rep4

description:
SDHD_4
Tumor with SDHD mutation.

source_name: Paraganglioma, carotid, SDHD

value: carotid paraganglioma

value: SDHD


title: krt18-/-_liver tissue_Tu2_MC229

description: untreated tumor liver tissue from 18 month-old krt18-/- mouse


title: krt18-/-_liver tissue_Tu2_MC131


title: Paraganglioma_carotid_rep3

description:
SDHD_3
Tumor with SDHD mutation.


title: krt18+/-_lung_tissue_Tu_M7126

value: 6 month old


title: krt18-/-_liver tissue_Tu2_C769


title: krt18-/-_liver tissue_Tu1_C769


title: MEF b1wt_L0 rep 1

city: Turku

first: Gunilla

last: Högnäs

address: Tykistökatu 6 B

department: Medical Biotechnology

country: Finland

institute: VTT

data_processing: The data were normalized using quantile normalisation with limma in R

source_name: Mouse embryonic fibroblast

label_protocol: For the Illumina gene expression analysis, 100 ng of purified total RNA was amplified and biotinylated in an overnight in vitro transcription reaction using the Illumina RNA TotalPrepTM amplification kit (Ambion, Applied Biosystems).

growth_protocol: MEFs were grown in high clucose DMEM supplemented with 10% FBS, 1% L-glutamine and 1% Penicillin/Streptomycin

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini handbook protocol.

treatment_protocol: The b1YYFF integrin mutation renders MEFs incapable of executing cytokinesis on b1 integrin specific matrixes. Repeated cytokinesis failure was induced by plating the clones on the β1 specific matrix component laminin in serum-free hybridoma medium over night. Normal medium was added the following day to allow for adhesion via β1 and β3 integrins and thus execution of normal cytokinesis. This procedure was repeated 4 or 8 times after which the cells were grown under normal conditions on plastic.

value: B1 wildtype

tag: cell type

value: Mouse embryonic fibroblast

tag: developmental stage

value: prepared from E13.11

tag: sex

tag: immortalization

value: SV-40 large T


title: MEF b1 integrin YYFF_L8 rep 1

value: b1 integrin YYFF

value: prepared from E13.17

value: female


title: MEF b1 integrin YYFF_L4 rep 1

value: prepared from E13.13


title: krt18-/-_liver tissue_Tu3_MC233

value: 18 month old


title: MEF b1wt_L8 rep 2

value: prepared from E13.10


title: krt18-/-_liver tissue_Tu1_MC233

value: tumor liver tissue


title: krt18-/-_liver tissue_Tu_C759

value: liver


title: MEF b1 integrin YYFF_L0 rep 2

value: prepared from E13.20


title: Paraganglioma_carotid_rep2

description:
SDHD_2
Tumor with SDHD mutation.


title: krt18-/-_liver tissue_Tu_C777


title: MEF b1 integrin YYFF_L4 rep 2

value: prepared from E13.14


title: krt18-/-_liver tissue_Tu_C770


title: MEF b1 integrin YYFF_L0 rep 1

value: prepared from E13.19


title: MEF b1wt_L0 rep 2

value: prepared from E13.12


title: MEF b1wt_L4 rep 2

value: prepared from E13.6


title: krt18+/-_liver tissue_M5246


title: MEF b1wt_L8 rep 1

value: B1 wildtype

value: prepared from E13.9


title: Paraganglioma_abdominal_rep3

description:
SDHB_8
Tumor with SDHB mutation.

source_name: Paraganglioma, abdominal, SDHB

value: abdominal paraganglioma

value: SDHB

value: male


title: Paraganglioma_carotid_rep1

description:
SDHD_1
Tumor with SDHD mutation.

value: carotid paraganglioma

value: SDHD


title: Paraganglioma_thoracic_rep4

description:
SDHB_7
Tumor with SDHB mutation.

source_name: Paraganglioma, thoracic, SDHB

value: thoracic paraganglioma

value: female


title: Paraganglioma_abdominal_rep2

description:
SDHB_6
Tumor with SDHB mutation.


