title: Enterococcus faecalis  OG1RF copY mutant Cu treatment 1

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

state: VI

address: Av. Libertador Bernardo OHiggins 611

department: ICI

country: Chile

institute: Universidad de OHiggins

description:
GEO_EFREYES2010_080625_Efae_V583_EXP_growth_medium_N_Cu_strain_E_faecalis_OG1RF_copY_mutant_rep1
This sample is of copY mutant Enterococcus faecalis V583 exposed to Cu treatment, correspond to the first of two biological replicates used in this experiment, each from separate cultures.

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

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

data_processing:
All data was processes automatically using DNASTAR software Array star 3.0. See www.dnastar.com.
Student's t-test  was used to identify significantly different gene expression levels with a p<0.05 and a 4-fold magnitude of change between the average value of each gene and its corresponding reference, using the DNASTAR software Array star 3.0. See www.dnastar.com.

organism: Enterococcus faecalis OG1RF

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

growth_protocol: Enterococcus faeclis OG1RF wild-type and copY mutant were grown to mid-log phase (O.D600nm 1.0), aerobically estandar condition at 37°C in N medium (Peptone 1 % (Difco), yeast extract 0.5 % (Difco), Na2HPO4 1 % (Merck) and glucose 1 % (Oxoid). For copper treatment, cultures were grown at the same condition by adding Cu (CuSO4 0.5 mM) to the control medium.

extract_protocol: The RNA was extracted using a Qiagen RNeasy mini kit (Qiagen). Residual contaminating genomic DNA was removed with RQ1 RNase-free DNase (Promega) treatment according to the manufacturer’s protocol. The integrity of the RNA was assessed by gel electrophoresis.

treatment_protocol: All Cu-treated cells were exposed for 3 hours prior to harvesting (at mid-log phase, OD600nm 1.0); the untreated cells were collected simultaneously.

value: copY deletion were constructed using the PheS* system (Kristich, Plasmid 2007, 57(2):131-144), resulting in non-polar deletion mutants genotype


title: Enterococcus faecalis  OG1RF copY mutant Cu treatment  2

status: Public on Feb 14 2011

type: RNA

description:
GEO_EFREYES2010_080625_Efae_V583_EXP_growth_medium_N_Cu_strain_E_faecalis_OG1RF_copY_mutant_rep2
This sample is of copY mutant Enterococcus faecalis V583 exposed to Cu treatment, correspond to the second of two biological replicates used in this experiment, each from separate cultures.

molecule: total RNA

tag: genotype


title: Enterococcus faecalis  OG1RF wild-type Cu treatment 1

description:
GEO_EFREYES2010_080625_Efae_V583_EXP_growth_medium_N_Cu_strain_E_faecalis_OG1RF_wild-type_rep1
This sample is of wild-type Enterococcus faecalis V583 exposed to Cu treatment, correspond to the first of two biological replicates used in this experiment, each from separate cultures.

value: Wild-type


title: Transitional B, rep 3

city: Boston

first: Michael

middle: Richard

last: Green

state: MA

address: 44 Binney Street

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: Gene expression data from purified B-cell population

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

scan_protocol: Scanned using an Affymetrix GCS3000 scanner

data_processing: Raw data was normalized for batch effects using robust multiarray (RMA) preprocessing with quantile normalization and a median polish using RMA Express, version 1.0.4.

label: biotin

organism: Mus musculus

source_name: Purified Transitional (B220-positive/Cd93-positive) B-cells

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

extract_protocol: Tripure (Roche) isolation of RNA was performed according to the manufacturers protocol. Total RNA was amplified to cRNA using Ovation RNA amplification system V2 (NuGen) according to the manufacturers protocol.

tag: strain

tag: tissue

value: Spleen

tag: cell type


title: Enterococcus faecalis  OG1RF copY mutant 1

description:
GEO_EFREYES2010_080625_Efae_V583_EXP_growth_medium_N_strain_E_faecalis_OG1RF_copY_mutant_rep1
This sample is of copY mutant Enterococcus faecalis V583, correspond to the first of two biological replicates used in this experiment, each from separate cultures.

source_name: Enterococcus faecalis  OG1RF copY mutant


title: Transitional B, rep 1

value: Purified Transitional (B220-positive/Cd93-positive) B-cells


title: Pre-B, rep 3

source_name: Purified Pre-B (B220-positive/CD43-low/IgM-negative) B-cells

value: Bone Marrow


title: Transitional B, rep 2


title: Enterococcus faecalis  OG1RF copY mutant 2

description:
GEO_EFREYES2010_080625_Efae_V583_EXP_growth_medium_N_strain_E_faecalis_OG1RF_copY_mutant_rep2
This sample is of copY mutant Enterococcus faecalis V583, correspond to the second of two biological replicates used in this experiment, each from separate cultures.


title: Pro-B, rep 3

source_name: Purified Pro-B (B220-positive/CD43-high/IgM-negative) B-cells


title: [CD4+ T-Cells]_[RO]_[2]

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

institute: Purdue

description: Mouse CD4 T cells were cultured in vitro to obtain RNA for the assay

