title: day 5 of ES cell differentiation, untreated

description:
ESC200c_Nt_day5.CEL
Gene expression data from day 5 of differentiation of ES cells

source_name: A2.miR200c, No treatment, day 5

value: untreated


title: L. lactis exponential phase ILV10 medium replicate 2

status: Public on Sep 22 2011

type: RNA

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

country: France

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

description: characterization of L. lactis response to isoleucine starvation

hyb_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.

data_processing: Local background was removed from the raw signals with the Bioplot software (Biochips Platform, INSA Toulouse, France, http://biopuce.insa-toulouse.fr).. Data were normalized by the all spot’s mean with Bioplot software.

molecule: total RNA

organism: Lactococcus lactis

source_name: L. lactis IL1403 exponential phase

growth_protocol: see manuscript in preparation Dressaire et al. 2008. Dynamic characterization of isoleucine starvation in Lactococcus lactis.

tag: strain IL1403

tag: exponential phase


title: day 4 of ES cell differentiation, untreated

city: Saint Louis

first: Jennifer

last: Gill

state: MO

address: 660 South Euclid Ave.

department: Pathology/Immunology

country: USA

institute: Washington University School of Medicine

description:
ESC200c_Nt_day4.CEL
Gene expression data from day 4 of differentiation of ES cells

hyb_protocol: The Affymetrix operating system (Command Console) was used to manage the washing and hybridization steps.

scan_protocol: The Affymetrix operating system (Command Console) was used for scanning.  Affymetrix analysis software (Genotyping Console) was used to derive Quality Control metrics, create .cel files and scaled expression data from the scanned Expresison array image files

data_processing: The data were analyzed with dChip 2008 using default analysis settings.  All samples were normalized to a single baseline array of median intensity (87).

label: biotin

organism: Mus musculus

source_name: A2.miR200c, No treatment, day 4

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

growth_protocol: ES cells were differentiated as embryoid bodies in petri dishes at a density of 15,000 cells/mL in differentiation media consisting of 10% FCS.

extract_protocol: RNA was isolated using Qiagen RNeasy kit per the manufacture's instructions.

treatment_protocol: In Ntdox conditions, doxycycline was added for a final concentration of 500ng/mL on days 2 and 4

tag: cell type

value: mouse embryonic stem cells

tag: cell line

tag: protocol

value: control

tag: agent

tag: time

value: day 4 of differentiation


title: EOS3F-24_2i_converted-rep3

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The data were analyzed with RMA as background correction, summarization & normalization method.

source_name: Partial iPS cells with 2i cocktail

label_protocol: Whole transcript sense target labeling assay

growth_protocol: Low passage primary MEFs were grown in DMEM (Wisent) supplemented with 10% FBS (Wisent), 10 μg/mL penicilin and streptomysin (Sigma), and 2 mM L-glutamine (Sigma). J1 ES cells and iPS cell clones were grown on arrested feeder cells under standard conditions in the presence of LIF. EOS3F-24, -28, and -29 iPS cells were mantained under 1 μg/ml puromycin selection.

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: 2i conversion was performed using MEK inhibitor (2 μM) and GSK inhibitor (12 μM) from StemGent in LIF supplemented ES media.

value: Partial iPS cells with 2i cocktail


title: day 4 of ES cell differentiation, dox-induced miR-200c/141

description:
ESC200c_Ntdox_day4.CEL
Gene expression data from day 4 of differentiation of ES cells inducibly expressing miR-200c/miR-141

source_name: A2.miR200c, Dox treatment, day 4

value: inducible expression of miR-200c/miR-141

value: doxycycline

tag: dose

value: 500 ng/mL


title: Patient 16 Preshift

status: Public on Sep 21 2011

city: Kaohsiung

first: Tzu Chi

last: Lee

address: Shihcyuan 1st Rd.

department: Department of Public Health

country: Taiwan

institute: Kaohsiung Medical University

description: sample 119

hyb_protocol: Then, 10 µg of fragmented biotin-labeled cRNA was hybridized on Phalanx Human OneArray™ by Phalanx hybridization buffer at 50oC in oven for 14-16 hrs using the bubble-mixing method.

scan_protocol: Finally, arrays were dried by centrifugation and scanned by DNA Microarray Scanner (Agilent Technologies, Santa Clara, US). Images from the scanned arrays were quantified using GenePix® Pro 4.0 (Molecular Devices, Sunnyvale, CA).

data_processing: Spots in each array with foreground median intensity of wavelength 532 nm greater than or equal to that of background median intensity plus 3 folds standard deviation of wavelength 532 nm were considered as the “Present” flag and included for the further analysis. In order to evaluate the quality of each array in the entire array experiment, three evaluation steps were performed: basic, reproducible, and diagram. In basic step, three parameters, including percentage of “Present” spots among all spots, the average intensity of “Present” spots, and coefficient of variation of intensity for control spots in the entire arrays were all considered. If any two parameters in one array were located outside the 1.5-folds interquartile range (25th-75th) of same parameters for all arrays, that array was excluded. The remaining arrays were then evaluated in reproducible steps which the repeated arrays of the same sample would pass, when their Pearson’s correlation coefficient was larger than 0.95 and “2-fold percentage” was less than 15% (sFig. 4). The “2-fold percentage” was the percentage of probes among all probes in which the ratio of the same probe between two arrays exceeded 2-fold. In the final diagram step, the density plot of repeated arrays was used to examine the intensity profile of each array. An array would pass if the profile was similar to the rest of arrays in the same phenotype groups. When the arrays passed all three steps, the raw intensity of spots were log-2 transformed for subsequent analysis. To adjust the systematic variation of experiments and dye effects, global Lowess normalizations were performed within repeated arrays of the same sample and between the samples.  Spot was included for further analysis when it was “Present” in at least one of the qualified arrays.

organism: Homo sapiens

source_name: Coke-oven worker

label_protocol: After non-specific binding targets were washed, the hybridization arrays were conjugated with fluorescent detector of Strepavidin-Cy3.

extract_protocol: One-half µg RNA of each sample was amplified by Illumina TotalPrep RNA Amplification Kit according to the manufacturer’s instructions (Ambion, Austin, TX).

tag: age

tag: time-point

value: Preshift

tag: work-place

value: Topside

tag: smoking

value: Yes


title: L. lactis exponential phase ILV10 medium replicate 1

scan_protocol: see Redon et al. 2005. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J Biol Chem 280(43):36380-385.

tag: growth status

value: exponential:µ= 0.877h-1


title: J1_ESCs_rep1

source_name: J1 Embryonic stem cells

value: J1 Embryonic stem cells


title: day 3 of ES cell differentiation, dox-induced miR-200c/141

description:
ESC200c_Ntdox_day3.CEL
Gene expression data from day 3 of differentiation of ES cells inducibly expressing miR-200c/miR-141

source_name: A2.miR200c, Dox treatment, day 3

value: day 3 of differentiation


title: day 3 of ES cell differentiation, untreated

description:
ESC200c_Nt_day3.CEL
Gene expression data from day 3 of differentiation of ES cells

source_name: A2.miR200c, No treatment, day 3


title: Patient 15 End-of-shift

description: sample 218

value: End-of-shift


title: Patient 16 End-of-shift

description: sample 219


title: EOS3F-24,2i_converted_rep1


title: Patient 14 End-of-shift

description: sample 216

value: Quit


title: EOS3F-24_2i_converted_rep2


title: prostate cancer sample 21

city: Boston

first: Changmeng

last: Cai

state: MA

address: 330 Brookline Avenue

department: hematology-oncology

institute: Beth Israel Deaconess Medical Center

description: gene expression data from prostate cancer sample #317R

hyb_protocol: After fragmentation, cRNA target were hybridized to Affymetrix 133A oligonucleotide microarrays

scan_protocol: High resolution GeneArray 3000 scaner

data_processing: Expression values were derived by probe set level analysis from the raw CEL files with R statitical software and BioConductor packages and libraries.

source_name: Primary localized prostate cancer

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

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

treatment_protocol: 22 primary cancer were hormone-naïve, while 29 metastatic cancer were castration-resistant (ADT treated).

tag: metastasis

value: localized prostate cancer

tag: androgen deprivation

value: no

value: positive


title: Patient 12 Preshift

description: sample 113


title: Patient 11 Preshift

description: sample 106

value: Sideoven


title: Patient 8 Preshift

description: sample 111


title: Patient 15 Preshift

description: sample 118


title: Patient 10 End-of-shift

description: sample 205

value: No


title: Patient 9 Preshift

description: sample 178


title: Patient 7 Preshift

description: sample 160


title: Patient 6 Preshift

description: sample 115


title: Patient 13 End-of-shift

description: sample 214


title: Patient 7 End-of-shift

description: sample 260


title: Patient 6 End-of-shift

description: sample 215


title: Patient 11 End-of-shift

description: sample 206


title: Patient 12 End-of-shift

description: sample 213


title: Patient 14 Preshift

description: sample 116


title: Patient 8 End-of-shift

description: sample 211


title: Patient 9 End-of-shift

description: sample 278


title: Patient 10 Preshift

description: sample 105


title: Patient 13 Preshift

description: sample 114


title: Patient 3 Preshift

description: sample 109


title: Patient 5 End-of-shift

description: sample 246


title: Patient 3 End-of-shift

description: sample 209


title: Patient 5 Preshift

description: sample 146


title: Patient 2 End-of-shift

description: sample 207


title: Patient 4 Preshift

description: sample 163


title: Patient 4 End-of-shift

description: sample 263


title: Patient 1 Preshift

description: sample 104


title: Patient 1 End-of-shift

description: sample 204


title: Patient 2 Preshift

description: sample 107


title: Follicular_Lymphoma_12

city: Toledo

first: Alberto

last: Arribas

state: Toledo

address: Avda Barber, 30

department: Molecular Pathology Research Unit

country: Spain

institute: Hospital Virgen de la Salud

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Gene Pix Pro Software (version 6.0).

data_processing: The background subtraction of microarray data was carried out using GEPAS 4.0 (http://gepas.bioinfo.cipf.es). The dataset was normalized by lowess within-array normalization and quantile between-array normalization.

label_protocol: The cDNA was fragmented, labeled and hybridized to Whole Human Genome Agilent 4X44K Oligonucleotide Microarray (Agilent Technologies, Inc., Santa Clara, CA).

extract_protocol: Total RNA  amplification and labeling were performed according to the standard Agilent protocol.

treatment_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), and purified and treated with RNase-free DNase I using the RNeasy kit (Qiagen Inc., Valencia, CA)

tag: tissue

value: freshly frozen lymph nodes

source_name: Universal Human Reference RNA from Stratagene

tag: sample origin

value: 10 human cell lines


title: Follicular_Lymphoma_14


title: UPN6

type: genomic

city: Stockholm

first: Stefan

last: Deneberg

department: Internal medicine/Huddinge

country: Sweden

institute: Karolinska Institutet

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: The beta values are formatted for use with BeadStudio software v3.2 and Genesis (TU Graz), meaning that -0.5 equals no methylation and +0.5 full methylation on a linear scale. Samples are mean normalized using Genesis.