title: U266 P - 24hr.AVG_Signal

description: U266 P - 24hr

tag: cell line

value: human myeloma cells

tag: treated with

value: 33 nM bortezomib

tag: bortezomib sensitivity

value: sensitive

tag: timepoint


title: U266 P - 16hr.AVG_Signal

description: U266 P - 16hr


title: MEF b1wt_L4 rep 1

value: Mouse embryonic fibroblast

value: prepared from E13.5

value: SV-40 large T


title: Paraganglioma_thoracic_rep2

description:
SDHB_3
Tumor with SDHB mutation.

tag: tissue


title: Paraganglioma_abdominal_rep1

description:
SDHB_4
Tumor with SDHB mutation.

tag: primary mutation


title: Paraganglioma_thoracic_rep3

description:
SDHB_5
Tumor with SDHB mutation.


title: Paraganglioma_thoracic_rep1

description:
SDHB_2
Tumor with SDHB mutation.


title: krt18+/-_liver tissue_Tu_C813

tag: strain

value: tumor liver tissue

value: 18 month old

value: liver


title: U266 P - 0hr.AVG_Signal

description: U266 P - 0hr


title: Pheochromocytoma_adrenal_rep1

description:
SDHB_1
Tumor with SDHB mutation.

source_name: Pheochromocytoma, adrenal, SDHB

value: adrenal pheochromocytoma


title: krt18+/-_liver tissue_Tu_C795


title: MM1_S - 24hr.AVG_Signal

description: MM1_S - 24hr

source_name: MM1_S - 24hr


title: krt18+/-_liver tissue_Tu_C812


title: MM1_S - 0hr.AVG_Signal

description: MM1_S - 0hr

source_name: MM1_S - 0hr


title: MM1_S - 16hr.AVG_Signal

description: MM1_S - 16hr

source_name: MM1_S - 16hr


title: AKP cell line, biological rep12

city: San Diego

first: Peter

last: Belmont

state: CA

address: 10724 Science Center Drive

institute: Pfizer Inc

description: Gene expression data from AKP cell line 12

hyb_protocol: per Affymetrix manufacturer instructions, performed at Expression Analysis (EA)

source_name: AKP cell line 12

growth_protocol: All cell lines grown in DMEM media supplemented with 10% FBS

extract_protocol: Qiagen RNEasy kit

treatment_protocol: No treatment

tag: genotype

value: AKP

value: Tumor

tag: Sex

value: Female


title: wt_liver tissue_Tu3_MC245

description: untreated tumor liver tissue from 18 month-old wt mouse

value: wild type


title: wt_liver tissue_Tu_C815


title: krt18+/-_liver tissue_Tu_MC144


title: wt_liver tissue_Tu3_MC243


title: wt_liver tissue_Tu_C779


title: wt_liver tissue_Tu1_MC245


title: 100nM CRH 24h

city: coventry

first: dimtiris

last: grammatopoulos

address: gibbet hill road

institute: warwick medical school

description: test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://pcrdataanalysis.sabiosciences.com/pcr/arrayanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data
Fold Change worksheet reports test/control ratios. Only genes with threshold ratios above 2 are shown.

label: SYBR Green

source_name: MCF7 cells

label_protocol: PCR assays were carried out using the Human Estrogen Receptor Signaling RT² Profiler™ PCR Array (SABioscience Corp.) according to the manufacturer instructions.

growth_protocol: MCF7 cells were cultured in Dulbecco’s modified Eagle Medium (DMEM) (Gibco/Invitrogen, UK), containing 10% fetal bovine serum, 1% glutamine and 0.1% penicillin/streptomycin. Cells were maintained at 37oC in a humidified atmosphere of 95% air and 5% CO2. 18h prior to treatments, cells were transferred to serum-free medium without phenol-red.

extract_protocol: Total RNA was extracted with Qiagen RNeasy Mini Kit (Qiagen Ltd, Crawley, UK) and 0.5-1μg was reverse transcribed using the RT² First Strand cDNA synthesis Kit (SABioscience Corp.)

treatment_protocol: cells were treated with 100nM or vehicle (1% acetic acid).