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with a GeneChip Hybridization Oven 640 for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 400 with fludics protocol EukGE_WS2v5 and user prepared solutions, as per protocols provided by Affymetrix in the GeneChip Expression Analysis Technical Manual, 2004. This included Enzo Life Sciences' BioArray Eukaryotic Hybridization Controls.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G enabled forHigh-Resolution Scanning.  The instruments were controlled using GCOS version1.4 software.

data_processing: The data were condensed with MAS 5.0 using the GeneChip Operation Software.

label: Biotin  (as a biotinylated nucleotide)

source_name: Mouse Spleen, peripheral lymph nodes, mesenteric lymph nodes

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA according to the Single Round RNA Amplification and Biotin Labeling System  (Enzo Life Sciences Intl.  Plymouth Meeting, PA)

extract_protocol:
Trizol
Qiagen Total RNA isolation kit

value: Spleen + Lymph Nodes

value: CD4+ T cells


title: CM11P17_240_617_1_1

status: Public on Feb 15 2011

type: genomic

city: SAN DIEGO

first: GULSAH

last: ALTUN

state: CA

address: 3030 Science Park Rd. 3rd floor, room 3020

institute: THE SCRIPPS RESEARCH INSTITUTE

description: Genomic DNA extracted was genotyped using HumanOmni1-Quad BeadChip Genotyping BeadChips (Illumina).

hyb_protocol: standard Illumina protocol

scan_protocol: Scanned on a BeadArray Reader (Illumina) using standard Illumina Protocol.

data_processing: We have used the Illumina Genome Studio software version 2010.2 to generate the SNP calls.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Undifferentiated hESC

label_protocol: standard Illumina protocol

extract_protocol: Qiagen DNeasy Blood and Tissue Kit

value: HESC

tag: passage number


title: Pro-B, rep 2

value: Purified Pro-B (B220-positive/CD43-high/IgM-negative) B-cells


title: Enterococcus faecalis  OG1RF wild-type Cu treatment 2

description:
GEO_EFREYES2010_080625_Efae_V583_EXP_growth_medium_N_Cu_strain_E_faecalis_OG1RF_wild-type_rep2
This sample is of wild-type Enterococcus faecalis V583 exposed to Cu treatment, correspond to the second of two biological replicates used in this experiment, each from separate cultures.


title: Pro-B, rep 1


title: ovules, rep2

city: Oeiras

first: Filipe

last: Borges

state: Lisbon

address: Rua da Quinta Grande, 6

country: Portugal

institute: Instituto Gulbenkian de Ciência

description:
At_ovules_L2
Gene expression analysis of pollen-pistil interactions in Arabidopsis

hyb_protocol: Fifteen micrograms of cRNA were used in a 300-mL hybridization containing added hybridization controls; 200 mL of mixture were hybridized on arrays for 16 h at 45°C. Standard posthybridization wash and double-stain protocols (EukGE-WS2v4) were used on an Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 2500.

data_processing: Scanned arrays were analyzed first with Affymetrix MAS 5.0 software to obtain Absent/Present calls and subsequent analysis was performed with dChip 1.3 (http://www.dchip.org, Wong Lab, Harvard). First, each GeneChip experiment was performed with biological replicates. Second, we used a samplewise normalization to the median median probe cell intensity (CEL) of all arrays: For each sample, the median CEL intensity of one of the replicates was scaled to the median median CEL intensity of all arrays. Then the remaining replicates were normalized to this array (baseline) applying an Invariant Set Normalization Method (Li and Wong, 2001)

organism: Arabidopsis thaliana

source_name: Arabidopsis ovules

label_protocol: 100 ng of total RNA were used in a reverse transcription reaction (SuperScript II; Invitrogen, Paisley, UK). double-stranded cDNA was used in an in vitro transcription reaction to generate cRNA (MEGAscript T7 kit; Ambion, Austin, TX); 400 ng of  cRNA were used for a second cDNA synthesis, followed by a second in vitro transcription reaction to generate biotinylated cRNA (ENZO BioArray High- Yield RNA Transcript Labeling kit; ENZO Diagnostics, Farmingdale, NY). Size distribution of the cRNA and fragmented cRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Seeds of Arabidopsis thaliana (L.), Heynh, ecotype Columbia (NASC, Nottingham, UK) were sown on soil and kept for three days at 4ºC in the dark to promote seed stratification. Seedlings were grown in short-day conditions (8h light/16h dark at 22-24ºC) for two weeks and then transferred to long-day conditions (16h light/8 h dark at 22-24ºC) to induce flowering.

extract_protocol: Total RNA was extracted from tissues using the RNeasy Mini Plant Kit (Qiagen, Hilden, Germany). Concentration and purity was determined by spectrophotometry and integrity was confirmed using an Agilent 2100 Bioanalyser with a RNA 6000 Nano assay (Agilent Technologies, Palo Alto, Ca).