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Ficoll separated fresh AML cells from diagnostic bone marrow samples were collected. DNA was extracted with the Dneasy kit(Qiagen)

treatment_protocol: EZ methylation kit

tag: aml type

value: de novo AML

tag: 2 year overall survival

value: n

tag: 2 year progression free survival

tag: complete remission (cr)

value: y

tag: npm1 status

value: Mut


title: UPN4


title: UPN30

value: WT


title: Follicular_Lymphoma_15


title: UPN32


title: UPN3


title: UPN9


title: Follicular_Lymphoma_13


title: UPN5


title: UPN31


title: UPN29


title: UPN7


title: Follicular_Lymphoma_8


title: UPN27


title: Follicular_Lymphoma_5


title: UPN26


title: Follicular_Lymphoma_9


title: UPN8


title: Follicular_Lymphoma_11


title: Follicular_Lymphoma_10


title: UPN28


title: Follicular_Lymphoma_16


title: UPN25


title: Follicular_Lymphoma_6


title: Follicular_Lymphoma_7


title: S288c MSS11 overexpressed, biological rep1 (MCB34)

city: Stellenbosch

first: Michael

middle: Christiaan

last: Bester

address: Victoria street

country: South Africa

institute: Institute for Wine Biotechnology

hyb_protocol: Performed according to standard Affymetrix protocol (Yeast 2.0)

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® scanner 3000and the Affymetrix GeneChip® Operating Software (GCOS) version 1.4.

data_processing: Data normalisation with RMA method, used software RMAExpress ver1.0.4

label: Biotin

organism: Saccharomyces cerevisiae

source_name: Wild type yeast transformed with muticopy vector carrying MSS11

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

growth_protocol: Yeast grown in 5 ml of synthetic dropout media (YNB) in test tubes. 2% Glucose as carbon source. 30 degrees Celsius as growth temperature

extract_protocol: Phenol-Chloroform exctraction with heat treatment (65 degrees Celsius 5 min.). Schmitt et al., 1990, A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res 18: 3091-3092.

treatment_protocol: Yeast cultures grown to early stationary phase, cells were seperated from growth medium, washed and mixed with extraction buffer and phenol/chloroform before being frozen in liquid nitrogen

tag: strain

value: BY4742, EUROSCARF

tag: genotype/variation

value: MSS11 over-expression


title: Σ1278b MSS11 overexpressed, biological rep1 (MCB31)

value: Σ1278b, H-U Moesch, MATα ura3-52 trp1Δ::hisG leu2Δ::hisG his3Δ::hisG


title: S288c wt, biological rep1 (MCB33)

source_name: Wild type yeast transformed with empty vector

value: wild type


title: UPN20


title: Lymph_Node_infiltrated_by_Marginal_Zone_Lyphoma_MALT_type_5


title: UPN22


title: Follicular_Lymphoma_3


title: UPN24


title: Lymph_Node_infiltrated_by_Splenic_Marginal_Zone_Lyphoma_2


title: UPN23


title: Σ1278b mss11 deleted, biological rep1 (MCB32)

source_name: Yeast carrying a deletion in MSS11 transformed with empty vector

value: MSS11 deletion


title: Lymph_Node_infiltrated_by_Splenic_Marginal_Zone_Lyphoma_1


title: Follicular_Lymphoma_4


title: UPN21


title: Lymph_Node_infiltrated_by_Marginal_Zone_Lyphoma_MALT_type_2


title: UPN2-B


title: Follicular_Lymphoma_2


title: Σ1278b FLO11 over-expression, biological rep3 (MCB22)

source_name: Wild type yeast transformed with muticopy vector carrying FLO11 under control of the constitutive strong promoter PGK1

value: FLO11 over-expression


title: Σ1278b wt, biological rep1 (MCB29)


title: Σ1278b FLO8 overexpressed, biological rep1 (MCB30)

source_name: Wild type yeast transformed with muticopy vector carrying FLO8

value: FLO8 over-expression


title: Lymph_Node_infiltrated_by_Splenic_Marginal_Zone_Lyphoma_3


title: Lymph_Node_infiltrated_by_Marginal_Zone_Lyphoma_MALT_type_1


title: Lymph_Node_infiltrated_by_Marginal_Zone_Lyphoma_MALT_type_3


title: Follicular_Lymphoma_1


title: Lymph_Node_infiltrated_by_Splenic_Marginal_Zone_Lyphoma_4


title: KO mouse heart at 6-weeks old, biological rep4

city: Houston

first: Zheng

last: Sun

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
Gene expression data from mouse heart
KO4

hyb_protocol: RNA were hybridized to the Mouse Gene 1.0 ST Array (Affymetrix).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS3000.

data_processing: Microarray image analysis was carried out using Partek Genomics Suite software. Subsequent analysis was carried out using BioConductor. Data from the 8 samples were subjected to background subtraction, quantile normalization, log2 transformation and probeset summarization using the RMA (Robust Multichip Average) algorithm. Only the probe sets that interrogate genes were retained and those meant for QC and normalization purposes were excluded from further analysis. The SAM procedure was then used to obtain multiple test corrected q-values for differential expression of genes between the hearts from MCH3-KO mice and control.

source_name: Mouse heart at 6-weeks old

label_protocol: GeneChip WT Terminal Labeling and Control Kit (Affymetrix)

growth_protocol: Mice were maintained on normal chow and the normal 24-hr light/dark cycle

treatment_protocol: Hearts were put into liquid nitrogen immediately after mice euthanization

value: heart

value: KO

value: 6-weeks old


title: KO mouse heart at 6-weeks old, biological rep3

description:
Gene expression data from mouse heart
KO3


title: KO mouse heart at 6-weeks old, biological rep2

description:
Gene expression data from mouse heart
KO2


title: UPN19


title: Lymph_Node_infiltrated_by_Marginal_Zone_Lyphoma_MALT_type_4

value: freshly frozen lymph nodes


title: Nodal_Marginal_Zone_Lymphoma_15

value: 10 human cell lines


title: UPN18

value: de novo AML


title: Σ1278b wt, biological rep3 (MCB19)


title: Σ1278b FLO11 over-expression, biological rep2 (MCB21)


title: Σ1278b FLO11 over-expression, biological rep1 (MCB20)


title: Nodal_Marginal_Zone_Lymphoma_13


title: UPN16


title: WT mouse heart at 6-weeks old, biological rep3

description:
Gene expression data from mouse heart
WT3


title: UPN17


title: Σ1278b wt, biological rep1 (MCB17)


title: UPN15


title: Nodal_Marginal_Zone_Lymphoma_14


title: Σ1278b wt, biological rep2 (MCB18)


title: WT mouse heart at 6-weeks old, biological rep2

description:
Gene expression data from mouse heart
WT2


title: Hip1Si-GFP/ Hip1Si-Hippi Replicate 4_Array A

city: Kolkata

first: Nitai

middle: Pada

last: Bhattacharyya

state: West Bengal

address: 1/AF Bidhannagar

department: Crystallography and Molecular Biology division

country: India

institute: Saha Institute of Nuclear Physics

description: Biological replicate 4 of 4, control: Hip1Si-GFP, test: Hip1Si-Hippi

hyb_protocol: Equal concentration of control and test cDNA lebelled with proper dye was mixed with Hybridization buffer supplied with the Chip (Ocimum Biosolutions, India) and heated at 95°C for 5 min. Then the mixture was loaded onto the slide and hybridization was carried out at 42°C for 16 hours in Hybstation (Genomic Solutions). After hybridization, slides were washed sequentially in the hybstation.

scan_protocol: Slides were scanned using GenePixPro 4200A scanner and image processing was done with GenePix Pro 6.0 soft ware

data_processing: GPR files were transferred to Acuity 4.0 software for analysis of data

source_name: Empty GFP vector transfected Hip1Si cells

label_protocol: 10 µg of total RNA was reverse transcribed and lebelled with Cy3 or Cy5 dye using CyScribe Post-Labeling Kit (GE Healthcare) according to manufacturer’s protocol.

growth_protocol: HeLa cells were grown in MEM supplemented with 10% FBS at 37°C in 5% CO2 atmosphere under humidified condition.

extract_protocol: Total RNA was extracted from cells using Rneasy Mini Kit (Qiagen, USA) following manufacturer’s protocol.

treatment_protocol: HeLa cells were stably transfected with HIP1 specific siRNA (Genescript) according to manufacterer's protocol. Colonies were selected by hygromycine resistance. selected colonies were checked for HIP1 knock down by western blot analysis. Stable HIP1 knocked down HeLa cells (Hip1Si) were then transiently transfected with either empty GFP vector or GFP-Hippi construct using lipofectamine transfection reagent (Invitrogen, USA) following manufacterer's protocol. Twenty four hours after transfection cells were taken for RNA isolation.

tag: cell line

value: HeLa cell

tag: cell type

value: Human cervical cancer

source_name: GFP-Hippi transfected Hip1Si cells


title: UPN12

tag: age

value: n

value: Mut


title: KO mouse heart at 6-weeks old, biological rep1

description:
Gene expression data from mouse heart
KO1


title: Nodal_Marginal_Zone_Lymphoma_12


title: UPN14

value: WT


title: WT mouse heart at 6-weeks old, biological rep4

description:
Gene expression data from mouse heart
WT4


title: Hip1Si-GFP/ Hip1Si-Hippi Replicate 3_Array A

description: Biological replicate 3 of 4, control: Hip1Si-GFP, test: Hip1Si-Hippi


title: Yeast smc2-8 mutant strains harboring pGAL:UME1 180min

city: Claremont

first: Biranchi

last: Patra

state: CA

address: 535 Watson Dr

institute: Keck Graduate Institute

hyb_protocol: Labelled probes were hybridized to Affymetrix Yeast Genome 2.0 Array.