tag: stimulus

value: 100nM CRH 24h


title: wt_liver tissue_Tu_C784


title: AKP cell line, biological rep10

description: Gene expression data from AKP cell line 10

scan_protocol: per Affymetrix manufacturer instructions, performed at Expression Analysis (EA)

source_name: AKP cell line 10

value: Male


title: AKP cell line, biological rep9

description: Gene expression data from AKP cell line 9

data_processing: per Affymetrix manufacturer instructions, performed at Expression Analysis (EA)

source_name: AKP cell line 9


title: wt_liver tissue_Tu2_MC245


title: wt_liver tissue_Tu_C753


title: Control_non-affected liver tissue_C3781

description: non-affected liver tissue from 18 month-old mouse

value: liver tissue


title: AKP cell line, biological rep11

description: Gene expression data from AKP cell line 11

source_name: AKP cell line 11

label_protocol: per Affymetrix manufacturer instructions, performed at Expression Analysis (EA)


title: Control_non-affected liver tissue_M781


title: wt_liver tissue_Tu2_MC243


title: AKP cell line, biological rep8

description: Gene expression data from AKP cell line 8

source_name: AKP cell line 8


title: AKP cell line, biological rep7

description: Gene expression data from AKP cell line 7

source_name: AKP cell line 7


title: AKP cell line, biological rep6

description: Gene expression data from AKP cell line 6

source_name: AKP cell line 6

value: Adenoma


title: sample.22 0 mg/kg DB[a,h]A

hyb_protocol: Hybridisations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Arrays were scanned at a resolution of 5 mm using an Agilent G2505B scanner.

data_processing: The log2 of median signal intensites were cyclic lowess normalized and the technical replicates were averaged using the median.

label: Cyanine 3-pCp

source_name: liver

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit (Agilent Tech, Mississauga, ON, Canada).

extract_protocol: Total RNA containing the small fraction was isolated from each sample using the miRVana miRNA Isolation Kit (Ambion), Streetsville, ON, Canada). Quality was confirmed using the Agilent 2100 Bioanalyzer and RNA Nano 6000 chips.

treatment_protocol: 10-week old male Muta™Mouse (i.e., transgenic mouse strain 40.6) were dosed daily via oral gavage for 28-days with DB[a,h]A dissolved in olive oil (6.25, 12.50 and 25 mg/kg body weight/day).  Each dose group contained 5 animals; 5 animals were also dosed with a vehicle (olive oil) control. Following a 3 day expression period after the last treatment, mice were euthanized with isofluorane followed by cervical dislocation. Liver was then excised, flash-frozen in liquid nitrogen, and stored at -80ºC until use.

tag: dose

value: 0 mg/kg DB[a,h]A

value: part of liver

tag: gender

value: male

value: 10 weeks

value: MutaMouse (transgenic mouse strain 40.6)

tag: date of exposure

value: January 24- February 22

tag: time post exposure

value: 3 days


title: sample.20 12.50 mg/kg DB[a,h]A

value: 12.50 mg/kg DB[a,h]A

tag: age

tag: genotype/variation


title: Control_non-affected liver tissue_MC774

source_name: liver tissue, aged 18 month, untreated

value: 18 month old

value: liver


title: AKP cell line, biological rep5

description: Gene expression data from AKP cell line 5

source_name: AKP cell line 5

value: AKP

value: Tumor


title: sample.19 0 mg/kg DB[a,h]A


title: AKP cell line, biological rep4

description: Gene expression data from AKP cell line 4

source_name: AKP cell line 4


title: AKP cell line, biological rep3

description: Gene expression data from AKP cell line 3

source_name: AKP cell line 3

value: Female


title: Control_non-affected liver tissue_C195

value: wild type


title: BPLER2_R2NX

city: Miami

first: Tan

middle: A

last: Ince

state: FL

address: 1501 NW 10th Avenue, Suite 913

department: Department of Pathology

institute: Interdisciplinary Stem Cell Institute and Braman Family Breast Cancer Institute, Miller School of Medicine, University of Miami

