title: IBM0298 Rep 1

source_name: IBM0298 Rep 1 input

source_name: IBM0298 Rep 1 IP


title: RMS6_N

status: Public on Aug 12 2013

type: genomic

city: Tokyo

first: Riki

last: Nishimura

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: University of Tokyo

description: Hybridized to 250K_Nsp

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by CNAG/AsCNAR 3.0

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: ERMS tumor specimen

label_protocol: Affymetrix standard protocol

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from resected fresh tumor blocks or freeze tumor blocks.

tag: disease

value: RMS

tag: histology subtype

value: ERMS


title: IBM0357 Rep 1

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

country: USA

institute: University of Minnesota

hyb_protocol: 20ug (30ug if possible) of labeled DNAs (30ug input DNA + 30ug IP DNA) were hybridized to the 12x270K arrays according to the array manufacturer protocol (42°C, 72hrs). Arrays were then washed according to the array manufacturers protocol.  (NimbleGen Arrays User’s Guide: CGH and CGH/LOH Arrays v9.1 chap. 4,5).

scan_protocol: Arrays were scanned according to the NimbleScan CGH User Guide protocol, which specifies parameters for the MS 200 Microarray Scanner and the MS 200 Data Collection Software was used to collect data.

data_processing:
Images were aligned and quantified using NimbleScan software (Roche NimbleGen) which produced .pair reports of raw data.
Pair files exported from Nimblescan were imported into the Bioconductor statistical environment (http://bioconductor.org/). Samples were frist normalized within arrays to minimize dye-bias,  and then normalized across arrays to achieve consistency between arrays. The normalized log2 (IP/input) ratio was used for downstream analyses.

organism: Zea mays

source_name: IBM0357 Rep 1 input

label_protocol: Amplified input and methylated DNA samples were labeled (.666 ug per subarray sample), hybridized to the 12x270K  feature array. Input DNAs were labeled using Cy3 and the immunoprecipitated methylated DNAs (IP) were labeled with Cy5. (NimbleGen Arrays User’s Guide: CGH and CGH/LOH Arrays v9.1 chap. 3).

extract_protocol: Genomic DNAs were extracted using CTAB and purified using phenol:chloroform/Na-Acetate purification and EtOH precipitation.  2ug of genomic DNA were sheared using a Covaris S220 Focused-ultrasonicator. Methylated DNAs were isolated from 400ng of sonicated DNA using the Zymo Research Methylated DNA IP kit (Cat # D5101) which contains the anti-5-methylcytosine monoclonal antibody.  50-100ng of methylated DNA and 50-100ng of corresponding sonicated (input control) DNAs were amplified using the Sigma Whole Genome Amplification kit (Cat # WGA2-50RXN).

treatment_protocol: genomic DNAs were sonicated, amplified, and fluorophore-labeled

tag: genotype

tag: replication

tag: tissue

value: seedling leaf (L3)

source_name: IBM0357 Rep 1 IP

treatment_protocol: genomic DNAs were sonicated, methylated DNAs were isolated, amplified, and fluorophore-labeled


title: IBM0099 Rep 1

source_name: IBM0099 Rep 1 input

source_name: IBM0099 Rep 1 IP


title: IBM0360 Rep 1

source_name: IBM0360 Rep 1 input

source_name: IBM0360 Rep 1 IP


title: cml133

description: This Sample represents up to 3 replicates.

hyb_protocol: 24-34ug of labeled DNAs (input DNA, IP DNA) were hybridized to the arrays according to the array manufacturer protocol (42°C, 16-20hrs).

scan_protocol: Arrays were scanned according to the NimbleScan CGH User Guide protocol, which specifies parameters for the GenePix4000B Scanner (Axon/Molecular Devices) or MS2000 Scanner (Nimblegen) used to collect data.

data_processing:
Images were aligned and quantified using NimbleScan software (Roche NimbleGen) which produced .pair reports of raw data.
Pair files for 2.1M and 1.4M platforms that were exported from NimbleScan were imported into the Bioconductor statistical environment (Gentleman et al., 2004). 2.1M platform pair files were subset to the 1.4M platform probes to facilitate combined analysis. For each genotype, designated as HapMap2 ‘HM’ lines (excluding B73), microarray data channels were assigned the following factors: B73, HM_line, B73 input, or HM_line input depending on sample derivation. For samples in which three replicates were not available, individual replicates were duplicated to maintain normalization methods across all samples. Non-maize probes and vendor-supplied process control probes were configured to have analytical weights of zero. Variance-stabilizing normalization was used to account for array-specific effects. Factor-specific hybridization coefficients were estimated by fitting fixed linear model accounting for dye and sample effects to the data using the limma package (Smyth 2004). To compute biologically relevant information about each HM line’s DNA methylation, the following contrasts were then computed: B73 IP vs B73 input (B73 methylation); HM_line input vs B73 input (CGH and differential hybridization efficiency); HM_line IP vs [HM_line input vs B73 input] (HM_line methylation corrected for differential hybridization efficiency); B73 IP vs HM_line IP vs [HM_line input vs B73 input]] (differential DNA methylation corrected for differential hybridization efficiency). Moderated t-statistics and the log-odds score for differential MeDIP enrichment were computed by empirical Bayes shrinkage of the standard errors with the False Discovery Rate controlled to 0.05 (Smyth 2004).

source_name: cml133 input

label_protocol: Amplified input and methylated DNA samples were labeled (3 x 1ug per reaction), hybridized to the array and washed according to the array manufacturers protocol.  Input DNAs were labeled using Cy3 and the immunoprecipitated methylated DNAs (IP) were labeled with Cy5.

extract_protocol: Genomic DNAs were extracted using CTAB and purified using phenol:chloroform/Na-Acetate purification and EtOH precipitation.  15-30ug of genomic DNA were sonicated (5 reps x 10 seconds with >1 minute on ice between reps).  Methylated DNAs were isolated from 400ng of sonicated DNA using the Zymo Research Methylated DNA IP kit (Cat # D5101) which contains the anti-5-methylcytosine monoclonal antibody.  50-100ng of methylated DNA and 50-100ng of sonicated (input control) DNAs were amplified using the Sigma Whole Genome Amplification kit (Cat # WGA2-10RXN).

tag: dna

value: input control

source_name: cml133 IP

tag: antibody

value: anti-5-methylcytosine monoclonal antibody (Zymo, Cat # D5101)

value: methylated DNA


title: RT Glucose 4d expression, sample 1

type: RNA

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

hyb_protocol: Cy5-labeled samples were competitively hybridized against the Cy3-labeled samples on custom glass slide 70-mer oligomer microarrays.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner (Axon Instruments/Molecular Devices).

data_processing:
Arrays were gridded using GenePix Pro, version 6.0 (Molecular Devices)
and median normalized using NOMAD 2.0 (http://nomad2.ucsf.edu/).  To
eliminate elements with low signal, we analyzed only elements for
which the sum of the medians for the 635 nm and 532 nm channels was >=
150 intensity units.  Median normalized ratios for elements passing this
threshold are given in the VALUE column.

molecule: total RNA

organism: Histoplasma capsulatum

source_name: RT Glucose 4d

label_protocol:
Fluorescently labeled cDNA was synthesized by
incorporating amino-allyl dUTP during reverse transcription with
Superscript II (Life Technologies) of 15 ug total RNA with
oligonucleotide-dT and random hexamers used as primers. Cy3 or Cy5 dyes (GE
Life Sciences) were coupled to the amino-allyl group as described
previously (Science 278: 680-686).

extract_protocol:
For the microarray time-course study, G217B yeast cells were grown at 37C
in HMM medium and subjected to passage at 1:25 dilution into HMM medium.
After 1 day of growth to early log phase, a portion of cells were harvested
for the t = 0 timepoints and the remaining cells were washed in PBS and
then resuspended with no dilution into 200 mL HMM (glucose) and HMM/100 mM
GlcNAc media for t =1 h, 4 h, and 24 h timepoints or resuspended with a
1:10 dilution into 200 mL HMM (glucose) and HMM/100 mM GlcNAc media for t =
4 d and 7 d timepoints. Cultures for all timepoints were allowed to
continue to grow at 37C under 5% CO2 for yeast-phase growth or transferred
to RT for filamentous-phase growth. For the endpoint microarray experiment,
G217B yeast cells were grown for 2 days at 37C in HMM glucose medium and
filamentous cells were grown for 4-6 weeks with passaging 3 times (1:5
dilution) into fresh HMM glucose medium at RT before reaching a sufficient
density of cells for harvesting. At each indicated timepoint,
cells were harvested by centrifugation or filtration and total RNA was
isolated using a guanidine thiocyanate lysis protocol as previously
described (Mol Biol Cell 14: 2314-2326).

tag: treatment

value: room temperature

tag: medium

value: Glucose

tag: time

tag: strain

value: Histoplasma capsulatum G217B

source_name: pooled reference

tag: sample type

value: pooled reference


title: RT Glucose 7d expression, sample 1

source_name: RT Glucose 7d


title: RMS12_N

description: Hybridized to 250K_Nsp


title: 37C GlcNAc 4d expression, sample 1

source_name: 37C GlcNAc 4d

value: GlcNAc


title: IBM0315 Rep 1

source_name: IBM0315 Rep 1 input

source_name: IBM0315 Rep 1 IP


title: STRM-30_H

description: Hybridized to 50K_Hind

source_name: RMS cell line


title: RMS4_N

description: Hybridized to 250K_Nsp


title: STRM-1_H

description: Hybridized to 50K_Hind


title: IBM0061 Rep 1

source_name: IBM0061 Rep 1 input

source_name: IBM0061 Rep 1 IP


title: STRM-18_H

description: Hybridized to 50K_Hind


title: RMS3_N

description: Hybridized to 250K_Nsp

source_name: ERMS tumor specimen


title: IBM0054 Rep 1

source_name: IBM0054 Rep 1 input

source_name: IBM0054 Rep 1 IP


title: RT GlcNAc 7d expression, sample 1

source_name: RT GlcNAc 7d


title: RT GlcNAc 4d expression, sample 1

source_name: RT GlcNAc 4d


title: RMS5_N

description: Hybridized to 250K_Nsp


title: 93-69-T-RMS_N

description: Hybridized to 250K_Nsp

source_name: ARMS tumor specimen

value: ARMS


title: 37C Glucose 7d expression, sample 1

source_name: 37C Glucose 7d


title: SCMC-RM2_H

description: Hybridized to 50K_Hind


title: IBM0008 Rep 1

source_name: IBM0008 Rep 1 input

source_name: IBM0008 Rep 1 IP


title: RD_H

description: Hybridized to 50K_Hind


title: Mo17 Rep 2

source_name: Mo17 Rep 2 input

source_name: Mo17 Rep 2 IP


title: 37C Glucose 4d expression, sample 1

source_name: 37C Glucose 4d

source_name: pooled reference


title: 98-T69-S97-204-RMS_N

description: Hybridized to 250K_Nsp


title: 2002-T57-RMS_N

description: Hybridized to 250K_Nsp


title: IBM0368 Rep 1

source_name: IBM0368 Rep 1 input

source_name: IBM0368 Rep 1 IP


title: RMS1_N

description: Hybridized to 250K_Nsp


title: Mo17 Rep 3

source_name: Mo17 Rep 3 input

source_name: Mo17 Rep 3 IP


title: A87-38(RM)_H

description: Hybridized to 50K_Hind

source_name: ERMS tumor specimen


title: Mo17 Rep 1

source_name: Mo17 Rep 1 input

source_name: Mo17 Rep 1 IP


title: 37C GlcNAc 7d expression, sample 1

source_name: 37C GlcNAc 7d


title: 4E_MK_Celegans_E_4

status: Public on Aug 11 2013

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: RMA normalization method of software Partek6.6

label: biotin

organism: Caenorhabditis elegans

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Celegans were collected from its standard growth protocol in the lab

