title: sip8_EBSS_3h

city: Quebec

first: Ezequiel

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

hyb_protocol: Biotinilated cRNA was hybridized to the arrays as described by the manufacturer (Affymetrix, Santa Clara, CA). The cRNA hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven. After 16 h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix-recommended protocol(http://media.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf.

scan_protocol: The arrays were scanned using the Affymetrix GCS 3000 7G and the Gene-Chip Operating Software (Affymetrix, Santa Clara, CA), to produce the intensity files.

data_processing:
The background subtraction and normalization of probe set intensities was performed using the method of Robust Multiarray Analysis (RMA(, using the Limma microarray package AffylmGUI (Bioconductor)
Values in the matrix table are in log2.

source_name: Cells transfected with  siNupr1  and cultured for 3  hrs in EBSS.

label_protocol: Total RNA (200 ng per sample) was labeled using the Affymetrix GeneChip® WT cDNA Synthesis and Amplification Kit protocol

growth_protocol: Cell culture and in vitro stress induction: MiaPaCa2 cells obtained from the American Type Culture Collection were maintained in DMEM medium (Invitrogen) supplemented with 10% FBS at 37°C with 5% CO2. Cells were at about 70% confluence for all experiments. To avoid additional stress, all media were warmed to 37°C, cells were washed twice with warm Phosphate Saline Buffer (PBS) before adding Earle’s Balanced Salt Solution (EBSS, Invitrogen), which is completely devoid of glucose, amino acids and growth factors.

extract_protocol: Total RNA was isolated by the Trizol (Gibco-BRL) procedure.

treatment_protocol: siRNA transfection: MiaPaCa2 and Panc1 cells were plated at 70% confluence in 100 mm dishes. INTERFErin™ reagent (POLYPLUS transfection) was used to perform siRNA transfections according to the manufacturer’s protocol. Nupr1, RelA/p65, RelB and IER3 were knocked-down using 140 ng of specific siRNAs. Scrambled siRNA targeting no known gene sequence was used as negative control. The sequences of Nupr1-specific siRNA (siNupr1 r(GGAGGACCCAGGACAGGAU)dTdT and siNupr1#2 r(AGGUCGCACCAAGAGAGAA)dTdT were previously reported (51) and RelA/p65- r(GAUCAAUGGCUACACAGG)dTdT, RelB- (siRelB r(GGAUUUGCCGAAUUAACAA)dTdT and siRelB#2 r(CUGCGGAUUUGCCGAAUUAUU)dTdT and IER3 (siIER3 r(GGAAGGAGAGCGUCGUUAA)dTdT and siIER3#2 r(AAGGCUUCUCUUUCUGCUG)dTdT-specific siRNAs were from Qiagen.


title: L102_555

status: Public on Feb 01 2012

type: RNA

city: Ithaca

first: Jesse

middle: D.

last: Munkvold

state: NY

address: 240 Emerson

department: Plant Breeding and Genetics

country: USA

institute: Cornell University

description: Array Batch: 20050

hyb_protocol: Perhybridization and hybridization was done using the Pronto! Hybridization Kit (Corning) with accompanying protocols. Labeled A555 and A647 samples were combined in balanced dye ratios and hybridization was done in Corning Microarray Hybridization chammber II with Erie Scientific Raised Coverslips (25x60mm). Hybridization was carried out for 18hrs. in a 42C water bath.

scan_protocol: Scanning was done using an Axon 6000B scanner with automatic PMT gain, 100% laser power, and 10um resolution.

data_processing: Array, block, and spot detection was done automatically and inspected by hand. Bad spots were automatically and hand-flagged.Background was calculated by morphological opening followed by closing using the GenePix 6 software.

label: Alexa 555

molecule: total RNA

organism: Triticum aestivum

source_name: CxC Line 102, embryo at physiological maturity

label_protocol: 10ug of total RNA were reverse transcribed using anchored poly-T primers and a 2:3 amino-allyl dUTP:dTTP ratio. RNA was hydrolyzed with NaOH and the amino-allyl cDNA was cleaned with a Qiagen Qiaquick column and phosphate buffers. Alexa 555 or 647 (Invitrogen #A32755) dyes were coupled according to accompanying protocols. Labeled cDNA  was cleaned using a Qiaquick column and incorporation was measured by spectrophotometry.

growth_protocol: Plants were grown in the  field (Helfer 2004) near Ithaca, NY. Spike samples were harvested at physiological maturity as described in Munkvold et al. 2009. TAG. 119. Samples were stored at -20C for two months while embryo samples were harvested. Primary and secondary position seeds were selected from five spikes and embryos (~100) were isolated by hand, frozen in liquid nitrogen, and stored at -80C.

extract_protocol: Total RNA extraction from isolated embryos was done using the Trizol reagent with only slight modifications to the manufacturer protocol. Total RNA was treated with RQ1 DNAse and cleaned using Qiagen Rneasy columns.

tag: population

value: Cayuga x Caledonia, DH

tag: field location

value: Helfer, Cornell University, Ithaca, NY

tag: year

tag: tissue

value: embryo at physiological maturity

label: Alexa 647

source_name: Pre-anthesis spike bulk

value: Pre-anthesis spike bulk


title: sip9_EBSS_9h

middle: L

label: Biotin

organism: Homo sapiens

source_name: Cells transfected with  siNupr1  and cultured for  9  hrs in EBSS.

tag: cell line


title: L105_555

description: Array Batch: 20050

source_name: CxC Line 105, embryo at physiological maturity


title: Melanocyte cell line SK_MEL-28-250K_Nsp

type: genomic

city: Rochester

first: xiaoyang

last: ruan

state: MN

address: 200 1st Street

department: Health Science Research

institute: Mayo Clinic

description:
Hybridized to 250K_Nsp
SK_MEL_28-250knsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G with AutoLoader.

data_processing: Genotype call was made by Affymetrix Power Tool (Linux, version 1.12.0) BRLMM algorithm. ROH was inferred by dChip (Version 2010/01) basic-HMM module, and PLINK (Version 1.07) ROH module. dChip ROH Call: L, R, and N; PLINK ROH Call: 0, 1 [dChip.txt, PLINK_coverted.txt, and PLINK_rawData.txt are provided as Series supplementary files.]

molecule: genomic DNA

source_name: Melanocyte cell line

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cells grown in RPMI 1640 with 5% FBS (Bio Whittaker, not heat inactivated) and 1% L-glutamine. Cells not grown past 80% confluencey for attached cells, or 0.5 x 10^6 cells for suspended. Trypsinize (for attached cells) cells with 5 ml trypsin-EDTA per T162, for 15 min., at 37C. Spin down suspended cells, and resuspend in ~3ml growth media. Count cells. Pass 1x10^6 cells into new T162's w 30 ml media.  Repeat growth cycle until desired amount of cells are available. Cells are not grown past passage 20.

extract_protocol: Genomic DNA was purified from cells using either the QIAamp DNA Blood Maxi Kit, or the Blood & Cell Culture DNA Maxi Kit (Qiagen Inc., Valencia, CA) according to manufacturer's instructions.  Quality was assessed by optical density 260/280 ratio using a spectrophotometer (Beckman-Coulter, Fullerton, CA) and by 0.8% agarose (SeaKem GTG, FMC BioProducts, Rockland, ME) gel electrophoresis in 1x TAE (Roche, Indianapolis, IN).

tag: tissue type

value: Melanocyte


title: Melanocyte cell line MDA-N-250K_Nsp

description:
Hybridized to 250K_Nsp
MDA_N-250knsp

source_name: Pleural effusion_Melanocyte cell line

value: MDA-N


title: Melanocyte cell line UACC-62-250K_Nsp

description:
Hybridized to 250K_Nsp
UACC_62-250knsp


title: Ctrl_EBSS_9h

source_name: Cells transfected with  siCtrl  and cultured for  9  hrs in EBSS.


title: Ctrl_EBSS_6h

source_name: Cells transfected with  siCtrl  and cultured for  6  hrs in EBSS.


title: sip8_DMEM_0h

source_name: Cells transfected with  siNupr1 and cultured for 0  hrs in EBSS.


title: CA EC1-3

city: Antwerpen

first: Nathalie

last: Dom

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

hyb_protocol: Prior to hybridization, arrays were incubated for 30-45 min at 42°C in a prehybridization solution (50% formamide, 5x saline sodium citrate (SSC), 0.1% sodium dodecyl sulphate (SDS), 0.1mg/mL BSA). The vacuum dried targets (both reference and treatment target) were resuspended in a hybridization solution (50% formamide, 5x SSC, 0.1% SDS, 0.1mg/mL BSA and 0.1mg/mL sheared salmon sperm) and denaturated at 95°C. The cooled targets were subsequently applied onto the prehybridized slides and incubated overnight at 42°C. After hybridization, arrays were washed in solutions with increasing stringency (decreasing concentrations of SSC and SDS) and dried with N2. The hybridization design was a universal reference design (a mixture of aliquots from control and exposed samples), which is recommended when class discovery is the main purpose of the experiment. One of the three biological replicates of each exposure condition was labelled with one dye, the remaining two samples were labelled with the second dye.

scan_protocol: Scanning and analysing of the slides was performed using the Genepix personal 4100 Scanner and Genepix pro Software (both Axon instruments, USA). Cy3 and Cy5 fluorescent signals were scanned at respectively 532 and 635nm and the PMT (photomultiplier tube) values were adjusted to reach a ratio (Cy5/Cy3) around 1. Spots were identified and ratio’s quantified by means of the Genepix software 5.0 (Axon Instruments).

data_processing: Statistical analyses were performed using the R package limma (linear models for microarray data). Spots for which red and green median foreground intensity < median background intensity + 2SD on all arrays were deleted before analysis. Median intensity data was background corrected using a normal-exponential convolution model. Subsequently, normalization between-arrays was performed using Variance Stabilization Normalization (vsn). For each probe, a linear model was fitted to intensity ratios, after which probes were ranked in order of evidence of differential expression using an empirical Bayes method. Both high and low concentrations of each chemical stressor were contrasted against their respective controls. Genes with p < 0.05 and log2FC < -0.75 or log2FC > 0.75 (log2 fold change) were considered as differentially transcribed gene fragments.