scan_protocol: Array was  scanned with Affymetrix GeneChip Scanner 3000.

data_processing:
The microarray data were analyzed with GeneSpring 6.2 software.
The Affymetrix data were processed using RMA - the RMA approach avoids the problems associated with noise at low signal values by ignoring the MM probe values. It models the PM values as a combination of an exponential distribution (for the signal) and a normal distribution (for the noise).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, Eukaryotic Sample and array processing,Affymetrix).

growth_protocol: Cells were grown in 5 mL S-URA media containing 2% raffinose for 24 hours at 28°C.

extract_protocol: Cells were harvested at 0, 45, 90 and 180 min by centrifugation. Total RNA was isolated using a hot phenol method as described by Schmitt, et al. (1990). The RNA was purified after DNase treatment and resuspended in 10 μL of ddH2O. The purified total RNA was quantified on a nanodrop spectrophotometer and were used for gene expression analysis

treatment_protocol: Samples were diluted to OD 0.02 in 150 mL S-URA media containing 2% raffinose and 2% galactose, and then grown overnight at 25°C in a water shaker.  The samples were shifted to a water shaker at 34.5°C

value: yeast cells

value: smc2-8 mutant strain

tag: plasmid

tag: time


title: Yeast smc2-8 mutant strains harboring pGAL:UME1 45min


title: Yeast smc2-8 mutant strains harboring pGAL:UME1 90min


title: UPN13


title: Hip1Si-GFP/ Hip1Si-Hippi Replicate 2_Array A

description: Biological replicate 2 of 4, control: Hip1Si-GFP, test: Hip1Si-Hippi


title: Nodal_Marginal_Zone_Lymphoma_9


title: Nodal_Marginal_Zone_Lymphoma_11


title: WT mouse heart at 6-weeks old, biological rep1

description:
Gene expression data from mouse heart
WT1


title: Nodal_Marginal_Zone_Lymphoma_10


title: Yeast smc2-8 mutant strains harboring pGAL:UME1 0 hr


title: HeLa-GFP/ HeLa-Hippi Replicate 4_Array A

description: Biological replicate 4 of 4, control: HeLa-GFP, test HeLa-Hippi

source_name: Empty GFP vector transfected HeLa cells

treatment_protocol: HeLa cells were transfected either with empty GFP vector or GFP-Hippi construct using lipofectamine transfection reagent (Invitrogen, USA) following manufacterer's protocol.

source_name: GFP-Hippi transfected HeLa cells


title: Yeast smc2-8 mutant strains harboring pGAL:SNU66 90min


title: UPN11

value: y


title: UPN10


title: Nodal_Marginal_Zone_Lymphoma_7


title: Nodal_Marginal_Zone_Lymphoma_8


title: Nodal_Marginal_Zone_Lymphoma_5


title: Yeast smc2-8 mutant strains harboring pGAL:SNU66 45min


title: Nodal_Marginal_Zone_Lymphoma_6


title: Yeast smc2-8 mutant strains harboring pGAL:SNU66 180min


title: HeLa-GFP/ HeLa-Hippi Replicate 2_Array A

description: Biological replicate 2 of 4, control: HeLa-GFP, test HeLa-Hippi


title: 5374669002_J

tag: idh1 status

tag: idh2 status


title: Nodal_Marginal_Zone_Lymphoma_3


title: Hip1Si-GFP/ Hip1Si-Hippi Replicate 1_Array A

description: Biological replicate 1 of 4, control: Hip1Si-GFP, test: Hip1Si-Hippi


title: Nodal_Marginal_Zone_Lymphoma_4


title: 5374669002_I


title: HeLa-GFP/ HeLa-Hippi Replicate 3_Array A

description: Biological replicate 3 of 4, control: HeLa-GFP, test HeLa-Hippi


title: 5374669002_H


title: Nodal_Marginal_Zone_Lymphoma_2


title: 5374669002_K


title: Yeast smc2-8 mutant strains harboring pGAL:SMC2 90min


title: 5374669002_E


title: HeLa-GFP/ HeLa-Hippi Replicate 1_Array A

description: Biological replicate 1 of 4, control: HeLa-GFP, test HeLa-Hippi


title: Yeast smc2-8 mutant strains harboring pGAL:SMC2 45min


title: 5374669002_G


title: Nodal_Marginal_Zone_Lymphoma_1


title: high-grade central osteosarcoma xenograft CTPx

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format.

hyb_protocol: As per manufacturer's instructions.

scan_protocol: As per manufacturer's instructions.

data_processing: Data were analyzed using the statistical language R. As Illumina identifiers are not stable and consistent between different chip versions, raw oligonucleotide sequences were converted to nuIDs. Data were transformed using the variance stabilizing transformation (vst) algorithm and subsequently normalized using robust spline normalization. Conversion to nuIDs, variance stabilizing transformation, and normalization of the data were all carried out using the Bioconductor package lumi. Quality control was performed using the Bioconductor package arrayQualityMetrics. Poor quality arrays were removed from further analyses.

label_protocol: As per manufacturer's instructions.

extract_protocol: Osteosarcoma and xenograft tissue was handled as previously described in Buddingh, Kuijjer et al (PMID: 21372215). Osteosarcoma cell lines were prepared as in Ottaviano et al. (PMID: 19787792)  RNA isolation, cDNA synthesis, cRNA amplification, Illumina Human-6 v2.0 Expression BeadChip hybridization, qPCR validation, and microarray data analysis were performed as previously described in Buddingh, Kuijjer et al. (PMID: 21372215)

tag: sample type

value: xenograft

tag: histological subtype

value: osteoblastic osteosarcoma


title: high-grade central osteosarcoma xenograft 46-464


title: Yeast smc2-8 mutant strains harboring pGAL:SNU66 0 hr


title: Yeast smc2-8 mutant strains harboring pGAL:SMC2 180min


title: Reactive_Lymhp_Node_Control_8

tag: tissue

tag: sample origin


title: 5374669002_D

tag: aml type

tag: 2 year overall survival


title: 5374669002_C

tag: 2 year progression free survival

tag: complete remission (cr)


title: Yeast smc2-8 mutant strains harboring pGAL:MEK1 45min

tag: strain


title: Reactive_Lymhp_Node_Control_6


title: Yeast smc2-8 mutant strains harboring pGAL:MEK1 180min


title: high-grade central osteosarcoma xenograft CHLx


title: Reactive_Lymhp_Node_Control_5


title: Yeast smc2-8 mutant strains harboring pGAL:MEK1 0 hr


title: 5374669002_A

tag: npm1 status


title: Reactive_Lymhp_Node_Control_7


title: Yeast smc2-8 mutant strains harboring pGAL:MEK1 90min


title: high-grade central osteosarcoma xenograft ALSKx

value: chondroblastic osteosarcoma


title: high-grade central osteosarcoma xenograft 400-31


title: Yeast smc2-8 mutant strains harboring pGAL:HTA2 90min

source_name: Yeast smc2-8 mutant strains harboring pGAL:UME1 90min


title: Reactive_Lymhp_Node_Control_3


title: high-grade central osteosarcoma xenograft 84-151


title: 5374669001_K


title: 5374669002_B


title: 5374669001_L


title: Reactive_Lymhp_Node_Control_2


title: high-grade central osteosarcoma xenograft 399-101


title: Yeast smc2-8 mutant strains harboring pGAL:SMC2 0 hr


title: high-grade central osteosarcoma xenograft Aox


title: 5374669001_J


title: high-grade central osteosarcoma xenograft 166-101


title: Yeast smc2-8 mutant strains harboring pGAL:HTA2 45min

source_name: Yeast smc2-8 mutant strains harboring pGAL:UME1 45min


title: high-grade central osteosarcoma xenograft 339-61


title: Yeast smc2-8 mutant strains harboring pGAL:HTA2 180min

source_name: Yeast smc2-8 mutant strains harboring pGAL:UME1 180min


title: Yeast smc2-8 mutant strains harboring pGAL:HTA2 0 hr


title: Hip1Si-GFP/ Hip1Si-Hippi Replicate 3_Array B

tag: cell line


title: Reactive_Lymhp_Node_Control_4


title: high-grade central osteosarcoma xenograft Okx


title: high-grade central osteosarcoma xenograft TSx


title: Hip1Si-GFP/ Hip1Si-Hippi Replicate 2_Array B

tag: cell type


title: Reactive_Lymhp_Node_Control_1


title: Yeast smc2-8 mutant strains harboring negative control 90min

description: 20100512_05_smc2-8_BG1766minus_90min.CEL

value: negative control


title: Hip1Si-GFP/ Hip1Si-Hippi Replicate 4_Array B


title: high-grade central osteosarcoma xenograft OHSx


title: Yeast smc2-8 mutant strains harboring negative control 180min

description: 20100512_11_smc2-8_BG1766minus_180min.CEL


title: 5374669001_F

tag: age


title: 5374669001_G


title: Yeast smc2-8 mutant strains harboring negative control 45min

description: 20100511_11_smc2-8_BG1766minus_45min.CEL

tag: plasmid


title: 5374669001_I


title: HeLa-GFP/ HeLa-Hippi Replicate 4_Array B


title: Yeast smc2-8 mutant strains harboring negative control 0 hr

tag: time


title: 5374669001_H

tag: idh1 status


title: HeLa-GFP/ HeLa-Hippi Replicate 3_Array B


title: high-grade central osteosarcoma xenograft MJSPx


title: high-grade central osteosarcoma xenograft MPAx


title: 5374669001_E

tag: idh2 status


title: Hip1Si-GFP/ Hip1Si-Hippi Replicate 1_Array B


title: 5374669001_D


title: 5374669001_C


title: HeLa-GFP/ HeLa-Hippi Replicate 2_Array B


title: 5374669001_A


title: 5260522010_L


title: Σ1278b wt, biological rep2, b

description: Gene expression data of yeast grown till early stationary phase in synthetic dropout media