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

treatment_protocol: RNA was isolated samples from Mutant and WT control genotype

tag: genotype/variation

value: mutant


title: 4c_MK_Celegans_Control_4

value: wild type


title: 2E_MK_Celegans_E_2


title: 90-T2-RMS_N

description: Hybridized to 250K_Nsp


title: t=0, 37C Glucose Late Time Course expression, sample 1

source_name: t=0, 37C Glucose Late Time Course


title: 1998-T71-RMS_N

description: Hybridized to 250K_Nsp

source_name: ARMS tumor specimen


title: RMS_H

description: Hybridized to 50K_Hind

source_name: RMS cell line


title: Sample 12_treated (IAA 0.022 mM)

city: Urbana

first: Michael

middle: J

last: Plewa

state: IL

address: 1101 W Peabody Dr

department: Crop Sciences

institute: University of Illinois at Urbana-Champaign

description: Test

data_processing:
Data analyses were performed using the web-based software package provided by SA Biosciences: http://sabiosciences.com/pcrarraydataanalysis.php
Threshold limit was arbitrarily set at 0.0147.  CT values were populated into the SA Biosciences PCR analysis software RT2 Profiler™ Data Analysis Template (downloaded from http://sabiosciences.com/pcrarraydataanalysis.php#Excel) with raw values generated from threshold cycle data.
ΔCt values were calculated on the data analysis template using the equation ΔCt = (Ct_Target − Ct_HKG). Gene expression levels were normalized to the average of 5 housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Gene expression was quantified using the equation 2^-ΔCt, and fold changes were calculated as 2^-ΔCt Test / 2^-ΔCt Control. The RankProd algorithm from the R Bioconductor package was used to test significance, with P ≤ 0.05 considered significant
Matrix non-normalized worksheet reports raw Ct values. Matrix normalized worksheet reports ΔCt values normalized to housekeeping genes.
Fold change worksheet reports treated/control expression ratios (i.e IAA treated/negative control)

label: SYBR Green

source_name: treated (IAA 0.022 mM)

label_protocol: PCR assays were performed using the human oxidative stress and antioxidant defense RT2 Profiler™ PCR Array (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. cDNA was prepared from RNA using RT2 PCR Array First Strand Kit (SA Biosciences, Frederick, MD), cDNA samples were diluted in nuclease free water and stored at −20°C. Transcriptome profiles were analyzed using an Oxidative Stress and Antioxidant Defense pathway specific PCR array (SA biosciences PAHS-065-24). Real-time PCR analysis was conducted using a two-step cycling program on a Stratagene Mx3000p thermocycler.

growth_protocol: Nontransformed human intestinal cells, line FHs Int 74, were purchased from American Tissue Culture Collection (Manassass, VA.) Cells were received at passage 12, and used until passage 17 or 18. Cells were maintained in Hybri-care 46X medium supplemented with 10% FBS, 1% antibiotic (10 units/mL penicillin G sodium, 10 µg/mL streptomycin sulfate, 25 µg/mL amphotericin B, 0.85% saline), and 30 ng/mL human epidermal growth factor at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: RNA was isolated using a Qiagen RNeasy Mini Kit (Valencia, CA) following the manufacturers protocol.  mRNA was stored at -80 °C when necessary.

tag: cell line

value: FHs INT 74

tag: cell type

value: embryonic intestinal epithelial

tag: activation agent

value: 0.022 mM IAA

tag: treatment time

value: 4 h


title: Sample 10_treated  (CAA 3.42 mM)

description: Test

source_name: treated  (CAA 3.42 mM)

value: 3.42 mM CAA


title: 1E_MK_Celegans_E_1


title: MK_Celegans_Control_1


title: 2c_MK_Celegans_Control_2


title: B73 Rep 2

source_name: B73 Rep 2 input

value: seedling leaf (L3)

source_name: B73 Rep 2 IP


title: Sample 8_negative control (BAA)

description: Control

source_name: negative control (BAA)

value: control


title: S96-529(RM)_H

description: Hybridized to 50K_Hind

tag: disease

value: RMS


title: Sample 6_treated (IAA 0.022 mM)

description: Test

value: 30 min


title: Sample 5_treated  (BAA 0.057 mM)

description: Test

source_name: treated  (BAA 0.057 mM)


title: Sample 4_treated  (CAA 3.42 mM)

description: Test


title: RMS901_N

description: Hybridized to 250K_Nsp

tag: histology subtype


title: Sample 2_negative control (BAA)

description: Control


title: Sample 1_negative control (CAA)

description: Control

source_name: negative control (CAA)


title: Sample 3_negative control (IAA)

description: Control

source_name: negative control (IAA)


title: RMS37_N

description: Hybridized to 250K_Nsp


title: S90-28(RM)_H

description: Hybridized to 50K_Hind

value: ERMS


title: Sample 9_negative control (IAA)

description: Control


title: B73 Rep 3

source_name: B73 Rep 3 input

tag: genotype

source_name: B73 Rep 3 IP


title: EC10-2_EC50-4_E.andrei_E2phenITC

city: Amsterdam

first: Elaine

last: van Ommen Kloeke

address: De Boelelaan 1085

department: Ecological Science

country: Netherlands

institute: VU University Amsterdam

description: One individual worm per biological replicate, sexually mature (visible clitellum), exposed for 4 days in a jar containing LUFA 2.2 soil non-spiked (acetone control).

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent Technologies) was used for hybridization, which was done at 65°C for 17 hours rotating at 10 rpm in an incubator. After hybridization the arrays were washed using Gene Expression Wash Buffer Kit (Agilent Technologies).

scan_protocol: The arrays were scanned on an Agilent DNA microarray scanner (Agilent Technologies), and fluorescence intensities were measured with Feature Extraction (version 10.5.1.1 or 10.7.3.1) Software (Agilent Technologies).

data_processing: Pre-processing and normalization was done using the limma package in the R (2.15.0) software environment (http://www.r-project.org/), which consisted of normexp background correction (set off = 30), loess normalization and aquantile normalization. Contrast ratios were obtained by fitting linear models using empirical Bayes methods. The Benjamini and Hochberg multiple testing correction was applied to control the false discovery rate. Genes were deemed significantly differentially expressed when the adjusted p-value < 0.01

organism: Eisenia andrei

source_name: 2-phenylethyl ITC spiked soil - EC10 exposure

label_protocol: 150 ng input was used for amplification and labeling with the Agilent Low-Input Quick Amp Labeling Kit (Agilent Technologies), according to the manufacturer’s guidelines. Labeled/amplified cRNA was purified using RNeasy (Qiagen).

extract_protocol: Total RNA was extracted from one individual worm per jar (biological replicate), using SV Total RNA isolation System (Promega).

source_name: 2-phenylethyl ITC spiked soil - EC50 exposure


title: EC10-1_EC50-3_E.andrei_E2phenITC

value: 2-phenylethyl ITC spiked soil - EC10 exposure

value: 2-phenylethyl ITC spiked soil - EC50 exposure


title: IBM0032 Rep 1

source_name: IBM0032 Rep 1 input

tag: replication

source_name: IBM0032 Rep 1 IP


title: Sample 7_negative control (CAA)

description: Control


title: RMS36_N

description: Hybridized to 250K_Nsp


title: RMS8_N

description: Hybridized to 250K_Nsp


title: EC50-1_AC3_E.andrei_E2phenITC

source_name: Acetone control soil exposure

value: Acetone control soil exposure


title: dCas9VP160/sgTetOmut

status: Public on Aug 10 2013

city: Cambridge

first: Albert

middle: W

last: Cheng

state: MA

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

description: Gene expression data from HEK293T transfected with dCas9VP160 and sgTetOmut

hyb_protocol: see manufacturer protocols

scan_protocol: see manufacturer protocols

data_processing: Gene expression values were processed and normalized using affy package for R

label_protocol: see manufacturer protocols

growth_protocol: HEK293T cells were cultured in DMEM with 10% inactivated FBS, 1% Penn/Strep, 1% Glutamine, 1% non-essential amino acids.

extract_protocol: RNAeasy mini kit was used to extract RNA from cells

treatment_protocol: Transfection was done using Fugene HD (Promega) using a 2:6 ratio (A total DNA amount of 2µg and 6µl of Fugene HD reagent) in 6-well plates.

tag: sgrna

value: sgTetOmut

tag: target

value: non-targeting control (mutant version of sgTetO)


title: AC2_EC10-4_E.andrei_E2phenITC


title: EC50-2_EC10-4_E.andrei_E2phenITC


title: dCas9VP160/sgTetO

description: Gene expression data from HEK293T transfected with dCas9VP160 and sgTetO

value: sgTetO

value: TetO promoter


title: AC1_EC10-3_E.andrei_E2phenITC


title: HN5 erlotinib resistant rep 3

city: Nedlands

first: Patrick

middle: Aaron

last: Candy

state: Western Australia

address: 6 Verdun St

department: Cancer Medicine

country: Australia

institute: Perkins Institute

description: biological replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumiR (version 2.12) using R

source_name: HN5 head and neck cancer cell

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Parental HN5 cells were cultured in gradually increasing concentrations of erlotinib with each passage until a concentration of 12.5 µM was reached at the end of a 3 month period. Cells were then maintained in 12.5 µM erlotinib for 6 months upon which they became the erlotinib resistant cells used in this experiment

tag: phenotype

value: Erlotinib resistant


title: EC10-1_AC3_E.andrei_E2phenITC

tag: treatment


title: HN5 parental rep 3

description: biological replicate 3

value: Erlotinib sensitive


title: dCas9VP160/sgIL1RN1~3

description: Gene expression data from HEK293T transfected with dCas9VP160 and sgIL1RN1~3

value: IL1RN promoter


title: HN5 erlotinib resistant rep 2

description: biological replicate 2


title: HN5 erlotinib resistant rep 1

description: biological replicate 1


title: Tumor IL11 #2

city: Heidelberg - Melbourne

first: Stefan

last: Thiem

state: Victoria

address: 145 Studley Road

department: Cancer Research

institute: Olivia Newton-John Cancer Research Institute

description:
IL11 Sample #1
IL11 #2

data_processing: The data were normalised using quantile normalisation with lumi package in R statistical software. Raw gene expression intensity values and detection P-values were extracted using Partek Genomics Suite software.

organism: Mus musculus

source_name: Gastric tumour from IL11-treated gp130Y575F/F mouse

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp RNA Amplification kit for Illumina arrays. The quantity of labelled product was ascertained using the Agilent Bioanalyser 2100 (NanoChip protocol).

