title: melanoma_AJCCstageIII_TumourID36

value: Female

value: Dead Melanoma


title: melanoma_AJCCstageIII_TumourID6

status: Public on Oct 06 2014

type: RNA

city: North Sydney

first: Graham

middle: J.

last: Mann

state: NSW

address: Poche Centre, 40 Rocklands Road

country: Australia

institute: Melanoma Institute Australia

hyb_protocol: Labelled material was hybridised to the arrays at 55C for 20hrs, rotating at 20rpm. Slides were washed with agilent wash buffers.

scan_protocol: Agilent High Resolution Scanner, G2505B was used. Agilent Feature Extractiob version 10.7.3.1. software was used for data extraction and protocol used by Fe software: miRNA 107 Sep09

data_processing: Data has been quantile normalised with no background subtraction.

molecule: total RNA

organism: Homo sapiens

source_name: melanoma lymph node, fresh frozen tissue (>80% tumor cell content, <30% necrosis)

label_protocol: 100ng of total RNA was used. miRNAs were fluorescently labelled by lagation of one Cyanine 3-pCp molecule to the 3' end of a RNA molecule

growth_protocol: All the tumour tissues were stored in liquid nitrogen untill extraction.

extract_protocol: Total RNA was extracted from fresh frozen tissues using the Roche High Pure miRNA Isolation kit (Cat No 05080576001, Roche Diagnostic, Indiana, IN, USA) in accordance with the manufacturer’s protocol. The quality and quantity of small RNAs present in the total RNA extract was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: tissue

value: lymph node

tag: diagnosis

value: melanoma

tag: patient age at primary dignosis (years)

tag: patient sex

tag: patient age at stage iii sample banked (years)

tag: survival from stage iii tumour banked (months)

tag: survival from primary melanoma (months)

tag: number of primary melanomas

tag: stage at primary diagnosis 5th edition

value: Stage II

tag: patient last status


title: melanoma_AJCCstageIII_TumourID28

value: Male

value: Stage I

value: Alive NSR


title: SMC_4h_M2

city: LA

first: Sungyong

last: You

state: CA

address: Beverly Blvd 8400

department: Surgery

country: USA

institute: Cedars-Sinai Medical Center

description: SAMPLE 10

hyb_protocol: The samples were hybridized to HuGene ST1.0 microarrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: The microarray data were preprocessed in Expression Consol software (Affymetrix) employing the probe logarithmic intensity error algorithm (PLIER, parameters - PM-GCBG background subtraction, quantile normalization, iterPLIER summarization)

label: Biotin

source_name: pBSMCs_PDGF 24hr

label_protocol: Total RNA was labeled employing the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer’s instructions (Affymetrix)

growth_protocol: Human primary bladder smooth muscle cells (pBSMCs) were cultured in smooth muscle cell medium (SMCM, Sciencell Research Laboratories, Carlsbad, CA) at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA from pBSMCs was extracted using the TRIzol reagent followed by RNeasy (QIAgen) method. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: pBSMCs were serum starved overnight and treated with 1 nM PDGF for 0, 4, and 24 h.

value: bladder

tag: cell type

tag: treated with

value: 1 nM PDGF-BB for 24hrs


title: melanoma_AJCCstageIII_TumourID16


title: melanoma_AJCCstageIII_TumourID69

value: Stage III


title: SMC_4h_M3

description: SAMPLE 11

value: Human primary bladder smooth muscle cells (pBSMCs)


title: SMC_24h_H3

description: SAMPLE 7

source_name: pBSMCs_PDGF 4hr

value: 1 nM PDGF-BB for 4hrs


title: SMC_24h_H4

description: SAMPLE 8


title: SMC_0h_L1

description: SAMPLE 1

value: none (0h control)


title: SMC_0h_L3

description: SAMPLE 3


title: SMC_24h_H2

description: SAMPLE 6


title: SMC_0h_L4

description: SAMPLE 4


title: SMC_24h_H1

description: SAMPLE 5


title: B4h_Alexa

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

description: raw data file: 252116912374_0004.gpr

hyb_protocol: 17 hours incubation at 65 degree with 10 rpm rotation.

scan_protocol: Slides were scanned after washing using GenePix 4200 AL (Axon Instruments) with pixel resolution 5µm and line average 2.

data_processing: Image analysis was done using GenePix Pro 6.1, bad spots were manually flagged (flag value -100). Data normalization in R with limma package using local background subtraction NormExp method with offset 50. Quantile-normalized log2-intensities were compared between treatments using linear model with contrasts. Significances were obtained using eBayes method, FDR was used for correcting multiple-testing.

organism: Arabidopsis thaliana

source_name: 1mm root tip

label_protocol: The Cy3, Cy5 and Alexa488 dye coupling with Amino Allyl MessageAmp™ II aRNA Amplification Kit (Life technologies) according to manufacturer’s instructions.

growth_protocol: 4 day-old seedlings were grown on the plant medium containing half Murashige and Skoog salt mix, 1% Sucrose, 0.05% MES  (pH 5.7) and 0.4% phytagel, with or without treatment.

extract_protocol: Total RNAs were isolated from 1 mm root tip by Quiagen RNeasy Mini kit (Quiagen).

treatment_protocol: 4 day-old seedlings were transfered to the plant medium containing half Murashige and Skoog salt mix, 1% Sucrose, 0.05% MES  (pH 5.7), 0.4% phytagel with 1 uM 17β-estradiol for 0, 4, 10, 18 or 36 hours.

tag: treatment

value: NAC45-ectopic induction

tag: timepoint

value: 4 hours

value: root tip


title: Amu_Alexa

description: raw data file: 252116912375_0006.gpr

tag: genotype/variation

value: nac45-2 nac86 double mutant


title: B36h_Alexa

description: raw data file: 252116912375_0005.gpr

value: 36 hours


title: B18h_Alexa

description: raw data file: 252116912374_0001.gpr

value: 18 hours


title: Awt_Alexa

description: raw data file: 252116912374_0003.gpr

value: col WT


title: B10h_Alexa

description: raw data file: 252116912376_0010.gpr

value: 10 hours


title: B18h_Cy5

description: raw data file: 252116912376_0012.gpr


title: Bno_Cy5

description: raw data file: 252116912375_0006.gpr

value: 0 hour


title: SMC_0h_L2

description: SAMPLE 2


title: B36h_Cy5

description: raw data file: 252116912374_0004.gpr


title: Amu_Cy5

description: raw data file: 252116912375_0005.gpr


title: Bno_Alexa

description: raw data file: 252116912375_0007.gpr


title: Awt_Cy5

description: raw data file: 252116912374_0002.gpr


title: B10h_Cy3

description: raw data file: 252116912376_0011.gpr


title: B4h_Cy5

description: raw data file: 252116912374_0003.gpr


title: melanoma_AJCCstageIII_TumourID231

value: lymph node

value: melanoma

value: Male


title: B36h_Cy3

description: raw data file: 252116912375_0006.gpr


title: Amu_Cy3

description: raw data file: 252116912374_0004.gpr


title: B18h_Cy3

description: raw data file: 252116912374_0003.gpr


title: Bno_Cy3

description: raw data file: 252116912375_0008.gpr


title: B4h_Cy3

description: raw data file: 252116912375_0005.gpr


title: Awt_Cy3

description: raw data file: 252116912374_0001.gpr


title: T2N0M0 NZR08

city: Beijing

first: Bangrong

last: Cao

address: NO.17 Panjiayuannanli, Chaoyang District, Beijing, P.R.China

country: China

institute: Cancer Institute & Hospital, Chinese Academy of Medical Sciences

description: Gene expression in noncancerous lung tissue adjacent to lung SCC

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% and 10%, dynamic range is extended).

data_processing: The scanned images were analyzed with Feature Extraction Software v9.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities. Log2 transformed raw intensities were normalized across a series of arrays with median-absolute scaled method using limma package of R software.

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

extract_protocol: RNA was prepared using TRIzol reagent(Invitrogen, Carlsbad, CA), and then purified using the RNeasy Mini Kit(Qiagen, Germantown, MD ), according to the manufacturer’s instructions. RNA was quantitated using a ND-1000 UV-VIS Spectrophotometer (NanoDrop Technologies, Wilmington, DE), and the integrity of the RNA was assessed with the RNA 6000 Labchip kit in combination with the Agilent 2100 Bioanalyzer (Agilent, Pal Alto, CA).

treatment_protocol: Noncancerous lung tissues were collected at the margin of the resection, mainly about 3-5 cm distant from the primary tumor. Fresh tissues were treated with RNAlaterTM (Ambion, Austin, TX, USA) and stored at -80℃ for subsequent molecular analysis.

tag: gender

value: Female

tag: age (years)

tag: ptnm

tag: pathologic t stage

tag: pathologic n stage

tag: disease state

value: lung squamous cell carcinoma


title: T2N1M0 NLY26

source_name: noncancerous lung tissue adjacent to lung SCC

tag: tissue


title: presenillin/wt replicate 1

city: Dresden

first: Judith

last: Paridaen

address: Pfotenhauerstr 108

country: Germany

institute: MPI-CBG

description:
replicate 1a:
Agilent-23-Medium.gpr (WT_Cy3, presenillin1 mutant_Cy5)
replicate 1b (dyeswap):
Agilent-24-Medium.gpr (WT_Cy5, presenillin1 mutant_Cy3)

hyb_protocol: Upon purification and fragmentation, labeled cRNA was hybridized to the zebrafish 22K 60-mer oligonucleotide microarray (G2518A-001, Agilent Technologies, Santa Clara, CA, USA) at 65ºC for 17 hours

scan_protocol: Arrays were scanned at 10 µm resolution with a dual-laser scanner (GenePix 4000B, Molecular Devices) using the GenePix 6 software.

data_processing: The raw data was transformed and normalized (Yang and Churchill, 2007) and a locally weighted regression smoother was applied to correct intensity-dependent signal patterns (Yang et al., 2002). All the hybridized chips for mutant vs. WT comparisons were scaled to a common median absolute deviation from median (MAD) of the logarithmic fold change (M value) (Yang et al., 2002). Statistical analysis was based on the assumption that the majority of genes are not changed in their expression and that the overall up- or down-regulated genes compensate each other in sum.

label: Cy3, Cy5

organism: Danio rerio

source_name: wildtype

label_protocol: cDNA was generated and labeled with Cy3 or Cy5-CTP using the low RNA input linear amplification kit (Perkin-Elmer).

extract_protocol: Total RNA from 3-4 brains of 17-month old adult psen1hu2547 or WT fish was extracted using RNeasy mini columns (Qiagen) and quality-checked using NanoDrop 1000 (Thermo Scientific) and formaldehyde gel electrophoresis.