treatment_protocol: Pistils were collected at 0, 0.5, 3.5 and 8 Hours After Pollination (HAP) and immediately frozen in liquid nitrogen. Two pistils from each time point were collected and stained with 0.1 % de-colorized aniline blue (Martin, 1959) as a control for pollen tube growth. Unfertilized ovules were collected by the funiculus from dissected UP and immediately frozen in liquid nitrogen.

tag: ecotype

value: Columbia

value: ovule


title: ovules, rep1

description:
At_ovules_L1
Gene expression analysis of pollen-pistil interactions in Arabidopsis


title: unpollinated pistil, rep1

description:
At_PPI_K7
Gene expression analysis of pollen-pistil interactions in Arabidopsis

source_name: Arabidopsis pistils unpollinated

value: pistil


title: Enterococcus faecalis  OG1RF wild-type 2

description:
GEO_EFREYES2010_080625_Efae_V583_EXP_growth_medium_N_strain_E_faecalis_OG1RF_wild-type_rep2
This sample is of wild-type Enterococcus faecalis V583, correspond to the second of two biological replicates used in this experiment, each from separate cultures.

source_name: Enterococcus faecalis  OG1RF wild-type


title: unpollinated pistil, rep2

description:
At_PPI_K8
Gene expression analysis of pollen-pistil interactions in Arabidopsis


title: Pre-B, rep 1

value: Purified Pre-B (B220-positive/CD43-low/IgM-negative) B-cells


title: pistil 8.0HAP, rep2

description:
At_PPI_K6
Gene expression analysis of pollen-pistil interactions in Arabidopsis

source_name: Arabidopsis pistils 8 hours after pollination

tag: time (hours after pollination)


title: [CD4+ T-Cells]_[RA]_[2]


title: pistil 3.5HAP, rep2

description:
At_PPI_J7
Gene expression analysis of pollen-pistil interactions in Arabidopsis

source_name: Arabidopsis pistils 3.5 hours after pollination


title: pistil 0.5HAP, rep1

description:
At_PPI_J4
Gene expression analysis of pollen-pistil interactions in Arabidopsis

source_name: Arabidopsis pistils 0.5 hours after pollination


title: pistil 3.5HAP, rep1

description:
At_PPI_J6
Gene expression analysis of pollen-pistil interactions in Arabidopsis


title: Bcl6 Trans, rep 4

description: Gene expression data from lymphoid tumor

source_name: Lymphoid tumor

value: Bcl6 transgenic (Catoretti et al., Cancer Cell 2005;7:445-455)

value: Tumor

value: Bcl6 knock-in

value: Lymphoid tumor


title: [CD4+ T-Cells]_[Ro]_[1]


title: pistil 8.0HAP, rep1

description:
At_PPI_K5
Gene expression analysis of pollen-pistil interactions in Arabidopsis


title: [CD4+ T-Cells]_[RA]_[1]


title: Enterococcus faecalis  OG1RF wild-type 1

description:
GEO_EFREYES2010_080625_Efae_V583_EXP_growth_medium_N_strain_E_faecalis_OG1RF_wild-type_rep1
This sample is of wild-type Enterococcus faecalis V583, correspond to the first of two biological replicates used in this experiment, each from separate cultures.


title: BG03P55_124_372_1_3


title: Pre-B, rep 2

description: Gene expression data from purified B-cell population


title: Animal 177 (-seizures) Left/Right

status: Public on Feb 13 2011

first: Kellen

last: Winden

address: 300 Longwood Ave

department: Neurology

institute: Boston Children's Hospital

description: dye swap

hyb_protocol: The microarray hybridizations were performed according to manufacturer's protocols.

scan_protocol: The microarray scanning were performed according to manufacturer's protocols.

data_processing: We imported the raw data from the Agilent microarrays into R (http://www.r-project.org/). We used available libraries from Bioconductor (http://www.bioconductor.org/) to analyze the two-color microarray designs. We used the linear models package (LIMMA). After the removal of flagged data, we used the default method for background subtraction and used quantile normalization to normalize values between arrays.

organism: Rattus norvegicus

source_name: Animal 177 (-seizures) Left

label_protocol: We used 100 ng of RNA as the initial starting template, which was labeled with Cy-3 or Cy-5 cytidine -5'-triphosphate (CTP) using the low input fluorescent linear amplification kit (Agilent). The labeled cRNA concentration was verified (Nanodrop) and RNA quality was checked on an Agilent Bioanalyzer (Agilent).

growth_protocol: Beginning 2 months after kainate injection, video monitoring was performed for all rats in order to detect spontaneous behavioral seizures. After eight months of video monitoring rats were divided for electrophysiological (n=12), microarray (n=10).

extract_protocol: Ten rats were taken for microarray studies: five with documented behavioral spontaneous seizures and five rats without spontaneous seizures. Rats were anesthetized with isofluorane, brains were quickly removed and sectioned by vibratome into 400 µm slices. Dentate gyri were removed under dissecting microscope and placed in -80C for further microarray experiments. The comparisons were performed between the area of dentate gyri (DG) adjacent to the KA lesion and non-lesioned contralateral side in each animal. RNA extraction was performed using Trizol (Invitrogen). RNA concentration and quality were evaluated using Nanodrop ND-1000 spectrophotometer (NanoDrop) and Agilent 2100 Bioanalyser (Agilent).