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Total RNA was quality ascertained using the Agilent Bioanalyser 2100 (NanoChip protocol).

treatment_protocol: Mice (6-8weeks, n=3 per treatment cohort) were subjected to a single i.p. injection of PBS (200ul), IL6 or IL11 (5ug diluted in 200ul PBS) 60 min prior to sacrifice. Gastric tumour tissue was resected and stored in RNAlater reagent.

value: mixed 129/BL6 background

tag: age

value: 6-8 weeks

tag: agent

tag: tissue

value: gastric tumours


title: HN5 parental rep 2

description: biological replicate 2


title: EC10-2_AC4_E.andrei_E2phenITC


title: Tumor IL6 #3

description:
IL6 Sample #1
IL6 #3

source_name: Gastric tumour from IL6-treated gp130Y575F/F mouse

tag: strain


title: AC2_EC50-4_E.andrei_E2phenITC


title: Tumor IL11 #1

description:
IL11 Sample #1
IL11 #1

tag: genotype/variation


title: Tumor IL11 #3

description:
IL11 Sample #1
IL11 #3


title: Tumor IL6 #2

description:
IL6 Sample #1
IL6 #2


title: RMS11_N

description: Hybridized to 250K_Nsp

source_name: ARMS tumor specimen

value: ARMS


title: AC1_EC50-3_E.andrei_E2phenITC


title: RMS2_N

description: Hybridized to 250K_Nsp

value: RMS


title: RMS903_N

description: Hybridized to 250K_Nsp


title: 4D T0-5

city: Vicksburg

first: Ping

last: Gong

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army ERDC

hyb_protocol: 600 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on GenePix 4200AL scanner at PMT gain level 350 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed with GenePix Pro 6.1 (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GEML grid file 021219_G2_D_F_20080811.xml to obtain signal intensities. Non-uniform spots and spots with a signal intensity outside the linear range were flagged. Signal intensity was converted into relative RNA concentration based on the linear standard curve of spike-in RNAs. The relative RNA concentration was normalized to the median value on each array.

organism: Eisenia fetida

source_name: Whole worm tissue, 0 days of exposure (4 days T0 control)

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

growth_protocol: Before being pulled out for use in the experiment, earthworms (Eisenia fetida) were kept in moistened sphagnum peat (pH 6.5–7.5, moisture content 50%) and fed ad libitum on a diet of Magic Worm Food (Carolina Biological Supply).

extract_protocol: Total RNA was extracted from thawed earthworm tissue using the RNeasy mini 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).

treatment_protocol: Adult earthworms bearing clitelum were pulled out of the culture and added to a non-spiked soil (blank control) or soils spiked with aceton (solvent control), 8, 16, 32, 64 or 128 mg [U-14C]-labeled HMX per gram of soil for 4, 14 and 28 days. Immediately after exposure termination, worms were picked out of the soil, rinsed with water, blotted on paper towel, flash frozen in liquid nitrogen, and stored at -80oC before being used for RNA extraction.

value: homoginized whole worm tissue

tag: gender

value: hermaphrodite

value: adult


title: Tumor PBS #3

description:
PBS Sample #3
Control #3

source_name: Gastric tumour from PBS-treated gp130Y575F/F mouse

value: PBS


title: 4D T0-6


title: 4D T0-2


title: Tumor PBS #1

description:
PBS Sample #1
Control #1


title: 4D T0-4


title: 4D C-4

source_name: Whole worm tissue, 4 days of exposure (blank control)


title: Tumor PBS #2

description:
PBS Sample #2
Control #2


title: B73 Rep 1

source_name: B73 Rep 1 input

value: seedling leaf (L3)

source_name: B73 Rep 1 IP


title: 4D T0-3


title: RMS38_N

description: Hybridized to 250K_Nsp


title: 4D C-5


title: 4D SC-10

source_name: Whole worm tissue, 4 days of exposure (solvent control)


title: 4D C-7


title: 4D SC-6


title: 4D SC-7


title: 4D C-10


title: 4D SC-1


title: 4D C-3


title: 4D SC-2


title: Tumor IL6 #1

description:
IL6 Sample #1
IL6 #1


title: 4D 8ppm-5

source_name: Whole worm tissue, 4 days of exposure to 8 mg HMX/g soil


title: 4D 8ppm-8


title: 4D 8ppm-3


title: 4D 64ppm-6

source_name: Whole worm tissue, 4 days of exposure to 64 mg HMX/g soil


title: HN5 parental rep 1

description: biological replicate 1

tag: cell line


title: 4D 8ppm-4


title: 4D 64ppm-2


title: Sample 11_treated  (BAA 0.057 mM)

description: Test

source_name: treated  (BAA 0.057 mM)

value: FHs INT 74

tag: cell type

value: embryonic intestinal epithelial

tag: activation agent

value: 4 h


title: 4D 64ppm-3


title: 4D 64ppm-4


title: 4D 16ppm-7

source_name: Whole worm tissue, 4 days of exposure to 16 mg HMX/g soil


title: 4D 64ppm-10


title: 4D 16ppm-8


title: 4D 32ppm-3

source_name: Whole worm tissue, 4 days of exposure to 32 mg HMX/g soil


title: 4D 128ppm-9

source_name: Whole worm tissue, 4 days of exposure to 128 mg HMX/g soil


title: 4D 16ppm-6


title: 4D 32ppm-8


title: 4D 16ppm-5


title: 4D 32ppm-5


title: 4D 32ppm-2


title: 4D 16ppm-2


title: 4D 32ppm-1


title: 4D 128ppm-7


title: 4D 128ppm-6


title: 28D T0-2

source_name: Whole worm tissue, 0 days of exposure (28 days T0 control)


title: EC50-1_EC10-3_E.andrei_E2phenITC

source_name: 2-phenylethyl ITC spiked soil - EC50 exposure

source_name: 2-phenylethyl ITC spiked soil - EC10 exposure


title: 4D 128ppm-10


title: 28D T0-5


title: 28D T0-4


title: 28D T0-1


title: 28D SC-5

source_name: Whole worm tissue, 28 days of exposure (solvent control)


title: 4D 128ppm-8


title: EC50-2_AC4_E.andrei_E2phenITC

value: 2-phenylethyl ITC spiked soil - EC50 exposure

source_name: Acetone control soil exposure

value: Acetone control soil exposure


title: 28D T0-3


title: 28D C-5

source_name: Whole worm tissue, 28 days of exposure (blank control)


title: 28D C-3


title: 28D SC-1


title: 28D SC-3


title: 28D C-2


title: 28D SC-2


title: 28D SC-4


title: 28D 8ppm-2

source_name: Whole worm tissue, 28 days of exposure to 8 mg HMX/g soil


title: 28D 8ppm-4


title: 28D 8ppm-1


title: 28D 8ppm-3


title: 28D 8ppm-5


title: 28D 64ppm-5

source_name: Whole worm tissue, 28 days of exposure to 64 mg HMX/g soil


title: 28D C-1


title: 28D 64ppm-2


title: 28D C-4


title: 28D 64ppm-1


title: 28D 64ppm-3


title: 28D 64ppm-4


title: Male Central Rep 3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expresion from male liver zone 3

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: Male Liver Zone 3

extract_protocol: RNAs were prepared using the Arcturus PicoPure Kit. Fifty ng of total RNA was amplified and labeled as directed in the NuGEN Ovation Pico WTA System protocol for Agilent microarrays. For each sample, 3 ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven. Slides were washed and then scanned with an Agilent Scanner

treatment_protocol: Zone 1 and zone 3 areas were captured from mouse liver sections by laser capture microdissection. For each individual mouse, 5 slides were used to capture zone 1 and 5 slides were used to capture zone 3 areas for RNA extractio

value: male

value: C3H/HeNCrlBR (C3H)

tag: zone


title: Female Central Rep 3

description: Gene expresion from female liver zone 3

hyb_protocol: For each sample, 3 ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

source_name: Female Liver Zone 3

label_protocol: Fifty ng of total RNA was amplified and labeled as directed in the NuGEN Ovation Pico WTA System protocol for Agilent microarrays.

value: female


title: Female Central Rep 2

description: Gene expresion from female liver zone 3


title: Female Portal Rep 2

description: Gene expresion from female liver zone 1

source_name: Female Liver Zone 1


title: Female Portal Rep 1

description: Gene expresion from female liver zone 1


title: Male Portal Rep 1

description: Gene expresion from male liver zone 1

source_name: Male Liver Zone 1


title: Male Portal Rep 3

description: Gene expresion from male liver zone 1


title: Female Central Rep 1

description: Gene expresion from female liver zone 3


title: Male Portal Rep2

description: Gene expresion from male liver zone 1


title: Female Portal Rep 3

description: Gene expresion from female liver zone 1


title: 28D 32ppm-4

source_name: Whole worm tissue, 28 days of exposure to 32 mg HMX/g soil


title: 28D 32ppm-5


title: 28D 32ppm-3


title: 28D 16ppm-5

source_name: Whole worm tissue, 28 days of exposure to 16 mg HMX/g soil


title: Male Central Rep 1

description: Gene expresion from male liver zone 3


title: 28D 16ppm-2


title: 28D 16ppm-3


title: Nr3-

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

description: Gene expression data from IL10-CD25+CD4+ T-cells from C57Bl/6 mice

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on a Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and vsn as normalization method

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT-Express Kit, Technical Manual,  Affymetrix).

growth_protocol: CD28 Superagonist D665 was injected i.p. into 6-12 weeks old C57BL/6 mice. After 3 days CD4+CD25+ of lymph nodes were isolated and cultured over night with anti-CD3 (2 µg/ml), anti-CD28 (5 µg/ml) and recombinant human IL-2 (200 U/ml) at 37° and 5% CO2 at 3e6 cells/well in 2 ml complete RPMI medium.

extract_protocol: Cells were lysed in Trizol reagent and complete RNA was isolated according to manufacturers instructions.

treatment_protocol: Cultured CD4+CD25+ T cells were stained for IL-10 and FACS sorted into IL-10+ and IL-10- CD25+ T cells.

value: IL10-CD25+CD4+ T-cells


title: 28D 128ppm-5

source_name: Whole worm tissue, 28 days of exposure to 128 mg HMX/g soil


title: 28D 128ppm-2


title: 28D 128ppm-4


title: 28D 128ppm-3


title: 28D 32ppm-2


title: 28D 16ppm-4


title: 28D 16ppm-1


title: 28D 32ppm-1


title: 28D 128ppm-1


title: Nr2+

description: Gene expression data from IL10+CD25+CD4+ T-cells from C57Bl/6 mice

value: IL10+CD25+CD4+ T-cells


title: Nr4-

source_name: IL10-CD25+CD4+ T-cells from C57Bl/6 mice


title: Nr1+

source_name: IL10+CD25+CD4+ T-cells from C57Bl/6 mice


title: Male Central Rep 2

description: Gene expresion from male liver zone 3


title: 14D T0-6

source_name: Whole worm tissue, 0 days of exposure (14 days T0 control)


title: MT knock-out mice without DOX treatment, biological rep2

city: Shanghai

first: Yi

last: Shuai

address: 1380, Zhongshan (W.)

department: Department of Toxicology

country: China

institute: Shanghai Municipal Center for Disease Control & Prevention

description: MT-/- mice without DOX treatment, biological rep2

hyb_protocol: 300 μl of hybridization cocktail containing 15 μg of fragmented and biotin-labeled cRNA were loaded onto each GeneChip® Mouse Genome 430 2.0 array chip. Hybridization was allowed to proceed overnight (16 h) at 45℃, followed by washing and staining on GeneChip fluidics station 450 (Affymetrix, Santa Clara, CA) with reagents provided by Affymetrix.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The scanned images were first assessed by visual inspection, then analyzed by GeneChip Operating Software (GCOS 1.4) supplied by Affymetrix to generate raw data files. Further processing was done using dChip software.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA

treatment_protocol: MT-Ⅰ/Ⅱ null (MT-/-) mice and corresponding wild-type mice (MT+/+) were administrated with a single dose of DOX (15 mg/kg, i.p.) or equal volume of saline. Animals were sacrificed on the 4th day after DOX administration and samples were collected for further analyses.