organism: Daphnia magna

source_name: CA EC1-3

label_protocol: The production of cDNA and subsequent amino-allyl labelling were performed according to the protocol described in detail by Vandenbrouck et al. (2009). In brief, 5µg of total RNA was mixed with Lucidea control mRNA spike mix (Amersham, UK) to be reverse-transcribed using the Superscript II, Random hexamer primers (both Invitrogen) in the presence of dNTPs with 2/3 aa-dTTP/dTTP (Sigma-Aldrich, Belgium). After an overnight incubation period (42°C) the amino-allyl-incorporated cDNA was purified using a modified Qiagen PCR spin colomn protocol (Van der Ven et al., 2005). In a next step, Cy5/Cy3 esters (Amersham) were used for covalent coupling to the amino-allyl labelled cDNA. The vacuum dried cDNA samples (dissolved in a 0,1M carbonate buffer (pH 9.0)) were mixed with the Cy3/Cy5 esters (dissolved in 100% DMSO) and incubated for an hour in the dark at room temperature. Hereafter, a second cleanup reaction was performed to establish the removal of the remaining uncoupled dyes (QIAquick PCR purification kit, Qiagen, USA). The quality of eluted and labelled cDNA was analysed using the Nanodrop® spectrophotometer. Samples with an FOI (frequence of incorporated dye) between 20 and 50 were selected for hybridization and an amount of 50 pmol labelled target was vacuum dried.

extract_protocol: Approximately 30 Daphnia/replicate were collected. Samples were shock-frozen in liquid nitrogen and stored in RNAlater (Ambion, USA) at -80°C. All RNA extractions were performed using the TRIzol® method (Invitrogen, Belgium) followed by a DNAse treatment using 1U RNAse-free DNAse and 1U RNAse inhibitor (Fermentas, Germany) per 30µl sample and subsequent phenol/chloroform extractions. The purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were respectively above 1.90 and 2.10. To verify the intactness of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed to visualize the 18S and 28S ribosomal bands.

treatment_protocol: Two sets of structural analogues, defined as narcotics (alcohols: ethanol, methanol and isopropanol) and as polar narcotics (chlorinated anilines: aniline, 4-chloroaniline, 3,5-dichloroaniline and 2,3,4-trichloroaniline) were selected for short-term toxicity experiments. Daphnia magna neonates (between 0 and 24h old) were exposed for 96h in glass recipients to each chemicals’ respective EC1-96h and EC10-96h (determined based on 96h immobilization experiments) to allow multi-level effect assessment (growth, energy reserves and gene transcription was assessed) of different chemicals at the same level of acute toxicity (exposure at equitoxic acute concentration). The experiments were performed in triplicate at a density of 1daphnid/5ml of reconstituted fresh water CaCl2.2H2O, 2mM; MgSO4.7H2O, 500μM; NaHCO3, 771μM; KCl, 77.1μM; water hardness, 250 mg CaCO3; pH 7.8; OECD guideline 203, annex 2). Test media were renewed every 24h for the alcohols (to account for their high(er) volatility) and every 48h for the anilines. Organisms were fed every other day with a mixture of P. subcapitata and C. reinhardtii in a 3:1 ratio. The necessary amounts of organisms for the respective endpoints (growth and energy use) were collected after 48h and 96h of exposure and for gene transcription analyses after 96h of exposures. 30 pooled daphnids per replica were used for gene transcription analyses.

value: whole body extracts (30 organisms)

tag: age

value: 96h old

tag: effect concentration

tag: agent

source_name: whole body extracts from reference sample

tag: sample type

value: reference


title: 11FlkF2

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
Amplification protocol
Target Amplified manufacturer/kit: Nugen WT-Ovation Pico RNA Amplification System (3300) and WT-Ovation Exon Module (2000)
Target Amplified protocol: Capel protocol: RNA extraction and sample preparation for Affymetrix Gene 1.0 ST arrays
Rounds of amplification: 1
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:13973

hyb_protocol: Affymetrix standard protocol The arrays were washed and stained using the Affymetrix Fluidics Station 450.  Fluidics Protocol FS450-0007. Amount labeled  target hybridization to array: Approximately 2.5 µg into the hybridization cocktail, approximately 2.1 µg were hybridized to the array.

scan_protocol: Probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G and Affymetrix GeneChip Command Console (AGCC) Software version 3.1.1.

data_processing:
Analysis method: Partek
GCOS Tgt value: 500

organism: Mus musculus

source_name: Gonad and mesonephros, 11.5 dpc female endothelial cells

label_protocol: Nugen Encore Biotin Module (4200)

treatment_protocol:
Pooled sample: Yes
Pool size: one or more litters
Dissection method: Dissected out the gonad and a portion of the mesonephros, trypsinized and FACS sorted.  Capel protocol: FACS Protocol
Experimental design: Female mice were time-mated and the embryos were collected. The gonads were removed and the males and females were separately pooled. The gonads were incubated in Trypsin EDTA for 5-10 minutes. The trypsin was removed, PBS (often with DNase) was added, and the gonadal cells were dissociated by pipetting and pulling through a syringe. The samples were passed through a strainer and then FACS sorted. Capel protocol: FACS protocol.

tag: gene reported

tag: strain

tag: Sex

value: female

tag: developmental stage

tag: theiler stage


title: CA EC10-1

source_name: CA EC10-1


title: CA EC10-2

source_name: CA  EC10-2


title: Melanocyte cell line SK_MEL-5-250K_Nsp

description:
Hybridized to 250K_Nsp
SK_MEL_5-250knsp

source_name: Metastasis_Melanocyte cell line


title: Melanocyte cell line MALME-3M-250K_Nsp

description:
Hybridized to 250K_Nsp
MALME_3M-250knsp


title: Melanocyte cell line MDA-MB-435-250K_Nsp

description:
Hybridized to 250K_Nsp
MDA_MB_435-250knsp


title: CA EC1-2

source_name: CA EC1_2


title: L97_555

description: Array Batch: 20050

source_name: CxC Line 97, embryo at physiological maturity


title: Ctrl_EBSS_3h

source_name: Cells transfected with siCtrl and cultured for 3  hrs in EBSS.


title: Ctrl_DMEM_0h

source_name: Cells transfected with siCtrl and cultured for 0  hrs in EBSS.


title: Melanocyte cell line LOXIMVI-250K_Nsp

description:
Hybridized to 250K_Nsp
LOXIMVI-250knsp

value: LOXIMVI


title: Melanocyte cell line M14-250K_Nsp

description:
Hybridized to 250K_Nsp
M14-250knsp


title: L98_555

description: Array Batch: 20038

source_name: CxC Line 98, embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: CA EC10-3

source_name: CA EC10-3


title: L96_555

description: Array Batch: 20050

source_name: CxC Line 96, embryo at physiological maturity


title: L100_555

description: Array Batch: 20050

source_name: CxC Line 100, embryo at physiological maturity


title: White blood cell line SR-250K_Nsp

description:
Hybridized to 250K_Nsp
SR-250knsp

source_name: White blood cell line

value: White blood cell

value: SR


title: sip8_EBSS_6h

source_name: Cells transfected with  siNupr1  and cultured for  6  hrs in EBSS.


title: CA Co3

source_name: CA Co3

value: unexposed control


title: CA EC1-1

source_name: whole body extracts from reference sample

source_name: CA EC1-1


title: CA Co2

source_name: CA Co2


title: L106_555

description: Array Batch: 20050

source_name: CxC Line 106, embryo at physiological maturity


title: siRelB_EBSS_9h

source_name: Cells transfected with siRelB and cultured for 9  hrs in EBSS.


title: L95_555

description: Array Batch: 20050

source_name: CxC Line 95, embryo at physiological maturity


title: CA Co1

source_name: CA Co1


title: siRelB_Mock_9h

source_name: Cells transfected with siRelB and cultured for 9  hrs in Mock.


title: sip65_Mock_9h

source_name: Cells transfected with siRelA/p65 and cultured for 9  hrs in Mock.


title: L93_555

description: Array Batch: 20050

source_name: CxC Line 93, embryo at physiological maturity


title: L87_555

description: Array Batch: 20038

source_name: CxC Line 87, embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: L89_555

description: Array Batch: 20050

source_name: CxC Line 89, embryo at physiological maturity


title: An EC10-3

source_name: An EC10-3

value: aniline


title: sic_Mock_9h

source_name: Cells transfected with siCtrl and cultured for 9  hrs in Mock.


title: An EC10-2

source_name: An EC10-2


title: White blood cell line K_562-250K_Nsp

description:
Hybridized to 250K_Nsp
K_562-250knsp

source_name: Pleural effusion_White blood cell line


title: White blood cell line RPMI_8226-250K_Nsp

description:
Hybridized to 250K_Nsp
RPMI_8226-250knsp

source_name: PB_White blood cell line


title: L86_555

description: Array Batch: 20038

source_name: CxC Line 86, embryo at physiological maturity


title: White blood cell line HL_60-250K_Nsp

description:
Hybridized to 250K_Nsp
HL_60-250knsp

source_name: PBL_White blood cell line


title: An EC10-1

source_name: An EC10-1

source_name: whole body extracts from reference sample


title: L84_555

description: Array Batch: 20050

source_name: CxC Line 84, embryo at physiological maturity


title: sic_EBSS_9h

source_name: Cells transfected with siCtrl and cultured for 9  hrs in EBSS.


title: sip65_EBSS_9h

source_name: Cells transfected with siRelA/p65 and cultured for 9  hrs in EBSS.


title: An EC1-3

source_name: An EC1-3


title: An EC1-1

source_name: An EC1-1


title: An EC1-2

source_name: An EC1-2


title: L79_555

description: Array Batch: 20038

source_name: CxC Line 79, embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: White blood cell line MOLT_4-250K_Nsp

description:
Hybridized to 250K_Nsp
MOLT_4-250knsp


title: White blood cell line CCRF_CEM-250K_Nsp

description:
Hybridized to 250K_Nsp
CCRF_CEM-250knsp

source_name: White blood cell line

value: CCRF-CEM


title: An Co2

source_name: An Co2


title: L82_555

description: Array Batch: 20050

source_name: CxC Line 82, embryo at physiological maturity


title: An Co3

source_name: An Co3


title: HEK293-WT-sample4

city: New York

first: Avi

last: Ma'ayan

address: One Gustave L. Levy Place Box 1215

department: Pharmacology and Systems Therapeutics

institute: Mount Sinai School of Medicine

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from HEK293 wild type biological rep4

hyb_protocol: Following standard procedures according to the manufacturer's instructions as applied at the MSSM core facility.

data_processing:
Expression Console (1.1.2800.29167), affymetrix-algorithm-name = rma
One-way analysis of variance test (ANOVA) with BH correction at 0.05 FDR was applied to the dataset to identify the genes that were differentially expressed between groups.

label: biotin

source_name: HEK293 wild type biological rep4

growth_protocol: Mice were sacrificed at 8 weeks. Each sample in the Tg and WT mice are from different individual animals. One mice developed significant scarring and since the array results were significantly different this sample was not used for further analysis. HEK 293 and HK2 cells were obtained from ATCC and cultured as described in Rosenstiel, P.E., et al. Kidney Int 74, 1049-1058 (2008).

extract_protocol: Total RNA was extracted from kidney cortices of five Tg26 and five WT for gene expression microarrays. RNA was isolated by using RNAesay kit from Qiagen.