treatment_protocol: Adult male rats were given atropine (0.04 mg i.m.), anesthetized with isofluorane 2%, and unilaterally injected with kainic acid (KA; 0.2 µl; 2.0 µg/µl normal saline) in the right posterior CA3 area of hippocampus (AP= -5.6 mm, ML= 4.0 mm, DV= 7.0 mm. A 30ga. needle attached to a Hamilton 1.0 µl syringe was lowered into the injection site and after 5 minutes, one half of the volume was injected. After another 5 minutes, the needle was raised 0.5 mm and the remainder of the solution was injected. After 20 minutes, the needle was withdrawn.

value: Dentate gyrus

tag: seizure

tag: side

value: left

source_name: Animal 177 (-seizures) Right

value: right


title: Animal 154 (-seizures) Right/Left

description: R/L (-Seizures)

source_name: Animal 154 (-seizures) Right

source_name: Animal 154 (-seizures) Left


title: Animal 154 (-seizures) Left/Right

description: dye swap


title: pistil 0.5HAP, rep2

description:
At_PPI_J5
Gene expression analysis of pollen-pistil interactions in Arabidopsis


title: 01N3J_Oligo

city: Cincinnati

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

hyb_protocol: Affymetrix Standard.

scan_protocol: Agilent G2500A GeneArray scanner

data_processing: RMA preprocessed values from a larger group of arrays.

label: Biotin

source_name: Peripheral Blood Mononuclear Cells

label_protocol: NuGEN Ovation V1

extract_protocol: Peripheral blood mononuclear cells (PBMC) were isolated by Ficoll (GE Healthcare, Piscataway, NJ) gradient centrifugation at the site of collection, and RNA was immediately stabilized in TRIzol (Invitrogen, Carlsbad, CA).

value: Peripheral blood mononuclear cells

tag: original diagnosis

value: oligoarticular JIA

tag: ttf

tag: race

value: Caucasian/White

tag: sex

value: Male


title: Animal 177 (-seizures) Right/Left

description: R/L (-Seizures)


title: Animal 183 (-seizures) Left/Right

description: dye swap

source_name: Animal 183 (-seizures) Left

source_name: Animal 183 (-seizures) Right


title: Animal 183 (-seizures) Right/Left

description: R/L (-Seizures)


title: Animal 181 (+seizures) Right/Left

description: R/L (+Seizures)

source_name: Animal 181 (+seizures) Right

source_name: Animal 181 (+seizures) Left


title: Animal 170 (+seizures) Left/Right

description: dye swap

source_name: Animal 170 (+seizures) Left

source_name: Animal 170 (+seizures) Right


title: Animal 152 (-seizures) Left/Right

description: dye swap

source_name: Animal 152 (-seizures) Left

source_name: Animal 152 (-seizures) Right


title: Animal 182 (+seizures) Left/Right

description: dye swap

source_name: Animal 182 (+seizures) Left

source_name: Animal 182 (+seizures) Right


title: Animal 170 (+seizures) Right/Left

description: R/L (+Seizures)


title: Animal 152 (-seizures) Right/Left

description: R/L (-Seizures)


title: Animal 169 (-seizures) Right/Left

description: R/L (-Seizures)

source_name: Animal 169 (-seizures) Right

source_name: Animal 169 (-seizures) Left


title: Animal 169 (-seizures) Left/Right

description: dye swap


title: Animal 180 (+seizures) Right/Left

description: R/L (+Seizures)

source_name: Animal 180 (+seizures) Right

source_name: Animal 180 (+seizures) Left


title: Animal 148 (+seizures) Left/Right

description: dye swap

source_name: Animal 148 (+seizures) Left

source_name: Animal 148 (+seizures) Right


title: Animal 181 (+seizures) Left/Right

description: dye swap


title: Animal 148 (+seizures) Right/Left

description: R/L (+Seizures)


title: Animal 182 (+seizures) Right/Left

description: R/L (+Seizures)


title: Animal 180 (+seizures) Left/Right

description: dye swap


title: Animal 152 (-Seizures) Left

description: L dg -Seizures

data_processing: We imported the raw data from the Codelink microarrays into R (http://www.r-project.org/). We used available libraries from Bioconductor (http://www.bioconductor.org/) to analyze the one-color microarray design. We used the linear models package (LIMMA). After the removal of flagged data, we used the default method for background subtraction and used quantile normalization to normalize values between arrays.

source_name: Animal 152 (-Seizures) Left

label_protocol: We used 100 ng of RNA as the initial starting template, which was labeled with biotin using the low input fluorescent linear amplification kit (Agilent). The labeled cRNA concentration was verified (Nanodrop) and RNA quality was checked on an Agilent Bioanalyzer (Agilent).