hyb_protocol: Performed according to standard Affymetrix protocol

data_processing: Data normalisation performed with GC-RMA

growth_protocol: Yeast grown in 5ml (test tubes on rotary wheel) synthetic dropout media (YNB) with 2% glucose at 30 degrees Celsius. Total RNA harvested at entry into stationary phase

value: Σ1278b, H-U Moesch

tag: genotype

value: MATα ura3-52 trp1Δ::hisG leu2Δ::hisG his3Δ::hisG


title: high-grade central osteosarcoma biopsy L3476

source_name: high-grade central osteosarcoma biopsy

tag: sample type

value: biopsy

tag: histological subtype

value: fibroblastic osteosarcoma


title: Σ1278b flo8 deleted, biological rep2

source_name: Yeast carrying a deletion in flo8 transformed with empty vector


title: Σ1278b flo8 deleted, biological rep1


title: Σ1278b FLO8 overexpressed, biological rep1


title: high-grade central osteosarcoma xenograft LBMx


title: Σ1278b FLO8 overexpressed, biological rep2


title: high-grade central osteosarcoma xenograft GKAMx


title: high-grade central osteosarcoma xenograft KPDx


title: HeLa-GFP/ HeLa-Hippi Replicate 1_Array B


title: high-grade central osteosarcoma biopsy L3444

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531303, but in this study, the sample is normalized on a larger dataset


title: 5374669001_B

value: de novo AML


title: 5260522010_G


title: high-grade central osteosarcoma biopsy L3443

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531302, but in this study, the sample is normalized on a larger dataset


title: high-grade central osteosarcoma biopsy L3475

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531305, but in this study, the sample is normalized on a larger dataset


title: Σ1278b wt, biological rep1, b


title: high-grade central osteosarcoma biopsy L3471


title: 5260522010_I


title: S288c MSS11 overexpressed, biological rep2

value: BY4742, EURODCARF

value: MATα his3Δ1 leu2Δ0 lys2Δ0 ura3Δ3


title: 5260522010_K


title: high-grade central osteosarcoma biopsy L3440

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531299, but in this study, the sample is normalized on a larger dataset


title: 5260522010_J

value: n


title: 5260522010_F


title: S288c wt, biological rep2

value: MATα his3Δ1 leu2Δ0 lys2Δ0 ura3Δ1


title: S288c MSS11 overexpressed, biological rep1

value: MATα his3Δ1 leu2Δ0 lys2Δ0 ura3Δ2


title: S288c wt, biological rep1

value: MATα his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0


title: Σ1278b MSS11 overexpressed, biological rep2


title: 5260522010_E

value: WT


title: 5260522010_D

value: y

value: Mut


title: 5260522010_C


title: high-grade central osteosarcoma biopsy L2620*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531331, but in this study, the sample is normalized on a larger dataset

value: osteoblastic osteosarcoma


title: high-grade central osteosarcoma biopsy L2292*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531320, but in this study, the sample is normalized on a larger dataset


title: Σ1278b MSS11 overexpressed, biological rep1


title: Σ1278b mss11 deleted, biological rep2


title: 5260522010_B


title: Σ1278b mss11 deleted, biological rep1


title: high-grade central osteosarcoma biopsy L3472


title: 5260522010_A


title: high-grade central osteosarcoma biopsy L1369*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531309, but in this study, the sample is normalized on a larger dataset


title: high-grade central osteosarcoma biopsy L2619*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531330, but in this study, the sample is normalized on a larger dataset


title: 5260522005_K


title: 5260522005_L


title: Σ1278b wt, biological rep1


title: 5260522005_J


title: high-grade central osteosarcoma biopsy L3460

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531288, but in this study, the sample is normalized on a larger dataset

value: chondroblastic osteosarcoma


title: high-grade central osteosarcoma biopsy L3441

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531300, but in this study, the sample is normalized on a larger dataset


title: colon_germ_free_inoculated_L.plantarum_(pool)

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: A54_09_COLON_LPLANT INOC

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using the multi-chip modified gamma Model for Oligonucleotide Signal (multi-mgMOS) [PMID: 16020470], using the PUMA package in Bioconductor.

source_name: colon from germ-free NMRI-KI mice, mono-associated with L. plantarum, pooled samples

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).

growth_protocol: Germ-free female NMRI-KI mice were inbred for >60 generations at the Laboratory of Medical Microbial Ecology at Karolinska Institute and they were housed in lightweight stainless-steel isolators. All mice had free access to a steam-sterilized standard mouse chow (R36; Lactamin, Vadstena, Sweden) and to sterilized water. Artificial light was available between 6 a.m. and 6 p.m.; the temperature was 24 ± 2.2°C, and the humidity was 55% ± 10%. The germ-free status was checked weekly by inoculating fecal samples in different media incubated both aerobically and anaerobically at 20 and 37°C for up to 4 weeks.

extract_protocol: After sampling, tissues were immediately preserved in 5 volumes of RNAlater (Ambion, Austin, Texas, USA) and stored at 4 ºC until use. Total RNA was prepared using TRIzol reagent and whereafter Purified total RNA was isolated using Qiagen RNEasy columns. For each part of the intestine, total RNA was pooled per intervention group (n=6).

treatment_protocol: The germ-free female NMRI-KI mice (45 – 65 days of age) were mono-associated using established protocols. In brief, 10 ml of cultures in late log phase of A. muciniphila MucT (ATTC BAA-835) and L. plantarum WCFS1 (NCIMB 8826) were centrifuged (4500 rpm, 10 min). Pellets were resuspended in 1 ml of sterile anaerobic Phosphate Buffer Saline (PBS) and dispensed into sterile ampoules which were heat-sealed. The external surface of each ampoule was sterilized with chromsulfuric acid before transfer into respective isolators. Inside the isolators, the ampoules were broken, and 0.2 ml (10^9 cfu/ml) of the strictly anaerobic A. muciniphila (n=6) was inoculated intragastrically; L. plantarum (n=6) was inoculated orally. Germ-free control mice (n=6) were housed in separate isolators. After 7 days of colonization, mice were killed by cervical dislocation and terminal ileum, cecum and ascending colon specimens were sampled.

value: NMRI-KI

tag: gender

value: female

tag: developmental stage

value: adult

tag: tissue

value: colon

tag: bacterial inoculation

value: Lactobacillus plantarum WCFS1


title: 5260522005_I

tag: aml type

value: de novo AML

tag: 2 year overall survival

tag: 2 year progression free survival

tag: complete remission (cr)


title: high-grade central osteosarcoma biopsy L3432

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531286, but in this study, the sample is normalized on a larger dataset

value: biopsy


title: 5260522005_G

tag: npm1 status


title: colon_germ_free_non_inoculated_(pool)

description: A54_07_COLON_NEG CTRL

source_name: colon from germ-free NMRI-KI mice, not inoculated, pooled samples

tag: strain

tag: age


title: colon_germ_free_inoculated_A.muciniphila_(pool)

description: A54_08_COLON_MUC INOC

source_name: colon from germ-free NMRI-KI mice, mono-associated with A. muciniphila, pooled samples

value: Akkermansia muciniphila MucT


title: Σ1278b wt, biological rep2

source_name: Wild type yeast transformed with empty vector

value: Σ1278b, H-U Moesch

value: MATα ura3-52 trp1Δ::hisG leu2Δ::hisG his3Δ::hisG

tag: plasmid


title: high-grade central osteosarcoma biopsy L3442

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531301, but in this study, the sample is normalized on a larger dataset


title: high-grade central osteosarcoma biopsy L3436

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531293, but in this study, the sample is normalized on a larger dataset


title: high-grade central osteosarcoma biopsy L3534

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531287, but in this study, the sample is normalized on a larger dataset

value: sclerosing


title: caecum_germ_free_inoculated_L.plantarum_(pool)

description: A54_06_CAECUM_LPLANT INOC

source_name: caecum from germ-free NMRI-KI mice, mono-associated with L. plantarum, pooled samples

value: caecum


title: genomic DNA of BSG900TD, DIPG

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

description: Gene expression data from pediatric DIPG patient.

hyb_protocol: Hybridizations were performed according the standard Affymetrix protocol

scan_protocol: Scanning performed according to the standard Affymetrix protocol

data_processing:
Affymetrix CEL files for the tumor and normal samples in the collection were analyzed using Genotyping Console software for initial quality control, followed by use of "Birdseed" algorithm to generate the SNP call files. The CEL and CHP files were first analyzed with dChipSNP to extract un-normalized signal intensity.  The intensity data was then normalized using reference normalization with selected diploid chromosomes within each sample.

Please contact Suzanne Baker at Suzanne.Baker@stjude.org for CEL files and genotype calls.

source_name: brainstem of pediatric DIPG patient collected Pretreatment

label_protocol: According to Affymetrix protocol

extract_protocol: Pulverized tissue was lysed in 200mM NaCl, 5mM EDTA, 0.2% SDS, 100mM Tris pH8.5, 100ug/ml proteinase K overnight at 55C, then extracted with phenol/chloroform.

tag: disease

value: DIPG

tag: age at diagonosis (years)

tag: survival (years)

tag: histology

value: ND

tag: sample collection

value: Pretreatment


title: high-grade central osteosarcoma biopsy L2611*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531326, but in this study, the sample is normalized on a larger dataset

tag: sample type

tag: histological subtype

value: osteoblastic osteosarcoma


title: 5260522005_F

value: y

value: Mut

tag: idh1 status

value: WT

tag: idh2 status


title: genomic DNA of BSG902TD, DIPG


title: caecum_germ_free_inoculated_A.muciniphila_(pool)

description: A54_05_CAECUM_MUC INOC

source_name: caecum from germ-free NMRI-KI mice, mono-associated with A. muciniphila, pooled samples

value: NMRI-KI

tag: gender

value: female

tag: developmental stage

value: adult

tag: tissue

tag: bacterial inoculation


title: high-grade central osteosarcoma biopsy L2295*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531321, but in this study, the sample is normalized on a larger dataset

value: anaplastic


title: 5260522005_E

tag: aml type

value: de novo AML

tag: 2 year overall survival

tag: 2 year progression free survival

tag: complete remission (cr)

tag: npm1 status


title: 5260522005_D

tag: age

value: n


title: high-grade central osteosarcoma biopsy L975*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531335, but in this study, the sample is normalized on a larger dataset

value: biopsy


title: high-grade central osteosarcoma biopsy L3455

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format.