value: heart


title: MT wild-type mice with DOX treatment, biological rep2

description: MT+/+ mice with DOX treatment, biological rep2


title: MT knock-out mice without DOX treatment, biological rep1

description: MT-/- mice without DOX treatment, biological rep1


title: MT knock-out mice with DOX treatment, biological rep2

description: MT-/- mice with DOX treatment, biological rep2


title: MT knock-out mice with DOX treatment, biological rep1

description: MT-/- mice with DOX treatment, biological rep1


title: 14D T0-5


title: MT wild-type mice with DOX treatment, biological rep1

description: MT+/+ mice with DOX treatment, biological rep1


title: WT_Cont_02

city: Madison

first: Sakae

last: Ikeda

state: WI

address: 425G Henry Mall

department: Medical Genetics

institute: University of Wisconsin - Madison

description:
WT control 2
gene expression data from 10 pooled WT  cornea

hyb_protocol: 1 µl (~114 ng) of puriﬁed, fragmented, labeled ss cDNA was hybridized to an array at 45°C for 16 h in an Affymetrix 640 hybridization oven.

scan_protocol: The post-hybridization process was performed in an Affymetrix 450 ﬂuidic station according to the manufacturer’s instructions.  All gene chips were scanned on an Affymetrix GC3000 G7 scanner

data_processing: Data were extracted from scanned images using Affymetrix Command Console (v.1.2.0.20). affymetrix-algorithm-name = rma-gene-full (v.1.0)

source_name: 10 pooled WT cornea

label_protocol: cRNA was synthesized using the Ambion WT Expression kit (Ambion). ss cDNA was synthesized and labeled using the Affymetrix WT Terminal Labeling kit.

growth_protocol: All mice were aged to P58

treatment_protocol: All mice were treated with Doxycycline (ip injection) from P28-P58.

tag: strain background

value: mixed; A.BY, C57BL6/J, 129, Swiss Black, and FVB

value: wild type

tag: dox treated

value: cornea


title: 14D T0-3

value: homoginized whole worm tissue

value: hermaphrodite

value: adult


title: WT_Cont_03

description:
WT control 3
gene expression data from 10 pooled WT  cornea


title: 4D 8ppm-10

source_name: Whole worm tissue, 4 days of exposure to 8 mg HMX/g soil


title: 14D SC-9

source_name: Whole worm tissue, 14 days of exposure (solvent control)


title: MT wild-type mice without DOX treatment, biological rep2

description: MT+/+ mice without DOX treatment, biological rep2


title: corn1_cont_03

description:
Corn1 control 3
gene expression data from 10 pooled Dstncorn1 mutant  cornea

source_name: 10 pooled Dstncorn1 mutant cornea

value: Dstncorn1 mutant


title: 14D T0-4


title: 14D T0-1


title: Res_02

description:
Rescued 2
gene expression data from 10 pooled Dstncorn1 rescued  cornea

source_name: 10 pooled Dstncorn1 rescued cornea

value: Dstncorn1 rescued


title: WT_Cont_01_2

description:
WT control 1
gene expression data from 10 pooled WT  cornea


title: MT wild-type mice without DOX treatment, biological rep1

description: MT+/+ mice without DOX treatment, biological rep1


title: corn1_cont_01

description:
Corn1 control 1
gene expression data from 10 pooled Dstncorn1 mutant  cornea


title: Res_01

description:
Rescued 1
gene expression data from 10 pooled Dstncorn1 rescued  cornea


title: Res_03

description:
Rescued 3
gene expression data from 10 pooled Dstncorn1 rescued  cornea


title: 14D C-6

source_name: Whole worm tissue, 14 days of exposure (blank control)


title: 14D C-7


title: 14D C-9


title: 14D SC-8


title: corn1_cont_02

description:
Corn1 control 2
gene expression data from 10 pooled Dstncorn1 mutant  cornea


title: 14D SC-4


title: 14D SC-2


title: 14D SC-10


title: 14D C-2


title: 14D C-5


title: 14D 8ppm-1

source_name: Whole worm tissue, 14 days of exposure to 8 mg HMX/g soil


title: 14D 8ppm-10


title: 14D 8ppm-3


title: 14D 8ppm-4


title: 14D 8ppm-7


title: 14D 64ppm-8

source_name: Whole worm tissue, 14 days of exposure to 64 mg HMX/g soil


title: 14D 64ppm-6


title: YXZ-N Lnc-RNAs

first: Wang

last: Kang

state: Shanghai

address: 225 Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital Second Military Medical University

description: This array contains ~19000 RefSeq coding genes and ~21000 long non-coding RNAs (lncRNA).

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: non-tumor tissues

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step.

value: liver parenchyma paired non-tumor nodules from a patient with HBV-positive hapatocellular carcinoma ,whose ID number is YXZ. HBV, hepatitis B


title: 14D 32ppm-4

source_name: Whole worm tissue, 14 days of exposure to 32 mg HMX/g soil


title: 14D 32ppm-5


title: MXC-N Lnc-RNAs

value: liver parenchyma paired non-tumor nodules from a patient with HBV-positive hapatocellular carcinoma ,whose ID number is MXC. HBV, hepatitis B


title: 14D 64ppm-7


title: 14D 32ppm-3


title: 14D 64ppm-4


title: ponAbe2  400k

city: Boston

first: Charles

last: Lee

address: 221 Longwood Ave., EBRC-422

department: Pathology

institute: Brigham and Women's Hospital/Harvard Medical School

description: Dye bias correction was performed using default settings in Agilent Feature Extraction.

hyb_protocol: Agilent recommended protocol

scan_protocol: scan at 3 uM resolution

data_processing: Agilent Feature Extraction software

organism: Pongo abelii

source_name: fibroblast cell line AG06209

label_protocol: Agilent recommended protocol

growth_protocol: standard for fibroblast cell lines

extract_protocol: standard DNA extraction from cell lines using cell lysis

value: fibroblast cell line

tag: coriell id

source_name: fibroblast cell line GM04272


title: WXM-N Lnc-RNAs

value: liver parenchyma paired non-tumor nodules from a patient with HBV-positive hapatocellular carcinoma ,whose ID number is WXM. HBV, hepatitis B


title: HQW-N Lnc-RNAs

value: liver parenchyma paired non-tumor nodules from a patient with HBV-positive hapatocellular carcinoma ,whose ID number is HQW. HBV, hepatitis B


title: WXM-T Lnc-RNAs

source_name: tumor tissue

value: liver parenchyma tumor nodules from a patient with HBV-positive hapatocellular carcinoma ,whose ID number is WXM.HBV, hepatitis B virus


title: RheMac2 400k

organism: Macaca mulatta

source_name: fibroblast cell line AG07110

source_name: fibroblast cell line AG06252


title: 14D 16ppm-2

source_name: Whole worm tissue, 14 days of exposure to 16 mg HMX/g soil


title: BHH-N Lnc-RNAs

value: liver parenchyma paired non-tumor nodules from a patient with HBV-positive hapatocellular carcinoma ,whose ID number is BHH. HBV, hepatitis B


title: HQW-T Lnc-RNAs

value: liver parenchyma tumor nodules from a patient with HBV-positive hapatocellular carcinoma ,whose ID number is HQW.HBV, hepatitis B virus


title: YXZ-T Lnc-RNAs

value: liver parenchyma tumor nodules from a patient with HBV-positive hapatocellular carcinoma ,whose ID number is YXZ.HBV, hepatitis B virus


title: 14D 16ppm-4


title: MXC-T Lnc-RNAs

value: liver parenchyma tumor nodules from a patient with HBV-positive hapatocellular carcinoma ,whose ID number is MXC.HBV, hepatitis B virus


title: 14D 16ppm-10


title: BHH-T Lnc-RNAs

value: liver parenchyma tumor nodules from a patient with HBV-positive hapatocellular carcinoma ,whose ID number is BHH.HBV, hepatitis B virus


title: 14D 64ppm-3


title: 14D 128ppm-5

source_name: Whole worm tissue, 14 days of exposure to 128 mg HMX/g soil


title: 14D 16ppm-1


title: 14D 32ppm-6


title: Pancreatic Cancer Cell line

city: Omaha

first: Ashley

middle: M

last: Mohr

state: NE

address: 985950 Nebraska Medical Center

institute: University of Nebraska Medical Center

hyb_protocol: Controls were added, RNA was labeled and hybridized according to manufacturer protocol (Exiqon).

scan_protocol: The arrays were scanned with the GenePix Pro 4000B and analyzed with GenePix Pro 6 (Molecular Devices).

data_processing: The array files were read in and preprocessed by background correction, within-array normalization through Loess normalization.  The normalized data was used to obtain values for the differential expression between samples.  For each cell line, microRNAs with average intensity values lower than the 5th percentile average intensity values of the arrays were filtered out.  MicroRNAs with at least 2-fold change were designated as differentially expressed.

source_name: Pancreatic Cancer Cell line, S2.013.Neo

label_protocol: RNA from S2.013.Neo and S2.013.MUC1 cells were labeled with Hy3 or Hy5 (respectively) according protocol, MiRCURY LNA microarray (Exiqon).

growth_protocol: S2.013.Neo and S2.013.MUC1 cells were grown in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum, 200 ug/mL G418 and ciprofloxacin.  Cells were cultured and maintained in a humidified chamber at 37°C with 5% CO2.

extract_protocol: Total RNA was isolated from cells at approximately 80% confluency using the mirVana miRNA Isolation Kit (Life Technologies).

treatment_protocol: S2.013 cells were previously stably transfected with a flag-epitope tagged MUC1 or control vector (S2.013.MUC1 or S2.013.Neo, respectively).

value: S2.013 - Transfected with Control vector

source_name: Pancreatic cancer cell line, S2.013.MUC1

value: S2.013 - transfected with overexpression of MUC1 cDNA


title: 14D 16ppm-9

value: homoginized whole worm tissue

value: hermaphrodite


title: 14D 128ppm-1

value: adult


title: 14D 128ppm-10


title: 14D 128ppm-7


title: 14D 128ppm-4


title: sand 60 mg/kg Cu 5

city: Bangor

first: Sharon

middle: E.

last: Hook

state: NSW

address: Private Mail Bag 7

department: Centre for Environmental Contaminants Research

institute: CSIRO

hyb_protocol: Microarray hybridizations were performed at the Ramaciotti Centre for Gene Function analysis (University of New South Wales, Sydney, Australia) following Agilent’s protocols.

scan_protocol: Data files were generated using Agilent’s feature extraction software

data_processing: Data were uploaded into GeneSpring 12.1 (Agilent) for subsequent analysis.

organism: Melita plumulosa

source_name: sand 60 mg/kg Cu 5

growth_protocol: As described in Simpson, S.L., Spadaro, D.A. (2011) Performance and sensitivity of rapid sublethal sediment toxicity tests with the amphipod Melita plumulosa and copepod Nitocra spinipes. Environ Toxicol Chem 30, 2326–2334.

extract_protocol: Organisms are homogenized in Trizol in MoBio's lysing matrix E with a fast prep system.  Extraction proceeded following the Trizol protocol, except that the aqueous phase was cleaned up using an Rneasy kit.

value: 10 pooled individual organisms

source_name: sand control


title: sand 10 mg/kg Cu 4

source_name: sand 10 mg/kg Cu 4

label_protocol: Microarray hybridizations were performed at the Ramaciotti Centre for Gene Function analysis (University of New South Wales, Sydney, Australia) following Agilent’s protocols.

treatment_protocol: As described in Simpson, S.L., Spadaro, D.A. (2011) Performance and sensitivity of rapid sublethal sediment toxicity tests with the amphipod Melita plumulosa and copepod Nitocra spinipes. Environ Toxicol Chem 30, 2326–2334.


title: 14D 32ppm-1


title: sand 10 mg/kg Cu 5

source_name: sand 10 mg/kg Cu 5


title: Pfalciparum Infected Aseptic Midgut

city: Baltimore

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

description: Mosquito tissues from the same treatment type were collected 24 hours after feeding on a P. falciparum infected blood meal (Cy5) and compared to mosquito tissues collected 24 hours after feeding on a non-infectious blood meal (Cy3). Raw data files are from 3 independent biological replicates and 1 pseudoreplicate (Contains an equal amount of Cy-5-labeled probe from each experimental biological replicate).