tag: age

value: whole brain

value: wildtype

source_name: psen1 hu2547

value: psen1 hu2547


title: T2N0M0 NLY20

value: noncancerous lung tissue adjacent to lung SCC


title: T2N0M0 NLY17


title: T2N1M0 NLY25


title: T3N2M0 NLY22


title: T2N2M0 NLY16


title: T2N0M0 NZR07


title: T2N0M0 NLY19


title: T2N0M0 NLY15


title: T2N2M0 NLY21


title: presenillin/wt replicate 3

description:
replicate 3a:
Agilent-27-Medium.gpr (WT_Cy3, presenillin1 mutant_Cy5)
replicate 3b (dyeswap):
Agilent-28-Medium.gpr (WT_Cy5, presenillin1 mutant_Cy3)


title: presenillin/wt replicate 2

description:
replicate 2a:
Agilent-25-Medium.gpr (WT_Cy3, presenillin1 mutant_Cy5)
replicate 2b (dyeswap):
Agilent-26-Medium.gpr (WT_Cy5, presenillin1 mutant_Cy3)


title: T2N2M0 NLY24


title: T2N2M0 NLY10


title: T2N2M0 NLY12


title: T3N1M0 NLY14


title: T2N0M0 NLY13


title: T3N1M0 NLY11


title: T3N1M0 NLY09


title: T2N2M0 NLY06


title: NBC 10 cultured with IL-4

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

country: Spain

institute: Hospital Clinico Universitario Virgen de la Arrixaca

hyb_protocol: Agilent Gene Expression Hybridization kit protocol following the manufacturer's instructions

scan_protocol: Agilent G2565CA scanner, Agilent Scan Control software, scanning at 5µm or at 3µm

data_processing: Lowess normalization using Agilent Feature Extraction software

source_name: pooled CLL and NBC Pre samples

label_protocol: Agilent Two Color Quick Amp Labeling and RNA Spike-In kits protocols following the manufacturer's instructions

growth_protocol: Culture for 18 hr in RPMI-1640 medium supplemented with 10% fetal calf serum

extract_protocol: miRNeasy mini kit (Qiagen) protocol following the manufacturer's instructions

treatment_protocol: 10 ng/ml IL-4 (BD Biosciences) or nothing or IL-4 plus specified inhibitors from Calbiochem

value: Peripheral blood B lymphocytes

value: CLL cells and normal B cells (NBC)

source_name: Normal B cells_18 hr with IL-4

value: Normal B cells

tag: sample group

value: IL-4 treated (10 ng/ml for 18hrs)


title: NBC 12 cultured with IL-4


title: T2N1M0 NLY07


title: NBC 11 cultured with IL-4


title: NBC 13 cultured with IL-4


title: T3N2M0 NLY08


title: T3N0M0 NLY03


title: NBC 9 cultured with IL-4


title: NBC 6 cultured with IL-4


title: NBC 8 cultured with IL-4


title: NBC 7 cultured with IL-4


title: T2N1M0 NLY04


title: NBC 4 cultured with IL-4


title: NBC 5 cultured with IL-4


title: NBC 1 cultured with IL-4


title: NBC 3 cultured with IL-4


title: T3N1M0 NL21


title: NBC 13 cultured with nothing

source_name: Normal B cells_18 hr with nothing

value: control samples (no-treatment)


title: NBC 12 cultured with nothing


title: T3N2M0 NLY02


title: T2N2M0 NCC83


title: T2N0M0 NCC09


title: T3N2M0 NCC51


title: T3N2M0 NCC27


title: T2N0M0 N91


title: T3N2M0 N98


title: T2N0M0 N85


title: NBC 2 cultured with IL-4


title: NBC 11 cultured with nothing


title: NBC 9 cultured with nothing


title: NBC 10 cultured with nothing


title: NBC 5 cultured with nothing


title: T2N1M0 N81


title: T2N0M0 N76


title: T3N0M0 N82


title: TRIM37KD H2Aub-Rep2

type: genomic

city: Davis

first: Sanchita

last: Bhatnagar

address: 1275 Health Sciences, Tupper Hall 3134

department: Medical Microbiology and Immunology

institute: University of California Davis

description: Sonicated DNA subjected to Chromatin Immunoprecipitation

hyb_protocol: Samples were prepared and hybridized to GeneChip Human Promoter 1.0R Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
ChIP-chip data was analyzed using Bioconductor package Starr for data read-in, normalizing and peak calling.  Quantile normalization was applied to normalize probe intensity before peak calling with default setting except that frag.length (sonication fragment length), minrun (minimum number of probes in a bound region), method (multiple test adjustment method), and alpha (False discovery rate cutoff) were set to  500, 2 and 0.1 respectively. Bound regions were annotated to nearest genes using Bioconductor package ChIPpeakAnno.
ChIP-chip data was analyzed using Bioconductor package Starr [1] [2] for data read-in, normalizing and peak calling.

molecule: genomic DNA

growth_protocol: MCF7 cells were cultured in DMEM media supplemented with 10% FBS at 37 degrees and 5% CO2.

extract_protocol: 1x10E8 cells were rinsed with PBS, scraped, and pelleted in a 50 mL conical tube. Cells were fixed in 1% formaldehyde for 10 minutes and 0.125M glycine was added to quench the cross-linking reaction. Cells were spun down and the pellet was re-suspended in Lysis buffer (50mM Hepes pH 8.0, 150mM NaCl, 1mM EDTA, 01% Na-Deoxycholate, 1% Triton X-100, 0.1% SDS, 1mM PMSF and protease inhibitors) and subjected to sonication by Bioruptor. Cell debris was removed by centrifugation at 1500g for 15 min and cleared superntant was used for Chromatin immunoprecipitation.

treatment_protocol: Cells were washed twice with PBS and then fixed with 1% Formaldehyde. The fixation was terminated with 2.5M glycine and

tag: cell line

tag: antibody


title: TRIM37KD H2Aub-Rep1

label_protocol: Samples were prepared and hybridized to GeneChip Human Promoter 1.0R Array according to Affymetrix specifications.


title: NBC 2 cultured with nothing


title: T2N1M0 N70


title: T3N2M0 N58


title: B10h_Cy5

description: raw data file: 252116912376_0009.gpr

value: NAC45-ectopic induction

value: root tip


title: IgG control-6

value: anti-IgG


title: NBC 9 before culture

source_name: Normal B cells

value: basal (Pre) samples; before culture


title: IgG control-5


title: T4N0M0 N64


title: NBC 3 cultured with nothing


title: T2N0M0 N57


title: NBC 8 before culture


title: TRIM37 KD H3K27me3-Rep1


title: NBC 4 cultured with nothing


title: TRIM37 KD H3K27me3-Rep2


title: IgG control-4


title: T1N2M0 N46


title: T2N0M0 N36


title: NBC 1 cultured with nothing


title: T3N0M0 N160


title: T2N1M0 N42


title: T2N0M0 N20


title: NBC 7 before culture


title: T2N2M0 N5


title: NBC 6 before culture


title: NBC 10 before culture


title: TRIM37 Rep1


title: T3N0M0 N153


title: T2N1M0 N45


title: NBC 5 before culture


title: TRIM37 Rep2


title: NBC 4 before culture


title: T4N1M0 N150


title: H2Aub-Rep2


title: T2N0M0 N16


title: NBC 3 before culture


title: T4N2M0 N136


title: H2Aub-Rep1


title: IgG control-3


title: T3N1M0 N126


title: NBC 2 before culture


title: T2N0M0 N127


title: T2N1M0 N15


title: H3K27me3-Rep2


title: H3K27me3-Rep1


title: T2N0M0 N149


title: T3N0M0 N123


title: NBC 1 before culture


title: CLL patient 1 cultured with IL-4 plus cyclin-Pifithrin-α

source_name: CLL cells_18 hr with IL-4 plus cyclin-Pifithrin-α

value: chronic lymphocytic leukemia (CLL) cells

value: IL-4 plus cyclin-Pifithrin-α treated


title: CLL patient 1 cultured with IL-4 plus NFkB activation inhibitor

source_name: CLL cells_18 hr with IL-4 plus an NFkB inhibitor

value: IL-4 plus an NFkB inhibitor treated


title: T1N0M0 N12

value: Male

value: lung squamous cell carcinoma


title: T2N1M0 N121


title: CLL patient 25 cultured with IL-4

source_name: CLL cells_18 hr with IL-4


title: Wild Type 5-7mm panicles rep2

city: Shanghai

first: Hu

last: Yun

state: Shanghai

address: 800 Dongchuan RD. Minhang District, Shanghai, China

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

description: Microarray data of genome-wide gene expression profile

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 7G.

data_processing: The data were analyzed with PARTEK genomic suit 6.4 using RMA normalization

label: biotin

organism: Oryza sativa

source_name: panicles in length of 5-7 mm

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (3_ivt_express_kit_manual Affymetrix).

growth_protocol: Rice plants grow in the paddyfield

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

treatment_protocol: No special treatment

value: Wild Type

tag: developmental stage

value: late flower development stage

value: panicles

tag: tissue size


title: CLL patient 24 cultured with IL-4

value: Peripheral blood B lymphocytes

tag: cell type


title: CLL patient 1 cultured with IL-4 plus ERK activation inhibitor peptide I

value: CLL cells and normal B cells (NBC)

source_name: CLL cells_18 hr with IL-4 plus an ERK inhibitor

value: IL-4 plus an ERK inhibitor treated


title: Wild Type 5-7mm panicles rep1


title: Wild Type 5-7mm panicles rep3


title: Ezh2-Rep2


title: osmads1 5-7mm panicles rep1


title: osmads1 5-7mm panicles rep2


title: Wild Type 2mm panicles rep3

source_name: panicles in length of 2mm

value: early flower development stage


title: Ezh2 -Rep1


title: T2N2M0 N103

value: noncancerous lung tissue adjacent to lung SCC


title: osmads1 5-7mm panicles rep3


title: Wild Type 2mm panicles rep2


title: osmads1 2mm panicles rep3


title: T1N0M0 N101


title: IgG control-1


title: Wild Type 2mm panicles rep1


title: BMP2 HUES24 H3K27me3

city: Marseille

first: michel

last: PUCEAT

address: 27 bd Jean moulin

department: University aix marseille

country: France

institute: INSERM

description: results for K27meHuES24

hyb_protocol: Samples were prepared and hybridized to Gne ChiP Human promoter  Tiling 1.0R Array according to Affymetrix specifications.