hyb_protocol: Fragmentation, hybridization, washing, staining, and scanning  were done according to the Affymetrix protocol. Briefly,  reagent preparation included 12X MES stock (1.22 M MES,  0.89 M [Na+]) and 2X hybridization buffer (1X hybridization  buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01%  Tween 20). The hybridization cocktail components and final  concentrations consisted of fragmented cDNA (.05 µg/µl),  control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization  controls bioB, bioC, bioD, and cre (1.5, 5, 25,  100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated  BSA (.5 mg/ml), 1X hybridization buffer with a final  volume of 300 µl. The GeneChip array was filled with 250 µl  of the hybridization cocktail and hybridized for 16 hours, rotated  at 60 RPM, and maintained at 45C.  Reagents prepared for washing and staining included a  nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent  wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween  20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+],  0.05% Tween 20). The wash procedure was carried out in  an Affymetrix Fluidics Station 400 controlled by Affymetrix  Microarray Suite 5.0 software resident on a personal computer.  The fluidics station first went through a priming step  and subsequently did the washing and staining by a software  protocol.

scan_protocol: The microarrays were scanned using the GeneArray scanner  per manufacturer’s instructions (Affymetrix, Santa Clara,  CA). The quality control algorithms for eliminating an array  are based on recommendations in both the Affymetrix and  dChip software packages.

label: Biotin

source_name: Primary tumor explants

label_protocol: As per Affymetrix instructions

growth_protocol: Cells injected in matrigel in immunocompromised mice

extract_protocol: The standard protocols followed were per Affymetrix’s instructions  (Genechip Expression Analysis Technical Manual  701021 Rev 4). Briefly, total RNA was isolated from tumors using  Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s  instructions. The RNA pellet was resuspended in 100 ul  of RNAse free water. The RNeasy Clean-up kit (Qiagen,  Valencia, CA) was utilized per manufacturer’s instructions  resulting in 30 ul total RNA sample. The total RNA concentration  and 260/280 ratio was evaluated on a NanoDrop ND-  1000 UV-Vis Spectrophotomter (NanoDrop Technologies,  Rockland, DE). Only samples with a 260/280 ratio greater  than 1.9 were further processed. An aliquot of 1 ul from each  of the samples was diluted to be within the dynamic range of  the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto,  CA), with a target of 100 ng. The Nano Labchip protocol was  followed as per manufacturer’s instructions and was placed  on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for  evaluation. Samples with the highest concentration, only 2  distinct 18 S and 28 S peaks, and no evidence of degradation  were further processed.  Six hundred units of SuperScript II reverse  transcriptase were used for the first strand cDNA synthesis  reaction.   The second strand DNA synthesis, the clean-up of  the double-stranded cDNA, the synthesis of the biotin-labeled  cRNA, and the clean-up of the biotin-labeled cRNA were  per Affymetrix instructions. The Genechip Sample Cleanup  module was used for the clean-up steps of the double stranded  cDNA and the biotin-labeled cRNA. Quantification  of the cRNA was evaluated on the NanoDrop.

tag: tumorigenic cell type

value: BPLER

tag: host strain

value: NOD/SCID mice


title: sample.18 6.25 mg/kg DB[a,h]A

value: 6.25 mg/kg DB[a,h]A


title: sample.23 25 mg/kg DB[a,h]A

value: 25 mg/kg DB[a,h]A


title: MEF b1 integrin YYFF_L8 rep 2

source_name: Mouse embryonic fibroblast

value: b1 integrin YYFF

tag: cell type

value: Mouse embryonic fibroblast

tag: developmental stage

value: prepared from E13.18

tag: sex

value: female

tag: immortalization

value: SV-40 large T


title: BPLER2_R2NX3


title: sample.16 25 mg/kg DB[a,h]A

tag: tissue

value: part of liver

value: male

value: 10 weeks

value: MutaMouse (transgenic mouse strain 40.6)