title: Animal 180 (+Seizures) Left

description: L dg +Seizures

source_name: Animal 180 (+Seizures) Left


title: Animal 169 (-Seizures) Right technical rep 2

description: R dg -Seizures

source_name: Animal 169 (-Seizures) Right


title: Animal 154 (-Seizures) Left

description: L dg -Seizures

source_name: Animal 154 (-Seizures) Left


title: Animal 154 (-Seizures) Right

description: R dg -Seizures

source_name: Animal 154 (-Seizures) Right


title: Animal 180 (+Seizures) Right

description: R dg +Seizures

source_name: Animal 180 (+Seizures) Right


title: Animal 183 (-Seizures) Left

description: L dg -Seizures

source_name: Animal 183 (-Seizures) Left


title: Animal 169 (-Seizures) Left technical rep 2

description: L dg -Seizures

source_name: Animal 169 (-Seizures) Left


title: Animal 181 (+Seizures) Left technical rep 2

description: L dg +Seizures

source_name: Animal 181 (+Seizures) Left


title: Animal 148 (+Seizures) Right

description: R dg +Seizures

source_name: Animal 148 (+Seizures) Right


title: Animal 152 (-Seizures) Right

description: R dg -Seizures

source_name: Animal 152 (-Seizures) Right


title: Animal 181 (+Seizures) Right technical rep 2

description: R dg +Seizures

source_name: Animal 181 (+Seizures) Right


title: Animal 148 (+Seizures) Left

description: L dg +Seizures

source_name: Animal 148 (+Seizures) Left


title: Animal 183 (-Seizures) Right

description: R dg -Seizures

source_name: Animal 183 (-Seizures) Right


title: Animal 177 (-Seizures) Right

description: R dg -Seizures

source_name: Animal 177 (-Seizures) Right


title: Animal 177 (-Seizures) Left

description: L dg -Seizures

source_name: Animal 177 (-Seizures) Left


title: PC3-NZD3

city: london

first: sandeep

middle: k

last: Nadendla

address: 2 newark street

department: ccr

country: United Kingdom

institute: qmul

description: Bone metastasis PCa cell line

hyb_protocol: Standard Illumina hybridization protocol (by DIRECT HYBRIDISATION): each cell line was analysed in triplicate.

scan_protocol: Scanning was done using the iScan control software-1.3.10+ with auto loader mode 2.0+ (i.e. according to Illumina's instructions)

data_processing: Data processing and normalisation was performed with Illumina Bead studio software

source_name: Established PCa cell line

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

growth_protocol: All cells were cultured in RPMI-1640 (Phenol red free) with 10% fetal bovine serum, pencillin (50 U/ml), streptamycin (50 mg/ml), glutamine (2 mM) and incubated at 37C. 5% CO2

extract_protocol: total RNA was extracted using the Qiagen RNeasy kit guidelines and quantified using thermoscientific nano drop spectrophotometer.

treatment_protocol: Cells were seeded at a density of 7000 cells/cm2 and RNA was harvested 3 days post-seeding: all cells were treated the same

tag: cell line

value: PCa

tag: type

value: Androgen independent

tag: morphology

value: Basal-like and fusiform

tag: chip loading

value: triplicate


title: DU145-NZD3

description: Brain metastasic PCa cell line

value: Compact and basal-like


title: DU145-NZD2

description: Brain metastasic PCa cell line


title: Animal 169 (-Seizures) Left

description: L dg -Seizures


title: Animal 170 (+Seizures) Left

description: L dg +Seizures

source_name: Animal 170 (+Seizures) Left


title: PC3-NZD2

description: Bone metastasis PCa cell line


title: PC3-NZD1

description: Bone metastasis PCa cell line


title: Animal 169 (-Seizures) Right

description: R dg -Seizures


title: LNCaP-GLI1-NZD3

description: Lymph node metastatic PCa cell line expressing ectopic GLI1 (from integrated pBabePuro-GLI1 vector)

source_name: Modified from established LNCaP cell line

value: LNCaP


title: DU145-NZD1

description: Brain metastasic PCa cell line


title: Animal 182 (+Seizures) Right

description: R dg +Seizures

source_name: Animal 182 (+Seizures) Right


title: LNCaP-GLI1-NZD2


title: LNCaP-GLI1-NZD1


title: Animal 181 (+Seizures) Left

description: L dg +Seizures


title: Animal 181 (+Seizures) Right

description: R dg +Seizures


title: LNCaP-pBP-NZD1

description: Lymph node metastatic PCa cell line with integrated empty pBapePuro retroviral vector (control sample)

value: Androgen dependent

value: Neuronal and fibroblast-like


title: Animal 182 (+Seizures) Left

description: L dg +Seizures

source_name: Animal 182 (+Seizures) Left


title: LNCaP-pBP-NZD2


title: LNCaP-pBP-NZD3


title: Case 678

status: Public on Feb 12 2011

city: Guangzhou

first: Qingming

last: Zhou

state: Guangdong

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University

hyb_protocol: The equal volumes of labeled cDNAs from HCC and matched NCL were mixed with 2x hybridization solution (10x Denhart’s solution, 1.0% SDS,5x SSC) in a total volume of 50 μL and applied onto a microarray in a hybridization chamber(Corning). Then the chamber was put in a BioMixerTM II hybridization oven (CapitalBio Inc.,Beijing, China) at 45 0C overnight. washed with 1xSSC/0.1%,0.5xSSC and 0.2xSSC.