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1.02) the identified binding sites were mapped to the gene promoter sites using Genomatrix
the identified binding sites were mapped to the gene promoter sites using Genomatrix

source_name: BMP2 HUES24 H3K27me3

growth_protocol: HUES cells were cultured as previously described (Stefanovic et al J cell biol 2009 186(5):665-73.

extract_protocol: cells were crosslinked and chromatin extracted as previously described (Zeineddine et al Dev Cell. 2006 ,11(4):535-46.)

treatment_protocol: cells were treated with 10 ng/ml BMP2 for two days

tag: treatment

tag: chip antibody


title: control HUES24 H3K27me3

description: results for K27meHuES24

source_name: control HUES24 H3K27me3

label_protocol: Samples were prepared and hybridized to Gne ChiP Human promoter  Tiling 1.0R Array according to Affymetrix specifications.


title: osmads1 2mm panicles rep2

tag: genotype/variation


title: CLL patient 23 cultured with IL-4

value: IL-4 treated (10 ng/ml for 18hrs)


title: control HUES24 H3K4me3

description: results for K4meHuES24

source_name: control HUES24 H3K4me3


title: CLL patient 20 cultured with IL-4


title: BMP2 HUES24 H3K4me3

description: results for K4meHuES24

source_name: BMP2 HUES24 H3K4me3


title: siNTE_D_96h

city: Varese (VA)

first: Marco

last: Fabbri

address: via dunant 5

country: Italy

institute: Università dell'Insubria

description: Gene expression control

hyb_protocol: standard Agilent protocol

scan_protocol: Scanned with the Agilent G2565BA Microarray Scanner (Agilent)

data_processing: The fluorescence intensities on scanned images were extracted and preprocessed by Agilent Feature Extraction Software (v10.5.1.1). The Agi4x44PreProcess Bioconductor package has been used to normalize data (quantile) and to specific filters (default parameters) have been applied to remove controls, probe  well above background, well above negative controls, saturation, population outliers, non uniform outliers and removing NAs. in-house script:  ddNORM=BGandNorm(ag1,BGmethod=half,NORMmethod=quantile,                   foreground=MeanSignal,background=BGMedianSignal,                   offset=50,makePLOTpre=FALSE,makePLOTpost=FALSE)    agddFILT=filter.probes(ddNORM,                  control=TRUE,                  wellaboveBG=TRUE,                  isfound=TRUE,                  wellaboveNEG=TRUE,                  sat=TRUE,                  PopnOL=TRUE,                  NonUnifOL=TRUE,                  nas=TRUE,                  limWellAbove=75,                  limISF=75,                  limNEG=75,                  limSAT=75,                  limPopnOL=75,                  limNonUnifOL=75,                  limNAS=100,                  makePLOT=F,annotation.package=human80x60.db,                  flag.counts=T,                  newtarget1)

source_name: NTE silenced hNT2 (96 hours)

label_protocol: standard Agilent protocol

growth_protocol: Undifferentiated hNT2 cells were cultured in 75 cm2 flasks at the density of 3 x 10 6 cells with 5% heat-inactivated foetal bovine serum (FBS) plus 50 U/ml penicillin and 100 µg/ml streptomycin in Opti-MEM media. After 24 hours and for initiating differentiation, a differentiation medium with 10 µM retinoic acid, 10% of FBS and antibiotics in DMEM-Glutamax was applied during 4 days. The medium was replaced at the beginning of day 3.

extract_protocol: RNA from hNT2 cells previously was purified using the RNeasy Plus kit (Qiagen, Germantown, MD, USA).

treatment_protocol: Briefly, 15 µl of lipofectamine were added to 250 µl of Opti-MEM medium and were incubated at room temperature for 15 min. In parallel, 1 pmol of each siRNA (siRNA for siPNPLA6 and non-specific siRNA for Negative Control) were added to 250 µl of Opti-MEM medium and also incubated at room temperature for 15 min. Both solutions were mixed and incubated at room temperature for 15 min with approximately 106 hNT2 cells. After an additional 15-min period, the transfection solution was diluted by adding 4 ml of fresh medium.

tag: time point

tag: sirna

value: siNTE


title: osmads1 2mm panicles rep1


title: CLL patient 19 cultured with IL-4


title: BMP2 HUES26 H3K27me3

description: results for K27meHuES26

source_name: BMP2 HUES26 H3K27me3


title: Neg_A_96h

description: Gene expression control

source_name: Non-specific siRNA hNT2 (96 hours)

value: Neg


title: CLL patient 21 cultured with IL-4

source_name: pooled CLL and NBC Pre samples


title: Neg_C_96h

description: Gene expression control


title: Tia-1 122973 spinal cord 6 month

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

institute: University of Tuebingen

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HT MG-430 PM Array Plates. Hybridization, washing, staining and scanning was performed fully automated on a Gene Titan instrument.

scan_protocol: standard Gene Titan instrument protocol

data_processing: The data were analysed using Bioconductor package 'oligo' 1.18.0 under R-2.14.0. Background correction, normalization and probe summarization was performed with RMA.

organism: Mus musculus

source_name: spinal cord, knock out, 6 month

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA using the 3'IVT Express Kit (Ambion).

growth_protocol: Mice were housed in Type II L cages (365x207x140 mm, floor area 530 cm2; IVC-based)at an environmental temperature 20-24°C, humidity: 55±10%and under 12/12 h light/dark cycle with food and water ad libitum.

extract_protocol: RNA  was extracted by using RNeasy Midi Kit (Qiagen) following manufacturers instructions for animal tissues.

treatment_protocol: not applicable

value: spinal cord

tag: strain

value: tia1 knock out

value: 6 months

tag: genetic background


title: Neg_C_24h

description: Gene expression control

source_name: Non-specific siRNA hNT2 (24 hours)


title: Neg_B_96h

description: Gene expression control


title: siNTE_A_96h

description: Gene expression control


title: BMP2 HUES26 H3K4me3

description: results for K4meHuES26

source_name: BMP2 HUES26 H3K4me3


title: CLL patient 16 cultured with IL-4

value: chronic lymphocytic leukemia (CLL) cells


title: CLL patient 17 cultured with IL-4


title: siNTE_B_96h

description: Gene expression control


title: CLL patient 18 cultured with IL-4


title: Neg_D_24h

description: Gene expression control


title: Tia-1 122972 spinal cord 6 month


title: CLL patient 15 cultured with IL-4


title: siNTE_C_24h

description: Gene expression control

source_name: NTE silenced hNT2 (24 hours)


title: Neg_A_24h

description: Gene expression control


title: control HUES26 H3K4me3

description: results for K4meHuES26

source_name: control HUES26 H3K4me3


title: Tia-1 122970 spinal cord 6 month


title: siNTE_B_24h

description: Gene expression control


title: siNTE_A_24h

description: Gene expression control


title: Tia-1 122973 liver 6 month

source_name: liver, knock out, 6 month

value: liver


title: control HUES26 H3K27me3

description: results for K27meHuES26

source_name: control HUES26 H3K27me3


title: CLL patient 12 cultured with IL-4

source_name: CLL cells_18 hr with IL-4


title: Tia-1 122970 liver 6 month


title: Tia-1 122972 liver 6 month


title: Ctrl_C_24h

description: Gene expression control

source_name: hNT2 in normal medium (24 hours)

value: Ctrl


title: Ctrl_D_24h

description: Gene expression control


title: CLL patient 14 cultured with IL-4


title: CLL patient 13 cultured with IL-4


title: CLL patient 10 cultured with IL-4


title: Ctrl_B_24h

description: Gene expression control


title: CLL patient 9 cultured with IL-4


title: Tia-1 122972 midbrain 6 month

source_name: midbrain, knock out, 6 month

value: midbrain


title: Primary_human_corneal_epithelial_cells_TNC_rep1

city: Québec

first: Karine

last: Zaniolo

state: Québec

address: 1050 Chemin Sainte-Foy

department: CUO-Recherche

country: Canada

institute: Centre de recherche du CHU de Québec

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Primary human corneal epithelial cells cultivatd on TNC, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification  (QIAGEN, Toronto, ON).  Dye incorporation and cRNA yield were checked with the Nanophotometer pearl(Montréal Biotech).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Toronto, ON)  from HCEC, HSEC, HCFC, HSFC, UVM isolated from normal eyes supplied by the National Eyes Bank from the CHU de Québec (QC, Canada), and from the uveal melanoma cell lines T115, T142 and T143 cultured from the primary tumors (115, 142 and 143) of patients diagnosed with uveal melanoma .

value: Primary human corneal epithelial cells

tag: culture conditions

value: TNC

tag: gender

value: unknown

value: 44 years


title: Primary_human_corneal_epithelial_cells_TNC_rep2

source_name: Primary human corneal epithelial cells cultivatd on TNC, replicate 2

value: 52 years


title: Tia-1 122973 midbrain 6 month

tag: tissue


title: CLL patient 7 cultured with IL-4

value: Peripheral blood B lymphocytes

value: CLL cells and normal B cells (NBC)


title: D80208_VPA012_244-FP_3mcgP

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

country: United Kingdom

institute: Institute of Cancer Research (ICR), London

description: Metastatic colorectal cancer samples with first-line FOLFIRI response

hyb_protocol: For each sample, the probes were then hybridized to human genome U133 chips (Affymetrix) containing more than 45,000 quanlifiers, corresponding to genes and expressed sequence tags.

scan_protocol: After hybridization, the probes were scanned using a laser scanner, and signal intensity for each transcript.

data_processing: Robust multiarray (RMA) processing was done using R and Bioconductor package (affy).

source_name: tumor

label_protocol: Labeled cRNA probes were then generated by reverse transcription followed by in vitro transcription, incorporating biotin labeling, as apart of the standard protocol (Affymetrix Inc, Santa Clara, CA).

extract_protocol: Rneasy Mini Kit (Qiagen)

treatment_protocol: Patients were treated with a combination of irinotecan with an LV5FU2 (folinic acid [or leucovorin] 200 mg/m2 as a 2-hour infusion followed by FU 400 mg/m2 bolus and 2,400 mg/m2 as a 46-hour continuous infusion) regimen (FOLFIRI) as first-line treatment. Ten patients participated in a multicenter phase II clinical trial aimed at assessing whether increasing the dose of irinotecan (from 180 to 260 mg/m2) in the FOLFIRI regimen would benefit patients with metastatic CRC. The remaining patients received a FOLFIRI regimen with a standard dose of irinotecan (180 mg/m2). For one patient, intravenous FU was replaced by an oral form of FU (uracil/ftorafur). Tumor response was evaluated according to WHO recommendations for the evaluation of cancer treatment in solid tumors.The size of the metastatic lesions was estimated from bidimensional measurements (the product of the longest diameter and the longest perpendicular diameter) using computed tomography scanning. Patients were evaluated for response before and after every four cycles of chemotherapy for a regimen of 3-week cycles and after every six cycles of chemotherapy for a regimen of 2-week cycles, to calculate the percent change from baseline. Best observed response was then used to classify patients into two groups. Patients with a decrease ≥ 50% of the metastatic lesion were classified as responders, and patients with a decrease less than 50% or with an increase in size of lesions were classified as nonresponders.