value: January 24- February 22

value: 3 days


title: sample.17 0 mg/kg DB[a,h]A

value: 0 mg/kg DB[a,h]A


title: AKP cell line, biological rep2

description: Gene expression data from AKP cell line 2

source_name: AKP cell line 2

tag: cell line

value: AKP

value: Tumor

value: Female


title: Control_non-affected liver tissue_C153

tag: strain

value: wild type

value: liver tissue

value: 18 month old

value: liver


title: AKP cell line, biological rep1

description: Gene expression data from AKP cell line 1

source_name: AKP cell line 1

tag: genotype

tag: Sex


title: BPLER3_R3NX3

value: BPLER

value: NOD/SCID mice


title: AP cell line, biological rep3

description: Gene expression data from AP cell line 3

source_name: AP cell line 3

value: AP


title: BPLER3_R3NX2


title: S2R+_HS

city: University Park

first: David

middle: Scott

last: Gilmour

state: Pennsylvania

address: 465 North Frear

department: Biochemistry and Molecular Biology

institute: Penn State University

description:
Permanganate ChIP-seq, heat shocked S2R+ cells
Library Strategy: Permanganate ChIP-seq

data_processing:
2 processed data files were generated: one identifying breaks occcuring at all nucleotides and the other identifying breaks at thymines.
Supplementary_files_format_and_content: all_reads file: Provides chromosome, location, and number of reads for all 4 nucleotides on the forward or reverse strand
Supplementary_files_format_and_content: T_reads file: Provides chromosome, location, and number of reads for T's on the forward or reverse strand

organism: Drosophila melanogaster

source_name: tissue culture cells

growth_protocol: Cells were grown in Schneider's media with 10% FBS at 24 degrees C

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min and quenched with 125 mM glycine.  Cells were dislodged from the culture dish and washed once in PBS followed by incubation in 10 mM KMnO4 in PBS for 1 min at room temperature.  The permanganate reaction was stopped by adding an equal volume of PBS containing 0.8 M beta-mercaptoethanol and 40 mM EDTA.  After washing once with PBS, cells were lysed and chromatin was sheared as previously described by Petesch, S.J. and J.T. Lis (2008) Cell 134, p 74-84. Chromatin from at least 20 million cells was used in one permanganate-ChIP-seq experiment, and RNA polymerase II was immunoprecipitated with antibody against Rpb3.
Polishing ChIP’ed DNA, first adaptor (P2) ligation and nick translation were done on protein A sepharose resin as described by Rhee and Pugh (2011), Cell 147, p. 1408. DNA with P2 adaptors on both ends was eluted from the resin with buffer containing 1% SDS and 0.1M NaHCO3. After reversing the crosslinks, the sample was digested with proteinase K, and extracted with phenol/chloroform. DNA was precipitated with ethanol and suspended in 90 ul of TE buffer (10 mM Tris pH 7.5, 1 mM EDTA). 10 ul of piperidine was added and the sample was incubated at 90 °C for 30 minutes. Piperidine was then removed by isobutanol and ether extraction and the DNA was ethanol precipitated as previously described by Gilmour and Fan (2009) Methods, 48, p. 368. The following steps of library preparation were done in solution as previously described Rhee and Pugh (2011). Briefly, the DNA was denatured at 95 °C and a primer hybridized to the P2 adaptor was extended with phi29 polymerase. After ligating the second adaptor (P1) to the piperidine cleaved ends, the DNA was purified with AMPure beads to remove free adaptors. After nick translation and PCR amplification with both P1 and P2 primers, the DNA was separated on a 2% agarose gel and fragments between 150-250 bp were selected for parallel sequencing. Emulsion PCR and SOLiD Sequencing were done at the Penn State Nucleic Acid facility on a SOLiD 2.0 sequencer.

treatment_protocol: Cells were heat shocked by replacing the media with media that had been prewarmed to 37 degrees C. The dish of cells was held at 37 degrees C in a water bath for 15 min.  At the end of the heat shock, an appropriate volumn of ice cold media was added to adjust the temperature to 24 degrees C.