tag: transfection

tag: gender


title: Lung cell line NCI_H460-250K_Nsp

description:
Hybridized to 250K_Nsp
NCI_H460-250knsp

source_name: Pleural effusion_Lung cell line

value: Lung


title: L72_555

description: Array Batch: 20050

source_name: CxC Line 72, embryo at physiological maturity

tag: population

value: Cayuga x Caledonia, DH


title: L73_555

description: Array Batch: 20050

source_name: CxC Line 73, embryo at physiological maturity

tag: field location

value: Helfer, Cornell University, Ithaca, NY


title: An Co1

source_name: whole body extracts from reference sample

source_name: An Co1


title: HEK293-WT-sample3

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from HEK293 wild type biological rep3

scan_protocol: Following standard procedures according to the manufacturer's instructions as applied at the MSSM core facility.

source_name: HEK293 wild type biological rep3


title: L76_555

description: Array Batch: 20050

source_name: CxC Line 76, embryo at physiological maturity

tag: year

value: embryo at physiological maturity


title: Lung cell line NCI_H522-250K_Nsp

description:
Hybridized to 250K_Nsp
NCI_H522-250knsp

source_name: Lung cell line


title: Lung cell line NCI_H226-250K_Nsp

description:
Hybridized to 250K_Nsp
NCI_H226-250knsp


title: HEK293-WT-sample2

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from HEK293 wild type biological rep2

source_name: HEK293 wild type biological rep2

label_protocol: Following standard procedures according to the manufacturer's instructions as applied at the MSSM core facility.


title: L71_555

description: Array Batch: 20050

source_name: CxC Line 71, embryo at physiological maturity

tag: tissue

value: Pre-anthesis spike bulk


title: Lung cell line HOP_62-250K_Nsp

description:
Hybridized to 250K_Nsp
HOP_62-250knsp

tag: cell line


title: Lung cell line HOP_92-250K_Nsp

description:
Hybridized to 250K_Nsp
HOP_92-250knsp

tag: tissue type


title: Lung cell line NCI_H322M-250K_Nsp

description:
Hybridized to 250K_Nsp
NCI_H322M-250knsp


title: Lung cell line NCI_H23-250K_Nsp

description:
Hybridized to 250K_Nsp
NCI_H23-250knsp


title: Hipocamp

city: Barcelona

first: Rory

last: Johnson

state: Catalonia

address: Calle Dr Aiguader, 88

department: Bioinformatics and Genomics

country: Spain

institute: Centre for Genomic Regulation

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT

data_processing:
The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).
Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: Hipocampus

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

value: Hipocampus


title: L70_555

description: Array Batch: 20050

source_name: CxC Line 70, embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: Lung cell line A549-250K_Nsp

description:
Hybridized to 250K_Nsp
A549-250knsp


title: Colon cell line SW_620-250K_Nsp

description:
Hybridized to 250K_Nsp
SW_620-250knsp

source_name: Colon cell line

value: Colon


title: HEK293-HIPK2-Vector-sample4

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from HEK293 transfected with HIPK2 vector biological rep4

value: HIPK2 vector


title: L101_555

description: Array Batch: 20050

source_name: CxC Line 101, embryo at physiological maturity


title: L67_555

description: Array Batch: 20050

source_name: CxC Line 67, embryo at physiological maturity


title: HEK293-WT-sample1

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from HEK293 wild type biological rep1

source_name: HEK293 wild type biological rep1


title: HEK293-HIPK2-Vector-sample3

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from HEK293 transfected with HIPK2 vector biological rep3


title: L68_555

description: Array Batch: 20050

source_name: CxC Line 68, embryo at physiological maturity


title: L69_555

description: Array Batch: 20038

source_name: CxC Line 69, embryo at physiological maturity


title: Mesencefal

source_name: Mesencefal

value: Mesencefal


title: Lung cell line EKVX-250K_Nsp

description:
Hybridized to 250K_Nsp
EKVX-250knsp

value: EKVX


title: Cerebel

source_name: Cerebellum

value: Cerebellum


title: L65_555

description: Array Batch: 20050

source_name: CxC Line 65, embryo at physiological maturity


title: Colon cell line KM12-250K_Nsp

description:
Hybridized to 250K_Nsp
KM12-250knsp


title: HEK293-HIPK2-Vector-sample1

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from HEK293 transfected with HIPK2 vector biological rep1


title: HEK293-HIPK2-Vector-sample2

description:
Mouse samples are labeled as investigator, id of sample, condition, gender, date. Human cellline samples are labled as facility, date, investigator, condition, sample id.
Gene expression from HEK293 transfected with HIPK2 vector biological rep2


title: L81_555

description: Array Batch: 20050

source_name: CxC Line 81, embryo at physiological maturity


title: L55_555

description: Array Batch: 20050

source_name: CxC Line 55, embryo at physiological maturity


title: Colon cell line HCT_15-250K_Nsp

description:
Hybridized to 250K_Nsp
HCT_15-250knsp


title: Temporal Superior

source_name: Temporal Superior

value: Temporal Superior


title: Esophagus

source_name: Esophagus

value: Esophagus


title: L60_555

description: Array Batch: 20038

source_name: CxC Line 60, embryo at physiological maturity


title: L62_555

description: Array Batch: 20050

source_name: CxC Line 62, embryo at physiological maturity


title: Cortex Parietal

source_name: Cortex Parietal

value: Cortex Parietal


title: Cortex Frontal

source_name: Cortex Frontal

value: Cortex Frontal


title: Kidney

source_name: Kidney

value: Kidney


title: Amigdala

source_name: Amigdala

value: Amigdala


title: L53_555

description: Array Batch: 20050

source_name: CxC Line 53, embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: Colon cell line HCT_116-250K_Nsp

description:
Hybridized to 250K_Nsp
HCT_116-250knsp

source_name: Colon cell line


title: Colon cell line HCC_2998-250K_Nsp

description:
Hybridized to 250K_Nsp
HCC_2998-250knsp


title: Cardiomyocytes derived from DCM iPSC treated by Serca2a, rep2

city: Stanford

first: Leng

last: Han

state: CA

address: 265 Campus Dr

institute: Stanford University

description:
Gene expression data from iPSC
DCM-Serca2a-2
DCM-Serca2a-2.CEL

hyb_protocol: Hybridization were followed standard Affymetrix protocol in Affymetrix GeneChip Hybridization Oven 640

scan_protocol: GeneChips were scanned using theAffymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings and RMA as normalization method.

source_name: DCM iPSC treated by Serca2a

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

growth_protocol: iPSCs were maitained with mTESR-1 medium on matrigel coated surfaces. iPSC-derived cardiomyocytes were maitained with DMEM plus 10% FBS in tissue culture dishes.

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

treatment_protocol: iPSC were treated by Adenovirus-Serca2a

tag: cell type

value: Cardiomyocytes (derived from DCM iPSC)

tag: genotype/variation

value: DCM

tag: gene therapy


title: Colon cell line HT29-250K_Nsp

description:
Hybridized to 250K_Nsp
HT29-250knsp

source_name: Primary_Colon cell line


title: Cardiomyocytes derived from DCM iPSC treated by Serca2a, rep1

description:
Gene expression data from iPSC
DCM-Serca2a-1
DCM-Serca2a-1.CEL


title: Central nervous system cell line U251-250K_Nsp

description:
Hybridized to 250K_Nsp
U251-250knsp

source_name: Central nervous system cell line

value: Central nervous system


title: Central nervous system cell line SNB_19-250K_Nsp

description:
Hybridized to 250K_Nsp
SNB_19-250knsp


title: Colon cell line COLO205-250K_Nsp

description:
Hybridized to 250K_Nsp
COLO205-250knsp

source_name: Ascites_Colon cell line


title: Cardiomyocytes derived from DCM iPSC, rep1

description:
Gene expression data from iPSC
DCM-1
DCM-1.CEL

source_name: DCM iPSC

value: control


title: Cardiomyocytes derived from normal iPSC treated by Serca2a, rep1

description:
Gene expression data from iPSC
Control-Serca2a-1
Control-Serca2a-1.CEL

source_name: Normal iPSC treated by Serca2a

value: Cardiomyocytes (derived from normal iPSC)

value: Normal


title: Cardiomyocytes derived from DCM iPSC, rep2

description:
Gene expression data from iPSC
DCM-2
DCM-2.CEL


title: Central nervous system cell line SNB_75-250K_Nsp

description:
Hybridized to 250K_Nsp
SNB_75-250knsp


title: Heart

source_name: Heart

value: Heart


title: L57_555

description: Array Batch: 20050

source_name: CxC Line 57, embryo at physiological maturity

value: Cayuga x Caledonia, DH

value: Helfer, Cornell University, Ithaca, NY

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: Entorrinal

source_name: Entorrinal

value: Entorrinal


title: Cardiomyocytes derived from normal iPSC, rep 2

description:
Gene expression data from iPSC
Control-2
Control-2.CEL

source_name: Normal iPSC


title: Liver

source_name: Liver

value: Liver


title: L50_555

description: Array Batch: 20050

source_name: CxC Line 50, embryo at physiological maturity


title: L41_555

description: Array Batch: 20050

source_name: CxC Line 41, embryo at physiological maturity


title: Colon

source_name: Colon

value: Colon


title: Central nervous system cell line SF_539-250K_Nsp

description:
Hybridized to 250K_Nsp
SF_539-250knsp


title: Central nervous system cell line SF_295-250K_Nsp

description:
Hybridized to 250K_Nsp
SF_295-250knsp


title: Cardiomyocytes derived from normal iPSC treated by Serca2a, rep2

description:
Gene expression data from iPSC
Control-Serca2a-2
Control-Serca2a-2.CEL


title: L44_555

description: Array Batch: 20050

source_name: CxC Line 44, embryo at physiological maturity


title: Induced pluripotent cells_patient III a

description:
Gene expression data from iPSC
iPS_III a
iPS_IIIa.CEL

source_name: iPSC for patient IIIa

value: iPS cells


title: Cervix

source_name: Cervix

value: Cervix


title: Cardiomyocytes derived from normal iPSC, rep 1

description:
Gene expression data from iPSC
Control-1
Control-1.CEL


title: Central nervous system cell line SF_268-250K_Nsp

description:
Hybridized to 250K_Nsp
SF_268-250knsp


title: Breast cell line MDA_MB_231-250K_Nsp

description:
Hybridized to 250K_Nsp
MDA_MB_231-250knsp

source_name: Pleural effusion_Breast cell line

value: Breast


title: L34_555

description: Array Batch: 20038

source_name: CxC Line 34, embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: Spleen