scan_protocol: scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China). Images were quantified using GenePix Pro (version 6.0).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Arraytools BRB 4.1 was used.

source_name: Hepatocellular carcinoma

label_protocol: Two μg of total RNA from HCCs or matched non-cancerous liver tissues (NC) were reverse-transcripted into cDNA and labeled with cyanine 5-dUTP or cyanine 3-dUTP, respectively,in a total volume of 20 μL

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

value: liver carcinoma

tag: survival time

tag: status (1-death,0-survival)

source_name: Matched noncancerous liver tissue of hepatocellular carcinoma

value: noncancerous liver tissue


title: Case 995

tag: tissue


title: Case 993


title: Case 989


title: Case 994


title: Case 674


title: Case 677


title: Case 997


title: PS-I Anthers

city: Las Cruces

first: Laura

last: Rodriguez-Uribe

state: NM

address: 945 College Dr. Skeen Hall RM 127

department: Plant and environmental Sciences

institute: New Mexico State University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip

scan_protocol: GeneChips were scanned GCS 3000 7G high resolution confocal laser scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method

organism: Gossypium barbadense

source_name: RNA from  Anther tissues  of  Cotton PS-1 Flowers

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: Anther and ovule tissues from Pima S-1 (also designated PS-1), a normal, non-semigametic yet obsolete G. barbadense cultivar, and Pima 57-4, its naturally occurring semigametic mutant were used.  Both genotypes were grown in a greenhouse in peat pots and transplanted to the field a month later.  The experimental design was a paired comparison with three replicates and the plot size was single row x 40 ft long. Seeding rate was 3 seed/ft and crop production was managed as recommended locally.

extract_protocol: Total RNA isolated by the modified hot Borate method

treatment_protocol: Anther and ovule tissues from 10 flowers of 57-4 and Pima S-1 was collected for each of the three replicates at zero days postanthesis (0 DPA) and placed in liquid nitrogen and stored at -80 °C.  Total RNA was isolated using a hot borate method and cRNA was hybridized to the Affymetrix Cotton Genome GeneChips.

value: anther

tag: cultivar

value: Pima PS-1


title: Animal 170 (+Seizures) Right

description: R dg +Seizures

source_name: Animal 170 (+Seizures) Right

value: Dentate gyrus

value: right


title: 57-4 Anthers

source_name: RNA from  Anther tissues  of  Cotton 57-4 Flowers

value: Pima 57-4


title: Case 669


title: PS-1 Ovules

source_name: RNA from  Ovule tissues  of  Cotton PS-1 Flowers

value: ovule

value: Pima S-1


title: 57-4 Ovules

source_name: RNA from  Ovule tissues  of  Cotton 57-4 Flowers


title: Case 663


title: Case 657


title: Case 652


title: Case 654


title: Case 648


title: Case 641


title: E-T2

city: Stanford

first: Patrick

middle: O

last: Brown

address: Beckman Center b439

department: Department of biochemistry

institute: Stanford university school of medicine

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74265.gif

hyb_protocol: not provided

scan_protocol: scanner: GenePix 4200A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Amplified Stratagene reference

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Amplified Stratagene reference

source_name: 18-2 primary tissue

extract_protocol: All cell lines were cultured according to the specifications outlined by ATCC. Cell lines were grown to 80% confluence, then serum-deprived in 0.5% FBS for 24 hours before harvesting. Cells were washed twice with Hank's Balanced Salt Solution (Invitrogen, Carlsbad, California) and drained. 1 mL of SDS extraction buffer (0.1M NaCl, 20 mM Trizma base, 25 mM EDTA, 0.5% w/v SDS) was added directly to the plate to lyse the cells. Cellular lysate was scraped off the plates, pipetted into a cryovial, and stored at 80C until DNA extraction. Lysates were treated with 200 ug/ml ProteinaseK at 50C overnight. DNA was precipitated with one volume of Isopropanol and dissolved in TE4 buffer

value: ovarian tumor tissue

tag: age

value: 43 years

tag: elevated risk for patient

value: N

tag: disease state

value: stage IIB

tag: tumor number


title: Case 646


title: S-T4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74263.gif

source_name: 23-3 primary tissue

value: 74 years

value: stage IIIC


title: S-T4a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74262.gif

source_name: 14-4 primary tissue


title: Case 611


title: OVCAR10 RNA6_81

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68526.gif

scan_protocol: scanner: GenePix 4000A

source_name: Amplified Stratagene Reference using AA MessageAmp II kit

source_name: OVCAR10 RNA6_81

tag: cell type

value: Cell-line, Ovarian

tag: phenotype (histology)

value: Adenocarcinoma


title: Case 605

value: liver carcinoma

value: noncancerous liver tissue


title: S-T3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74258.gif

source_name: 13-3 primary tissue

value: 77 years


title: TOV21G RNA6_57

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68594.gif

value: Amplified Stratagene Reference using AA MessageAmp II kit

source_name: TOV21G RNA6_57

value: Clear Cell


title: Case 597


title: ES-2_RNA5_11

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68704.gif

source_name: Stratagene Reference amplified with AA MessageAmp II kit from Ambion