value: metastatic colorectal cancer tumor

tag: response

value: FOLFIRI S (sensitive)


title: CLL patient 8 cultured with IL-4

tag: sample group

value: IL-4 treated (10 ng/ml for 18hrs)


title: T4N0M0 N13

source_name: noncancerous lung tissue adjacent to lung SCC

value: Male

tag: age (years)

tag: ptnm

tag: pathologic t stage

tag: pathologic n stage

tag: disease state

value: lung squamous cell carcinoma


title: D80208_VPA012_223-GB_3mcgP

value: FOLFIRI R (resistant)


title: Tia-1 122973 cerebellum 6 month

source_name: cerebellum, knock out, 6 month

value: cerebellum

value: tia1 knock out

tag: age

value: 6 months


title: D80306_VPA013_119PM_3mcgP


title: CLL patient 6 cultured with IL-4

tag: cell type

value: chronic lymphocytic leukemia (CLL) cells


title: Tia-1 122970 midbrain 6 month

value: midbrain


title: Tia-1 122972 cerebellum 6 month


title: CLL patient 5 cultured with IL-4


title: D80208_VPA012_222-PEC_3mcgP


title: Primary_human_corneal_epithelial_cells_BSA_rep2

source_name: Primary human corneal epithelial cells cultivated on BSA, replicate 2

value: Primary human corneal epithelial cells

value: BSA


title: D80208_VPA012_213-RG_3mcgP


title: IgG control-2

tag: cell line

tag: antibody

value: anti-IgG


title: Tia-1 122970 cerebellum 6 month


title: CLL patient 4 cultured with IL-4

source_name: pooled CLL and NBC Pre samples


title: Primary_human_corneal_epithelial_cells_BSA_rep1

source_name: Primary human corneal epithelial cells cultivated on BSA, replicate 1

value: unknown

value: 44 years


title: Uveal_melanoma_derivative_cell_line_T143_rep1

source_name: Uveal melanoma derivative cell line, replicate 1

value: Uveal melanoma derivative cell line T143

value: male

value: 55 years


title: D80208_VPA012_196-TD_3mcgP

value: metastatic colorectal cancer tumor


title: Uveal_melanoma_derivative_cell_line_T142_rep1

value: Uveal melanoma derivative cell line T142

value: 54 years


title: WT 2 spinal cord 6 month

source_name: spinal cord, wild type, 6 month

value: spinal cord

value: wild type


title: CLL patient 3 cultured with IL-4

value: Peripheral blood B lymphocytes

value: CLL cells and normal B cells (NBC)

value: IL-4 treated (10 ng/ml for 18hrs)


title: D80208_VPA012_149-JGI_3mcgP

value: FOLFIRI S (sensitive)


title: WT 1 spinal cord 6 month

value: 6 months


title: CLL patient 25 cultured with nothing

source_name: CLL cells_18 hr with nothing

value: chronic lymphocytic leukemia (CLL) cells

value: control samples (no-treatment)


title: D80208_VPA012_189-JR_3mcgP

value: FOLFIRI R (resistant)


title: WT 3 spinal cord 6 month


title: CLL patient 1 cultured with IL-4


title: CLL patient 24 cultured with nothing


title: Uveal_melanoma_derivative_cell_line_T143_rep2

source_name: Uveal melanoma derivative cell line, replicate 2


title: WT 3 liver 6 month

source_name: liver, wild type, 6 month

value: liver


title: Uveal_melanoma_derivative_cell_line_T115_rep2

value: Uveal melanoma derivative cell line T115

value: female

value: 43 years


title: D80208_VPA012_130-YL_3mcgP

value: metastatic colorectal cancer tumor


title: Uveal_melanoma_derivative_cell_line_T142_rep2

value: Uveal melanoma derivative cell line T142

value: male


title: WT 2 liver 6 month


title: D80208_VPA012_115-CB_3mcgP


title: D80208_VPA012_044-MB_3mcgP


title: Uveal_melanoma_derivative_cell_line_T115_rep3

source_name: Uveal melanoma derivative cell line, replicate 3


title: WT 1 liver 6 month


title: CLL patient 2 cultured with IL-4

source_name: CLL cells_18 hr with IL-4


title: D80130_VPA012_94-AM_3mcgP


title: CLL patient 23 cultured with nothing


title: Primary_human_uveal_melanocyte_cells_rep3

source_name: Primary human uveal melanocyte cells, replicate 3

value: Primary human uveal melanocyte cells

value: 83 years


title: D80130_VPA012_89-NC_3mcgP


title: WT 2 midbrain 6 month

source_name: midbrain, wild type, 6 month

value: midbrain

value: wild type


title: Primary_human_uveal_melanocyte_cells_rep2

source_name: Primary human uveal melanocyte cells, replicate 2

value: 59 years


title: D80130_VPA012_061-CM_3mcgP

value: FOLFIRI S (sensitive)


title: Primary_human_uveal_melanocyte_cells_rep1

source_name: Primary human uveal melanocyte cells, replicate 1

value: 51 years


title: Primary_human_skin_fibroblast_cells_rep3

source_name: Primary human skin fibroblast cells, replicate 3

value: Primary human skin fibroblast cells

value: unknown

value: 21 years


title: CLL patient 20 cultured with nothing

value: Peripheral blood B lymphocytes

value: CLL cells and normal B cells (NBC)

value: chronic lymphocytic leukemia (CLL) cells

value: control samples (no-treatment)


title: Uveal_melanoma_derivative_cell_line_T115_rep1

value: Uveal melanoma derivative cell line T115

value: female

value: 43 years


title: WT 1 midbrain 6 month

value: 6 months


title: Primary_human_skin_fibroblast_cells_rep2

source_name: Primary human skin fibroblast cells, replicate 2

value: 25 years


title: WT 1 cerebellum 6 month

source_name: cerebellum, wild type, 6 month

value: cerebellum


title: D80130_VPA012_059-MT_3mcgP

source_name: tumor

value: metastatic colorectal cancer tumor


title: D80130_VPA012_045-JC_3mcgP

value: FOLFIRI R (resistant)


title: D80130_VPA012_056-MC_3mcgP


title: CLL patient 19 cultured with nothing

source_name: pooled CLL and NBC Pre samples


title: CLL patient 21 cultured with nothing


title: WT 2 cerebellum 6 month

value: wild type


title: D80130_VPA012_73-PD_3mcgP


title: WT 3 cerebellum 6 month


title: CLL patient 18 cultured with nothing


title: Tia-1 122973 spinal cord 3 month

source_name: spinal cord, knock out, 3 month

value: spinal cord

value: tia1 knock out

value: 3 months


title: CLL patient 17 cultured with nothing


title: Primary_human_corneal_fibroblast_cells_rep3

source_name: Primary human corneal fibroblast cells, replicate 3

value: Primary human corneal fibroblast cells

value: unknown

value: 0.74 years


title: D80130_VPA012_016-MV_3mcgP

value: FOLFIRI S (sensitive)


title: CLL patient 15 cultured with nothing

value: Peripheral blood B lymphocytes

value: CLL cells and normal B cells (NBC)

value: chronic lymphocytic leukemia (CLL) cells

value: control samples (no-treatment)


title: D60801_VPA10_227_SS_3mcgP


title: CLL patient 16 cultured with nothing


title: Tia-1 122970 spinal cord 3 month


title: Primary_human_skin_fibroblast_cells_rep1

source_name: Primary human skin fibroblast cells, replicate 1

value: Primary human skin fibroblast cells


title: Tia-1 122972 spinal cord 3 month


title: Primary_human_skin_epithelial_cells_rep4

source_name: Primary human skin epithelial cells, replicate 4

value: Primary human skin epithelial cells

value: female

value: 30 years


title: Primary_human_corneal_fibroblast_cells_rep1

source_name: Primary human corneal fibroblast cells, replicate 1


title: D60801_VPA10_022_JB_3mcgP

value: metastatic colorectal cancer tumor


title: CLL patient 13 cultured with nothing

source_name: CLL cells_18 hr with nothing


title: Tia-1 122972 liver 3 month

source_name: liver, knock out, 3 month

value: liver


title: CLL patient 14 cultured with nothing


title: CLL patient 9 cultured with nothing


title: C7H2/FOXO3 4OHT treated

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

description: C7H2/FOXO3 4OHT treated

hyb_protocol: Target samples were hybridized to Human HGU133 Plus 2.0 microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned in an Affymetrix 3000 scanner.

data_processing: Raw microarray data has been background adjusted using the GCRMA method (gcrma package version 2.32.0) and quantile normalized. Thus adjusted probe intensities have been summarized using the fitPLM function from the affyPLM package (version 1.36.0).

label_protocol: 500 ng total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix). All procedures were performed according to the manufacturer’s protocols.

growth_protocol: All cell lines were cultured in RPMI1640 (Lonza, Basel, Switzerland) containing 10% fetal calf serum, 100 U/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine (Gibco BRL, Paisley, GB) at 5% CO2 and 37 °C in saturated humidity.

extract_protocol: Total RNA was prepared from 5000000 cells using TRIzolTM Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions.

treatment_protocol: SH-EP/FOXO3, SH-EP, NB15/FOXO3, NB15, C7H2/FOXO3 and C7H2 were treated for 3 hours with 100nM 4-hydroxy-tamoxifen (4OHT)

tag: treatment


title: CLL patient 10 cultured with nothing


title: Primary_human_skin_epithelial_cells_rep2

source_name: Primary human skin epithelial cells, replicate 2

value: 36 years


title: Tia-1 122973 liver 3 month

tag: strain

value: tia1 knock out


title: NB15 4OHT treated

description: NB15 4OHT treated


title: Tia-1 122973 midbrain 3 month

source_name: midbrain, knock out, 3 month

value: midbrain

value: 3 months

tag: genetic background


title: C7H2/FOXO3 untreated

description: C7H2/FOXO3 untreated


title: Tia-1 122970 liver 3 month


title: C7H2 4OHT treated

description: C7H2 4OHT treated


title: Primary_human_corneal_fibroblast_cells_rep2

source_name: Primary human corneal fibroblast cells, replicate 2

value: Primary human corneal fibroblast cells

value: unknown

value: 34 years


title: CLL patient 8 cultured with nothing

value: Peripheral blood B lymphocytes


title: Primary_human_skin_epithelial_cells_rep1

source_name: Primary human skin epithelial cells, replicate 1

value: 1 year


title: Primary_human_skin_epithelial_cells_rep3

source_name: Primary human skin epithelial cells, replicate 3


title: Primary_human_corneal_epithelial_cells_rep8

source_name: Primary human corneal epithelial cells, replicate 8

value: Primary human corneal epithelial cells

value: 52 years


title: CLL patient 12 cultured with nothing

value: CLL cells and normal B cells (NBC)

value: chronic lymphocytic leukemia (CLL) cells

value: control samples (no-treatment)


title: Tia-1 122970 midbrain 3 month


title: NB15/FOXO3 untreated

description: NB15/FOXO3 untreated


title: Primary_human_corneal_epithelial_cells_rep7

source_name: Primary human corneal epithelial cells, replicate 7

value: 44 years


title: CLL patient 7 cultured with nothing


title: Tia-1 122972 midbrain 3 month


title: NB15/FOXO3 4OHT treated

description: NB15/FOXO3 4OHT treated


title: Tia-1 122972 cerebellum 3 month

source_name: cerebellum, knock out, 3 month

value: cerebellum


title: CLL patient 5 cultured with nothing


title: CLL patient 6 cultured with nothing


title: t-BOOHt-repetition4

city: Thiverval - Grignon

first: Djamila

last: Onesime

address: CBAI

department: MICA

institute: INRA

hyb_protocol: Hybridizations were performed as recommended by the manufacturer (Two-Colour Microarray-Based Gene Protocol, version 6.5, May 2010, from Agilent Technologies).  300 ng of Cy-3 and Cy-5 labelled cRNA were combined with 10x blocking agent, and 25x fragmentation buffer at 60ºC for exactly 30 min. The reaction was stopped with 2x GE hybridization buffer HI-RPM and hybridized to the oligo microarray for 17 h at 65ºC with continuing rotation (10 r.p.m). After hybridization, slides were washed for 1 min at room temperature, using GE wash buffer 1, and 1 min at 37ºC with GE wash buffer 2.

scan_protocol: Agilent G2565 Scanner in extended dynamic range with a resolution of 5 nm per pixel The scanned images were quantified using Agilent Feature Extraction Software (version10.7.3.1).

data_processing: Intensity-dependent normalization was performed with the LOESS procedure followed by subtraction of the log-ratio median calculated over the values for an entire block from each individual log-ratio using the anapuce package of R. Differental analysis was performed with the varmixt package of R.