source_name: Spleen

value: Spleen


title: Adipose

source_name: Adipose

value: Adipose


title: Ovary

source_name: Ovary

value: Ovary


title: L42_555

description: Array Batch: 20038

source_name: CxC Line 42, embryo at physiological maturity


title: HepG2


title: Induced pluripotent cells_patient II b

description:
Gene expression data from iPSC
iPS_II b
iPS_IIb.CEL

source_name: iPSC for patient IIb

value: DCM


title: Induced pluripotent cells_patient II c

description:
Gene expression data from iPSC
iPS_II c
iPS_IIc.CEL

source_name: iPSC for patient IIc


title: L30_555

description: Array Batch: 20050

source_name: CxC Line 30, embryo at physiological maturity


title: Breast cell line T47D-250K_Nsp

description:
Hybridized to 250K_Nsp
T47D-250knsp

source_name: Breast cell line


title: L29_555

description: Array Batch: 20050

source_name: CxC Line 29, embryo at physiological maturity


title: Breast cell line HS578T-250K_Nsp

description:
Hybridized to 250K_Nsp
HS578T-250knsp

source_name: Primary_Breast cell line


title: Breast cell line MCF7-250K_Nsp

description:
Hybridized to 250K_Nsp
MCF7-250knsp


title: Breast cell line BT_549-250K_Nsp

description:
Hybridized to 250K_Nsp
BT_549-250knsp

source_name: Metastasis_Breast cell line


title: Bladder

source_name: Bladder

value: Bladder


title: Induced pluripotent cells_patient Ib

description:
Gene expression data from iPSC
iPS_Ib
iPS_Ib.CEL

source_name: iPSC for patient Ib

value: Normal


title: Induced pluripotent cells_patient IIa

description:
Gene expression data from iPSC
iPS_IIa
iPS_IIa.CEL

source_name: iPSC for patient IIa


title: L28_555

description: Array Batch: 20038

source_name: CxC Line 28, embryo at physiological maturity


title: 251486826202-4

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: myc 4

hyb_protocol: Agilent : 500.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using Axon Scanner.

data_processing: OneChannelGui data processing; Log2(signal) quantile normalized.

molecule: polyA RNA

source_name: myc 4

label_protocol: Agilent low RNA

extract_protocol: Chomzynski

value: B splenocytes

value: c-myc/Cdk4(R24C) lymphoma

tag: amount in (µg)


title: Induced pluripotent cells_patient Ia

description:
Gene expression data from iPSC
iPS_Ia
iPS_Ia.CEL

source_name: iPSC for patient Ia


title: L20_555

description: Array Batch: 20050

source_name: CxC Line20, embryo at physiological maturity

value: Cayuga x Caledonia, DH

value: Helfer, Cornell University, Ithaca, NY

source_name: Pre-anthesis spike bulk


title: Thymus

source_name: Thymus

value: Thymus


title: 251486826202-3

description: myc 3

source_name: myc 3


title: L18_555

description: Array Batch: 20050

source_name: CxC Line 18, embryo at physiological maturity

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: human embyonic stem cells (H7)

description:
Gene expression data from human embyonic stem cells.
HES
HES.CEL

source_name: human embyonic stem cells

value: embyonic stem cells


title: Trachea

source_name: Trachea

value: Trachea


title: L22_555

description: Array Batch: 20038

source_name: CxC Line 22, embryo at physiological maturity


title: HeLa DGCR8 siRNA #3, mRNA

first: Scott

middle: H

last: Olejniczak

address: 417 E68th St

institute: Memorial Sloan Kettering Cancer Center

description: Gene expression data from DGCR8 siRNA #3-transfected HeLa cells.

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99C for 5 min and hybridized for 16 h at 45C to Affymetrix Human Gene 1.0 ST microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: An Affymetrix GCS3000 laser scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.

source_name: HeLa cells, DGCR8 siRNA-3

label_protocol: 2ug of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: HeLa cells were grown in DMEM containing 10% FCS.

extract_protocol: Total RNA was isolated using Trizol reagent according to the manufacturer's instructions.

treatment_protocol: HeLa cells were transfected with siRNAs using RNAiMAX (Invitrogen) according to the manufacturer's recommendations.

value: HeLa

value: cervical adenocarcinoma

tag: treatment

value: DGCR8 siRNA-3


title: 251486826202-1

description: control 3

source_name: control 3

tag: strain

value: wt


title: Human Testis

source_name: Human Testis

value: Human Testis


title: 251486826202-2

description: control 4

source_name: control 4


title: 251486826201-4

description: myc 2

source_name: myc 2


title: Skin Fibroblast

description:
Gene expression data from firboblast
Fibroblast
Fibroblast.CEL

source_name: Human fibroblast

value: fibroblast cells


title: GM12878


title: L14_555

description: Array Batch: 20050

source_name: CxC Line 14, embryo at physiological maturity


title: 251486826201-3

description: myc 1

source_name: myc 1


title: HelaS3


title: 251486826201-2

description: control 2

source_name: control 2


title: L9_555

description: Array Batch: 20038

source_name: CxC Line 9, embryo at physiological maturity


title: 251486826201-1

description: control 1

source_name: control 1


title: L11_555

description: Array Batch: 20038

source_name: CxC Line 11, embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: Placenta

source_name: Placenta

value: Placenta


title: 28-2 cells, 5% lowest LMP1-mRFP Replicate 3

city: Madison

first: Zachary

last: Pratt

state: WI

address: 1400 University Avenue

department: Oncology

institute: University of Wisconsin-Madison

description: Biological replicate 3 of 3.  5% of 28-2 cells expressing the lowest levels of LMP1-mRFP, isolated by flow cytometry of single cells, harvested immediately after sorting.

hyb_protocol: Equal masses of Cy3- and Cy5-labeled samples were co-hybridized to microarrays.

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

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and normalization.

source_name: 28-2 cells, 5% lowest LMP1-mRFP

label_protocol: 150 ng of RNA was reverse transcribed with an oligo d(T) promoter primer into cDNA using the Agilent Quick Amp Kit, Two Color per manufacturer's protocol.  The cDNA was then transcribed into cRNA containing Cy3 or Cy5 using the Agilent T7 RNA polymerase transcription kit.

growth_protocol: 28-2 cells were grown in RPMI-1640 and 10% fetal bovine serum (supplemented with penicillin and streptomycin).

extract_protocol: Total RNA was extracted using TRIzol reagent per manufacturer's protocol

treatment_protocol: There were no additional treatments applied to these cells.

tag: ebv-status

value: Positive

tag: lmp1-mrfp expression level

value: Low

value: B-cell

tag: phenotype

value: 5% lowest LMP1-mRFP

source_name: 28-2 cells, unsorted pool

tag: ebv status

value: 28-2 cells, unsorted pool


title: HeLa DGCR8 siRNA #2, mRNA

description: Gene expression data from DGCR8 siRNA #2-transfected HeLa cells.

source_name: HeLa cells, DGCR8 siRNA-2

value: DGCR8 siRNA-2


title: ShSy5y


title: Intestine

source_name: Intestine

value: Intestine


title: HeLa DGCR8 siRNA #1, mRNA

description: Gene expression data from DGCR8 siRNA #1-transfected HeLa cells.

source_name: HeLa cells, DGCR8 siRNA-1

value: DGCR8 siRNA-1


title: L8_555

description: Array Batch: 20050

source_name: CxC Line 8, embryo at physiological maturity

value: Cayuga x Caledonia, DH

value: Helfer, Cornell University, Ithaca, NY

value: embryo at physiological maturity

value: Pre-anthesis spike bulk


title: L5_555

description: Array Batch: 20050

source_name: CxC Line 5, embryo at physiological maturity


title: 28-2 cells, 5% lowest LMP1-mRFP Replicate 2

description: Biological replicate 2 of 3.  5% of 28-2 cells expressing the lowest levels of LMP1-mRFP, isolated by flow cytometry of single cells, harvested immediately after sorting.


title: 28-2 cells, 5% lowest LMP1-mRFP Replicate 1

description: Biological replicate 1 of 3.  5% of 28-2 cells expressing the lowest levels of LMP1-mRFP, isolated by flow cytometry of single cells, harvested immediately after sorting.


title: K562


title: L4_555

description: Array Batch: 20050

source_name: CxC Line 4, embryo at physiological maturity


title: Lung

source_name: Lung

value: Lung


title: HeLa Ars2 siRNA #2, mRNA

description: Gene expression data from Ars2 siRNA #2-transfected HeLa cells.

source_name: HeLa cells, Ars2 siRNA-2

value: HeLa

value: cervical adenocarcinoma

value: Ars2 siRNA-2


title: L7_555

description: Array Batch: 20050

source_name: CxC Line 7, embryo at physiological maturity


title: HeLa Ars2 siRNA #1, mRNA

description: Gene expression data from Ars2 siRNA #1-transfected HeLa cells.

source_name: HeLa cells, Ars2 siRNA-1

value: Ars2 siRNA-1


title: Skeletal Muscle

source_name: Skeletal Muscle

value: Skeletal Muscle


title: Human Brain

source_name: Human Brain

value: Human Brain


title: HeLa Ars2 siRNA #3, mRNA

description: Gene expression data from Ars2 siRNA #3-transfected HeLa cells.

source_name: HeLa cells, Ars2 siRNA-3

value: Ars2 siRNA-3


title: 28-2 cells, 5% highest LMP1-mRFP Replicate 3

description: Biological replicate 3 of 3.  5% of 28-2 cells expressing the highest levels of LMP1-mRFP, isolated by flow cytometry of single cells, harvested immediately after sorting.

source_name: 28-2 cells, 5% highest LMP1-mRFP

value: Positive

value: High

value: B-cell

value: 5% highest LMP1-mRFP


title: 28-2 cells, 5% highest LMP1-mRFP Replicate 1

description: Biological replicate 1 of 3.  5% of 28-2 cells expressing the highest levels of LMP1-mRFP, isolated by flow cytometry of single cells, harvested immediately after sorting.

value: 28-2 cells, unsorted pool


title: 28-2 cells, 5% highest LMP1-mRFP Replicate 2

description: Biological replicate 2 of 3.  5% of 28-2 cells expressing the highest levels of LMP1-mRFP, isolated by flow cytometry of single cells, harvested immediately after sorting.


title: WTvsKOcomX CDML replicate 3

status: Public on Jan 31 2012

city: Louvain-La-Neuve

first: Pascal

last: Hols

address: Place Croix du Sud 5

department: Institut des Sciences de la Vie

institute: Université catholique de louvain

description: Biological replicate 1 of  2, dye swap

hyb_protocol: Hybridization of the labeled cDNA (0.3 microg per sample) were added to hybridization buffer (Agilent In Situ Hybridization Kit Plus)  and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially according to Agilent instructions.