hyb_protocol: Probes prepared from the RNA of P. falciparum-infected mosquitoes (labeled with Cy5-dUTP fluorescent nucleotides) were co-hybridized with probes prepared from the RNA obtained from uninfected blood-fed mosquitoes (labeled with Cy3-dUTP fluorescent nucleotides).

scan_protocol: Agilent Scanner (Agilent Technologies)

data_processing: Background-subtracted median fluorescent values were normalized with the LOWESS normalization method, and Cy5/Cy3 ratios from replicate assays were subjected to t-tests at a significance level of p<0.05 using TIGR MIDAS and MeV software. Expression data from replicate assays were averaged with the GEPAS microarray software (http://www.gepas.org) and logarithm (base 2)-transformed.

organism: Anopheles gambiae

source_name: A. gambiae midgut

label_protocol: The Cy5- and Cy3-labeled probes were synthesized using the Low RNA Input Fluorescent Linear Amplification Kit from Agilent Technologies (Santa Clara, California, USA).

growth_protocol: A. gambiae Keele strain mosquitoes were reared at 27°C in 70% humidity, and adults were maintained on a 10% sucrose solution on a 12-h light/dark cycle, according to standard rearing conditions.

extract_protocol: 20 midguts and carcasses were collected from each treatment and infection type. RNA was extracted from dissected tissues using an RNeasy kit (Qiagen, Valencia, California, USA) according to standard methodology.

treatment_protocol: A. gambiae mosquitoes were fed on either an infectious blood meal containing P. falciparum gametocytes or a non-infectious blood meal. 24-hours post-feeding, mosquitoes were anesthetized on ice and midguts and remaining carcasses were collected.

value: Keele

value: Midgut

value: Antibiotics

tag: infection

value: Plasmodium falciparum NF54W

value: uninfected blood meal


title: sand 60 mg/kg Cu 1

source_name: sand 60 mg/kg Cu 1


title: Pfalciparum Infected Aseptic Carcass

source_name: A. gambiae carcass

value: Carcass


title: Pfalciparum Infected Septic Midgut

value: Untreated


title: PanTro2 (4 of 9)

organism: Pan troglodytes

source_name: fibroblast cell line PR001171

value: fibroblast cell line

source_name: fibroblast cell line PR00818


title: PanTro2 (3 of 9)


title: sand 10 mg/kg Cu 3

source_name: sand 10 mg/kg Cu 3


title: sand 10 mg/kg Cu 2

source_name: sand 10 mg/kg Cu 2


title: sand 60 mg/kg Cu 2

source_name: sand 60 mg/kg Cu 2


title: Pfalciparum Infected Septic Carcass


title: PanTro2 (2 of 9)


title: sand 60 mg/kg Cu 3

source_name: sand 60 mg/kg Cu 3


title: PanTro2 (5 of 9)


title: RheMac2 (8 of 9)

source_name: fibroblast cell line AG07110

source_name: fibroblast cell line AG06252


title: sand 10 mg/kg Cu 1

source_name: sand 10 mg/kg Cu 1


title: silt 500 mg/Kg Cu 4

source_name: silt 500 mg/Kg Cu 4

source_name: silt control


title: silt 200 mg/Kg Cu 2

source_name: silt 200 mg/Kg Cu 2


title: silt 500 mg/Kg Cu 1

source_name: silt 500 mg/Kg Cu 1


title: 50:50 sand:silt 250 mg/kg Cu 4

source_name: 50:50 sand:silt 250 mg/kg Cu 4

source_name: Sand:silt control


title: silt 500 mg/Kg Cu 3

source_name: silt 500 mg/Kg Cu 3


title: silt 200 mg/Kg Cu 1

source_name: silt 200 mg/Kg Cu 1


title: silt 200 mg/Kg Cu 4

source_name: silt 200 mg/Kg Cu 4


title: silt 500 mg/Kg Cu 5

source_name: silt 500 mg/Kg Cu 5


title: 50:50 sand:silt 250 mg/kg Cu 5

source_name: 50:50 sand:silt 250 mg/kg Cu 5


title: silt 200 mg/Kg Cu 5

source_name: silt 200 mg/Kg Cu 5


title: 50:50 sand:silt 250 mg/kg Cu 1

source_name: 50:50 sand:silt 250 mg/kg Cu 1


title: 50:50 sand:silt 250 mg/kg Cu 2

source_name: 50:50 sand:silt 250 mg/kg Cu 2


title: Con86

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software (v9.5) formed a composite of the two scans and calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided here is Quantile Normalization.

organism: Micropterus salmoides

source_name: control

label_protocol: Agilent one color protocol for Cy3

extract_protocol: STAT60 protocol for total RNA

value: whole ovary

value: female


title: Flu45

source_name: flutamide


title: Con91


title: Flu50


title: ponAbe2 (5 of 9)

source_name: fibroblast cell line AG06209

source_name: fibroblast cell line GM04272


title: DDE106

source_name: p,p'- Dichlorodiphenyldichloroethylene


title: Flu42


title: Con90


title: MXC134

source_name: methoxychlor


title: PanTro2 (6 of 9)

source_name: fibroblast cell line PR001171

source_name: fibroblast cell line PR00818


title: Flu54


title: ponAbe2 (8 of 9)


title: DDE110


title: MXC129


title: DDE101


title: silt 200 mg/Kg Cu 3

source_name: silt 200 mg/Kg Cu 3

source_name: silt control


title: sand 60 mg/kg Cu 4

source_name: sand 60 mg/kg Cu 4

source_name: sand control


title: Con96


title: MXC135


title: DDE108


title: ponAbe2 (6 of 9)


title: MXC133


title: 50:50 sand:silt 250 mg/kg Cu 3

source_name: 50:50 sand:silt 250 mg/kg Cu 3

source_name: Sand:silt control


title: PanTro2 (8 of 9)


title: PanTro2 (1 of 9)


title: silt 500 mg/Kg Cu 2

source_name: silt 500 mg/Kg Cu 2


title: RheMac2 (5 of 9)

source_name: fibroblast cell line AG07110

source_name: fibroblast cell line AG06252


title: Patient #3

status: Public on Aug 09 2013

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

description:
ColonN_252800414877_1_2
Gene expression analysis of human patient sample

hyb_protocol: Labeled cDNA was hybridized to SurePrint G3 Human GE 8x60 Agilent® Microarray chip (ID: G4858A-028004) using Gene Expression Hybridization Kit Cat. # 5188-5242).

scan_protocol: Microarray Scanner Agilent G2505X class C

data_processing: The data were normalized with Bioconductor software using quantiles.

source_name: colon surgical resection

label_protocol: For future sample normalization, RNA was treated with One-Color RNA Spike-In Kit cat. # 5188-5282 (Agilent). 200ng of RNA were used for cDNA preparation with Low Input Quick Amp Labeling Kit, one-color Cat. # 5190-2305, Agilent®. Sample labelling with dye (Cy3) fluorophore was made with previous cited kit. Labelled cDNA was purified with RNeasy MinElute Cleanup Kit Cat.# 74204 (Izasa/Qiagen).

growth_protocol: Surgical resection of normal colorectal tissue samples.

extract_protocol: The samples were homogenized with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

value: normal colon

tag: disease status

value: colorectal cancer

tag: patient identifier


title: Patient #2

description:
ColonN_252800414877_1_1
Gene expression analysis of human patient sample


title: CC18CO normal colon cell line

description:
ColonLN_252800414888_2_4
Gene expression analysis of human patient sample

source_name: normal colon cell line

value: normal colon cells


title: PanTro2 400k


title: Patient #39

description:
RectoN_252800415216_1_4
Gene expression analysis of human patient sample

source_name: rectum surgical resection

value: normal rectum


title: RheMac2 (7 of 9)


title: ponAbe2 (7 of 9)

source_name: fibroblast cell line AG06209

source_name: fibroblast cell line GM04272


title: ponAbe2 (1 of 9)


title: Patient #45

description:
RectoN_252800415131_2_1
Gene expression analysis of human patient sample


title: Patient #44

description:
RectoN_252800415129_2_1
Gene expression analysis of human patient sample


title: Patient #42

description:
RectoN_252800414888_2_1
Gene expression analysis of human patient sample


title: ponAbe2 (9 of 9)


title: RheMac2 (4 of 9)


title: RheMac2 (6 of 9)


title: the tested sample of a Yangxin pig

city: Wuhan

first: Fenge

last: Li

state: Hubei

address: Shizishan Street

institute: Huazhong Agricultural University

hyb_protocol: Labeled DNA was co-hybridized to the custom-made NimbleGen comparative genome hybridization (CGH) array (3 × 720 K) according to the manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Hybridized microarray slides were scanned using a microarray scanner MS200 (Roche NimbleGen) according to the manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan v2.5 software.

organism: Sus scrofa

source_name: male Yangxin semen

label_protocol: Test DNA and reference DNA samples were independently labeled with Cy3 and Cy5 dyes respectively according to the manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: The genomic DNA of 13 pig samples was extracted from semen, whole blood or ear notch by phenol extraction and ethanol precipitation.

tag: breed

value: Yangxin

value: male

value: semen

tag: developmental stage

source_name: female Duroc blood

value: Duroc

value: blood


title: Patient #41

description:
RectoN_252800414878_2_1
Gene expression analysis of human patient sample


title: ponAbe2 (4 of 9)


title: RheMac2 (9 of 9)


title: ponAbe2 (2 of 9)


title: Patient #11

description:
ColonN_252800415228_2_1
Gene expression analysis of human patient sample


title: Patient #10

description:
ColonN_252800415228_1_4
Gene expression analysis of human patient sample


title: Patient #40

description:
RectoN_252800415216_2_1
Gene expression analysis of human patient sample


title: PanTro2 (7 of 9)

source_name: fibroblast cell line PR001171

source_name: fibroblast cell line PR00818


title: the tested sample of a White Duroc pig

source_name: female White Duroc blood

value: White Duroc

value: adult


title: Patient #38

description:
RectoN_252800414877_2_1
Gene expression analysis of human patient sample


title: RheMac2 (3 of 9)


title: the tested sample of Landrace 2

source_name: male Landrace 2 semen

value: Landrace


title: Patient #14

description:
ColonN_252800415129_1_2
Gene expression analysis of human patient sample


title: Patient #17

description:
ColonN_252800415216_1_1
Gene expression analysis of human patient sample


title: the tested sample of Landrace 1

source_name: male Landrace 1 semen


title: the tested sample of Landrace x DIV pig 2

source_name: female LD2 blood

value: Landrace x DIV


title: ponAbe2 (3 of 9)


title: Patient #13

description:
ColonN_252800415129_1_1
Gene expression analysis of human patient sample


title: Patient #9

description:
ColonN_252800415128_1_1
Gene expression analysis of human patient sample


title: RheMac2 (2 of 9)

description: Dye bias correction was performed using default settings in Agilent Feature Extraction.