tag: treatment

value: heat shock


title: AP cell line, biological rep2

description: Gene expression data from AP cell line 2

source_name: AP cell line 2

value: Male


title: AP cell line, biological rep1

description: Gene expression data from AP cell line 1

source_name: AP cell line 1


title: sample.12 6.25 mg/kg DB[a,h]A

tag: dose

value: 6.25 mg/kg DB[a,h]A

value: part of liver

tag: gender

value: male

value: 10 weeks


title: sample.14 12.50 mg/kg DB[a,h]A

value: 12.50 mg/kg DB[a,h]A

value: MutaMouse (transgenic mouse strain 40.6)

tag: date of exposure

value: January 24- February 22

tag: time post exposure

value: 3 days


title: sample.15 25 mg/kg DB[a,h]A

value: 25 mg/kg DB[a,h]A

tag: age

tag: genotype/variation


title: sample.11 6.25 mg/kg DB[a,h]A


title: sample.8 25 mg/kg DB[a,h]A


title: BPLER3_R3NX4C

tag: tumorigenic cell type

tag: host strain


title: BPLER3_R3NX4


title: 35S:AtERF4-HA_over_control_2wk_seedlings-rep4

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

description: Biological replicate 4 of 4.

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LOWESS normalization. After that, signal of each probe was divided by median value of filter-passed probes.

organism: Arabidopsis thaliana

source_name: 35S:NLS-GFP-HA (control), 2wk-seedlings of Arabidopsis thaliana.

label_protocol: 1 µg of total RNA was used for labeling procedure using QickAmp Labeling kit (Two-color) (Agilent).

growth_protocol: All plants were grown in MS (0.5% sucrose) agar media in 16hr light / 8hr dark cycle in 23 Celsius degree. Many plants of the transgenic and control were grown in same one plate for each replicate.

extract_protocol: Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

value: seedling

tag: ecotype

source_name: 35S:AtERF4-HA, 2wk-seedlings of Arabidopsis thaliana.


title: S2R+_NHS

description:
Permanganate ChIP-seq, nonheat shocked S2R+ cells
Library Strategy: Permanganate ChIP-seq

value: no heat shock


title: sample.7 25 mg/kg DB[a,h]A


title: HP+NCFM_Rep2

city: Clayton

first: Sam

last: Forster

state: Victoria

address: 27 - 31 Wright Street

department: Monash Institute

country: Australia

institute: Monash University

description: Gene expression after 5 hours combined treatment with Helicobacter pylori and Lacobacillus acidophillus

hyb_protocol: The resulting cRNA was fragmented, hybridized to Agilent 4x44k Whole Mouse Genome Expression Microarrays and the slides washed according to manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing using an Agilent DNA Microarray Scanner (G2505B) according to manufacters instructions

data_processing: Feature extraction was performed with Agilent Feature Extraction Software 9.5 using default parameters excluding non-uniform flagged outliers

source_name: Bone marrow derived macrophages

label_protocol: 200 ng of RNA was Cy3 labeled with the one colour low RNA input Quick Amplification kit (Agilent) according to manufacters instructions

growth_protocol: For the generation of murine bone marrow-derived macrophages (BMDMs) bone marrow from female 6-10 weeks old C57BL/6 mice was flushed out from the femur and tibia and washed in PBS. The cells were re-suspended in RPMI 1640 medium (Gibco, VIC, Australia) containing 10 % (v/v) heat-inactivated fetal calf serum (Thermo Electron, VIC, Australia) supplemented with 1% penicillin/streptomycin (Gibco), 1% Glutamax (Gibco), and 20% of growth supernatant of L929 cells

extract_protocol: The BMDMs were harvested 5 h after addition of H. pylori and RNA was extracted using Qiagen RNeasy mini column with on-column DNAse digestion according to manufacturers instructions

treatment_protocol: Overnight cultures of L. acidophilus and H. pylori were harvested by centrifugation at 1250 x g for 10 min at 4º C and washed twice in sterile phosphate-buffered saline (PBS).  Bacteria were re-suspended in RPMI 1640 medium (without FCS and antibiotics) and, unless stated otherwise, added (100 µl/well) to the BMDMs at a MOI of 1:1 (or medium for a final volume of 600 µl/well). The cell cultures were incubated at 37 ºC in 5 % CO2. In the inhibitor experiments, BMDMs were pre-incubated for 30 min with the endosomal acidification blockers Chloroquine (final concentration 10 μM) and Bafilomycin A1 (final concentration 25 μM) prior to stimulation with L. acidophilus

value: female

value: 6-10 weeks old

value: Helicobacter pylori + Lactobacillus

tag: cell type

value: Bone marrow derived macrophages


title: NCFM_Alone_Rep2

description: Gene expression after 5 hour stimulation with Lactobacillus acidophillus

value: Lactobacillus


title: NCFM_Alone_Rep1


title: 35S:AtERF4-HA_over_control_2wk_seedlings-rep2

description: Biological replicate 2 of 4.