scan_protocol: Scanned on an Agilent Scanner G2565B Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

label: Alexa Fluor 555

organism: Streptococcus thermophilus

source_name: LMD-9WT CDML OD 0.4

label_protocol:
First strand cDNA was synthetized from 10 microg RNA. Synthesized cDNA were purified and labeled with Alexa Fluor 555 and Alexa Fluor 647. Experiments were carried out according to instructions of the Superscript Plus Indirect cDNA Labeling system (Invitrogen).
The quality of the labeled cDNA and its concentration were respectively measured with the 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA) and ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

growth_protocol: Strains LMD-9 WT and CB003 were grown at 37°C during 16h in M17 medium supplemented with lactose 1% (M17L), washed twice (5,000 x g, 9 min, room temperature) in one volume of CDM medium supplemented with lactose 1% (CDML) and resuspended in one volume of CDML. Cultures were then 30-fold diluted in CDML. When cells reached the mid-log phase (OD600 of 0.4), 25-ml aliquots were collected for total RNA extraction.

extract_protocol: Cells were harvested by centrifugation (7,000 x g for 4 min) and mechanically broken with 0.18-mm-diameter glass beads in a Braun Homogenizer (three 1-min periods of homogenization with 1-min intervals on ice). Total RNA was extracted using the High Pure RNA isolation kit (ROCHE, Basel, Switzerland)

tag: isolate

value: clone 1

label: Alexa Fluor 647

source_name: KOcomX CDML OD 0.4


title: WTvsKOmecA THBG replicate 2

description: Biological replicate 2 of  2

source_name: LMD-9WT THBG OD 0.4

growth_protocol: Strains LMD-9 WT and CB052 were grown during 16h at 37°C in THB medium supplemented with glucose 1% (THBG). Cultures were then 30-fold diluted in THBG. When cells reached the mid-log phase (OD600 of 0.4), 25-ml aliquots were collected for total RNA extraction.

extract_protocol: Cells were harvested by centrifugation (7,000 x g for 4 min), and mechanically broken with 0.18-mm-diameter glass beads in a Braun Homogenizer (three 1-min periods of homogenization with 1-min intervals on ice). Total RNA was extracted using the High Pure RNA isolation kit (ROCHE, Basel, Switzerland)

value: clone 2

source_name: KOmecA THBG OD 0.4


title: L33_555

description: Array Batch: 20038

source_name: CxC Line 33, embryo at physiological maturity

tag: population

value: Cayuga x Caledonia, DH

value: Helfer, Cornell University, Ithaca, NY

value: embryo at physiological maturity

source_name: Pre-anthesis spike bulk


title: WTvsKOcomX CDML replicate 1

description: Biological replicate 1 of  2


title: HeLa ctl siRNA, biological replicate 1, mRNA

description: Gene expression data from control siRNA-transfected HeLa cells, biological replicate #1.

source_name: HeLa cells, control siRNA

value: HeLa

value: control siRNA


title: L1_555

description: Array Batch: 20050

source_name: CxC Line 1, embryo at physiological maturity

tag: field location

value: Pre-anthesis spike bulk


title: HeLa ctl siRNA, biological replicate 3, mRNA

description: Gene expression data from control siRNA-transfected HeLa cells, biological replicate #3.

value: cervical adenocarcinoma


title: L23_555

description: Array Batch: 20038

source_name: CxC Line 23, embryo at physiological maturity

tag: year


title: WTvsKOcomX CDML replicate 2

description: Biological replicate 2 of  2


title: Induced pluripotent cells_patient III b

description:
Gene expression data from iPSC
iPS_III b
iPS_IIIb.CEL

source_name: iPSC for patient IIIb

value: iPS cells

value: Normal


title: WTvsKOmecA THBG replicate 3

description: Biological replicate 2 of  2, dye swap


title: Malignant melanoma 0664 cellular RNA

city: Charlestown

first: Johan

last: Skog

state: MA

address: 149 13th street

department: Molecular Neurogenetics

institute: Massachusetts General Hospital

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was analyzed using GenomeStudio v1.1

source_name: Malignant melanoma cell RNA from low passage cell culture

label_protocol: Standard Illumina labelling protocol

growth_protocol: DMEM medium supplemented with 5% microvesicle free fetal bovine serum.

extract_protocol: RNA was extracted with the Ambion miRNeasy RNA extraction kit, followed by quality assessment on a Bioanalyzer RNA pico chip.

treatment_protocol: Cells were washed and fresh media was added. Exosomes/microvesicles were harvested after 48 hrs. At the same time, the cells were harvested for RNA extraction. Exosomes/microvesicles were isolated by differential centrifugation according to previously published protocol (Skog J et al. Nat Cell Biol 2008)

tag: disease state

value: Malignant melanoma

tag: rna source

value: cell RNA from low passage cell culture


title: NA19239

status: Public on Jan 30 2012

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using the standard Illumina protocol.

scan_protocol: BeadChips were imaged using iScan with the standard recommended Illumina scanner setting.

data_processing: Raw intensities were extracted using GenomeStudio v2010.1. Background normalization was conducted by subtracting averaged negative probe intensity from signal A and B. Then quantile normalization was done to control for chip-to-chip variation. Finally, average beta was recalculated from normalized intensities: methylated intensity/(methylated + unmethylated intensities). Data points with bad detection P values were removed and then imputed. One CpG site, cg22903370, was removed due to >50% of data points missing.

label: Cy3 and Cy5

source_name: Lymphoblastoid Cell Line (HapMap), YRI

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was obtained from the Coriell Cell Repository. DNA quantity and purity was assessed using Nanodrop.

tag: coriell cell line

value: lymphoblastoid

value: YRI

tag: gender

value: male


title: Glioblastoma 20/3 cellular RNA_replicate 2

source_name: Glioblastoma cell RNA from low passage cell culture

value: Glioblastoma


title: NA19240

tag: cell type

value: female


title: Glioblastoma 11/5 exosomes/microvesicles_media supernatant_replicate 2

source_name: Glioblastoma exosomes/microvesicle RNA

value: exosomes/microvesicle RNA


title: Glioblastoma 11/5 cellular RNA


title: NA19238


title: Glioblastoma 20/3 cellular RNA_replicate 1


title: NA19209


title: Malignant melanoma 0664 exosomes/microvesicles_media supernatant_replicate 2

source_name: Malignant melanoma exosomes/microvesicle RNA


title: NA19221

description: This Sample represents 2 technical replicates (a, b).

data_processing: Raw intensities were extracted using GenomeStudio v2010.1. Background normalization was conducted by subtracting averaged negative probe intensity from signal A and B. Then quantile normalization was done to control for chip-to-chip variation. Finally, average beta was recalculated from normalized intensities: methylated intensity/(methylated + unmethylated intensities). The technical replicates were processed individually, and then the median was calculated from the processed average beta of the replicates. Data points with bad detection P values were removed and then imputed. One CpG site, cg22903370, was removed due to >50% of data points missing.


title: NA19208


title: Malignant melanoma 0105 exosomes/microvesicles_media supernatant


title: NA19210


title: Glioblastoma 11/5 exosomes/microvesicles_media supernatant_replicate 1


title: Malignant melanoma 0105 cellular RNA


title: WTvsKOmecA THBG replicate 1

description: Biological replicate 1 of  2

value: clone 1


title: NA19205


title: NA19207


title: NA19223


title: NA19222


title: Glioblastoma 20/3 exosomes/microvesicles_media supernatant


title: HeLa ctl siRNA, biological replicate 2, mRNA

description: Gene expression data from control siRNA-transfected HeLa cells, biological replicate #2.

tag: cell line


title: NA19211


title: NA19206


title: NA19202


title: NA19204


title: NA19201


title: NA19193


title: NA19192


title: NA19194


title: NA19203


title: NA19159


title: NA19154


title: NA19200


title: Malignant melanoma 0664 exosomes/microvesicles_media supernatant_replicate 1


title: NA19171


title: NA19152


title: NA19173


title: NA19172


title: NA19153


title: NA19145


title: NA19160


title: NA19143


title: NA19161


title: NA19139


title: NA19140


title: NA19132


title: NA19138


title: NA19144


title: NA19141


title: NA19131


title: NA19142


title: NA19137


title: NA19127


title: NA19130


title: NA19129


title: NA19120


title: NA19102


title: NA19119


title: NA19116


title: NA19128


title: NA19099


title: NA19093


title: NA19094


title: NA19098


title: NA19101


title: NA18913


title: NA18912


title: NA18871


title: NA19092


title: NA19103


title: NA18914


title: NA18872


title: NA18870


title: NA18860


title: NA18857


title: NA18856


title: NA18863


title: NA18862


title: NA18858


title: NA18853


title: NA18521


title: NA18859


title: NA18855


title: NA19100


title: NA18522


title: NA18854


title: NA18516


title: NA18852


title: NA18517


title: NA18515


title: NA18523


title: NA18507


title: NA18508


title: NA18504


title: NA18505


title: NA18503


title: NA12892

source_name: Lymphoblastoid Cell Line (HapMap), CEU

value: CEU


title: NA18501


title: NA18502


title: NA18500


title: NA12891


title: NA12874


title: NA12875


title: NA12878


title: NA12872


title: NA12813


title: NA12873


title: NA12812


title: NA12864


title: NA12814


title: NA12815


title: NA12802


title: NA12762


title: NA12801


title: NA12761


title: NA12763

description: This Sample represents 3 technical replicates (a, b, c).


title: NA12752


title: NA12865


title: NA12760


title: NA12264


title: NA12753


title: NA12750


title: NA12751


title: NA12716


title: NA18861


title: NA12740


title: NA12248


title: NA12239


title: NA12249


title: NA12707


title: NA12234


title: NA12717


title: NA12155


title: NA12146


title: NA12236


title: NA12145


title: NA12156


title: NA12144


title: NA12154


title: NA12056


title: NA12006


title: NA12044


title: NA12043


title: NA12003


title: NA12005


title: NA12057


title: NA11993


title: NA11995


title: NA12004


title: NA11994


title: NA11881


title: NA11831


title: NA11829


title: NA10854


title: NA11839


title: NA11992


title: NA11840


title: NA10863


title: NA10857


title: NA11830


title: NA10856


title: NA10855


title: NA10861


title: NA10860


title: NA11832


title: NA10851


title: NA11882


title: NA10839


title: NA10846


title: NA10859


title: NA18506


title: NA10847


title: NA10835


title: NA10838


title: NA07348


title: NA07357


title: NA10831


title: NA10830


title: NA07029


title: NA07055


title: NA07034


title: NA07345


title: NA07048


title: NA07019


title: NA06993


title: NA07022


title: Isolated cardiomyocytes treated for 24 h with fresh culture medium

status: Public on Jan 28 2012

city: Helsinki

first: Antti

last: Siltanen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki, Institute of Biomedicine

description: CTRL

hyb_protocol: According to the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Chip scanning was performed with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data analysis was performed with GeneSpring GX software, version 11.0.1 (Agilent Technologies). Data were normalized with the RMA algorithm, and baseline transformation to the median was performed.