organism: Kluyveromyces lactis

source_name: Klyap8∆-30 min exposure to 0.25 mM tert-butyl hydroperoxide (t-BOOH)

label_protocol: RNA was linearly amplified and labeled with  two different fluorescent dyes ; cyanine 3-CTP (cy-3) and cyanine5-CTP (cy-5), using the Agilent Low Input Quick Amp Labelling kit (version 6.5, May 2010)

growth_protocol: K. lactis cells exponentially grown in YPD medium were exposed  or not to a stress for 30 min.  The cells were harvested, pelleted and frozen for further analysis.

extract_protocol: Total RNA was extracted by trizol treatment following manufacturer's instructions (Invitrogen, Carlsbad, CA, USA)

treatment_protocol: Cells were exposed or not to a stress for 30 min: 0.1 mM sodium arsenite, NaASO2 or 0.25 mM t-BOOH

source_name: Klwt-30 min exposure to 0.25 mM tert-butyl hydroperoxide t-BOOH (reference)

value: Klwt


title: Primary_human_corneal_epithelial_cells_rep6

source_name: Primary human corneal epithelial cells, replicate 6

value: 3 years


title: SH-EP/FOXO3 4OHT treated

description: SH-EP/FOXO3 4OHT treated


title: CLL patient 3 cultured with nothing

source_name: pooled CLL and NBC Pre samples


title: t-BOOHt-repetition3

value: 30 min exposure to 0.25 mM tert-butyl hydroperoxide (t-BOOH)


title: WT 3 spinal cord 3 month

source_name: spinal cord, wild type, 3 month

value: spinal cord

value: wild type


title: Tia-1 122973 cerebellum 3 month

value: tia1 knock out

value: 3 months


title: SH-EP/FOXO3 untreated

description: SH-EP/FOXO3 untreated


title: CLL patient 4 cultured with nothing


title: SH-EP 4OHT treated

description: SH-EP 4OHT treated

source_name: SH-EP

value: SH-EP


title: Primary_human_corneal_epithelial_cells_rep5

source_name: Primary human corneal epithelial cells, replicate 5

value: unknown


title: Tia-1 122970 cerebellum 3 month


title: CLL patient 2 cultured with nothing

value: Peripheral blood B lymphocytes

source_name: CLL cells_18 hr with nothing


title: WT 2 spinal cord 3 month


title: Primary_human_corneal_epithelial_cells_rep4

source_name: Primary human corneal epithelial cells, replicate 4

value: Primary human corneal epithelial cells


title: Primary_human_corneal_epithelial_cells_rep2

source_name: Primary human corneal epithelial cells, replicate 2

value: 71 years


title: CLL patient 1 cultured with nothing

value: CLL cells and normal B cells (NBC)


title: t-BOOH-repetition2


title: t-BOOH-repetition1


title: As(III) -repetition4

source_name: Klwt-30 min exposure to 25mM sodium arsenite As(III) (reference)

source_name: Klyap8∆-30 min exposure to 25mM sodium arsenite (As(III))


title: Primary_human_corneal_epithelial_cells_rep3

source_name: Primary human corneal epithelial cells, replicate 3


title: As(III) -repetition3

value: 30 min exposure to 25mM sodium arsenite (As(III))


title: Primary_human_corneal_epithelial_cells_rep1

source_name: Primary human corneal epithelial cells, replicate 1


title: WT 3 midbrain 6 month

source_name: midbrain, wild type, 6 month

value: midbrain

value: 6 months


title: CLL patient 10 before culture

source_name: CLL cells

value: chronic lymphocytic leukemia (CLL) cells

value: basal (Pre) samples; before culture


title: WT 3 liver 3 month

source_name: liver, wild type, 3 month

value: liver


title: WT 2 liver 3 month


title: CLL patient 8 before culture


title: CLL patient 7 before culture


title: WT 1 liver 3 month


title: As(III) -repetition2

value: Klwt


title: siZC3H14 Replicate 3

city: Atlanta

first: Callie

last: Wigington

state: GA

address: 1510 Clifton Road RRC 4158

department: Biochemistry

institute: Emory University

description:
SAMPLE 9
Replicate 3
Estrogen Receptor (+) breast adenocarcinoma, derived from metastatic site by pleural effusion

hyb_protocol: Standard Illumina hybridization protocol (WG Gene Expression Direct Hybridization Assay)

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: MCF-7 cells (ATCC HTB-22)

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep-96 RNA Amplication Kit - for Array Analysis (cat # 4393637)

growth_protocol: MCF-7 cells were maintained in Dulbecco's Modified Eagle Media supplemented with 10% FBS and Pen-Strep.

extract_protocol: Cells were disrupted using Qiagen Qiashredder columns followed by RNA extraction and purification using the QIAGEN RNeasy mini kit according to manufacturer's instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were transfected with Lipofectamine2000 according to manufacturer's protocol. Briefly, 3x10^6 cells were plated into 35-mm tissue culture dishes. 24 hours after plating cells were treated with 100 pmoles of the respective siRNAs. Media was changed 24 hours after transfection and cells were harvested 48 hours after the initial transfection.

value: MCF-7 breast cancer cells

tag: genotype/variation


title: As(III) -repetition1


title: CLL patient 9 before culture


title: WT 3 midbrain 3 month

source_name: midbrain, wild type, 3 month

value: wild type


title: siZC3H14 Replicate 2

description:
SAMPLE 8
Replicate 2
Estrogen Receptor (+) breast adenocarcinoma, derived from metastatic site by pleural effusion


title: WT 2 midbrain 3 month


title: CLL patient 6 before culture


title: CLL patient 5 before culture


title: siZC3H14 Replicate 1

description:
SAMPLE 7
Replicate 1
Estrogen Receptor (+) breast adenocarcinoma, derived from metastatic site by pleural effusion


title: siPABPN1 Replicate 3

description:
SAMPLE 6
Replicate 3
Estrogen Receptor (+) breast adenocarcinoma, derived from metastatic site by pleural effusion


title: Untreated-repetition1

value: Untreated

source_name: Klwt-Untreated (reference)


title: Untreated-repetition2


title: siPABPN1 Replicate 2

description:
SAMPLE 5
Replicate 2
Estrogen Receptor (+) breast adenocarcinoma, derived from metastatic site by pleural effusion


title: WT 1 midbrain 3 month

value: 3 months


title: CLL patient 4 before culture

source_name: pooled CLL and NBC Pre samples


title: CLL patient 3 before culture


title: Untreated-repetition4


title: Untreated-repetition3


title: siPABPN1 Replicate 1

description:
SAMPLE 4
Replicate 1
Estrogen Receptor (+) breast adenocarcinoma, derived from metastatic site by pleural effusion


title: siScramble Replicate 3

description:
SAMPLE 3
Replicate 3
Estrogen Receptor (+) breast adenocarcinoma, derived from metastatic site by pleural effusion

value: siScramble


title: WT 2 cerebellum 3 month

source_name: cerebellum, wild type, 3 month

value: cerebellum


title: CLL patient 2 before culture

value: Peripheral blood B lymphocytes


title: WT 3 cerebellum 3 month


title: siScramble Replicate 1

description:
SAMPLE 1
Replicate 1
Estrogen Receptor (+) breast adenocarcinoma, derived from metastatic site by pleural effusion


title: CLL patient 1 before culture


title: WT 1 cerebellum 3 month


title: siScramble Replicate 2

description:
SAMPLE 2
Replicate 2
Estrogen Receptor (+) breast adenocarcinoma, derived from metastatic site by pleural effusion


title: Arabidopsis Treated Root 3 [exon level]

status: Public on Oct 05 2014

city: BOWLING GREEN

first: shivendra

middle: v.

last: sahi

state: KENTUCKY

address: 1906 college heights

department: Biology

institute: western kentucky university

description:
E3_051613_(AraGene-1_0-st)
Exon level.
RMA expression value derived from Expression Console software.

hyb_protocol: Samples were hybridized with GeneChip Arabidopsis Gene 1.0 ST Arrays (Affymetrix).

scan_protocol: Arrays were scanned at the UK Microarray Core Facility, Kentucky, USA. Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: Raw data were processed with the Expression Console (Affymetrix) for background correction and normalization using RMA algorithm. Secondary analysis of the data was performed by Transcriptome analysis console (Affymetrix).

source_name: Gold-treated root 12 h

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Mature seeds of the Arabidopsis thaliana cv. Col-0 were sterilized and grown hydroponically in 0.5X MS medium for 5 days followed by transfer into 1X MS medium for 7 days.

extract_protocol: RNA was isolated from 100 mg of root tissue with the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. All samples were treated with RNase-free DNase (Promega) to remove trace amounts of genomic DNA.

treatment_protocol: The 12-day-old plantlets were transferred to 10 ppm gold (HAuClO4) solution for 12 h at pH 4.2.

tag: ecotype

tag: developmental stage

value: 12-day-old seedling

value: root

value: gold (HAuClO4) exposure


title: Arabidopsis Control Root 1 [exon level]

description:
C1_051613_(AraGene-1_0-st)
Exon level.
RMA expression value derived from Expression Console software.

source_name: Control root

tag: tissue

value: control


title: Arabidopsis Treated Root 2 [exon level]

description:
E2_051613_(AraGene-1_0-st)
Exon level.
RMA expression value derived from Expression Console software.


title: LU1152_N

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using the standard recommended Illumina scanner setting.

data_processing: Signal intensities were obtained from GenomeStudio (Illumina), converted to beta-values, filtered, and normalized to remove biases between Infinium I and II probes

source_name: Normal lung tissue

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Genomic DNA from fresh frozen lung tumor/normal tissue was extracted using Allprep (Qiagen).

value: normal


title: Arabidopsis Control Root 3 [exon level]

description:
C3_051613_(AraGene-1_0-st)
Exon level.
RMA expression value derived from Expression Console software.


title: LU1114_N


title: WT 1 spinal cord 3 month

source_name: spinal cord, wild type, 3 month

value: spinal cord


title: LU1138_N


title: Arabidopsis Control Root 2 [exon level]

description:
C2_051613_(AraGene-1_0-st)
Exon level.
RMA expression value derived from Expression Console software.


title: LU1149_N


title: LU1152

source_name: Lung tumor

value: lung carcinomas


title: LU1134_N


title: LU1157


title: LU976_N


title: LU1138


title: LU1151


title: LU1090_N


title: LU1162


title: LU1098_N


title: LU1167


title: LU1096_N


title: LU1115_N


title: LU1117_N


title: LU1153


title: LU1163


title: LU1136


title: LU1134


title: LU1149


title: LU1121


title: LU1124


title: LU1136_N


title: LU1114


title: LU1117


title: LU1110


title: LU1098


title: Arabidopsis Treated Root 1 [exon level]

description:
E1_051613_(AraGene-1_0-st)
Exon level.
RMA expression value derived from Expression Console software.