value: chondroblastic osteosarcoma


title: ileum_germ_free_inoculated_L.plantarum_(pool)

description: A54_03_ILEUM_LPLANT INOC

source_name: ileum from germ-free NMRI-KI mice, mono-associated with L. plantarum, pooled samples

tag: strain

value: ileum

value: Lactobacillus plantarum WCFS1


title: genomic DNA of BSG529T, DIPG

source_name: brainstem of pediatric DIPG patient collected Postmortem

tag: disease

value: DIPG

tag: age at diagonosis (years)

tag: survival (years)

tag: histology

value: Glioblastoma

value: Postmortem


title: 5260522005_B

tag: idh1 status


title: genomic DNA of BSG046T, DIPG

tag: sample collection


title: genomic DNA of BSG901TD, DIPG

value: ND

value: Pretreatment


title: genomic DNA of BSG047T, DIPG

value: Diffuse astrocytoma


title: genomic DNA of BSG047N, matched normal to BSG047T

description: Normal samples

source_name: matched normal to BSG047T

value: Normal


title: 5260522005_C

value: WT


title: 5260522005_H

value: y

tag: idh2 status


title: ileum_germ_free_non_inoculated_(pool)

description: A54_01_ILEUM_NEG CTRL

source_name: ileum from germ-free NMRI-KI mice, not inoculated, pooled samples

value: NMRI-KI

tag: gender

value: female

tag: developmental stage

value: adult


title: high-grade central osteosarcoma biopsy L3469

tag: sample type

tag: histological subtype


title: ileum_germ_free_inoculated_A.muciniphila_(pool)

description: A54_02_ILEUM_MUC INOC

source_name: ileum from germ-free NMRI-KI mice, mono-associated with A. muciniphila, pooled samples

tag: tissue

tag: bacterial inoculation

value: Akkermansia muciniphila MucT


title: genomic DNA of BSG509T, DIPG


title: high-grade central osteosarcoma biopsy L3535

value: biopsy

value: giant cell rich


title: 5260522005_A

tag: aml type

value: de novo AML

tag: complete remission (cr)

value: Mut


title: genomic DNA of BSG045N, matched normal to BSG045T

description: Normal samples

source_name: matched normal to BSG045T


title: liver_BPAHighDose_rep6

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

institute: INRAE

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >13.8 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min) and Stabilization and Drying Solution (Agilent Technologies, 30 sec).

scan_protocol: Slides were scanned immediately after washing on a GenePix™ 4000B array scanner

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014868_D_20070207). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot):  myfunw<-function(x)  {okType<-x$ControlType==0  okFoundGreen<-x$gIsFound==1  okPos=x$gIsPosAndSignif==1  okWellAbove<- x$gIsWellAboveBG==1  as.numeric(okType & okFoundGreen & okPos & okWellAbove)}  We selected the spots with a weight of 1 for 15 out of 18 microarrays or with a weight of 1 in all 6 microarrays from at least one experimental group. At this step, 23930 spots out of 45018 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 22514 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: liver, exposed to BPA at 5000 µg/Kg/day, replicate 6

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 1 µg of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions,  followed by RNeasy column purification (QIAGEN, Courtaboeuf, France).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Four week-old male CD-1 mice were purchased from Charles River (Les Oncins, France). Mice were acclimatized for one week, housed in polypropylene cages at 22+2°C on a 12 hour light/dark cycle and allowed free access to water (polypropylene bottles) and food. The in vivo study was conducted under the European Union Guidelines for the use and care of laboratory animals and were approved by an independent ethics committee.

extract_protocol: Immediately following euthanasia, liver was removed, weighted, dissected (~100 mg fragments from the large lobe), snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted from frozen liver samples with TRIzol reagent (Invitrogen) following  manufacturer's instructions. Total RNA samples were controlled for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies) and assayed at 260nm on a Nanodrop ND-1000 spectrophotometer (Thermo Scientific)

treatment_protocol: Five week-old mice were randomly divided into 3 groups (n = 6/group). Bisphenol-A was incorporated into a powedered diet (ingredients from SAFE Diets) containing (w/w) 49% starch, 14% casein, 2% cellulose, 24.4% sucrose, 2.5% arachis oil, 2.5% canola oil, 5% Minerals Mix (Ref 205b, SAFE), 0.5% Vitamins mix (Ref 200, SAFE) and 0.1% DL-methionine. Three diets were formulated to obtain an average BPA exposure of the animals of 0, 50 or 5000 µg/Kg/day. To calculate BPA exposure we considered a daily food consumption corresponding to 10% of body weight. Mice were exposed to the different diets for 28 days.

value: male

tag: age

value: 9 weeks

value: liver

tag: treatment

value: exposed to BPA at 5000 µg/Kg/day


title: genomic DNA of BSG044T, DIPG

tag: disease

value: DIPG

value: Glioblastoma

value: Postmortem


title: 4770230047_G

tag: 2 year overall survival

tag: 2 year progression free survival

tag: npm1 status

value: WT


title: genomic DNA of BSG046N, matched normal to BSG046T

description: Normal samples

source_name: matched normal to BSG046T

value: Normal


title: liver_BPAHighDose_rep5

source_name: liver, exposed to BPA at 5000 µg/Kg/day, replicate 5

tag: strain


title: genomic DNA of BSG043T, DIPG

tag: age at diagonosis (years)

tag: survival (years)

tag: histology

tag: sample collection


title: liver_BPAHighDose_rep4

source_name: liver, exposed to BPA at 5000 µg/Kg/day, replicate 4

tag: gender


title: caecum_germ_free_non_inoculated_(pool)

description: A54_04_CAECUM_NEG CTRL

source_name: caecum from germ-free NMRI-KI mice, not inoculated, pooled samples

value: NMRI-KI

tag: developmental stage

value: caecum


title: 4770230047_H

value: y

tag: idh1 status

tag: idh2 status


title: 4770230047_F

tag: aml type


title: high-grade central osteosarcoma biopsy L3536

source_name: high-grade central osteosarcoma biopsy

tag: sample type

tag: histological subtype

value: sclerosing


title: liver_BPAHighDose_rep2

source_name: liver, exposed to BPA at 5000 µg/Kg/day, replicate 2

tag: age

tag: tissue

tag: treatment


title: high-grade central osteosarcoma biopsy L3533

value: biopsy

value: fibroblastic & giant cell rich


title: 4770230047_B

value: de novo AML

tag: 2 year overall survival

tag: 2 year progression free survival

tag: complete remission (cr)


title: liver_BPAHighDose_rep3

source_name: liver, exposed to BPA at 5000 µg/Kg/day, replicate 3

tag: strain


title: 4770230047_C

value: n

tag: npm1 status

value: Mut


title: genomic DNA of BSG045T, DIPG

tag: disease

tag: age at diagonosis (years)

tag: survival (years)

tag: histology


title: high-grade central osteosarcoma biopsy L997*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531351, but in this study, the sample is normalized on a larger dataset

value: osteoblastic osteosarcoma


title: genomic DNA of BSG042T, DIPG

tag: sample collection


title: high-grade central osteosarcoma biopsy L1085*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531307, but in this study, the sample is normalized on a larger dataset

value: chondroblastic osteosarcoma


title: liver_BPAHighDose_rep1

source_name: liver, exposed to BPA at 5000 µg/Kg/day, replicate 1

tag: gender

value: male

value: 9 weeks

value: liver

value: exposed to BPA at 5000 µg/Kg/day


title: 4770230042_I

tag: aml type

value: WT

tag: idh1 status

tag: idh2 status


title: high-grade central osteosarcoma biopsy L3457

tag: sample type

tag: histological subtype


title: genomic DNA of BSG040T, DIPG

value: DIPG

value: Glioblastoma

value: Postmortem


title: liver_BPALowDose_rep6

source_name: liver, exposed to BPA at 50 µg/Kg/day, replicate 6

tag: age

tag: tissue

tag: treatment

value: exposed to BPA at 50 µg/Kg/day


title: genomic DNA of BSG043N, matched normal to BSG043T

description: Normal samples

source_name: matched normal to BSG043T

value: Normal


title: high-grade central osteosarcoma biopsy L1386*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531319, but in this study, the sample is normalized on a larger dataset

value: biopsy


title: high-grade central osteosarcoma biopsy L3434

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531290, but in this study, the sample is normalized on a larger dataset


title: 4770230042_F

tag: 2 year overall survival

tag: 2 year progression free survival

tag: complete remission (cr)


title: 4770230042_G

value: y

tag: npm1 status


title: high-grade central osteosarcoma biopsy L3431

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531285, but in this study, the sample is normalized on a larger dataset


title: genomic DNA of BSG044N, matched normal to BSG044T

description: Normal samples

source_name: matched normal to BSG044T

tag: disease


title: liver_BPALowDose_rep3

source_name: liver, exposed to BPA at 50 µg/Kg/day, replicate 3

tag: strain


title: liver_BPALowDose_rep5

source_name: liver, exposed to BPA at 50 µg/Kg/day, replicate 5


title: genomic DNA of BSG039N, matched normal to BSG039T

description: Normal samples

source_name: matched normal to BSG039T


title: genomic DNA of BSG042N, matched normal to BSG042T

description: Normal samples

source_name: matched normal to BSG042T


title: liver_BPALowDose_rep4

source_name: liver, exposed to BPA at 50 µg/Kg/day, replicate 4


title: high-grade central osteosarcoma biopsy L3456

value: fibroblastic osteosarcoma


title: Fibroblast CRL-2429 - mAdbID:108273

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 108273

hyb_protocol: Sample Hybridization Protocol Other: Hybridization was performed using a ULS aRNA Fluorescent Labeling and Hybridization Kit (Kreatech, Amsterdam, Netherlands).