organism: Rattus norvegicus

source_name: Fetal Wistar rat isolated cardiomyocytes, control

label_protocol: According to the Affymetrix GeneChip 3' IVT Express Kit.

growth_protocol: Cardiomyocytes were isolated by enzyme digestion and plated for 48 hours.

extract_protocol: RNeasy mini (Qiagen) according to kit protocol.

treatment_protocol: Samples were treated for 24 hours with fresh culture medium, myoblast-conditioned medium, or cardiac fibroblast-conditioned medium.

value: Wistar

tag: developmental stage

value: fetal

value: cardiomyocytes

value: fresh culture medium


title: Isolated cardiomyocytes treated for 24 h with cardiac fibroblast-conditioned medium

description: Cardiac fibroblast

source_name: Fetal Wistar rat isolated cardiomyocytes, cardiac fibroblast-conditioned medium

tag: treatment

value: cardiac fibroblast-conditioned medium


title: NA06994


title: NA07056


title: NA07000


title: NA06985


title: 2464_G3

status: Public on Jan 01 2012

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

description: aCGH analysis

hyb_protocol: Labelled DNAs were hybridized to whole-genome oligonucleotide 1x244K or 2x105K or 4x44K microarrays (Agilent Technologies) following the manufacture's instructions ("Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, fluorescent-labeled reference and tumor DNAs (3 ug each) were mixed with 50 ug of human Cot-1 DNA (Invitrogen Life Technologies) and control targets (Agilent Technologies). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65°C for 40 hrs. After hybridization, the slides were washed with Oligo aCGH Wash Buffer 1(Agilent Technologies) at room temperature for 5 min, with Oligo aCGH Wash Buffer 2 (Agilent Technologies) at 37°C for 1 min, with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 1x244k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel 1 is set to Red & Green, Red PMT is set to 100%, Green PMT is set to 100%) . Microarray performance was assessed by QC metric tool.

data_processing:
The scanned TIFF images were loaded into the Feature Extraction (v9.5 Agilent technologies), Feature Extraction files were analyzed by CGH Analytics Software (v. 3.5.14 Agilent Technologies) applying Z-Score algorithm.

Z-score data is not available for GEO submission.

source_name: reference

label_protocol: We followed the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, 2 ug of sample and reference genomic DNAs (for reference were used Human Genomic DNA: male Cat G1471, female Cat G1521, Promega, Madison, WI)  were separately digested with AluI/RsaI restriction enzyme mix (Promega). Fragmented DNA was labeled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 ueach), dUTP (60 uM) and Cy3-dUTP (60 uM) or Cy5-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by NanoDrop 1000 (ThermoScientific) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

extract_protocol: Genomic DNA was extracted overnight with lysis buffer containing K proteinase (0.2 mg/ml) followed by standard phenol/chloroform extraction. DNA content and quality were measured by Biophotometer (Eppendorf)

tag: group

source_name: tumor sample

tag: tissue

value: Neuroblastoma

tag: histology

value: stroma poor

tag: tumor stage

tag: patient nationality

value: Italian


title: 1965_G3

description: aCGH analysis


title: NA06991


title: 1869_G3

description: aCGH analysis


title: 1995_G3

description: aCGH analysis


title: 1560_G3

description: aCGH analysis


title: 1900_G3

description: aCGH analysis


title: 1699_G3

description: aCGH analysis


title: Isolated cardiomyocytes treated for 24 h with myoblast-conditioned medium

description: Myoblast

source_name: Fetal Wistar rat isolated cardiomyocytes, skeletal myoblast-conditioned medium

tag: strain

value: skeletal myoblast-conditioned medium


title: 1585_G3

description: aCGH analysis


title: 1640_G3

description: aCGH analysis


title: 1562_G3

description: aCGH analysis


title: 1292_G3

description: aCGH analysis


title: 1768_G3

description: aCGH analysis


title: 2136_G3

description: aCGH analysis


title: 2181_G3

description: aCGH analysis


title: 1439_G3

description: aCGH analysis


title: 2122_G3

description: aCGH analysis


title: 1228_G3

description: aCGH analysis


title: 1276_G3

description: aCGH analysis


title: 1506_G3

description: aCGH analysis


title: 1198_G3

description: aCGH analysis


title: 806_G3

description: aCGH analysis


title: 535_G3

description: aCGH analysis


title: 2235_G2

description: aCGH analysis


title: 2129_G2

description: aCGH analysis


title: 2130_G2

description: aCGH analysis


title: 2035_G2

description: aCGH analysis


title: 2397_G2

description: aCGH analysis


title: 2111_G2

description: aCGH analysis


title: 2006_G2

description: aCGH analysis


title: 1861_G2

description: aCGH analysis


title: 1498_G2

description: aCGH analysis


title: 1026_G2

description: aCGH analysis


title: 1275_G2

description: aCGH analysis


title: 1332_G2

description: aCGH analysis


title: 1104_G2

description: aCGH analysis


title: 1401_G2

description: aCGH analysis


title: 2028_G2

description: aCGH analysis


title: 1905_G2

description: aCGH analysis


title: 2175_G2

description: aCGH analysis


title: 1921_G2

description: aCGH analysis


title: 2148_G2

description: aCGH analysis


title: 1845_G2

description: aCGH analysis


title: 1041_G2

description: aCGH analysis


title: 1447_G2

description: aCGH analysis


title: 1030_G2

description: aCGH analysis


title: 2868_G1

description: aCGH analysis


title: 2405_G1

description: aCGH analysis


title: 1327_G2

description: aCGH analysis


title: G3_Cologne_251469810679_1_2.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251469810679_1_2.txt

value: German


title: G2_Cologne_251469812851_1_1.txt

description:
aCGH
Agilent Feature Extraction File name: G2_Cologne_251469812851_1_1.txt


title: G3_Cologne_251469810687_1_2.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251469810687_1_2.txt


title: 1431_G1

description: aCGH analysis


title: G2_Cologne_251469812851_1_2.txt

description:
aCGH
Agilent Feature Extraction File name: G2_Cologne_251469812851_1_2.txt


title: 1731_G1

description: aCGH analysis


title: G3_Cologne_251469810686_1_2.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251469810686_1_2.txt


title: 1912_G1

description: aCGH analysis


title: 1115_G1

description: aCGH analysis


title: 2036_G1

description: aCGH analysis


title: 1722_G1

description: aCGH analysis


title: 2207_G1

description: aCGH analysis


title: 2220_G1

description: aCGH analysis


title: 1946_G1

description: aCGH analysis


title: 2277_G1

description: aCGH analysis


title: 2024_G1

description: aCGH analysis


title: 1682_G1

description: aCGH analysis


title: 869_G2

description: aCGH analysis


title: G2_Cologne_251469812850_1_2.txt

description:
aCGH
Agilent Feature Extraction File name: G2_Cologne_251469812850_1_2.txt


title: 2717_G1

description: aCGH analysis


title: 2052_G1

description: aCGH analysis


title: G1_Cologne_251469812543_1_2.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469812543_1_2.txt


title: 2216_G1

description: aCGH analysis


title: G1_Cologne_251469810680_1_2.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469810680_1_2.txt


title: G2_Cologne_251469812850_1_1.txt

description:
aCGH
Agilent Feature Extraction File name: G2_Cologne_251469812850_1_1.txt


title: G1_Cologne_251469810679_1_1.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469810679_1_1.txt


title: G1_Cologne_251469810667_1_2.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469810667_1_2.txt


title: 2215_G3

description: aCGH analysis


title: 830_G3

description: aCGH analysis


title: G1_Cologne_251469812734_1_1.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469812734_1_1.txt


title: G1_Cologne_251469810782_1_2.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469810782_1_2.txt


title: G1_Cologne_251469812733_1_2.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469812733_1_2.txt


title: 1243_G3

description: aCGH analysis


title: G3_Cologne_251275011636.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011636.txt


title: G3_Cologne_251275011639.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011639.txt


title: G1_Cologne_251469812541_1_1.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469812541_1_1.txt


title: G1_Cologne_251469812543_1_1.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469812543_1_1.txt


title: G3_Cologne_251275011658.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011658.txt


title: G1_Cologne_251469812732_1_1.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469812732_1_1.txt


title: G3_Cologne_251270012622.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251270012622.txt


title: G1_Cologne_251469812733_1_1.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469812733_1_1.txt


title: G1_Cologne_251469812718_1_1.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469812718_1_1.txt


title: G3_Cologne_251275011661.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011661.txt


title: G3_Cologne_251275011660.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011660.txt


title: 984_G3

description: aCGH analysis


title: G1_Cologne_251469812732_1_2.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469812732_1_2.txt


title: G3_Cologne_251275011669.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011669.txt


title: G3_Cologne_251275011662.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011662.txt


title: G3_Cologne_251275011773.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011773.txt


title: G1_Cologne_251469812542_1_1.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469812542_1_1.txt


title: G3_Cologne_251275011610.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011610.txt


title: G3_Cologne_251275011771.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011771.txt


title: G3_Cologne_251328219276.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251328219276.txt


title: G3_Cologne_251275011596.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011596.txt


title: G1_Cologne_251469812541_1_2.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469812541_1_2.txt


title: G1_Cologne_251469810082_1_1.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469810082_1_1.txt


title: G1_Cologne_251328219285.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251328219285.txt


title: G1_Cologne_251469812734_1_2.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251469812734_1_2.txt


title: G1_Cologne_251328224477.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251328224477.txt


title: G1_Cologne_251328220149.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251328220149.txt


title: G1_Cologne_251328220491.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251328220491.txt


title: G3_Cologne_251275011614.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011614.txt


title: G1_Cologne_251275011688.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251275011688.txt


title: G3_Cologne_251275011613.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011613.txt


title: G3_Cologne_251275011766.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011766.txt


title: G2_Cologne_251275011692.txt

description:
aCGH
Agilent Feature Extraction File name: G2_Cologne_251275011692.txt


title: G2_Cologne_251275011659.txt

description:
aCGH
Agilent Feature Extraction File name: G2_Cologne_251275011659.txt


title: G3_Cologne_251275011628.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011628.txt


title: G1_Cologne_251328219422.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251328219422.txt


title: G1_Cologne_251275011682.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251275011682.txt


title: G2_Cologne_251270010387.txt

description:
aCGH
Agilent Feature Extraction File name: G2_Cologne_251270010387.txt


title: G1_Cologne_251275011617.txt

description:
aCGH
Agilent Feature Extraction File name: g1_Cologne_251275011617.txt


title: G2_Cologne_251275011655.txt

description:
aCGH
Agilent Feature Extraction File name: G2_Cologne_251275011655.txt


title: G2_Cologne_251275011663.txt

description:
aCGH
Agilent Feature Extraction File name: G2_Cologne_251275011663.txt