title: LU1097


title: LU1118


title: LU1096


title: LU1089


title: LU1020


title: LU968


title: LU1041


title: LU987


title: LU976


title: LU887


title: LU998


title: LU1074


title: LU1094


title: LU856


title: LU990


title: LU851


title: LU876


title: LU1040


title: LU866


title: LU847


title: LU859


title: LU826


title: LU1054


title: LU820


title: LU983


title: LU804


title: LU785


title: LU1115


title: LU788


title: LU755


title: LU782


title: LU717


title: LU738


title: LU727


title: LU867


title: LU709


title: LU667


title: LU749


title: LU672


title: LU673


title: LU681


title: LU768


title: LU752


title: LU648


title: LU647


title: LU510


title: LU635


title: LU666


title: LU704


title: LU485


title: LU500


title: LU583


title: LU821


title: LU797


title: LU468


title: LU660


title: LU464


title: LU773


title: LU402


title: LU460


title: LU411


title: LU434


title: LU418


title: LU627


title: LU1090


title: LU449


title: LU473


title: LU444


title: LU370


title: LU382


title: LU436


title: LU302


title: LU330


title: LU427


title: LU372


title: LU352


title: LU318


title: LU350


title: LU376


title: LU276


title: LU332


title: LU324


title: LU271


title: LU262


title: LU375


title: LU398


title: LU257


title: LU400


title: LU277


title: LU215


title: LU164


title: LU295


title: LU190


title: Arabidopsis Treated Root 3 [gene level]

description:
E3_051613_(AraGene-1_0-st)
Gene level.
RMA expression value derived from Expression Console software.


title: Legionella ITS 014

status: Public on Oct 04 2014

city: Tianjin

first: Boyang

address: #23 HongDa Street

institute: Nankai Univ

hyb_protocol: All labeled PCR products were precipitated using 100% cold ethanol, centrifuged at 13,000 g for 10 min, washed with 75% ethanol, and dried at room temperature. The dried, labeled DNA was diluted in 16 µL of hybridization buffer (50% formamide, 6× SSC, 5× Denhardt, and 0.5% SDS) and then hybridized with the prepared microarray at 45°C for 12 h. After hybridization, the slide was washed with solution A (1× SSC and 0.1% SDS) for 3 min, solution B (0.05× SSC) for 3 min, and solution C (95% ethanol) for 1.5 min.

scan_protocol: The microarray was dried under a gentle air stream and scanned with a laser beam of 532 nm using the GenePix biochip scanner 4100A (Axon Instruments, CA, USA) set to the following parameters: photomultiplier tube gain, 600, and pixel size, 5 µm.

data_processing: The signal-to-noise ratio (SNR) was calculated for each spot using the built-in software, GenePix Pro 6.0, with the threshold set at 3.0. A signal was considered positive when 70% of the probes to a respective target gene generated hybridization signals above the SNR threshold.

organism:
Legionella longbeachae
Legionella micdadei
Legionella maceachernii

source_name: bacterial strain

label_protocol: To label the PCR products, 10 µL of the PCR products generated from the first run and the reverse primer and 0.3 µL of 25 nM Cy3-dUTP were added to the PCR mixture, and PCR was carried out using the same PCR conditions described for the first step.

growth_protocol: Legionella strains were cultured onto buffered charcoal yeast extract (BCYE) agar plates (Hope Bio-technology Co., Ltd, Qingdao, China) and incubated in a 5% CO2 incubator at 37°C for 2–4 days.

extract_protocol: Genomic DNA was extracted from pure cultures using bacterial genomic DNA purification kit (Tiangen Biotech Co., Ltd., Beijing, China).

tag: sample type

value: culture


title: LU219


title: Arabidopsis Control Root 3 [gene level]

description:
C3_051613_(AraGene-1_0-st)
Gene level.
RMA expression value derived from Expression Console software.


title: LU1097_gene_expression

hyb_protocol: Illumina hybridization protocol

scan_protocol: Standard Illumina iScan scanning protocol; scan setting file: Direct Hyb

data_processing: The data were normalised using quantile normalisation implemented in BASE, http://base.thep.lu.se/

extract_protocol: Total RNA from fresh frozen lung tumor tissue was extracted using the Qiagen AllPrep kit according to manufacturer's instructions. RNA concentrations were measured using a Nanodrop (NanoDrop Technologies). RNA integrity was determined by an Agilent Bioanalyzer.

tag: histological subtype

value: AdenoSq


title: Legionella ITS 011

organism:
Fluoribacter dumoffii
Legionella anisa


title: Legionella ITS 010

organism: Legionella maceachernii


title: Legionella ITS 008

organism: Legionella longbeachae


title: Legionella ITS 012

organism:
Legionella longbeachae
Legionella anisa


title: Legionella ITS 007

organism: Legionella jordanis


title: LU143


title: LU145


title: Arabidopsis Treated Root 2 [gene level]

description:
E2_051613_(AraGene-1_0-st)
Gene level.
RMA expression value derived from Expression Console software.


title: Arabidopsis Treated Root 1 [gene level]

description:
E1_051613_(AraGene-1_0-st)
Gene level.
RMA expression value derived from Expression Console software.


title: Arabidopsis Control Root 2 [gene level]

description:
C2_051613_(AraGene-1_0-st)
Gene level.
RMA expression value derived from Expression Console software.


title: LU85


title: LU137


title: LU70


title: Legionella ITS 004

organism: Fluoribacter dumoffii


title: Legionella ITS 001

organism: Legionella pneumophila


title: Legionella ITS 002

organism: Legionella anisa


title: Legionella ITS 003

organism: Legionella bozemanae


title: Legionella ITS 013

organism:
Legionella jordanis
Fluoribacter gormanii
Legionella fairfieldensis


title: Legionella ITS 009

organism: Legionella micdadei


title: Legionella ITS 005

organism: Legionella fairfieldensis


title: LU79

organism: Homo sapiens


title: LU66


title: LU123


title: LU16


title: LU14


title: LU2


title: SCLC_tissue_cluster 2 [GTB.32330]

city: Koto

first: YUICHI

last: SAITO

state: Tokyo

address: 3-8-31 Ariake

department: Pathology

country: Japan

institute: The Cancer Institute of Japanese Foundation Cancer Research

hyb_protocol: Hybridization and Microarray Wash according to the manufacturer’s instructions.

scan_protocol: Agilent SureScan microarray scanner was used for microarray scanning according to the manufacturer’s instructions.

data_processing: Agilent Feature Extraction software was used to output the Feature Extraction QC report. RNA Integrity Number (RIN) index was calculated for each sample using Agilent 2100 Expert software. In order to reduce experimental biases in microarray analysis due to poor RNA quality, only RNA samples with RIN number > 4 were further processed.

source_name: Ganken Tissue Bank

label_protocol: Fluorescent Labeling of samples according to the manufacturer’s instructions.

extract_protocol: RNAeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: All specimens were grossly dissected and snap-frozen in liquid nitrogen typically within 15 min of removal, and were kept frozen at -80℃ until use

value: frozen tissue

tag: cimp

value: cluster 2

tag: gender

value: male


title: SCLC_tissue_cluster 1 [GTB.31173]

description: RNAeasy Mini Kit (Qiagen, Hilden, Germany)

value: cluster 1


title: stalk_cult_Wnt1_rep1

city: Stanford

first: Maya

middle: Elise

last: Kumar

address: 279 Campus Drive, room B469

institute: Stanford University School of Medicine

hyb_protocol: hybridized to  a Mouse Genome 430 2.0 Array (Affymetrix) following manufacturer's protocols

scan_protocol: standard scanning protocols from Stanford PAN facility

data_processing: Expression Console, MAS 5.0

source_name: stalk mes, culture, Wnt1 medium

label_protocol: cDNA was synthesized using a two cycle cDNA synthesis kit (Affymetrix)

growth_protocol: Tissue exctracted from staged embryonic lungs dissected from timed pregnant female mice.

extract_protocol: total RNA was prepared by incubating the tissue in lysis buffer (0.5% SDS, 5 mM EDTA, 50 mM Tris, pH 7.5, 50 mM NaCl) containing 250 μg/ml proteinase K (Roche) at 42°C for 25 min.The lysate was extracted twice with phenol, precipitated in the presence of 10 μg glycogen, treated with RQ1 DNase (Promega), and precipitated again.

treatment_protocol: no culture' samples were extracted directly after dissection.  'Culture' samples were cultured for 12 hours on TC plastic in either in control growth medium ('control') or growth medium plus 400 ng/ml WNT1 ('Wnt1')

value: lung mesenchyme


title: stalk_cult_Wnt1_rep2


title: LU136


title: SCLC_tissue_cluster 2 [GTB.23034]


title: stalk_cult_control_rep1

source_name: stalk mes, culture, control medium


title: SCLC_tissue_cluster 1 [GTB.19596]


title: LU87


title: SCLC_tissue_cluster 2 [GTB.17989]


title: stalk_nocult_rep1

source_name: mesenchyme, lung branch stalk e11.5-12.5 mouse

value: lung mesenchyme, lung branch stalk


title: tip_nocult_rep1

source_name: mesenchyme, lung branch tip, e11.5-12.5 mouse

value: lung mesenchyme, lung branch tip


title: MeCP2KO, VPA, biological rep3

city: Shinagawa-ku

first: KATSUHIDE

last: IGARASHI

department: Life Science Tokyo Advanced Research center (L-StaR)

institute: Hoshi University School of Pharmacy and Pharmaceutical Science

hyb_protocol: For hybridization to the GeneChip Mouse Expression Array 430A or 430B or Mouse Genome 430 2.0 Array (Affymetrix), 15 µg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 1x eukaryotic hybridization control, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, and 1x hybridization buffer in a 45°C rotisserie oven for 16 h. Washing and staining were performed by using a GeneChip Fluidic Station (Affymetrix) according to the manufacturer's protocol(Fluidics Protocol: EuKGE-WS2v4).

scan_protocol: Phycoerythrin-stained arrays were scanned as digital image files with GeneChip Scanner 3000 7G with AutoLoader.

data_processing: Data transformation algorithm and normalization was done by Affymetrix GCOS. Scaling:All Probe Sets, Target Signal=500; Normalization value: 1; Parameters: defalut settings; MAS5 processing

source_name: MeCP2KO mouse VPA administered half brain

label_protocol: Total RNA was purified by using an RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. First-strand cDNA was synthesized from 5 µg of RNA by using 200 units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), 100 pmol T7-(dT)24 primer [5'-GGCCAGTGA AT TGTA ATACGACTCACTATAGGGAGGCGG-(dT)24-3'], 1x first-strand buffer, and 0.5 mM dNTPs at 42°C for 1 h. Second-strand synthesis was performed by incubating first-strand cDNA with 10 units of Escherichia coli ligase (Invitrogen), 40 units of DNA polymerase I (Invitrogen), 2 units of RNase H (Invitrogen), 1x reaction buffer, and 0.2 mM dNTPs at 16°C for 2 h, followed by 10 units of T4 DNA polymerase (Invitrogen) and incubation for another 5 min at 16°C. Double-stranded cDNA was purified by using GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions and labeled by in vitro transcription by using a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY). Briefly, dsDNA was mixed with 1x HY reaction buffer, 1x biotin-labeled ribonucleotides (NTPs with Bio-UTP and BioCTP), 1x DTT, 1x RNase inhibitor mix, and 1x T7 RNA polymerase and incubated at 37°C for 4 h. Labeled cRNA was then purified by using GeneChip Sample Cleanup Module and fragmented in 1x fragmentation buffer at 94°C for 35 min.

growth_protocol: When mice reached 6 weeks old, they received daily injections of VPA (300 mg/kg) for 2 weeks. After that, half brain was collected and used for gene expression analysis.