title: HP+NCFM_Rep1


title: 35S:AtERF4-HA_over_control_2wk_seedlings-rep3

description: Biological replicate 3 of 4.


title: sample.10 0 mg/kg DB[a,h]A

value: 0 mg/kg DB[a,h]A


title: HP+NCFM_Rep3


title: HP_Alone_Rep2

description: Gene expression after 5 hour stimulation with Helicobacter pylori

value: Helicobacter pylori


title: 35S:AtERF4-HA_over_control_2wk_seedlings-rep1

description: Biological replicate 1 of 4.


title: BG3_NHS

description:
Permanganate ChIP-seq, nonheat shocked BG3 cells
Library Strategy: Permanganate ChIP-seq


title: sample.3 6.25 mg/kg DB[a,h]A

value: 6.25 mg/kg DB[a,h]A

value: part of liver


title: sample.6 12.50 mg/kg DB[a,h]A

value: male

value: 10 weeks


title: sample.1 0 mg/kg DB[a,h]A

value: MutaMouse (transgenic mouse strain 40.6)


title: NCFM_Alone_Rep3


title: HP_Alone_Rep1


title: HP_Alone_Rep3


title: hALT_30y

status: Public on Jul 01 2013

city: Yokohama City

first: Yasuharu

last: Ueno

state: Kanagawa

address: 3-9  Fuku-ura, Kanazawa-ku

department: Graduate School of Medicine

institute: Yokohama City University

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 High-Resolution Microarray Scanner using one color scan setting for 4x44k v2 array slides.

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.
The raw signal intensities of samples were log2-transformed and normalised by the quantile algorithm.
(A total of 16,523 orthologs across the human 4x44K v.2 Agilent oligonucleotide array, and the mouse 4x44K v.2 Agilent oligonucleotide array.)

source_name: human adult (30 years old) liver tissues

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Purification kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Total liver cells


title: hFLC-LB

source_name: hFLC-derived LB


title: hiPSC-LB

source_name: hiPSC-derived LB


title: 14286639 - Benzene-3h_BR2 vs Ctrl-3h_BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Improving the knowledge of the metabolic pathways of benzene in higher plants.

hyb_protocol: Ctrl-3h_BR2 Cy5 / Benzene-3h_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Brassica oleracea

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: caulin leaf - Media=Compost hygrometry Temperature=20°C Light

extract_protocol: Ctrl-3h_BR2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: variety

value: Var. Prover

tag: harvest date

extract_protocol: Benzene-3h_BR2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Benzene 3h - environmental treatment - abiotic stress,benzene:time 3hour . 2 months old cabbages are exposed to 3ppm of atmospheric benzene in a 300 liters hermetic chamber. Exposures were conducted over periods of 1h, 3h and 24h. We made biological replicates of exposures of 1h and 3h. As controls, non-exposed plants are located next the exposure chamber for each experiment. At the end of the exposure, pieces of leaves from 3 different plants were pooled and immediatly flash-frozen with liquid nitrogen and stored at -80°C until RNA extraction.


title: 14286636 - Ctrl-3h_BR1 vs Benzene-3h_BR1

hyb_protocol: Benzene-3h_BR1 Cy5 / Ctrl-3h_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Benzene-3h_BR1:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: Ctrl-3h_BR1:5ug. (Qiagen_RNeasy.pdf)


title: 14286656 - col-NaCl vs col

description: Characterization to raptor mutants (partner of the kinase TOR) and of their answer to the salt stress.