title: PanTro2 (9 of 9)


title: Patient #5

description:
ColonN_252800414878_1_2
Gene expression analysis of human patient sample


title: Patient #6

description:
ColonN_252800414888_1_1
Gene expression analysis of human patient sample


title: the tested sample of an Erhualian pig

source_name: female Erhualian blood

value: Erhualian


title: Patient #4

description:
ColonN_252800414878_1_1
Gene expression analysis of human patient sample


title: the tested sample of a Tongcheng pig

source_name: female Tongcheng blood

value: Tongcheng


title: 4_one_month_after

city: Toskushima

first: Yuki

last: Kuwano

address: Kuramoto-cho

department: Pathophysiology

institute: The University of Tokushima Graduate School

description: miRNA expression one month after the exam in blood

hyb_protocol: For hybridization, the samples were resuspended in 17 microliters of DEPC-treated water. To each sample, 1 microliter of diluted Hybridization Spike Control, 4.5 mkl of 10X GE Blocking Agent (Agilent Technologies) and 22.5 microliters of 2X HiRPM Hybridization Buffer (Agilent Technologies) were added. The samples were heated to 100oC for 5 minutes and transferred immediately to an ice water bath for 5 minutes. The samples were then loaded onto Human miRNA Microarray (V3, 8x15K array). Hybridization was performed at 55oC for 20 hours.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA).

data_processing: Data extracted using Agilent's Feature Extraction software, version 9.5 (P/N G2567AA). Raw data output was imported into Genespring GX11 (Agilent) and normalized each chip to the 75th percentile of all measurements (per chip normalization).

source_name: whole blood

label_protocol: otal RNA was labeled with Cyanine 3-Cytidine biphosphate (pCp) using the Agilent’s miRNA Complete Labeling and Hybridization Kit (Agilent Technologies).Briefly, 100 ng of total RNA was combined with diluted Labeling Spike In controls. The samples were dephosphorylated using Calf Intestinal Phosphatase at 37oC for 30 minutes, followed by denaturation with 10% DMSO at 100oC for 10 minutes and incubation in an ice water bath. The Cyanine 3-pCp was then ligated onto the miRNA molecule using T4 RNA Ligase at 16oC for 2 hr.

extract_protocol: From the stored samples, total RNA containing small RNAs using the PAXgene Blood miRNA kit (Qiagen, Hilden, Germany) was extracted according to the manufacturer’s protocol.

treatment_protocol: Blood was collected after saliva sampling (between 16:00 and 17:00) and immediately poured into PAXgeneTM blood RNA tubes (Becton Dickinson, Franklin Lakes, NJ, USA). After sufficient mixing, tubes were stored for 2 h at room temperature, followed by storage at -80°C.

tag: age

tag: time

value: one month after the exam in blood

tag: treatment

value: chronic stress


title: 4_two_months_before

description: miRNA expression two months before the exam in blood

value: two months before the exam in blood

tag: tissue


title: Patient #12

description:
ColonN_252800415128_1_2
Gene expression analysis of human patient sample

value: normal colon

value: colorectal cancer


title: MS2 let-7a-5p (13)

city: Basel

first: Lukas

last: Baeriswyl

address: Fabrikstrasse 10

department: Human Genetics and Genomics

country: Switzerland

institute: Novartis Pharma AG

description: microRNA expression data

hyb_protocol: 400ng of biotinylated RNA (small RNAs) were hybridized for 42 hr at 45C on GeneChip hsMiR Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner GCS 3000 7G

data_processing: The microarray data are prepared for further analysis using the Affymetrix Power Tools (APT) version 1.14.3 The rma-bg function that performs an RMA style background adjustment. The perfect match option (Pm-only) then uses the unmodified PM intensity values of the probes and calculates the median value.

source_name: MS2 phage RNA and 5x106 copies let-7a-5p /ug RNA

label_protocol: Biotinylated RNA were prepared from 400 ng total RNA according to the FlashTag protocol (FlashTag Biotin HSR RNA Labeling Kit, 2012, Affymetrix Inc.).

extract_protocol: Diluted commercial RNA samples [Universal Human miRNA reference RNA (Agilent Technologies, #750700), human brain total RNA (Life Technologies, #AM6050), human liver total RNA (Life Technologies, # AM7960) and MS2 phage RNA (Roche, #10165948001); Synthetic miRNA templates for let-7a-5p, let-7b-5p, let-7c, let-7d-5p, miR-302a-3p, miR-302b-3p, miR-302c-3p, miR-302d-3p (Integrated DNA Technologies)].

tag: rna source


title: MS2 let-7b-5p (14)

description: microRNA expression data

source_name: MS2 phage RNA and 5x106 copies let-7b-5p /ug RNA


title: MS2 let-7d-5p (16)

description: microRNA expression data

source_name: MS2 phage RNA and 5x106 copies let-7d-5p /ug RNA


title: MS2 let-7c (15)

description: microRNA expression data

source_name: MS2 phage RNA and 5x106 copies let-7c /ug RNA


title: the tested sample of Chinese new pig line DIV2

source_name: female DIV2 blood

value: DIV

tag: gender

value: female


title: RheMac2 (1 of 9)

source_name: fibroblast cell line AG07110

tag: cell type

value: fibroblast cell line

source_name: fibroblast cell line AG06252


title: 3_one_month_after

value: male


title: the tested sample of Chinese new pig line DIV1

source_name: female DIV1 blood

source_name: female Duroc blood

value: Duroc


title: liver miR-302d (12)

description: microRNA expression data

source_name: human liver total RNA and 5x106 copies miR-302d-3p /ug RNA


title: the tested sample of a Pietrain pig

source_name: male Pietrain semen

value: Pietrain

value: semen

value: blood


title: 3_two_days_before

description: miRNA expression two days before the exam in blood

value: two days before the exam in blood


title: 2_one_month_after


title: Patient #37

description:
RectoN_252800414877_1_4
Gene expression analysis of human patient sample

source_name: rectum surgical resection

value: normal rectum


title: liver miR-302c (11)

description: microRNA expression data

source_name: human liver total RNA and 5x106 copies miR-302c-3p /ug RNA


title: 1_two_days_before


title: 2_two_days_before


title: 1_two_months_before


title: 2_two_months_before


title: the tested sample of Landrace x DIV pig 1

source_name: male LD1 semen

value: Landrace x DIV

value: adult


title: liver miR-302a (9)

description: microRNA expression data

source_name: human liver total RNA and 5x106 copies miR-302a-3p /ug RNA


title: miRQC D repeat (8)

description: microRNA expression data


title: liver miR-302b (10)

description: microRNA expression data

source_name: human liver total RNA and 5x106 copies miR-302b-3p /ug RNA


title: miRQC D (7)

description: microRNA expression data


title: miRQC C repeat (6)

description: microRNA expression data


title: Δpp-1 6h vs Δpp-1 5h

city: Berkeley

first: Abby

last: Leeder

address: 111 Koshland Hall

institute: UC Berkeley

hyb_protocol: Hybridizations were performed using Pronto kits (Promega) according to the manufacturer's protocol and as described by Tian et al (2007 - Eukaryotic cell 6(6)1018:29)

scan_protocol: Scanned on an Axon GenePix 4000B

data_processing:
GenePix Pro 6 software (Molecular Devices) was used to quantify hybridization signals and collect raw data.
Normalized Cy5/Cy3 expression values (See Townsend and Hartl 2002) were analyzed by using BAGEL (Bayesian Analysis of Gene Expression Levels). bagel output - norm. log ratio Cy5/3, where the ratios of the expression of each gene are analyzed as a closed loop among all the slides [PMID: 16287898] and are shown in columns C-L of the spreadsheet.

organism: Neurospora crassa OR74A

source_name: Δpp-1 conidia, 30 degree incubation

label_protocol: The ChipShot Indirect cDNA Synthesis and labelling protocol from Promega/Corning (Promega) was used according to the manufacturer's instructions, with the following exceptions: 10μg dried cDNA was resuspended in 9 μl 0.06 M sodium bicarbonate, and quenching was accomplished by the addition of 4.5 μl 4 M hydroxylamine

growth_protocol: N. crassa conidia were grown for 3-8h at 30 degrees in constant light.

extract_protocol: RNA was extracted using Trizol

value: 6 hours growth

value: 5 hours growth


title: miRQC B repeat (4)

description: microRNA expression data

source_name: 100% human brain total RNA (Ambion #AM6050)


title: Δpp-1 5h vs Δpp-1 4h

value: 4 hours growth


title: WT 8h vs WT 6h repeat 2

source_name: WT (FGSC 2489) conidia, 30 degree incubation

value: 8 hours growth


title: WT 6h vs Δpp-1 6h repeat 2


title: Δpp-1 8h vs Δpp-1 6h repeat 1


title: Patient #16

description:
ColonN_252800415131_1_2
Gene expression analysis of human patient sample

source_name: colon surgical resection

value: normal colon

value: colorectal cancer


title: Δpp-1 8h vs Δpp-1 6h repeat 2


title: H2Aub_ChIP

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

hyb_protocol: Hybridization cocktails were generated using the labeled DNA fragments (2 μg labeled DNA, 1x MES, 3M TMAC, 40 pM Affymetrix control oligo B2, 100 μg/mL salmon sperm DNA, and 0.02% Triton X-100). Each chip was pre-hybridized with 200 μl of 1X MES-triton for 1 hour in the Affymetrix Hybridization 645 oven at 45 rpm and 45oC. Samples in hybridization cocktail were heated for 10 minutes at 99oC then incubated to a 45oC for 10 minutes. Samples are spun in a microcentrifuge at maximum speed for 3 min. 200 μl of a sample was injected in to a chip. Hybridization was carry out in the hybridization oven at 45 rpm and 45oC for 18 hours. The arrays were washed and stained on the GeneChip Fluidics Station 450 series.

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

data_processing: MAT software (Johnson et al. 2006) was used to calculate ChIP enrichment in the H2Aub ChIP samples relative to the Input samples and sites of significant binding across the non-repetitive Drosophila genome. MAT score.bar files contain MAT scores for each probe as generated using MAT software (Johnson et al. 2006). .bed files, also generated using MAT software, indicate binding at p-value less than or equal to 10E-3.

organism: Drosophila melanogaster

source_name: ML-DmBG3-c2 cells derived from larval central nervous system

label_protocol: Immunoprecipitated DNA and input chromatin DNA was amplified using the GenomePlex Complete Whole Genome Amplification Kit (Sigma) and fragmented using controlled DNAse I reactions. Fragmented DNA was labeled with bio-11-ddATP (Perkin Elmer) using a Terminal Transferase labeling kit (Roche).

growth_protocol: ML-DmBG3 cells were cultured in Schneider's media with 10% FCS and 10 μg per ml insulin at 25oC.

extract_protocol: BG3 cells were grown to a concentration of 5x10E6 per mL, then crosslinked by addition of 36% formaldehyde directly to the cell culture media to a final concentration of 1%, and incubation for 10 minutes at room temperature on a rocking platform. The reaction was stopped by addition of glycine pH 7.0 to a final concentration of 0.125 M. Cells were washed once with 1x PBS and once each with Wash Buffers A (10 mM HEPES pH 7.6; 10 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.25% Triton X100) and B (10 mM HEPES pH 7.6; 200 mM NaCl; 1 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.01% Triton X-100) for 10 minutes each. Cells were resuspended in sonication buffer to a concentration of 1x10E9/3 mL, and sonicated using a BioRuptor Sonicator for 14-20 cycles of 30 s on, 30 s off. Na-lauroylsarcosine was added to 0.5% and incubated for 10 minutes, rotating. Chromatin was centrifuged at 12,000g for 5 minutes at 4°C to pellet insoluble material, and 200 mL chromatin aliquots, each representing ~50x10E6 cells, were snap frozen on dry ice. For immunoprecipitation, 200 μL aliquots of chromatin (50x10E6 BG3 cells) were adjusted to RIPA buffer in a final volume of 500 μL. Adjusted chromatin was pre-cleared for 2 hours with Protein A agarose beads, then incubated with primary antibody overnight at 4°C.The ChIP antibody used was anti-ubiquityl-Histone H2A (Lys119) (D27C4) XP® Rabbit mAb from Cell Signaling Technology (cat. no. 8240). Chromatin complexes were pulled down by incubation with Protein A/G agarose beads for 4 hours at 4°C, and beads were washed consecutively with RIPA, LiCl buffer, and TE. Samples were treated with RNAse A for 30 minutes at 37°C, then DNA crosslinks were reversed by overnight treatment at 65°C with Proteinase K, and DNA was recovered using Qiagen MinElute columns. The input samples were prepared from chromatin without immunoprecipitation.