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.12;; 5.14 Temperature: 25.35

data_processing:
BRB ArrayTool Data Processing
Calculation Method: Analyzed using BRBArrayTools developed by the Biometric Research Branch, National Cancer Institute (http://linus.nci.nih.gov/BRB-ArrayTools.html ). Briefly, the raw data set was filtered according to standard procedure to exclude spots with minimum intensity that arbitrarily was set to an intensity parameter of 200 for in both fluorescence channels. If the fluorescence intensity of one channel was great than 200 and that of the other but was below 200, the fluorescence of the low intensity channel was arbitrarily set to 200. Spots with diameters < 10um and flagged spots were also excluded from the analyses. Then, the filtered data were normalized using Lowess Smoother for gene expression microarray.

source_name: Fibroblast CRL-2429

label_protocol:
Cy5 Sample Labeling Protocol
Other: Samples were directly labeled using a ULS aRNA Fluorescent Labeling Kit (Kreatech, Amsterdam, Netherlands) with Cy5.

extract_protocol:
Trizol Sample Extraction Protocol
Other: Total RNA was extracted from all cell type using Trizol (Invitrogen, Carlsbad, CA).

tag: cell line

value: CCD-1112Sk (ATCC, Manassas, VA)

tag: cell type

value: Fibroblast

source_name: Pooled PBMC Reference Sample

label_protocol:
Cy3 Sample Labeling Protocol
Other: Samples were directly labeled using a ULS aRNA Fluorescent Labeling Kit (Kreatech, Amsterdam, Netherlands) with Cy3.

value: Peripheral blood mononuclear cells (PBMC)

tag: other

value: Sample Pooling Protocol:Total RNA from a pool of PBMCs from six healthy subjects was extracted and amplified into aRNA to serve as a reference.


title: Fibroblast NuFF1 - mAdbID:108274

description: mAdb experiment ID: 108274

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.11;; 5.13 Temperature: 24.01

source_name: Fibroblast NuFF1

value: NuFF1 (Global Stem Inc, Rockville, MD)


title: liver_BPALowDose_rep2

source_name: liver, exposed to BPA at 50 µg/Kg/day, replicate 2

tag: gender

value: male

value: 9 weeks


title: high-grade central osteosarcoma biopsy L3459

value: osteoblastic osteosarcoma


title: high-grade central osteosarcoma biopsy L3433

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531289, but in this study, the sample is normalized on a larger dataset


title: liver_BPALowDose_rep1

source_name: liver, exposed to BPA at 50 µg/Kg/day, replicate 1

value: liver


title: 4770230042_E

tag: aml type

value: de novo AML

value: n

value: WT

tag: idh1 status

value: Mut


title: genomic DNA of BSG039T, DIPG

source_name: brainstem of pediatric DIPG patient collected Postmortem

value: DIPG

tag: age at diagonosis (years)

tag: survival (years)

tag: histology

value: Glioblastoma

tag: sample collection

value: Postmortem


title: high-grade central osteosarcoma biopsy L3458

source_name: high-grade central osteosarcoma biopsy

tag: sample type

value: biopsy

tag: histological subtype


title: genomic DNA of BSG038T, DIPG


title: genomic DNA of BSG040N, matched normal to BSG040T

description: Normal samples

source_name: matched normal to BSG040T

value: Normal


title: high-grade central osteosarcoma biopsy L2301*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531324, but in this study, the sample is normalized on a larger dataset


title: BMSC-4 - mAdbID:104749

description: mAdb experiment ID: 104749

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.02 Temperature: 33.44

value: Bone marrow stroma cells (BMSC)


title: high-grade central osteosarcoma biopsy L3461


title: Fibroblast CRL-2352 - mAdbID:108272

description: mAdb experiment ID: 108272

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 5.03 Temperature: 27.06

source_name: Fibroblast CRL-2352

value: CCD 1108Sk (ATCC, Manassas, VA)

value: Fibroblast

value: Peripheral blood mononuclear cells (PBMC)


title: liver_control_rep6

source_name: liver, control, replicate 6

value: male

tag: age

tag: tissue

tag: treatment

value: control


title: liver_control_rep5

source_name: liver, control, replicate 5

value: 9 weeks


title: genomic DNA of BSG037T, DIPG

tag: disease


title: high-grade central osteosarcoma biopsy L1368*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531308, but in this study, the sample is normalized on a larger dataset

value: osteoblastic osteosarcoma


title: liver_control_rep3

source_name: liver, control, replicate 3

tag: strain

value: liver


title: liver_control_rep4

source_name: liver, control, replicate 4


title: BMSC-7 - mAdbID:108271

description: mAdb experiment ID: 108271

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.14;; 4.96 Temperature: 27.61

tag: cell line

value: Sample Pooling Protocol:Total RNA from a pool of PBMCs from six healthy subjects was extracted and amplified into aRNA to serve as a reference.


title: BMSC-5 - mAdbID:108269

description: mAdb experiment ID: 108269

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 5.09 Temperature: 26.54

tag: cell type


title: BMSC-6 - mAdbID:108270

description: mAdb experiment ID: 108270

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.14;; 4.81 Temperature: 27.12

tag: other


title: genomic DNA of BSG037N, matched normal to BSG037T

description: Normal samples

source_name: matched normal to BSG037T


title: genomic DNA of BSG038N, matched normal to BSG038T

description: Normal samples

source_name: matched normal to BSG038T


title: high-grade central osteosarcoma biopsy L1370*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531310, but in this study, the sample is normalized on a larger dataset


title: liver_control_rep2

source_name: liver, control, replicate 2

tag: gender


title: BMSC-3 - mAdbID:104748

description: mAdb experiment ID: 104748

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.07 Temperature: 33.41


title: liver_control_rep1

source_name: liver, control, replicate 1


title: high-grade central osteosarcoma biopsy L1385*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531314, but in this study, the sample is normalized on a larger dataset


title: Nodal Marginal Zone Lymphoma_1368

hyb_protocol: The miRNA microarray experiments were done using the Agilent Human miRNA Microarray (V1), 8 x 15K (Agilent Technologies). For each tissue sample, 100 ng total RNA were hybridized with the miRNA array and further processed as previously described (Ach RA, Wang H, Curry B. BMC Biotechnol. 2008).

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.0).

data_processing: Agilent Feature Extraction Software (version 9.0) was used for background subtraction and LOWESS normalization.

source_name: Nodal Marginal Zone Lymphoma (NMZL)

label_protocol: Total RNA  amplification and labeling were performed according to the standard Agilent protocol.

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), and purified and treated with RNase-free DNase I using the RNeasy kit (Qiagen Inc., Valencia, CA).

tag: tissue source

value: B-cell non-Hodgkin lymphoma patients

value: freshly frozen lymph nodes


title: BMSC-2 - mAdbID:104747

description: mAdb experiment ID: 104747

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.16;; 3.58 Temperature: 33.38

source_name: Pooled PBMC Reference Sample


title: Nodal Marginal Zone Lymphoma_1515


title: BMSC-1 - mAdbID:104746

description: mAdb experiment ID: 104746

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.04 Temperature: 33.25


title: high-grade central osteosarcoma biopsy L3447

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM530899, but in this study, the sample is normalized on a larger dataset


title: high-grade central osteosarcoma biopsy L3453


title: high-grade central osteosarcoma biopsy L3448

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531283, but in this study, the sample is normalized on a larger dataset


title: genomic DNA of BSG035N, matched normal to BSG035T

description: Normal samples

source_name: matched normal to BSG035T


title: hESCL BG10V - mAdbID:104745

description: mAdb experiment ID: 104745

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.1 Temperature: 33.07

source_name: hESCL BG01V

value: Human embryonic stem cells (hESCs)


title: Nodal Marginal Zone Lymphoma_1367


title: Nodal Marginal Zone Lymphoma_1379


title: hESCL H1 - mAdbID:104744

description: mAdb experiment ID: 104744

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.58 Temperature: 33.07

source_name: hESCL H1

value: H1 (WiCell Research Institute, Madison, WI)


title: genomic DNA of BSG034N, matched normal to BSG034T

description: Normal samples

source_name: matched normal to BSG034T


title: genomic DNA of BSG033N, matched normal to BSG033T

description: Normal samples

source_name: matched normal to BSG033T


title: high-grade central osteosarcoma biopsy L3449

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531284, but in this study, the sample is normalized on a larger dataset

scan_protocol: As per manufacturer's instructions.

source_name: high-grade central osteosarcoma biopsy

value: fibroblastic osteosarcoma


title: Follicular Lymphoma_00031982

source_name: Follicular Lymphoma (FL)


title: genomic DNA of BSG033T, DIPG

description: Gene expression data from pediatric DIPG patient.

source_name: brainstem of pediatric DIPG patient collected Postmortem

value: DIPG

value: Glioblastoma

value: Postmortem


title: high-grade central osteosarcoma biopsy L3466

value: biopsy


title: hESCL H9 - mAdbID:104743

description: mAdb experiment ID: 104743

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.14;; 5.05 Temperature: 33.1

source_name: hESCL H9

value: H9 (WiCell Research Institute, Madison, WI)


title: genomic DNA of BSG031T, DIPG

scan_protocol: Scanning performed according to the standard Affymetrix protocol


title: Follicular Lymphoma_00032172


title: genomic DNA of BSG035T, DIPG


title: Hematopoietic stem cells CD34-3 - mAdbID:104742

description: mAdb experiment ID: 104742

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 5.05 Temperature: 32.86

source_name: Hematopoietic stem cells CD34-3

value: G-CSF-mobilized peripheral blood stem cells (PBSC)

value: Peripheral blood mononuclear cells (PBMC)


title: Follicular Lymphoma_00031266


title: Hematopoietic stem cells CD34-2 - mAdbID:104741

description: mAdb experiment ID: 104741

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 5.07 Temperature: 32.71

source_name: Hematopoietic stem cells CD34-2


title: Follicular Lymphoma_00011094


title: high-grade central osteosarcoma biopsy L3465

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531294, but in this study, the sample is normalized on a larger dataset

value: chondroblastic osteosarcoma


title: Hematopoietic stem cells CD34-1 - mAdbID:104740

description: mAdb experiment ID: 104740

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 5.07 Temperature: 32.61

source_name: Hematopoietic stem cells CD34-1


title: Follicular Lymphoma_00001013


title: high-grade central osteosarcoma biopsy L3454


title: 4770230042_D

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

tag: aml type

value: de novo AML

tag: 2 year overall survival

value: y

tag: 2 year progression free survival

tag: complete remission (cr)

tag: npm1 status

value: Mut

tag: idh1 status

value: WT

tag: idh2 status


title: genomic DNA of BSG032N, matched normal to BSG032T

description: Normal samples

source_name: matched normal to BSG032T

value: Normal


title: Follicular Lymphoma_00010064

value: B-cell non-Hodgkin lymphoma patients

value: freshly frozen lymph nodes


title: genomic DNA of BSG031N, matched normal to BSG031T

description: Normal samples

source_name: matched normal to BSG031T


title: 4770230042_C

tag: age


title: high-grade central osteosarcoma biopsy L2302*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531325, but in this study, the sample is normalized on a larger dataset

tag: sample type

tag: histological subtype


title: high-grade central osteosarcoma biopsy L3474

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format.