hyb_protocol: col Cy5 / col-NaCl Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: col

growth_protocol: whole plant - Media=MS/2 hygrometry=in vitro, Room 70% Temperature=22°C Light=Light

extract_protocol: col:5ug. (Qiagen_RNeasy.pdf)

value: columbia

value: wild type

tag: dev.stage (boyes et al. plant cell 2001)

value: boyes 1.04

source_name: col-NaCl

extract_protocol: col-NaCl:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:NaCl - abiotic stress - abiotic stress,nacl 200 mm:quantity 200mM time 3hour . Sowing on metal grids on MS/2 medium with continuous light (90 μE/m2/s 22°C). Transfer after 12 days of culture for 3h to liquid MS/2 medium containing or not 200 mM NaCl.


title: 14286635 - Benzene-1h_BR2 vs Ctrl-1h_BR2

hyb_protocol: Ctrl-1h_BR2 Cy5 / Benzene-1h_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Ctrl-1h_BR2:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: Benzene-1h_BR2:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Benzene 1h - environmental treatment - abiotic stress,benzene:time 1hour . 2 months old cabbages are exposed to 3ppm of atmospheric benzene in a 300 liters hermetic chamber. Exposures were conducted over periods of 1h, 3h and 24h. We made biological replicates of exposures of 1h and 3h. As controls, non-exposed plants are located next the exposure chamber for each experiment. At the end of the exposure, pieces of leaves from 3 different plants were pooled and immediatly flash-frozen with liquid nitrogen and stored at -80°C until RNA extraction.


title: 14286638 - Ctrl-3h_BR2 vs Benzene-3h_BR2

hyb_protocol: Benzene-3h_BR2 Cy5 / Ctrl-3h_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 0hr_Unstim_Rep2

description: Gene expression in unstimulated bone marrow macrophages

extract_protocol: The BMDMs were harvested 4 h after addition of H. pylori and RNA was extracted using Qiagen RNeasy mini column with on-column DNAse digestion according to manufacturers instructions

tag: strain

value: female

value: Untreated


title: 14286637 - Benzene-3h_BR1 vs Ctrl-3h_BR1

hyb_protocol: Ctrl-3h_BR1 Cy5 / Benzene-3h_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286633 - Benzene-1h_BR1 vs Ctrl-1h_BR1

hyb_protocol: Ctrl-1h_BR1 Cy5 / Benzene-1h_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Ctrl-1h_BR1:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: Benzene-1h_BR1:5ug. (Qiagen_RNeasy.pdf)


title: 0hr_Unstim_Rep1

extract_protocol: The BMDMs were harvested and RNA was extracted using Qiagen RNeasy mini column with on-column DNAse digestion according to manufacturers instructions

value: 6-10 weeks old


title: vehicle

description: control

source_name: MCF7 cells

extract_protocol: Total RNA was extracted with Qiagen RNeasy Mini Kit (Qiagen Ltd, Crawley, UK) and 0.5-1μg was reverse transcribed using the RT² First Strand cDNA synthesis Kit (SABioscience Corp.)

tag: stimulus

value: vehicle


title: 14286651 - col-NaCl vs Rap22-NaCl

hyb_protocol: Rap22-NaCl Cy5 / col-NaCl Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Rap22-NaCl:5ug. (Qiagen_RNeasy.pdf)

value: raptor mutants (rap22)


title: sample.5 12.50 mg/kg DB[a,h]A

source_name: liver

extract_protocol: Total RNA containing the small fraction was isolated from each sample using the miRVana miRNA Isolation Kit (Ambion), Streetsville, ON, Canada). Quality was confirmed using the Agilent 2100 Bioanalyzer and RNA Nano 6000 chips.

value: 12.50 mg/kg DB[a,h]A

tag: tissue

value: January 24- February 22

value: 3 days


title: 14286652 - Rap22-NaCl vs col-NaCl

hyb_protocol: col-NaCl Cy5 / Rap22-NaCl Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286648 - col vs Rap78

hyb_protocol: Rap78 Cy5 / col Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Rap78:5ug. (Qiagen_RNeasy.pdf)


title: 14286654 - Rap78-NaCl vs col-NaCl

hyb_protocol: col-NaCl Cy5 / Rap78-NaCl Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Rap78-NaCl:5ug. (Qiagen_RNeasy.pdf)


title: 14286655 - col vs col-NaCl

hyb_protocol: col-NaCl Cy5 / col Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.