source_name: ES-2_RNA5_11 amplified with AA MessageAmp II from Ambion


title: CAOV3 RNA5_59

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68524.gif

source_name: CAOV3 RNA5_61


title: S-T5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74257.gif

source_name: 16-1 primary tissue


title: Case 590

source_name: Hepatocellular carcinoma

source_name: Matched noncancerous liver tissue of hepatocellular carcinoma


title: Mammary_OD14-HIGH_cyno 5732

city: Winston-Salem

first: Charles

last: Wood

state: NC

address: Medical Center Blvd

department: Pathology

institute: Wake Forest University School of Medicine

description: post-menopausal;ovariectomized

hyb_protocol: 10ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre was hybridized to an Affymetrix Rhesus Microarray for 16 hours at 45̊˚C. All arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station.

scan_protocol: Stained arrays were scanned with an Affymetrix GeneChip Scanner 3000.

data_processing: Data analysis was carried out using Affymetrix GCOS and Expression Console.

organism: Macaca fascicularis

source_name: Mammary tissue;OD14-HIGH treated

label_protocol: Samples were labeled according to original animal number.

extract_protocol: Samples were homogenized using Tri-reagent(MRC) and BCP and then cleaned using Qiagen Rneasy Mini-kit. Protocol was modified to include the Tri-reagent and then manufacturers protocol was followed.

tag: gender

value: female

tag: developmental stage

value: post-menopausal

tag: surgery

value: ovariectomized

tag: treatment

value: 0.2 mg/kg tibolone

value: mammary


title: Case 586


title: Mammary_OD14-HIGH_cyno 5727

description: post-menopausal;ovariectomized


title: Mammary_OD14-HIGH_cyno 5765

description: post-menopausal;ovariectomized


title: Mammary_CEE+MPA_cyno 5773

description: post-menopausal;ovariectomized

source_name: Mammary tissue;CEE+MPA treated

value: 0.042 mg/kg conjugated equine estrogens + 0.167 mg/kg medroxyprogesterone acetate


title: ES-2 RNA6_12_(Repeat)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68791.gif

source_name: Stratagene Reference amplified with Ambion MessageAmp II kit

source_name: ES-2 RNA6_12 amplified with Ambion MessageAmp II kit

tag: cell line


title: Mammary_CEE+MPA_cyno 5711

description: post-menopausal;ovariectomized


title: OV90 RNA5_49a_Repeat

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68797.gif

source_name: Stratagene Reference amplified with Ambion AA MessageAmp II kit

source_name: OV90 RNA5_49a amplified with Ambion AA MessageAmp II kit

value: Serous


title: Case 569


title: Mammary_CEE+MPA_cyno 5709

description: post-menopausal;ovariectomized


title: Mammary_OD14-HIGH_cyno 5700

description: post-menopausal;ovariectomized


title: HEY RNA6_30  DO NOT USE!

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68699.gif

value: Stratagene Reference amplified with AA MessageAmp II kit from Ambion

source_name: HEY RNA6_30 amplified with AA MessageAmp II from Ambion

value: HEY


title: OV90 RNA6_49a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68592.gif

source_name: Amplified Stratagene Reference using AA MessageAmp II kit

source_name: OV90 RNA6_49a


title: Mammary_CEE_cyno 5836

description: post-menopausal;ovariectomized

source_name: Mammary tissue;CEE treated

value: 0.042 mg/kg conjugated equine estrogens


title: Mammary_CEE+MPA_cyno 5805

description: post-menopausal;ovariectomized


title: TOV112D RNA6_6a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68790.gif

value: Stratagene Reference amplified with Ambion MessageAmp II kit

source_name: TOV112D RNA6_6a amplified with Ambion MessageAmp II kit

value: Cell-line, Ovarian

value: Endometrioid


title: OVCAR10_RNA5_25

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68690.gif

source_name: Stratagene Reference amplified with AA MessageAmp II kit from Ambion

source_name: OVCAR10_RNA5_25 amplified with AA MessageAmp II from Ambion

value: Adenocarcinoma


title: OV90_RNA6_10a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68706.gif

source_name: OV90_RNA6_10a  amplified with AA MessageAmp II from Ambion


title: OV90 RNA5a_47

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68589.gif

source_name: OV90 RNA5a_47


title: Case 563

source_name: Hepatocellular carcinoma

value: liver carcinoma

value: noncancerous liver tissue


title: HEY RNA6_89

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68705.gif

source_name: HEY RNA6_89 amplified with AA MessageAmp II from Ambion


title: Mammary_CEE_cyno 5832

description: post-menopausal;ovariectomized


title: SKOV3 RNA5_3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68789.gif