value: osteoblastic osteosarcoma


title: high-grade central osteosarcoma biopsy L436*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531334, but in this study, the sample is normalized on a larger dataset


title: Follicular Lymphoma_00000918

tag: tissue


title: Follicular Lymphoma_00020298


title: high-grade central osteosarcoma biopsy L428*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531332, but in this study, the sample is normalized on a larger dataset


title: 4770230042_B


title: 4770230042_A

value: n


title: high-grade central osteosarcoma cell line IOR-OS9

growth_protocol: As described in Ottaviano et al. (PMID: 19787792)

value: cell line


title: genomic DNA of BSG030T, DIPG

tag: disease

value: DIPG

tag: age at diagonosis (years)

tag: survival (years)

tag: histology

value: Glioblastoma

tag: sample collection


title: mRNA of BSG901TD, DIPG

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GCS 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: brain of pediatric DIPG patient collected Pretreatment

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

tag: age at diagnosis (years)

value: ND

value: Pretreatment


title: high-grade central osteosarcoma biopsy L2296*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531322, but in this study, the sample is normalized on a larger dataset

value: biopsy


title: Follicular Lymphoma_00011873

tag: tissue source


title: Follicular Lymphoma_00022588


title: genomic DNA of BSG032T, DIPG

value: Postmortem


title: genomic DNA of BSG029T, DIPG


title: high-grade central osteosarcoma biopsy L432*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531333, but in this study, the sample is normalized on a larger dataset

value: pleomorphic


title: Follicular Lymphoma_00011881


title: genomic DNA of BSG026T, DIPG


title: genomic DNA of BSG034T, DIPG


title: mRNA of BSG044T, DIPG

source_name: brain of pediatric DIPG patient collected Postmortem


title: high-grade central osteosarcoma cell line IOR-MOS

tag: cell line

value: IOR-MOS


title: high-grade central osteosarcoma biopsy L3437

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531295, but in this study, the sample is normalized on a larger dataset


title: mRNA of BSG040T, DIPG


title: Follicular Lymphoma_00020426


title: mRNA of BSG042T, DIPG


title: genomic DNA of BSG027TD, DIPG

source_name: brainstem of pediatric DIPG patient collected Pretreatment

value: Anaplastic astrocytoma


title: Follicular Lymphoma_00022092


title: Follicular Lymphoma_00020542


title: genomic DNA of BSG026N, matched normal to BSG026T

description: Normal samples

source_name: matched normal to BSG026T


title: high-grade central osteosarcoma biopsy L1382*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531313, but in this study, the sample is normalized on a larger dataset


title: mRNA of BSG039T, DIPG


title: genomic DNA of BSG029N, matched normal to BSG029T

description: Normal samples

source_name: matched normal to BSG029T


title: genomic DNA of BSG024TD, DIPG


title: genomic DNA of BSG025N, matched normal to BSG025T

description: Normal samples

source_name: matched normal to BSG025T


title: Follicular Lymphoma_00020899


title: genomic DNA of BSG030N, matched normal to BSG030T

description: Normal samples

source_name: matched normal to BSG030T


title: genomic DNA of BSG025T, DIPG


title: mRNA of BSG037T, DIPG


title: high-grade central osteosarcoma cell line IOR-OS18


title: mRNA of BSG035T, DIPG


title: high-grade central osteosarcoma biopsy L1016*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531306, but in this study, the sample is normalized on a larger dataset


title: Follicular Lymphoma_00020182


title: genomic DNA of BSG024T, DIPG

source_name: brainstem of pediatric DIPG patient collected Postmortem matched with pretreatment sample BSG024TD


title: mRNA of BSG509T, DIPG


title: mRNA of BSG034T, DIPG


title: genomic DNA of BSG023T, DIPG


title: high-grade central osteosarcoma biopsy L2297*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531323, but in this study, the sample is normalized on a larger dataset

source_name: high-grade central osteosarcoma biopsy


title: Follicular Lymphoma_00021804

source_name: Follicular Lymphoma (FL)


title: mRNA of BSG032T, DIPG


title: high-grade central osteosarcoma biopsy L3477

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531352, but this sample is normalized on a larger dataset


title: high-grade central osteosarcoma cell line OSA

value: OSA

value: fibroblastic osteosarcoma


title: Lymph node_22464

source_name: lymph node with reactive lymphoid hyperplasia (RLN)


title: high-grade central osteosarcoma biopsy L1378

value: fibroblastic MFH-like


title: genomic DNA of BSG023N, matched normal to BSG023T

description: Normal samples

source_name: matched normal to BSG023T

value: Normal


title: mRNA of BSG033T, DIPG


title: genomic DNA of BSG022W, matched normal to BSG022T and BSG022TD

description: Normal samples

source_name: matched normal to BSG022T and BSG022TD


title: genomic DNA of BSG022TD, DIPG


title: high-grade central osteosarcoma cell line OHS

value: OHS


title: genomic DNA of BSG022T, DIPG

source_name: brainstem of pediatric DIPG patient collected Postmortem matched with pretreatment sample BSG022TD


title: Lymph node_21688

value: freshly frozen lymph nodes


title: mRNA of BSG031T, DIPG


title: Lymph node_22382


title: Lymph node_30802


title: mRNA of BSG030T, DIPG


title: high-grade central osteosarcoma cell line IOR-OS15

value: osteoblastic osteosarcoma


title: mRNA of BSG024TD, DIPG


title: mRNA of BSG024T, DIPG

source_name: brain of pediatric DIPG patient collected Postmortem sample matched to pretreatment sample BSG024TD


title: high-grade central osteosarcoma cell line IOR-MG63

value: cell line


title: high-grade central osteosarcoma cell line IOR-OS14


title: Follicular Lymphoma_00030568

value: B-cell non-Hodgkin lymphoma patients


title: Follicular Lymphoma_00030305


title: mRNA of BSG023T, DIPG

value: DIPG

value: Glioblastoma


title: high-grade central osteosarcoma cell line IOR-OS10


title: high-grade central osteosarcoma biopsy L3473


title: genomic DNA of BSG019T, DIPG

source_name: brainstem of pediatric DIPG patient collected Postmortem


title: high-grade central osteosarcoma cell line MHM

value: MHM


title: mRNA of BSG022T, DIPG


title: Follicular Lymphoma_31048


title: genomic DNA of BSG022N, matched normal to BSG022T and BSG022TD

description: Normal samples


title: Follicular Lymphoma_22196


title: mRNA of BSG020T, DIPG


title: genomic DNA of BSG020N, matched normal to BSG020T

description: Normal samples

source_name: matched normal to BSG020T


title: Follicular Lymphoma_811


title: high-grade central osteosarcoma cell line IOR-SARG

value: IOR-SARG


title: high-grade central osteosarcoma biopsy L3462

value: biopsy


title: high-grade central osteosarcoma cell line KPD

value: KPD


title: genomic DNA of BSG021T, DIPG

value: Postmortem


title: Follicular Lymphoma_802


title: genomic DNA of BSG020T, DIPG


title: Follicular Lymphoma_423


title: Follicular Lymphoma_00020612


title: mRNA of BSG012T, DIPG


title: genomic DNA of BSG017N, matched normal to BSG017T

description: Normal samples

source_name: matched normal to BSG017T


title: mRNA of BSG017T, DIPG

source_name: brain of pediatric DIPG patient collected Postmortem


title: mRNA of BSG015T, DIPG


title: high-grade central osteosarcoma biopsy L3463

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531291, but in this study, the sample is normalized on a larger dataset


title: high-grade central osteosarcoma biopsy L3435

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531292, but in this study, the sample is normalized on a larger dataset


title: Lymph node_1010


title: genomic DNA of BSG019N, matched normal to BSG019T

description: Normal samples

source_name: matched normal to BSG019T


title: mRNA of BSG010T, DIPG


title: genomic DNA of BSG015T, DIPG


title: Nodal Marginal Zone Lymphoma_02040336

source_name: Nodal Marginal Zone Lymphoma (NMZL)


title: high-grade central osteosarcoma biopsy L3464


title: mRNA of BSG009T, DIPG


title: mRNA of BSG005T, DIPG


title: mRNA of BSG004TD, DIPG

source_name: brain of pediatric DIPG patient collected Pretreatment collected postmortem

value: Pretreatment collected postmortem


title: high-grade central osteosarcoma biopsy L3470

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531298, but in this study, the sample is normalized on a larger dataset


title: high-grade central osteosarcoma biopsy L3468

value: chondroblastic osteosarcoma


title: Lymph node_1118


title: Nodal Marginal Zone Lymphoma_02050469


title: mRNA of BSG001T, DIPG

value: ND


title: Nodal Marginal Zone Lymphoma_00030109


title: high-grade central osteosarcoma biopsy L2618*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531329, but this sample is normalized on a larger dataset


title: Nodal Marginal Zone Lymphoma_00021904


title: genomic DNA of BSG005T, DIPG

description: Gene expression data from pediatric DIPG patient.


title: Nodal Marginal Zone Lymphoma_02040450


title: genomic DNA of BSG010N, matched normal to BSG010T

description: Normal samples

source_name: matched normal to BSG010T


title: genomic DNA of BSG024N, matched normal to BSG024T and BSG024TD

description: Normal samples

source_name: matched normal to BSG024T and BSG024TD


title: high-grade central osteosarcoma biopsy L2616*

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531328, but this sample is normalized on a larger dataset


title: mRNA of BSG003T(CB), DIPG


title: LTB4_5

city: Bethesda

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the U133+ 2.0 GeneChip  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChip Scanner 7G was used to scan the microarrays

data_processing: Affymetrix Microarray Suite version 5.0

source_name: Elutriated Human Monocytes

growth_protocol: cultured human elutriated peripherial  blood monocytes

extract_protocol: Rneasy Mini Kit Qiagen

treatment_protocol: LTB4 50nM for 30 minutes

tag: cell type

value: monocyte

tag: treatment


title: Nodal Marginal Zone Lymphoma_02060229


title: LTB4_4


title: high-grade central osteosarcoma biopsy L2614*

description:
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format.
Note: this is the same as GEO accession GSM531327, but this sample is normalized on a larger dataset

source_name: high-grade central osteosarcoma biopsy


title: LTB4_3


title: high-grade central osteosarcoma biopsy L2615

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format.