extract_protocol: Half brain samples were prepared from the mice of WT, KOS and KOV groups. Samples were homogenized and lysed in 500 ul of RLT buffer (QIAGEN, Valencia, CA) and total RNA extracted according to the manufacturer’s instructions using the RNeasy  Kit (QIAGEN) for GeneChip analysis.

treatment_protocol: Three groups were designated as wild type mouse (WT), MeCP2KO mouse with saline treatment (KOS) and MeCP2KO mouse with VPA treatment (KOV). At 6weeks old, KOV group received intraperitoneal (i.p.) injection of 300 mg/kg VPA dayly for two weeks.

tag: strain/genotype

value: half brain


title: SCLC_tissue_cluster 2 [GTB.12822]


title: stalk_nocult_rep2


title: SCLC_tissue_cluster 2 [GTB.12005]


title: SCLC_tissue_cluster 1 [GTB.8289]


title: SCLC_tissue_cluster 2 [GTB.10482]

value: female


title: MeCP2KO, VPA, biological rep2


title: SCLC_tissue_cluster 1 [GTB.25232]


title: MeCP2KO, VPA, biological rep1


title: SCLC_tissue_cluster 2 [GTB.32120]


title: MeCP2KO, Saline, biological rep3

source_name: MeCP2KO mouse saline administered half brain


title: SCLC_tissue_cluster 2 [GTB.7853]


title: SCLC_tissue_cluster 2 [GTB.5395]


title: SCLC_tissue_cluster 1 [GTB.6013]


title: MeCP2KO, Saline, biological rep2


title: stalk_cult_conrol_rep2


title: WT, biological rep2

source_name: Wild type mouse half brain

value: wild type


title: SCLC_tissue_cluster 2 [GTB.4271]


title: WT, biological rep3


title: SCLC_tissue_cluster 2 [GTB.2760]


title: Arabidopsis Control Root 1 [gene level]

description:
C1_051613_(AraGene-1_0-st)
Gene level.
RMA expression value derived from Expression Console software.

organism: Arabidopsis thaliana

value: 12-day-old seedling

value: root


title: MeCP2KO, Saline, biological rep1

organism: Mus musculus


title: SCLC_tissue_cluster 2 [GTB.3105]


title: SCLC_tissue_cluster 1 [GTB.2942]


title: 28d

city: Matsumoto City

first: Fuminori

last: Kawano

state: Nagano

address: Niimura 2095-1

department: Graduate School of Health Sciences

institute: Matsumoto University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE 8×60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: Soleus muscle 28 days after denervation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was exracted from tissue segment of skeletal muscle using Isogen (NIPPON GENE) followed by isopropanol precipitation.

tag: strain background

value: Wistar Honnover

value: Muscle


title: SCLC_tissue_cluster 1 [GTB.3170]

tag: age


title: SCLC_tissue_cluster 2 [GTB.2425]


title: Post

source_name: Normal soleus muscle


title: Constipated rats -AEtLP

city: Miryang

first: Dae Youn

last: Hwang

address: 50 Cheonghak-ri, Samnangjin-eup

country: South Korea

institute: Pusan National University

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: SD rat

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: All animals were handled at the Pusan National University Laboratory Animal Resources Center accredited by AAALAC International (Accredited Unit Number; 001525) according to the National Institutes of Health guidelines.

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

treatment_protocol: Constipation was induced in SD rats by subcutaneous injection of loperamide (4 mg/kg weight) in 0.9% sodium chloride twice (9 AM and 6 PM) a day for 3 days, whereas the non-constipation group was injected with 0.9% sodium chloride alone as described in previous study. At 15 hr after the final treatment of loperamide, the constipation group was further divided into a vehicle-treated constipation group and AEtLP-treated constipation group. They were received a consistent volume of water or 15 uL/g body weight of AEtLP (1,000 mg/kg weight) via oral administration for once at 9 AM. At 24h after the treatment of AEtLP and vehicle, all animals were immediately euthanatized using CO2 gas and tissue samples were acquired and stored in Eppendorf tubes at -70℃ until assaued.

value: Distal colon

value: 8 weeks

value: SD

value: AEtLP-treated constipation


title: Constipated rats -No treatment


title: SCLC_tissue_cluster 1 [GTB.2213]

value: frozen tissue


title: Legionella ITS 006

last: Cao

organism: Fluoribacter gormanii

value: culture


title: Constipated rats -Vehicle

value: male

value: vehicle-treated constipation


title: WT, biological rep1


title: tip_nocult_rep2


title: SCLC_tissue_cluster 2 [GTB.2241]

value: cluster 2


title: SCLC_tissue_cluster 1 [GTB.545]

value: cluster 1


title: Double mutant under -P condition repeat1

status: Public on Oct 03 2014

city: Hangzhou

first: Chuanzao

last: Mao

address: 866 Yu Hang Tang Road

institute: Zhejiang University

description: Gene expression data from double mutant under -P condition

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix Genechip Scanner 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 100.

organism: Oryza sativa

source_name: Double mutant under -P condition

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (GeneChip® 3’ IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: Hydroponic experiments were conducted using rice culture solution with NaH2PO4 (0, or 200 Î¼M Pi). Nutrient solution was adjusted to pH 5.5 using 1 M NaOH and replaced every 2 days. Experiments were carried out in a greenhouse with a 12 h day (30º)/12 h night (22º) photoperiod, 200 Î¼mol m-2 s-1 photon density, and 60% humidity.

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

treatment_protocol: Fourteen days plants growth under hydroponic +P condition (200 µM) were treated with +P(200µM) or –P (no phosphate) for another 7 days, shoot of plants from 3 biological repeats were sampled for Affymetrix microarray analysis.

value: Leaf

value: double mutant under -P condition


title: Double mutant under +P condition repeat3

description: Gene expression data from double mutant under +P condition

source_name: Double mutant under +P condition

value: double mutant under +P condition


title: SCLC_tissue_cluster 2 [GTB.2229]


title: PL

source_name: Normal plantaris


title: Double mutant under -P condition repeat2


title: Double mutant under +P condition repeat2


title: Double mutant under -P condition repeat3


title: Wildtype Nipponbare under -P condition repeat2

description: Gene expression data from wildtype Nipponbare under -P condition

source_name: Wildtype Nipponbare under -P condition

value: wildtype Nipponbare under -P condition


title: Wildtype Nipponbare under +P condition repeat1

description: Gene expression data from wildtype Nipponbare under +P condition

source_name: Wildtype Nipponbare under +P condition

value: wildtype Nipponbare under +P condition


title: Wildtype Nipponbare under -P condition repeat1


title: SCLC_tissue_cluster 2 [GTB.409]


title: Wildtype Nipponbare under +P condition repeat2


title: 34c, biological rep3

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: 34c, Dicer/Pten Double knockout (DKO) mouse tumor cell line

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: RNA quality was determined on a 2100 Bioanalyzer. Gene expression profiles were generated on Mouse WG-6 version 2.0 Beadchips (Illumina) at University of Texas Health Science Center Microarray Core Laboratory. The array platform consists of 45,281 transcript probes representing 30,854 unique genes. Data was normalized in Bioconductor.

label_protocol: According to Illumina protocol.

growth_protocol: We used a mouse genetics strategy to conditionally delete both Dicer and the Pten tumor suppressor in the female reproductive tract using anti-Müllerian hormone receptor type 2 (Amhr2-Cre). These Dicer-Pten DKO (Dicer flox/flox Pten flox/flox Amhr2 cre/+) mice universally develop high-grade serous epithelial cancers. Tumor cell lines were established from mouse primary tumors and miR-34c was expressed in these cell lines.

extract_protocol: Total RNA was extracted from DKO tumor cell lines transfected with miR-34c (n=3) and control miRNA (n=3) using the RNeasy mini RNA isolation kit (Qiagen).

value: DKO tumor

tag: transfection


title: 34c, biological rep2

source_name: Dicer/Pten Double knockout (DKO) mouse tumor cell line

tag: cell line


title: Control, biological rep2

description: Control, Dicer/Pten Double knockout (DKO) mouse tumor cell line

value: control


title: Double mutant under +P condition repeat1


title: 34c, biological rep1


title: Control, biological rep1


title: Control, biological rep3


title: Rbp53 normal mammary tissue MCRP1510

city: Guelph

first: Robert

last: Jones

address: 50 Stone Rd

department: Biomedical Sciences

institute: University of Guelph

description: gene expression data from normal mammary tissue derived from Rbp53 mice

hyb_protocol: standard Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

data_processing: Microarray Data were normalized using RMA method via Partek Genomics Suite (v.5.6) and absolute expression values were obtained

source_name: normal mammary tissue

growth_protocol: Samples from independent primary mammary tumors from MMTV-Cre:Rbp53,MMTV-Cre:p53, Ad-Cre:Rbp53 models and normal mammary tissue were frozen and kept in -80 degree.

extract_protocol: Total RNA was extracted with Trizol reagent twice. Quality control was performed with Agilent Bioanalyser

treatment_protocol: Total RNA obtained from primary tumors and normal mammary tissue were used for microarray analysis to determine differentially regulated genes. Cluster analysis and pathway analysis based on gene expression were then performed to determine significant genes/pathways

value: mixed

tag: tumor model

value: normal mammary tissue


title: Rbp53 normal mammary tissue MCRP-1508

scan_protocol: standard Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)


title: MMTV-Cre:p53 primary tumor C53-25

description: gene expression data from p53 deleted mammary tumor

source_name: Primary mammary tumor p53 deleted

label_protocol: standard Affymetrix Mouse Gene 1.0 st microarray experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

value: MMTV-Cre

value: Primary mammary tumor p53 deleted


title: Rbp53 normal mammary tissue MCRP-1512


title: Ad-Cre:Rbp53 primary tumor ACRP-1

description: gene expression data from Rbp53 deleted mammary tumor

source_name: Primary mammary tumor Rbp53 deleted

value: Ad-CMVcre (Transplant)

value: Primary mammary tumor Rbp53 deleted


title: MMTV-Cre:Rbp53 primnary tumor MCRP-1280


title: Ad-Cre:Rbp53 primary tumor ACRP-2


title: Wildtype Nipponbare under +P condition repeat3


title: MMTV-Cre:p53 primary tumor TP53-1


title: Rbp53 normal mammary tissue MCRP-1511


title: MMTV-Cre:Rbp53 primary tumor TMCRP-1

value: MMTV-Cre (Transplant)


title: MMTV-Cre:Rbp53 primary tumor TMCRP-1123


title: MMTV-Cre:p53 primary tumor C53-18


title: MMTV-Cre:Rbp53 primary tumor TMCRP-3


title: Rbp53 normal mammary tissue MCRP-1509


title: MMTV-Cre:Rbp53 TMCPR-1014


title: MMTV-Cre:Rbp53 primary tumor MCRP-1175

value: MMTV-Cre (nulliparous)


title: Metabolically adaptable MA1 cells

first: Anthony

last: Lucci

state: Texas

address: 1515 Holcombe Blvd

department: Surgical Oncology

institute: UT MD Anderson Cancer Center

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit. Briefly, 600 ng of cyanine 3-labeled fragmented complementary RNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo 8×60K Microarrays.

scan_protocol: The fluorescence signals of the hybridized microarrays were detected using the Agilent Microarray Scanner System.