title: G1_Cologne_251275011616.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251275011616.txt


title: G2_Cologne_251275011631.txt

description:
aCGH
Agilent Feature Extraction File name: G2_Cologne_251275011631.txt


title: G3_Cologne_251275011598.txt

description:
aCGH
Agilent Feature Extraction File name: G3_Cologne_251275011598.txt


title: 1968_G2

description: aCGH analysis


title: G1_Cologne_251275011664.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251275011664.txt


title: G1_Cologne_251275011615.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251275011615.txt


title: ER71 EYFP E8.0 embryo wildtype EYFP positive replicate 1

status: Public on Nov 02 2011

city: Minneapolis

first: Fengli

last: Fu

address: 312 Church Street SE

institute: University of Minnesota

description: amplified twice

hyb_protocol: Amplified aRNAs were hybridized to Affymetrix mouse 430 2.0 full genome array chips at the BioMedical Genomics Center of the University of Minnesota  BioMedical Genomics Center of the University of Minnesota

scan_protocol: GeneChip were scanned according to Affymetrix standard protocols

data_processing: The data were processed with affymetrix RMA method

source_name: ER71 EYFP; ER71 wildtype, E8.0 embryo

label_protocol: MessageAmpII-Biotin Enhanced Kit

extract_protocol: trizol

treatment_protocol: digested with trypsin and sorted on a BD FACSAria

value: ER71 embryonic ER71 wildtype EYFP positive cells

tag: age

tag: eyfp

value: positive

tag: genotype

value: ER71 wildtype

tag: genetic background

value: C57BL/6 and FVB mixed line


title: G2_Cologne_251275011670.txt

description:
aCGH
Agilent Feature Extraction File name: G2_Cologne_251275011670.txt

value: female


title: G1_Cologne_251275011689.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251275011689.txt


title: ER71 EYFP E8.0 embryo ER71 mutant EYFP positive replicate 2

description: amplified twice

source_name: ER71 EYFP; ER71 mutant, E8.0 embryo

value: ER71 embryonic mutant EYFP positive cells

value: ER71 mutant


title: AT/RT tumor sample ID00663

status: Public on Sep 22 2011

city: Aurora

first: Diane

middle: K

last: Birks

state: CO

department: Neurosurgery

institute: University of Colorado, Denver - Anschutz Medical Campus

description: Atypical Teratoid / Rhabdoid Tumor patient sample

hyb_protocol: For all samples, 11.5 micrograms of fragmented, biotinylated cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 GeneChip array for 16 hours at 45-C. After hybridization, the arrays were washed and stained according to  the standard Amplification for Eukaryotic Targets Protocol (Affymetrix Inc.).

scan_protocol: All GeneChip arrays were scanned at 488 and 570 nm with a confocal G2500A Gene-Array Scanner (Agilent Technologies, Palo Alto, CA).

data_processing: Data were background corrected and normalized using the gcRMA algorithm in R, as implemented in Bioconductor (www.bioconductor.org). The resulting data are gene expression values in log2 scale. These 18 AT/RT samples are a subset of a total of 228 microarray tumor and control samples input to gcRMA.

source_name: patient tumor sample

label_protocol: For all samples other than ID03161, five micrograms of total RNA was reverse-transcribed using a T7-(dT) 24 oligomer and Superscript II Reverse Transcriptase (Invitrogen Corp., Carlsbad, CA). Subsequently, biotin-labeled cRNA was generated from the double-stranded cDNA template by in vitro transcription using T7 RNA polymerase and a BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). Biotinylated cRNA (20 micrograms) was fragmented to an average size of 35 to 200 bases with fragmentation buffer.  For sample ID03161, limited amount of starting RNA precluded use of this protocol. Instead ID03161 RNA was prepared using the Ambion Message Amp Premier RNA Amplification Kit (Applied Biosystems), according to manufacturer's directions, using a starting amount of 400 nanograms of RNA.

extract_protocol: RNA was extracted from each sample using an RNeasy or DNA/RNA AllPrep kit (Qiagen) according to the manufacturer’s directions

treatment_protocol: all samples were collected at time of surgery

value: F

tag: tumor location

value: posterior fossa

tag: chromosome 22 monosomy

value: ring chromosome 22

tag: age at diagnosis (months)

tag: overall survival (months)

tag: status

value: died of disease

value: atypical teratoid / rhabdoid tumor


title: AT/RT tumor sample ID00517

tag: gender

value: M

value: yes

value: Unknown

value: Lost to follow-up


title: AT/RT tumor sample ID00515

value: frontal lobe

value: no

value: Alive, no evidence of disease


title: AT/RT tumor sample ID00413


title: GBM_57

status: Public on Oct 31 2011

first: Andrew

middle: M

last: Donson

department: Pediatrics

institute: CU Anschutz Medical Campus

description: Gene expression data from surgical tumor sample of high grade astrocytoma

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values. The Affymetrix HG-U133 plus 2 microarray contains 54,675 probe sets including multiple probe sets for the same gene. In order to reduce error associated with multiple testing we used only a single probe set for each gene that possessed the highest gcRMA expression level across all our samples. This filtered list of the best expressed probe sets contained 20,722 genes.

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

extract_protocol:
Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500).
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: brain tumor (high grade astrocytoma)

tag: survival (months)


title: AT/RT tumor sample ID90005

value: unknown


title: AT/RT tumor sample ID00605


title: G1_Cologne_251275011667.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251275011667.txt

value: Neuroblastoma

value: stroma poor

value: German

value: male

tag: group


title: AT/RT tumor sample ID90004

value: F

value: posterior fossa

tag: tissue


title: G1_Cologne_251275011668.txt

description:
aCGH
Agilent Feature Extraction File name: G1_Cologne_251275011668.txt

tag: histology


title: AT/RT tumor sample ID00370

value: died of disease


title: AT/RT tumor sample ID90007

value: temporal

value: atypical teratoid / rhabdoid tumor


title: AT/RT tumor sample ID00737

value: M

value: Alive with recurrence


title: GBM_678


title: Huntington's disease 874H

status: Public on Sep 01 2011

city: Cambridge

first: Bin

last: Zheng

address: 65 Landsdowne Street

department: Center for Neurologic Diseases

institute: Brigham and Women's hospital

hyb_protocol: standard Affymetrix protocols

scan_protocol: standard Affymetrix protocols

data_processing: The data were processed and scaled to a target intensity of 100 for all probe sets by MAS5 in Biocondutor affy package.

source_name: Huntington's disease

extract_protocol: PAXgene blood RNA kit

tag: age at blood draw

value: whole blood


title: Control 894B

source_name: Control


title: AT/RT tumor sample ID00404

value: yes


title: AT/RT tumor sample ID00119


title: AT/RT tumor sample ID00687

value: died of complications


title: GBM_89


title: AT/RT tumor sample ID00514

value: parietal / occipital lobes

value: no


title: AT/RT tumor sample ID00504


title: AT/RT tumor sample ID00343

value: unknown


title: AT/RT tumor sample ID03161

value: Alive, no evidence of disease


title: Control 874G


title: Control 874E


title: Huntington's disease 874F


title: Huntington's disease 820F


title: Huntington's disease 874A


title: 675NT_Macro

status: Public on Aug 26 2011

city: Bronx

first: Miao

last: Shi

address: 1301 Morris Park ave

institute: Albert einstein College of Medicine

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the CHP files.

source_name: Macro Samples

label_protocol: 100ng total RNA was amplified using Ambion WT Expression Kit following the manufacturer’s instructions. 5.5 µg of amplification products were labeled with Affymetrix WT Terminal Labeling Kit hybridized to Affymetrix HG Gene 1.0ST chips using Affymetrix Hybridization Control Kit and washed and stained using Affymetrix Wash and Stain Kit. All steps were done following the manufacturer’s instructions.

extract_protocol: 50mg to 80mg of snap frozen lung tissue was added to a tube containing 1 ml of ice cold trizol and homogenized until tissue was totally homogenized. After incubation for 5 min at room temperature, 0.2ml of chloroform was added; tube was shaked vigorously by hand for 15 sec and then incubated for 3 min at room temperature. Then samples were centrifuged for 20 min at 12000g at 4C. Aqueous phase was transfered to a clean 1.5-ml tube and 1 x volume of 70% ethanol was added into the aqueous phase. Sample was applied to the Rneasy column and centrifuged at 8000g for 30 sec. Further procedure was done using Rneasy mini kit according to the manufactures suggestions including an optional 30 min DNase I treatment.

tag: disease state

value: Non-Tumor

tag: cell type

value: Adeno carcinoma


title: Control 874D


title: Control 874C


title: Huntington's disease 820E


title: 688NT_Macro


title: Huntington's disease 820D


title: 675T_Macro

value: Tumor


title: 670NT_Macro

value: Adeno Squamous-cell carcinoma


title: 688T_Macro


title: 618NT_Macro


title: 692NT_Macro


title: 670T_Macro


title: AT/RT tumor sample ID00003

value: F

value: posterior fossa


title: Huntington's disease 820C


title: 618T_Macro


title: Huntington's disease 874B


title: Control 820B


title: 653T_Macro


title: 642T_Macro


title: 642NT_Macro


title: 551NT_Macro

value: Squamous-cell carcinoma


title: 611T_Macro


title: 1958_G1

description: aCGH analysis

value: Neuroblastoma

value: stroma poor

tag: tumor stage

tag: patient nationality

value: Italian

value: female


title: 692T_Macro


title: 607T_Macro


title: 619T_Macro


title: 606NT_Macro


title: 558T_Macro


title: 610NT_Macro


title: 619NT_Macro


title: 539T_Macro


title: 610T_Macro


title: 653NT_Macro


title: 538NT_Macro


title: 542NT_Macro


title: 558NT_Macro


title: 542T_Macro


title: 539NT_Macro


title: 560T_Macro


title: 560NT_Macro


title: 604NT_Macro


title: 607NT_Macro


title: 603T_Macro


title: 543T_Macro


title: 507NT_Macro


title: 534T_Macro


title: 538T_Macro


title: 551T_Macro


title: 507T_Macro


title: 603NT_Macro


title: 543NT_Macro


title: 534NT_Macro


title: 596NT_Macro


title: 566T_Macro


title: 552T_Macro


title: 566NT_Macro


title: 581T_Macro


title: 561T_Macro


title: 596T_Macro


title: 541NT_Macro


title: 552NT_Macro


title: 325T(2)_Macro


title: 541T_Macro


title: 325NT(2)_Macro


title: 325NT_Macro


title: 561NT_Macro


title: 581NT_Macro


title: 670T_LCM

source_name: LCM Samples

label_protocol: 1ng total RNA was used as input for the Pico amplification and 4ug of amplified cDNA was used for Exon Module amplification. cDNA amplification products were fragmented and labeled with biotin using the NuGEN FL module, hybridized to HG Gene 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix Hybridization Control Kit. And washed and stained using Affymetrix Wash and Stain kit. All steps were processed following the manufactures suggestions.