tag: cell line

tag: chip antibody

value: anti-ubiquityl-Histone H2A (Lys119)

tag: chip antibody manufacturer

value: Cell Signaling

tag: chip antibody catalog #

value: input DNA


title: Δpp-1 4h vs WT 4h


title: miRQC B (3)

description: microRNA expression data

value: 100% human brain total RNA (Ambion #AM6050)


title: WT 6h vs WT 5h repeat 2


title: miRQC C (5)

description: microRNA expression data


title: miRQC A repeat (2)

description: microRNA expression data

source_name: 100% Universal Human miRNA reference (Agilent #750700)


title: WT 5h vs WT 6h repeat 2


title: WT 6h vs WT 8h repeat 1


title: the tested sample of a Large White pig

source_name: female Large White ear notch

value: Large White

value: female

value: ear notch

value: Duroc


title: miRQC A (1)

description: microRNA expression data

value: 100% Universal Human miRNA reference (Agilent #750700)


title: Δpp-1 8h vs WT 8h repeat 2


title: WT 3h vs WT 4h repeat 2

value: 3 hours growth


title: Δpp-1 6h vs WT 6h


title: Patient #15

description:
ColonN_252800415131_1_1
Gene expression analysis of human patient sample


title: 4_two_days_before

source_name: whole blood

value: male

value: two days before the exam in blood

value: chronic stress

value: blood


title: WT 8h vs Δpp-1 8h

value: 8 hours growth


title: Δpp-1 4h vs Δpp-1 3h

value: 4 hours growth


title: WT 3h vs Δpp-1 3h


title: Δpp-1 3h vs Δpp-1 4h


title: Wild type control_1

city: Vienna

first: Sebastian

last: Nijman

address: Lazarettgasse 14

country: Austria

institute: Research Center for Molecular Medicine

description:
Gene expression from unstimulated control cells
Sample WT_1

hyb_protocol: Affymetrix GeneChip® Human PrimeView arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Express Kit User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

source_name: Wild type control

label_protocol: 100ng of total RNA were amplified and labeled using the  Affymetix Genechip 3` IVT Express Kit (Catalog Number 901228, Affymetrix, Santa Clara, CA)

growth_protocol: KBM7 cells were maintained in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% fetal calf serum and 1% penicillin/streptomycin.

extract_protocol: RNA was isolated with the RNeasy Mini Kit from Qiagen with the help of the QIAcube robot.

treatment_protocol: Log phase proliferating cells were stimulated with IFN-gamma (100ng/ml,  Peprotech) or TNF-alpha (10ng/ml, Peprotech) for 6 hours or left untreated. Sample WT_1 corresponds with the control sample for the IFN-gamma stimulation; Sample WT_2 corresponds with the control sample for the TNF-alpha stimulation.

value: KBM7 chronic myeloid leukemia (CML) cells

tag: genotype/variation

value: Wild type

tag: agent

value: unstimulated


title: TNFRSF1A

description:
Gene expression from unstimulated cells lacking expression of TNFR1
Sample TNFRSF1A

source_name: TNFRSF1A mutant

value: TNFRSF1A mutant


title: WT 4h vs Δpp-1 4h


title: Δpp-1 5h vs WT 5h

value: 5 hours growth


title: JAK2 mutant + IFN-gamma

description:
Gene expression from cells lacking JAK2 expression stimulated with IFN-gamma
Sample JAK2_IFN

source_name: JAK2 mutant + IFN-gamma

value: JAK2 mutant

value: IFN-gamma


title: JAK2 mutant

description:
Gene expression from unstimulated cells lacking JAK2 expression
Sample JAK2

source_name: JAK2 mutant


title: MEF_Wapl(-/F)+4OHT_4

first: Roman

last: Stocsits

address: Campus-Vienna-Biocenter 1

institute: IMP - Research Institute of Molecular Pathology

description: Wapl (-/F) + 4-OHT

hyb_protocol: Probe- Prehybridisation (TECAN HS4800)      Protocol for 40 domain chips:    Combine: 50µl Labeled DNA     29µl    20x SSPE    4µl 50x Denhardts solution    50µl Form amid    1.5µl   mouse block    3.5µl 20% SDS (last component to be added)      Incubate at 94°C for 2 min  Prehybridise probe for at least 1 hour at 50°C    • start prehybridization of the slides    • After prehyb of the samples and the slides pipette 135 µl onto each slide   If you have duplicates then pool and use 135µl per slide    • split and pipette 140 µl onto each slide    • Continue with hybridization on TECAN HS4800  for 12hours 45°C

scan_protocol: Scanner: GenePix 4000B

data_processing: Image Analysis: GenPix Pro 6.0. Data analysis: The statistical computing software R version 2.11.0 http://www.R-project.org and the limma package [Smyth 2004] was used for data normalization and calculation of fold changes and differential expression. In brief, we first removed all clones with missing signal intensities. Micro Array expression intensities were then background corrected using RMA and normalized within arrays with default settings. Only clones with reasonable (>250) expression values in at least 25% of the samples were analyzed further. Differentially expressed genes were obtained by applying limma's linear model fit and subsequent Benjamini Hochberg p-value adjustment. Genes with adjusted p-value smaller than 0.01 were called significant.

source_name: G0 phase synchronized MEFs

label_protocol: Labeling with a Reactive Fluorescent Dye/ Molecular probes (Alexa 555, 647)    Thoroughly dissolve the amine-modified 4µg DNA in 5µl  nuclease free H2O (warming to 42°C for 5 min if necessary)  Add 3µl  Labeling buffer  (Just before use dissolve one vial of reactive dye in 10-20µl DMSO or use aliquots from –80°C)  Add 2µl  reactive dye to the samples, vortex briefly to mix (do not spin)  Incubate for 1 hour in the dark at room temperature

growth_protocol: MEFs were starved in OptMEM containing 2% serum for seven days before RNA extraction

extract_protocol: Total RNA extracted using RNeasy Mini Kit (QIAGEN) following manufacturer's instructions

treatment_protocol: 4-OHT was added to the starvation medium to a final concentration of 500 nM

tag: strain

value: mixed C57BL/6 and 129

value: G0 phase synchronized MEFs

tag: sample group

tag: genotype

value: Wapl (-/F) ERCre/+

value: starvation + 4-OHT

tag: hybridisation chip

source_name: pool

tag: reference

value: pool


title: MEF_Wapl(-/F)_4

description: Wapl (-/F)

tag: age

value: starvation


title: TNFRSF1A mutant + TNF-alpha

description:
Gene expression from cell lacking expression of TNFR1 stimulated with TNF-alpha
Sample TNFRSF1A_TNF

source_name: TNFRSF1A mutant + TNF-alpha

value: TNF-alpha


title: Wild type control_1 +IFN-gamma

description:
Gene expression from control cells stimulated with IFN-gamma
Sample WT_IFN

source_name: Wild type control +IFN-gamma


title: Wild type control_2 + TNF-alpha

description:
Gene expression from control cells stimulated with TNF-alpha
Sample WT_TNF

source_name: Wild type control + TNF-alpha


title: Wild type control_2

description:
Gene expression from unstimulated control cells
Sample WT_2


title: WT 6h vs WT 5h repeat 1

tag: developmental stage

value: 6 hours growth


title: Δpp-1 4h vs Δpp-1 5h

source_name: Δpp-1 conidia, 30 degree incubation


title: WT 5h vs Δpp-1 5h repeat 2


title: WT 8h vs WT 6h repeat 1

value: 8 hours growth


title: MEF_Wapl(-/F)_2

description: Wapl (-/F)

tag: treatment


title: MEF_Wapl(-/F)_3

description: Wapl (-/F)


title: WT 5h vs WT 4h

value: 4 hours growth


title: Δpp-1 6h vs Δpp-1 8h


title: Δpp-1 3h vs WT 3h

value: 3 hours growth


title: MEF_Wapl(-/F)+4OHT_2

description: Wapl (-/F) + 4-OHT


title: 3_two_months_before

value: male

tag: time

value: two months before the exam in blood

value: chronic stress

tag: tissue

value: blood


title: SW480 empty vector control

city: Munich

first: Marc

last: Taenzer

address: Ismaningerstr 22

institute: MRI

description: Gene expression data

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA

source_name: SW480 cells

label_protocol: Affymetrix standard protocol

growth_protocol: Cells were selected with Geneticin and grown for several weeks. Single clones were picked and checked for expression of TFAP2E.

extract_protocol: RNA was extracted with Rneasy Kit (Quiagen).

treatment_protocol: SW480 stable clones were used for RNA extraction.

tag: expression

value: control


title: MEF_Wapl(-/F)+4OHT_3

description: Wapl (-/F) + 4-OHT

tag: cell type


title: SW480 cells with TFAP2E CDS overexpression

description: Gene expression data

tag: cell line

value: TFAP2E CDS overexpression


title: MEF_Wapl(-/F)_1

description: Wapl (-/F)

value: mixed C57BL/6 and 129


title: WT 5h vs WT 6h repeat 1

source_name: WT (FGSC 2489) conidia, 30 degree incubation

value: 5 hours growth


title: WT 4h vs WT 3h


title: 1_one_month_after

tag: gender

value: one month after the exam in blood


title: Meg_rep3

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

description: Primary megakaryocytes (MEG) were obtained by expansion and differentiation of fetal liver progenitors followed by CD41 immunoselection.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data analysis was performed using the BioConductor packages ‘affy’library in R. Using the RMA method, hybridization signals were corrected for background, quantile-normalized and log2-transformed.

source_name: Megakaryocytes

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol

value: fetal liver

value: Megakaryocytes


title: Δpp-1 5h vs Δpp-1 6h

state: CA


title: Meg_rep4


title: Meg_rep2


title: Δpp-1 8h vs WT 8h repeat 1


title: ERY_rep4

source_name: Erythroblasts

value: Erythroblasts


title: WT 3h vs WT 4h repeat 1


title: MEF_Wapl(-/F)+4OHT_1

description: Wapl (-/F) + 4-OHT

value: G0 phase synchronized MEFs

value: Wapl (-/F) ERCre/+

value: starvation + 4-OHT

value: pool


title: Meg_rep1


title: MEF_Wapl(+/F)+4OHT_4

description: Wapl (+/F) + 4-OHT

value: Wapl (+/F) ERCre/+


title: MEF_Wapl(+/F)_3

description: Wapl (+/F)

value: starvation


title: MEF_Wapl(+/F)_4

description: Wapl (+/F)


title: ERY_rep3


title: WT 5h vs Δpp-1 5h repeat 1


title: MEF_Wapl(+/F)_2

description: Wapl (+/F)


title: MEF_Wapl(+/F)+4OHT_3

description: Wapl (+/F) + 4-OHT


title: RProia9_9_LA_Mouse430_2_9_9KO-und

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: RMA nomanization method of software Partek6.6

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse were collected from NIDDK animal core facility. Primary keratinocytes from the skin of Sgpp1+/+ and Sgpp1-/- mice were grown in 0.05mM Ca2+-containing EMEM medium plus 8% fetal calf serum (low Ca2+ medium) for 3-4 days and harvested for isolation of mRNA.