data_processing: Agilent G2567AA Feature Extraction Software version 10.7.3.1 was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers, and calculates statistical confidences. To determine differential gene expression, Feature Extraction Software-derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

source_name: cell line

label_protocol: To produce cyanine 3-labeled complementary RNA, the 100-ng RNA samples were amplified by linear T7 polymerase-based amplification and labeled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer’s protocol.

growth_protocol: We cultured both MA1 and MA2 variants and the parental cell line in a medium containing Gln and dialyzed FBS; we used dialyzed FBS since it was used for selecting the MA variants in Gln-free medium.

extract_protocol: RNA was isolated using standard RNA extraction protocols (NucleoSpin RNA II, Macherey-Nagel, Bethlehem, PA) and quality checked with the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: No treatment. MA1 and MA2 are rare cells are derived from rare cells (less than 0.01% in pupulation) that were able to survive and grow without added glutamine in the culture medium.

value: breast cancer

value: female

value: MA1 variant

value: derived from SUM149-Luc


title: MMTV-Cre:Rbp53 primary tumor MCRP-1241

value: MMTV-Cre (Parous)


title: Metabolically adaptable MA2 cells

value: MA2 variant


title: Parental SUM149-Luc cell line

description: Control

value: Parental


title: CAL1_CRTL_2

city: Bologna

first: Fabio

last: Fuligni

address: Via Massarenti 9

department: Department of Experimental, Diagnostic, and Specialty Medicine Bologna University Medical School

institute: University of Bologna

description: CAL1 Cell line Control

hyb_protocol: Standard 29K Whole-Genome DASL HT Assay hybridization protocol (WGDASL HT Assay Guide (15018210 D)

scan_protocol: Standard 29K Whole-Genome DASL HT Assay scan protocol (WGDASL HT Assay Guide (15018210 D)

data_processing: Gene expression analysis was carried according to MIAME guidelines.

source_name: CAL1 Cell line

label_protocol: Standard 29K Whole-Genome DASL HT Assay label protocol (WGDASL HT Assay Guide (15018210 D)

extract_protocol: total RNA from cryopreserved and FFPE samples was extracted using TRIzol reagent (Invitrogen) and the RecoverAll Total Nucleic Acid Isolation Kit (Ambion, Austin, TX), respectively, following the manufacturer's protocols

treatment_protocol: Treatment with imatinib mesylate (0 and 1 microM) for 6 hours

tag: phenotype


title: C3

description: plasmacytoid dendritic cell (pDC) samples isolated from the peripheral blood of healthy donors

source_name: pDC Cell Line

tag: cell type

value: plasmacytoid dendritic cell (pDC)

value: healthy donor


title: C4


title: CAL1_6H_3

description: CAL-1 cells incubated for 6 hours with IC50 30 nM concentration of Bortezomib


title: CAL1_CRTL_1

description: CAL1 Cell line Control


title: MMTV-Cre:Rbp53 primary tumor TMCRP-985

value: mixed


title: vng1179Ccmyc_1_1

city: Seattle

first: Christopher

middle: L

last: Plaisier

state: Washington

address: 401 Terry Avenue North

institute: Institute for Systems Biology

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
VNG1179C cMyc-tagged and sampled at early growth, biological replicate 1.

hyb_protocol: According to Agilent protocol.

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software.

data_processing:
Agilent Feature Extraction for spotfinding/quantitation.
Normalized log10 intensity of X_INT/Y_INT (IP/WCE) averaged over dye flip between IP and WCE DNA. Second raw data file contains Agilent Feature Extraction file for the dye flip experiment.

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium sp. NRC-1 VNG1179C cMyc-tagged strain IP fraction

label_protocol: See Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35.

growth_protocol: Halobacterium salinarum NRC-1 strains were batch cultured in complete defined media (CDM) with 19 amino acids in flasks at 37°C with constant shaking (125 rpm).

extract_protocol: Chromatin immunoprecipitation (IP) was conducted as described in Facciotti, MT, Reiss, DJ, Pan, M, Kaur, A, Vuthoori, M, Bonneau, R, Shannon, P, Srivastava, A, Donohoe, SM, Hood, LE and Baliga, NS. General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A. 2007;104: 4630-4635. Optimizations of the ChIP protocol are described in Schmid AK, Pan M, Sharma K, Baliga NS.2011. Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon. Nucleic Acids Res.39(7):2519-33. Primary antibody is the Covance 9E10 monoclonal antibody (anti-c-myc) from mouse, cat #MMS-150P, and secondary antibody is ECL mouse IgG HRP-linked whole antibody from sheep, Amersham cat #NA931.

treatment_protocol: Over-expression of c-Myc-tagged FFRPs allowed enrichment of genomic regions bound by each FFRP in either early or late growth in CDM.

tag: strain

tag: condition

value: early

tag: replicate

value: over-expression

tag: chip antibody

value: anti-c-myc (9E10) monoclonal antibody

label: Cy5, Cy3

source_name: Halobacterium sp. NRC-1 VNG1179C cMyc-tagged strain whole cell extract (WCE) fraction


title: vng1237Ccmyc_2_2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
VNG1237C cMyc-tagged and sampled at late growth, biological replicate 2.

source_name: Halobacterium sp. NRC-1 VNG1237C cMyc-tagged strain IP fraction

value: late

source_name: Halobacterium sp. NRC-1 VNG1237C cMyc-tagged strain whole cell extract (WCE) fraction


title: CAL1_6H_2


title: vng1237Ccmyc_1_2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
VNG1237C cMyc-tagged and sampled at late growth, biological replicate 1.


title: CAL1_6H_1


title: vng1179Ccmyc_1_2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
VNG1179C cMyc-tagged and sampled at late growth, biological replicate 1.


title: vng1237Ccmyc_1_1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
VNG1237C cMyc-tagged and sampled at early growth, biological replicate 1.


title: vng1179Ccmyc_2_1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
VNG1179C cMyc-tagged and sampled at early growth, biological replicate 2.


title: C2


title: C1


title: vng1237Ccmyc_2_1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
VNG1237C cMyc-tagged and sampled at early growth, biological replicate 2.


title: vng1179Ccmyc_2_2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
VNG1179C cMyc-tagged and sampled at late growth, biological replicate 2.


title: trh7cmyc_1_1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh7 cMyc-tagged and sampled at early growth, biological replicate 1.

source_name: Halobacterium sp. NRC-1 Trh7 cMyc-tagged strain IP fraction

source_name: Halobacterium sp. NRC-1 Trh7 cMyc-tagged strain whole cell extract (WCE) fraction


title: trh7cmyc_2_2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh7 cMyc-tagged and sampled at late growth, biological replicate 2.


title: trh7cmyc_1_2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh7 cMyc-tagged and sampled at late growth, biological replicate 1.


title: trh6cmyc_2_2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh6 cMyc-tagged and sampled at late growth, biological replicate 2.

source_name: Halobacterium sp. NRC-1 Trh6 cMyc-tagged strain IP fraction

source_name: Halobacterium sp. NRC-1 Trh6 cMyc-tagged strain whole cell extract (WCE) fraction


title: trh6cmyc_2_1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh6 cMyc-tagged and sampled at early growth, biological replicate 2.


title: trh6cmyc_1_2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh6 cMyc-tagged and sampled at late growth, biological replicate 1.


title: trh7cmyc_2_1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh7 cMyc-tagged and sampled at early growth, biological replicate 2.


title: BPDCN_34

source_name: BPDCN Patient

tag: tumor type

value: BPDCN

value: BPDCN Patient


title: BPDCN_8


title: trh4cmyc_2_2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh4 cMyc-tagged and sampled at late growth, biological replicate 1.

source_name: Halobacterium sp. NRC-1 Trh4 cMyc-tagged strain IP fraction

source_name: Halobacterium sp. NRC-1 Trh4 cMyc-tagged strain whole cell extract (WCE) fraction


title: BPDCN_33


title: trh4cmyc_2_1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh4 cMyc-tagged and sampled at early growth, biological replicate 2.


title: BPDCN_32


title: Metabolically adaptable variant MA2 compared to parental

description: Parental cell line control

hyb_protocol: Hybridization was performed according to the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol version 7.1 using the SureTag DNA Labeling Kit. The corresponding cyanine 3- and cyanine 5-labeled DNAs were combined and hybridized at 65 °C for 40 hours to an Agilent Human Genome CGH 1M Microarray.

scan_protocol: The fluorescence signals of the hybridized Agilent Human Genome CGH microarrays were detected using the Agilent DNA microarray scanner.

data_processing: Agilent Feature Extraction Software was used to read out and process the microarray image files. Further analysis and visualization of the hybridization results were performed with the Agilent Genomic Workbench Lite 6.5. We used the following stringent filter settings for aberrations: (i) minimum number of probes present in an aberrant region = 5, (ii) minimum absolute average log2 ratio for region = 0.4 (corresponds to a fold change of 1.32), and (iii) threshold = 5. The statistical analysis of aberrant regions was based on the aberration detection method ADM-2. The ADM-2 algorithm identifies all aberrant intervals in a genome with consistently high or low log ratios based on the statistical score.

source_name: MA2 variants selected from SUM149-Luc cell line

label_protocol: The digested DNA was used as template for a genomic DNA labeling reaction using the SureTag DNA Labeling Kit (Agilent Technologies) according to the manufacturer’s protocol. The yields of labeled DNA and the dye incorporation rate after Klenow labeling were determined with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: For CGH array analysis, cells were cultured in parallel with those used for the gene expression microarray. We cultured both MA1 and MA2 variants and the parental cell line in a medium containing Gln and dialyzed FBS; we used dialyzed FBS since it was used for selecting the MA variants in Gln-free medium.

extract_protocol: Genomic DNA was purified using the Gentra Puregene Cell kit (Qiagen). The integrity of the genomic DNA samples was assessed by agarose gel electrophoresis. A 2.5-μg quantity of each DNA sample was digested with the restriction enzymes AluI and RsaI.

value: originally cultured from 35 yrs old patient

tag: tissue

value: Breast cancer cell line

value: triple-negative inflammatory breast cancer cell line

source_name: control parental cell line SUM149-Luc

value: breast cancer cell line


title: trh4cmyc_1_1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh4 cMyc-tagged and sampled at early growth, biological replicate 1.


title: Metabolically adaptable variant MA1 compared to parental

description: Parental cell line control

source_name: MA1 variants selected from SUM149-Luc cell line


title: BPDCN_5


title: trh6cmyc_1_1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh6 cMyc-tagged and sampled at early growth, biological replicate 1.


title: Wildtype Nipponbare under -P condition repeat3

description: Gene expression data from wildtype Nipponbare under -P condition

source_name: Wildtype Nipponbare under -P condition

value: Leaf

tag: genotype/variation

value: wildtype Nipponbare under -P condition


title: trh3cmyc_2_2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh3 cMyc-tagged and sampled at late growth, biological replicate 2.

source_name: Halobacterium sp. NRC-1 Trh3 cMyc-tagged strain IP fraction

source_name: Halobacterium sp. NRC-1 Trh3 cMyc-tagged strain whole cell extract (WCE) fraction


title: trh3cmyc_2_1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh3 cMyc-tagged and sampled at early growth, biological replicate 2.