extract_protocol:
LCM of lung tissue: Snap frozen tissue was reembedded in cold Tissue-Tek optimal cutting temperature medium (Sakura Finetek USA, Inc.) Three sections (12uM thick) from each frozen tumor and non-tumor block were cut in a refrigerated cryostat at −25°C and placed on nuclease and human nucleic acid free membrane slides (Leica, Herborn, Germany). The sections were stored at -80°C until use or immediately stained with a rapid H&E staining protocol (95% ethanol (10 s), Rnase free water (10s) Gills hematoxylin (2min), Rnase free water (10s), blueing reagent (30s), 70% Ethanol (10s), Eosin Y (2s), 95% Ethanol (10s), 100% ethanol (30s), 100 % Ethanol (1 min). Once slide was air dried, slide was placed on the stage for microdissection and desired cells were microdissected within 30 minutes into the cap of a 200 µl PCR tubes filed with 20 µl RLT/β-ME buffer (Qiagen), using Leica AS LMD LCM system for each sample. This procedure was repeated on the next slide until a total of 1000 cells were captured for that case. The number of slides used per case varied from 1 to 3, as every case and every tumor block had different sized tumors. Distinguishing Tumor cells from two different types of Non-Tumor lung tissue compartments (AC versus BEC) could be done with confidence in these snap-frozen samples, given the quality of real-time images guiding microdissection.
For each patient, a pathologist assessed an H&E stained slide from each frozen tumor block and normal block.
RNA extraction of LCM Samples and amplification for Microarray: RNA samples for amplification with the Pico kit were isolated from 1000 cells using the RNeasy Micro Kit (Qiagen) including the optional DNase treatment, according to the manufacturer's instructions. Total RNA was quantified using a Nanodrop Spectrophotometer 2000 (Thermo Scientific Inc., Waltham, MA, USA) and the quality confirmed on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA amplifications were carried out using Nugen Pico WTA amplification system according to the manufacturers’ suggestions followed by an additional amplification step using Nugen Exon Module.


title: 304T_Macro


title: 159NT_Macro


title: 618NT_LCM


title: 642T_LCM


title: 610T_LCM


title: 325T_Macro


title: 159T_Macro


title: 619NT_LCM


title: 611T_LCM


title: 670NT_LCM


title: 610NT_LCM


title: 604NTB_LCM

value: Non-Tumor Bronchy


title: 604NT_LCM


title: 603NT_LCM


title: 603T_LCM


title: 566T_LCM


title: 558T_LCM


title: 596T_LCM


title: 606T_Macro


title: 596NT_LCM


title: 552T_LCM


title: 560NT_LCM


title: 606T_LCM


title: 581T_LCM


title: 566NT_LCM


title: 561T_LCM


title: 561NTB_LCM


title: 581NT_LCM


title: 552NTB_LCM


title: 561NT_LCM


title: 552NT_LCM


title: 551T_LCM


title: 539NT_LCM


title: 551NT_LCM


title: 539T_LCM


title: 543T_LCM


title: 542NT_LCM


title: 542T_LCM


title: 534NT_LCM


title: 538T_LCM


title: 534NTB_LCM


title: 538NT_LCM


title: 534T_LCM


title: 507T_LCM


title: 325NTB_LCM


title: 304NT_Macro


title: 325T_LCM


title: 325NT_LCM


title: Pig13_Failure

status: Public on Aug 24 2011

city: Uppsala

first: Per

last: Vikholm

address: Akademiska sjukhuset

department: Cardiothoracic Surgery

country: Sweden

institute: Uppsala University

hyb_protocol: Affymetrix GeneChip® expression arrays (Porcine Genome Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev2, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450

scan_protocol: GeneChips were scanned using a GeneChip® Scanner 3000 7G

data_processing: The raw data was processed using Partek Genomic Suite software (Partek Inc, St Louis, MO). Two-way analysis of variance (ANOVA) method was used to calculate p values.

organism: Sus scrofa

source_name: Right ventricular free wall, ischemia 120 min

label_protocol: 250 nanograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® 3’ IVT Express Kit Manual (PN 702646 Rev1, Affymetrix Inc., Santa Clara, CA)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified using RNeasy columns (Quiagen)

tag: pig number

value: Right ventricule

tag: breed

value: mixed breed of Hampshire, Yorkshire and Swedish Landrace

tag: treatment group

value: Failure


title: Pig13_Baseline

source_name: Right ventricular free wall, baseline

value: Baseline


title: Pig11_Failure


title: 507NT_LCM


title: Pig12_Baseline


title: Pig11_Baseline


title: 304NT_LCM


title: Pig9_Failure


title: 304T_LCM


title: Pig9_Baseline


title: Pig6_Failure


title: Pig8_Failure


title: Ependymoma 101

status: Public on Aug 15 2011

city: Houston

first: Stephen

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

institute: Baylor College of Medicine

description: PLIER expression value derived from Expression Console (v1.1) software, core-gene level analysis

hyb_protocol: Samples were hybridized to the Affymetrix Exon 1.0ST arrays at the London Regional Genomics Centre (London, Ontario)

scan_protocol: Array scanning was performed according to manufacturers instructions (Affymetrix).

data_processing: Raw data were processed with Affymetrix Expression Console (version 1.1). Gene Level (CORE content) analysis was performed using the following settings: PLIER summarization, PM-GCBG background correction, Quantile (sketch) normalization. Probesets were then annotated using the human genome (HG19) build within Expression Console.

source_name: Brain Tumor

label_protocol: 2 micrograms of RNA was used for single-strand cDNA synthesis then labeling using the Affymetrix WT sense target labeling assay all performed according to Affymetrix manufacturers instructions.

extract_protocol: Fresh frozen tumors were immersed in liquid nitrogen, then pulverized into a powder using a mortar and pestle. RNA was then extracted using the Trizol (Invitrogen) method according to manufacturers directions. Concentration of mRNA was determined using a NanoDrop. Quality of mRNA and assessment of DNA contamination was determined by analysis of 50-200ng RNA on the Agilent Bioanalyzer.

value: Ependymoma brain tumor

tag: age

tag: location

value: Supratentorial Region


title: Ependymoma 100

value: M

value: Posterior Fossa


title: Ependymoma 99


title: Ependymoma 102


title: Pig6_Baseline


title: Ependymoma 96


title: Ependymoma 97


title: Ependymoma 92


title: Ependymoma 95


title: Ependymoma 88


title: Ependymoma 93


title: Ependymoma 89

value: Spinal Cord


title: Ependymoma 84

value: F


title: Ependymoma 87


title: Pig12_Failure


title: Ependymoma 85


title: Pig8_Baseline


title: Ependymoma 94


title: Ependymoma 76


title: Ependymoma 77


title: Ependymoma 82


title: Ependymoma 79


title: Ependymoma 74


title: Ependymoma 98


title: Ependymoma 80


title: Ependymoma 81


title: Ependymoma 75


title: Ependymoma 78


title: Ependymoma 86


title: Ependymoma 73


title: Ependymoma 91


title: Ependymoma 83


title: Ependymoma 90


title: 642NTB_LCM

value: Adeno carcinoma


title: Ependymoma 72


title: Ependymoma 68


title: Ependymoma 67


title: Ependymoma 70


title: Ependymoma 66


title: Ependymoma 65


title: Ependymoma 60


title: Ependymoma 62


title: Ependymoma 59


title: Ependymoma 57


title: Ependymoma 49


title: Ependymoma 69


title: Ependymoma 58


title: Ependymoma 61


title: Ependymoma 71


title: Ependymoma 54


title: Ependymoma 50


title: Ependymoma 55


title: Ependymoma 38


title: Ependymoma 56


title: Ependymoma 39


title: Ependymoma 48


title: Ependymoma 47


title: Ependymoma 63


title: Ependymoma 46


title: Ependymoma 64


title: Ependymoma 40


title: Ependymoma 37


title: Ependymoma 34


title: Ependymoma 42


title: Ependymoma 30


title: Ependymoma 31


title: Ependymoma 51


title: Ependymoma 36


title: Ependymoma 25


title: Ependymoma 43


title: Ependymoma 26


title: Ependymoma 23


title: Ependymoma 45


title: Ependymoma 35


title: Ependymoma 52


title: Ependymoma 27


title: Ependymoma 44


title: Ependymoma 21


title: Ependymoma 32


title: Ependymoma 22


title: Ependymoma 53


title: Ependymoma 18


title: Ependymoma 19


title: Ependymoma 41


title: Ependymoma 33


title: Ependymoma 17


title: Ependymoma 28


title: Ependymoma 20


title: Ependymoma 12


title: Ependymoma 16


title: Ependymoma 11


title: Ependymoma 15


title: Ependymoma 10


title: Ependymoma 6


title: Ependymoma 13


title: Ependymoma 4


title: Ependymoma 8


title: Ependymoma 5


title: Ependymoma 14


title: Ependymoma 24


title: PS-M1-

status: Public on Jun 09 2011

city: Bangalore

first: Sudhir

last: Krishna

state: Karnataka

address: UAS-GKVK Campus, Bellary Road

country: India

institute: National Centre for Biological Sciences, TIFR

description: Gene expression from freshly isolated cancer biopsy

hyb_protocol: 1650ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent Technologies G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1  and 10.5.1.1)

data_processing: The normalization was done using GeneSpring GX 11 Software.

source_name: Lin- CD66-

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: The primary cancer samples (PS-M1) were used without culturing. The CaSki spheres were grown for 14 days in non-adherent condition in sphere medium and the adherent weregrwon in DMEM with serum.

extract_protocol: Qiagen mini kit for CaSki adherent and sphere following the manufacturer's recommendations. Trizol method for patient samples.RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: primary squamous cell cervical cancarcinoma

tag: tumor class

value: FIGO Stage IIIB


title: PS-M2+

source_name: Lin- CD66+


title: Ependymoma 9


title: Ependymoma 7


title: Ependymoma 3


title: Ependymoma 2


title: PS-M3+


title: PS-M1+


title: PS-M4+


title: Ependymoma 1


title: Sphere2

description: Gene expression from cell line grown in sphere medium

hyb_protocol: 1650ng of cy3 labeled samples for  4x44k arrays and 600 ng  cy3 labeled samples for 8x15 arrays were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

source_name: cell line grown in sphere medium

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the  samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: The primary cancer samples (PS-M1) were used without culturing. The CaSki spheres were grown for 14days in non-adherent condition in sphere medium and the adherent weregrwon in DMEM with serum.

tag: cell line

value: CaSki

value: cell line derived from metastatic lesion


title: Adherent1

description: Gene expression from cell line grown in serum

source_name: cell line grown in serum


title: Adherent2