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

treatment_protocol: RNA was isolated samples from KO and WT genotype

value: Primary keratinocytes

tag: genotype/variaion


title: MEF_Wapl(+/F)_1

description: Wapl (+/F)


title: WT 4h vs WT 5h

value: 4 hours growth


title: RProia7_23_LA_Mouse430_2_7_23KO-und


title: RProia8_8_LA_Mouse430_2_8_8KO-und


title: RProia6_21_LA_Mouse430_2_6_21KO-und


title: ERY_rep1


title: WT 6h vs WT 8h

value: 6 hours growth

value: 8 hours growth


title: MEF_Wapl(+/F)+4OHT_2

description: Wapl (+/F) + 4-OHT


title: HSC_rep3

source_name: Hematopoietic Stem Cell

value: Hematopoietic Stem Cell


title: HSC_rep4


title: MEF_Wapl(+/F)+4OHT_1

description: Wapl (+/F) + 4-OHT

value: mixed C57BL/6 and 129


title: WT 6h vs Δpp-1 6h repeat 1


title: RProia5_5_LA_Mouse430_2_5_5WT-und


title: ERY_rep2


title: HSC_rep2


title: angio2_3

city: Iowa City

first: Timothy

middle: Marvin

last: Bahr

state: IA

department: Pediatrics

institute: University of Iowa

description: Gene expression in fetal heart tissue after daily infusion of angiotensin

hyb_protocol: Fragmented RNA was hybridized for 17 hours at 65˚C and 10 rpm.  Slides were washed using Agilent Gene Expression Wash Buffers.

scan_protocol: Slides were scanned immediately after washing on an Agilent C scanner (20 bit) at 5 µm resolution.

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software using default parameters.

organism: Ovis aries

source_name: fetus, heart tissue, daily angiotensin 2 infusion

label_protocol: Three µg of amplified RNA was labeled with Cy-5 using the Kreatech ULS Labeling Kit, 1.65 µg was fragmented according to Agilent specifications and Kreablock was added before hybridizing to the Agilent sheep gene expression microarray.

extract_protocol: The samples were homogenized in Trizol® reagent and total RNA was purified by phenol/chloroform extraction followed by cleanup using the RNeasy® kit.  High quality RNA (RNA Integrity Number of 7.5-10 and 28S/18S ratio of 1.6-2.1) was confirmed with an Agilent Bioanalyzer.

treatment_protocol: The uterus of pregnant ewes at 125-126 days gestation (term 145 days) with twin fetal pregnancies was opened, and catheters were placed in the fetal right femoral artery and vein.  To examine heart and cardiomyocyte growth in response to ANG II, 4 catheterized fetuses received a continuous intravenous infusion of ANG II.  Likewise, 4 catheterized fetuses received a continuous intravenous infusion of losartan, an AT1 receptor antagonist.  Following five days of treatment, fetuses were exteriorized and their hearts were excised.  A portion of the left ventricular free wall and septum of each heart was excised, frozen, and stored at -80C.

tag: twin set

value: left ventricle free wall


title: angio2_4


title: control_l_4

description: Gene expression in fetal heart tissue of control fetus

source_name: fetus, heart tissue, no infusion


title: control_a_4


title: losartan_4

description: Gene expression in fetal heart tissue after daily infusion of losartan

source_name: fetus, heart tissue, daily losartan infusion


title: control_a_3


title: RProia3_3_LA_Mouse430_2_3_3WT-und


title: PINT inhibition, rep3

description:
ASO_PINT_3
Gene expression after transfection with ASO PINT and 12h of doxorubicine 150nM treatment

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix MoGene-1_0-st-v1 chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized with Bioconductor software using the RMA algorithm.

source_name: MEF lsl, ASO PINT, treated with doxorrubicine 150nM, 12h

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: MEF LSL were grown with DMEM (Invitrogen) 10% FBS (Invitrogen) at 37 °C, 5% CO2.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: For p53 restoration, p53LSL/LSL MEFs were infected with AdenoCre virus for 24h (University of Iowa) at moi of 5. After p53 restoration, MEFs were transfected with ASOs and siRNAs. 24h after transfection, cells were treated with doxorubicine hydrochloride (Sigma D1515) for 12h to activate p53 mediated response by DNA damage.

value: MEF LSL

tag: strain/background

tag: aso

value: PINT

value: doxorubicine


title: HSC_rep1

value: fetal liver


title: RProia4_4_LA_Mouse430_2_4_4WT-und


title: losartan_3


title: Tumor cells (MiaPaCa2) treated with pre-stimulated stellate cells (PSC), 24h

city: Heidelberg

first: Matt

middle: Zbigniew

last: Rogon

address: Meyerhofstrasse 1

department: SCB

institute: EMBL

description: MiaPaca2 post TC-primed PSC-treatment

hyb_protocol: Following fragmentation, 10 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 400.

data_processing: The data were processed with R using RMA normalization procedure (justRMA package), annotated with the corresponding library (hgu133plus2.db), and extracted in both unfiltered (normalized, complete set), and filtered (IQR filtering 0.35).

organism: Homo sapiens

source_name: MiaPaCa2 cell line

growth_protocol: regular frowth to 70% confuence at 37oC

extract_protocol: Qiagen RNA kit extraction according to manufacturer's protocol

treatment_protocol: Stellate-cell supernatant was added 24, 7,6,5,4,3,2, and  1hour prior harvest

tag: pancreatic tumor cell line


title: HeLa serum starvation 36h + 30 uM zinc

city: Tokyo

first: Kengo

last: Homma

address: 3-1, 7-Chome, Hongo, Bunkyo-ku

department: Graduate School of Pharmaceutical Sciences

institute: The University of Tokyo

description: SAMPLE 4

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 μg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven.Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) v.9.1 was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. The signal intensities from the single-experiment raw data lists are normalized by dividing the intensity values by their median. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

source_name: HeLa serum starvation + zinc addition

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit (Agilent Technologies) following the manufacture's protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: The total RNA was isolated from cells using the Isogen reagent (Wako) following the manufacturer's recommendations.

value: HeLa

tag: treament condition

value: serum starvation 36h + 30 uM zinc


title: Tumor cells (MiaPaCa2) treated with pre-stimulated stellate cells (PSC), 7h

description: MiaPaca2 post TC-primed PSC-treatment


title: RProia2_2_LA_Mouse430_2_2_2WT-und


title: RProia10_10_LA_Mouse430_2_10_10KO-und


title: Tumor cells (MiaPaCa2) treated with pre-stimulated stellate cells (PSC), 4h

description: MiaPaca2 post TC-primed PSC-treatment


title: Tumor cells (MiaPaCa2) treated with pre-stimulated stellate cells (PSC), control at 24h

description: Miapaca2 control


title: Tumor cells (MiaPaCa2) treated with pre-stimulated stellate cells (PSC), 5h

description: MiaPaca2 post TC-primed PSC-treatment


title: RProia1_1_LA_Mouse430_2_1_1WT-und


title: Tumor cells (MiaPaCa2) treated with pre-stimulated stellate cells (PSC), control at 0h

description: Miapaca2 control


title: PINT inhibition, rep1

description:
ASO_PINT_1
Gene expression after transfection with ASO PINT and 12h of doxorubicine 150nM treatment


title: Tumor cells (MiaPaCa2) treated with pre-stimulated stellate cells (PSC), 6h

description: MiaPaca2 post TC-primed PSC-treatment


title: PINT control inhibition, rep2

description:
ASO_control_3
Gene expression after transfection with ASO control and 12h of doxorubicine 150nM treatment

source_name: MEF lsl, ASO CONTROL, treated with doxorrubicine 150nM, 12h

value: control


title: HeLa serum starvation 36h

description: SAMPLE 3

source_name: HeLa serum starvation

value: serum starvation


title: LM8 hPHD4 clone

city: Dresden

first: Georg

last: Breier

department: Institut für Pathologie

institute: TU Dresden

hyb_protocol: The fragmented cRNA was hybridized to the GeneChip array MOE430A over night at 45°C under rotation (60 rpm).

scan_protocol: The arrays were washed, stained and scanned ba standard Affymetrix protocols using the Affymetrix GeneChip Fluidic station 400 and the Agilent GeneArray scanner 2500 (Agilent, Technologies, Palo Alto, CA, USA

data_processing: Images were quantified with MAS 5.0 software and GeneSpring software 9.0, using MAS5  normalisation and no baseline transformation.

source_name: LM8 osteosarcoma cells

label_protocol: Biotinylatetd targets were prepared according to the Affymetrix Eukaryotic Hybridization protocol (Affymetrix, Santa Clara, CA, http:\\www.affymetrix.com)  from 5 µg total RNA.

growth_protocol: LM8 osteosarcoma cells were transfected eith a full length hPHD4 cDNA clone in a pcDNA3.1 vector using transfection reagent (Lipofectamine TM 200; Invitrogen, Carlsbad),

extract_protocol: RNA was isolatedfrom cell pellets using the Rneasy Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer's protocol.

treatment_protocol: and selected in medium supplemented with 0,5 mg/ml G418. Cells transfected with empty pcDNA3.1 vector served as control for all experiments.

value: stable transfected clone


title: LM8 control clone

value: control clone transfected with empty vector


title: control_a_2


title: control_l_3


title: PINT control inhibition, rep1

description:
ASO_control_2
Gene expression after transfection with ASO control and 12h of doxorubicine 150nM treatment


title: Tumor cells (MiaPaCa2) treated with pre-stimulated stellate cells (PSC), 3h

description: MiaPaca2 post TC-primed PSC-treatment


title: losartan_2


title: PINT inhibition, rep2

description:
ASO_PINT_2
Gene expression after transfection with ASO PINT and 12h of doxorubicine 150nM treatment


title: p53 control inhibition, rep3

description:
siRNA_control_3
Gene expression after transfection with siRNA control and 12h of doxorubicine 150nM treatment

source_name: MEF lsl, siRNA control, treated with doxorrubicine 150nM, 12h

tag: sirna


title: HeLa 8µM TPEN 9h

description: SAMPLE 2

source_name: HeLa zinc depletion

value: 8µM TPEN for 9h


title: control_a_1


title: Tumor cells (MiaPaCa2) treated with naive stellate cells (PSC), 7h

description: MiaPaca2 post naive PSC-treatment


title: p53 inhibition, rep3

description:
siRNA_p53_3
Gene expression after transfection with siRNA p53 and 12h of doxorubicine 150nM treatment

source_name: MEF lsl, siRNA p53, treated with doxorrubicine 150nM, 12h


title: Tumor cells (MiaPaCa2) treated with naive stellate cells (PSC), 24h

description: MiaPaca2 post naive PSC-treatment


title: angio2_1


title: angio2_2


title: Tumor cells (MiaPaCa2) treated with pre-stimulated stellate cells (PSC), 1h

description: MiaPaca2 post TC-primed PSC-treatment


title: Tumor cells (MiaPaCa2) treated with naive stellate cells (PSC), control at 24h

description: Miapaca2 control


title: p53 inhibition, rep2

description:
siRNA_p53_2
Gene expression after transfection with siRNA p53 and 12h of doxorubicine 150nM treatment


title: control_l_2


title: HeLa control

description: SAMPLE 1

source_name: HeLa control


title: p53 control inhibition, rep1

description:
siRNA_control_1
Gene expression after transfection with siRNA control and 12h of doxorubicine 150nM treatment


title: Tumor cells (MiaPaCa2) treated with pre-stimulated stellate cells (PSC), 2h

description: MiaPaca2 post TC-primed PSC-treatment


title: p53 inhibition, rep1

description:
siRNA_p53_1
Gene expression after transfection with siRNA p53 and 12h of doxorubicine 150nM treatment


title: p53 control inhibition, rep2

description:
siRNA_control_2
Gene expression after transfection with siRNA control and 12h of doxorubicine 150nM treatment


title: losartan_1


title: control_l_1