title: Nodal Marginal Zone Lymphoma_02030091


title: Nodal Marginal Zone Lymphoma_00020184


title: genomic DNA of BSG012W, matched normal to BSG012T

description: Normal samples

source_name: matched normal to BSG012T

value: Normal


title: high-grade central osteosarcoma biopsy L2613


title: genomic DNA of BSG012T, DIPG


title: genomic DNA of BSG005N, matched normal to BSG005T

description: Normal samples

source_name: matched normal to BSG005T


title: genomic DNA of BSG004TD, DIPG

source_name: brainstem of pediatric DIPG patient collected Pretreatment collected postmortem


title: Nodal Marginal Zone Lymphoma_00011953


title: LTB4_2


title: genomic DNA of BSG003T(CB), DIPG


title: LTB4_1


title: Control_5

treatment_protocol: untreated control

value: control


title: high-grade central osteosarcoma biopsy L3446

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM530667, but in this study, the sample is normalized on a larger dataset

value: giant cell rich


title: Nodal Marginal Zone Lymphoma_00000119

value: freshly frozen lymph nodes


title: genomic DNA of BSG003T(BS), DIPG


title: genomic DNA of BSG004N, matched normal to BSG004TD

description: Normal samples

source_name: matched normal to BSG004TD


title: high-grade central osteosarcoma biopsy L3439

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Note: this is the same as GEO accession GSM531297, but in this study, the sample is normalized on a larger dataset

value: chondromyxoid fibroma-like


title: Control_4


title: Control_3


title: Nodal Marginal Zone Lymphoma_00011021

value: B-cell non-Hodgkin lymphoma patients


title: genomic DNA of BSG021N, matched normal to BSG021T

description: Normal samples

source_name: matched normal to BSG021T


title: genomic DNA of BSG003Ncx, matched normal to BSG003T(BS) and BSG003T(CB)

description: Normal samples


title: genomic DNA of BSG001N, matched normal to BSG001T

description: Normal samples

source_name: matched normal to BSG001T


title: high-grade central osteosarcoma biopsy L2617

value: osteoblastic osteosarcoma


title: genomic DNA of BSG009T, DIPG

source_name: brainstem of pediatric DIPG patient collected Postmortem

value: DIPG

value: Glioblastoma


title: genomic DNA of BSG903T, brainstem LGG

description: Gene expression data from pediatric brainstem LGG patient.

source_name: brainstem of pediatric LGG patient collected Pretreatment

value: brainstem LGG

value: Pilocytic Astrocytoma

value: Pretreatment


title: high-grade central osteosarcoma biopsy L3467

value: biopsy


title: Control_2


title: genomic DNA of BSG017T, DIPG

value: Postmortem


title: FFPE liver patient 4624

status: Public on Sep 20 2011

city: shanghai

first: xiaonan

last: zhang

address: caolang road 2901, Jinshan district

department: research unit

country: China

institute: Shanghai public health clinical center

description: miRNA expression in FFPE

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction software 10.7(Agilent technologies, Santa Clara, CA, US) with default settings，Scan resolution=5μm, PMT 100%，10%.

source_name: FFPE, before treatment

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: reponse to therapy

value: Rapid response

value: FFPE

value: liver

tag: disease state

value: hepatatis B

tag: individual

value: patient 4624


title: FFPE liver patient 4616

description: miRNA expression in FFPE

value: No response

value: patient 4616


title: high-grade central osteosarcoma biopsy L3438

description:
Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format.
Note: this is the same as GEO accession GSM531296, but in this study, the sample is normalized on a larger dataset


title: genomic DNA of BSG904T, brainstem LGG


title: high-grade central osteosarcoma cell line ZK-58

value: cell line


title: FFPE liver patient 4614

description: miRNA expression in FFPE

value: patient 4614


title: Control_1

value: monocyte

value: control


title: FFPE liver patient 4611

description: miRNA expression in FFPE

value: patient 4611


title: FFPE liver patient 4617

description: miRNA expression in FFPE

value: patient 4617


title: genomic DNA of BSG001T, DIPG

value: DIPG

value: ND


title: EWS knock-down replicate 3 Dye-Swap

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

institute: Center for genomic regulation

description: Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

hyb_protocol: Slides were hybridized following manufacturer protocol, with the exception that we hybridized 6 micrograms of each amplified cRNA sample and the Agilent hybridization oven was set to 60ºC.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing: Raw data were processed using SAPO (http://bioinfo.ciberehd.org/SAP.ang.htm) and CGEM (http://bioinfo.ciberehd.org/CGEM.ang.html) alternative splicing analysis tools, obtaining lowess normalized log2ratios.

source_name: EWS siRNA knock-down in HeLa cell line replicate 3

label_protocol: Sample was labeled using the Quick-Amp labeling kit, no dye (Agilent 5190-0447) and cyanine 5-CTP and cyanine 3-CTP (Perkin-Elmer NEL580, NEL581). Purified using Quiagen RNeasy mini kit. Quality control assessed by Agilent Bioanalyzer 2100.

growth_protocol: Cell were grown in complete media (DMEM + 10% FBS + penicillin/streptomycin). Before transfection, HeLa cells were plated the day before at 4X10E3 per well in 35mm plates in DMEM 10%FBS without antibiotics.

extract_protocol:
RNeasy mini kit (QUIAGEN, cat.no. 74104) and DNase treated on-column with DNase RNase-free (QUIAGEN, cat no. 79254)
Quality assesment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

treatment_protocol: HeLa cells were plated the day before transfection at 4X10E3 per well in 35mm plates in DMEM 10%FBS without antibiotics and transfected with 20micromolar of a scrambled RNA or EWS siRNA oligonucleotides using Lipofectamine RNA iMAX (Cat. No 13778-150, Invitrogen) in optimem media (Invitrogen). Five hours after transfection, the media was removed and replaced by complete media (DMEM + 10% FBS + penicillin/streptomycin). Cell were harvested after 72 hours after transfection.

value: HeLa

tag: genotype/variation

value: knockdown with a EWS siRNA oligo

source_name: HeLa siRNA control of trasfection replicate 3

value: transfected with a scrambled oligo


title: FFPE liver patient 4620

description: miRNA expression in FFPE

tag: sample type

value: FFPE

value: patient 4620


title: FFPE liver patient 4625

description: miRNA expression in FFPE

value: liver

value: hepatatis B

value: patient 4625


title: FFPE liver patient 4607

description: miRNA expression in FFPE

value: Rapid response

value: patient 4607


title: genomic DNA of BSG009N, matched normal to BSG009T

description: Normal samples

source_name: matched normal to BSG009T

value: Normal


title: EWS knock-down replicate 2 Dye-Swap

source_name: EWS siRNA knock-down in HeLa cell line replicate 2

source_name: HeLa siRNA control of trasfection replicate 2


title: FFPE liver patient 4602

description: miRNA expression in FFPE

value: patient 4602


title: FFPE liver patient 4623

description: miRNA expression in FFPE

value: patient 4623


title: EWS knock-down replicate 1 Dye-Swap

source_name: EWS siRNA knock-down in HeLa cell line replicate 1

source_name: HeLa siRNA control of trasfection replicate 1


title: FFPE liver patient 4603

description: miRNA expression in FFPE

value: No response

value: patient 4603


title: genomic DNA of BSG018T, brainstem LGG

value: brainstem LGG

value: Low-grade astrocytoma

value: Pretreatment


title: PA14-mexR QSM C30 2hr 37C planktonic cell

city: College Station

first: Mingming

last: Pu

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A&M University

description: RNA extracted from planktonic cells of PA14_mexR after 2 hr growth after adding 50 µM C30 in QSM minimal medium when OD600 reaches 0.25.

hyb_protocol: Following affymetrix protocol.cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).”

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Pseudomonas aeruginosa PA14

source_name: Channel 1

extract_protocol: Overnight culture in LB+Tc75 was washed with 1 volume of QSM medium (OS minimal medium + 0.1% Adenosine as carbon source) twice, and re-inoculated into 200 ml QSM medium in 1 L flask start with OD600= 0.02. The culture was incubated at 37 ºC with shaking at 250 rpm. When culture grows to mid-exponential phase (OD600=0.25), C30 was added to a final concentration of 50 µM and the culture was incubated for additional 2 hr. Cells were harvested, total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

value: planctonic cells

tag: strain

tag: medium

value: QSM minimal medium

tag: compound

tag: time

value: 2 hr

tag: temp

value: 37 ºC


title: EWS knock-down replicate 3

value: HeLa

value: knockdown with a EWS siRNA oligo

value: transfected with a scrambled oligo


title: FFPE liver patient 4601

description: miRNA expression in FFPE

value: Rapid response

value: FFPE

tag: tissue

value: liver

value: hepatatis B

value: patient 4601


title: plasma patient 4728

description: miRNA expression in plamsa

source_name: plasma, before treatment

value: No response

value: plasma

value: patient 4728


title: plasma patient 4729

description: miRNA expression in plamsa

value: patient 4729


title: FFPE liver patient 4622

description: miRNA expression in FFPE

value: patient 4622


title: EWS knock-down replicate 2


title: PA14-WT QSM C30 2hr 37C planktonic cell

description: RNA extracted from planktonic cells of PA14 wild type after 2 hr growth after adding 50 µM C30 in QSM minimal medium when OD600 reaches 0.25.

label_protocol: Following affymetrix protocol.cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: Overnight culture in LB was washed with 1 volume of QSM medium (OS minimal medium + 0.1% Adenosine as carbon source) twice, and re-inoculated into 200 ml QSM medium in 1 L flask start with OD600= 0.02. The culture was incubated at 37 ºC with shaking at 250 rpm. When culture grows to mid-exponential phase (OD600=0.25), C30 was added to a final concentration of 50 µM and the culture was incubated for additional 2 hr. Cells were harvested, total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

value: planctonic cells

value: PA14 wild type


title: plasma patient 4726

description: miRNA expression in plamsa

value: patient 4726