source_name: SKOV3 RNA5_3 amplified with Ambion MessageAmp II kit


title: Mammary_CEE_cyno 5799

description: post-menopausal;ovariectomized


title: 2008_RNA6_24

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68691.gif

source_name: 2008_RNA6_24  amplified with AA MessageAmp II from Ambion


title: Case 559

source_name: Matched noncancerous liver tissue of hepatocellular carcinoma


title: SKOV3 RNA5_3a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68509.gif

value: Amplified Stratagene Reference using AA MessageAmp II kit

source_name: SKOV3 RNA5_3a


title: TOV112D RNA5_5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68515.gif

source_name: TOV112D RNA5_5


title: Case 556


title: Case 555


title: Case 554


title: PEO1_RNA6_85

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68687.gif

source_name: PEO1_RNA6_85 amplified with AA MessageAmp II from Ambion


title: Case 551


title: Case 550


title: Salv CKO 2 H04-1060912354

city: Houston

first: Todd

middle: Ryan

last: Heallen

state: Texas

address: One Baylor Plaza

department: Molecular Physiology and Biophysics

institute: Baylor College of Medicine

hyb_protocol: Phalanx Hybridization Protocol (http://www.phalanxbiotech.com/)

scan_protocol: Scanned by Phalanx Biotech Group (http://www.phalanxbiotech.com/)

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities. We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.

source_name: murine embryonic heart tissue

label_protocol: AminoAllyl aRNA labeling. The reactive amino group of 5-(3-aminoallyl)-UTP/5-(3-aminoallyl)-dUTP was used to conjugate the purified aRNA with the NHS-CyDye.

extract_protocol: Dissected E9.5 hearts were placed in RNAlater for tissue stabilization. Total RNA was then extracted using the RNeasy Micro Kit (Qiagen) and optical density was measured by NanoDrop ND-1000, Agilent RNA 6000 Nano Assay and agarose electrophoresis.

value: whole heart

tag: strain

value: C57bl/6 x129 hybrid

tag: genotype/variation

value: Salv CKO


title: Salv CKO 1 H03-1060912355


title: Mammary_CEE_cyno 5784

description: post-menopausal;ovariectomized

value: female

value: post-menopausal

value: ovariectomized


title: Control 1 H01-1060912349

value: wild-type


title: Mammary_control_cyno 5703

description: post-menopausal;ovariectomized

source_name: Mammary tissue; no treatment

value: control

value: mammary


title: Control 2 H02-1060912350


title: Mammary_control_cyno 5754

description: post-menopausal;ovariectomized


title: Mammary_control_cyno 5716

description: post-menopausal;ovariectomized


title: M5 Leukimia patient YJF with DNMT3a R882 mutant

city: Shanghai

first: Zhaohui

last: Gu

state: Shanghai

address: 197 Rui Jin Road II

department: School of Medicine

institute: Shanghai Jiao Tong University

description: Gene expression data from bone marrow of YJF at diagnosis

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

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 and GeneChip® Command Console Software (AGCC)

data_processing: The data were analyzed with Partek Genomics Suite 6.5 under default procedure for background correction on the PM values, quantile normalization across all the chips in the experiment and Log2 transformation

source_name: Bone Marrow from YJF at diagnosis

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

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

value: Bone Marrow

tag: tumor

value: Acute monocytic leukemia

tag: sample type

value: DNMT3a R882 mutant


title: M5 Leukimia patient DAX of DNMT3a R882 wild type

description: Gene expression data from bone marrow of DAX at diagnosis

source_name: Bone Marrow from DAX at diagnosis

tag: tissue

value: DNMT3a R882 wild type


title: A1847 RNA5_17_Repeat)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68792.gif

source_name: Stratagene Reference amplified with Ambion AA MessageAmp II kit

tag: reference

source_name: A1847 RNA5_17 amplified with Ambion AA MessageAmp II kit

value: Cell-line, Ovarian

value: Adenocarcinoma


title: M5 Leukimia patient HLG of DNMT3a R882 wild type

description: Gene expression data from bone marrow of HLG at diagnosis

source_name: Bone Marrow from HLG at diagnosis


title: Case 536

value: liver carcinoma

tag: survival time

tag: status (1-death,0-survival)

value: noncancerous liver tissue


title: Case 541


title: M5 Leukimia patient SXX of DNMT3a R882 wild type

description: Gene expression data from bone marrow of SXXL at diagnosis

source_name: Bone Marrow from SXX at diagnosis


title: M5 Leukimia patient LJX of DNMT3a R882 wild type

description: Gene expression data from bone marrow of LJX at diagnosis

source_name: Bone Marrow from LJX at diagnosis


title: IGROVE1_RNA5_19

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68694.gif

source_name: Stratagene Reference amplified with AA MessageAmp II kit from Ambion

source_name: IGROVE1_RNA5_19 amplified with AA MessageAmp II from Ambion

value: Endometrioid


title: Case 534

source_name: Hepatocellular carcinoma


title: SKOV3 RNA5_35a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68511.gif

source_name: Amplified Stratagene Reference using AA MessageAmp II kit

source_name: SKOV3 RNA5_35a


title: M5 Leukimia patient WJH with DNMT3a R882 mutant

description: Gene expression data from bone marrow of WJH at diagnosis

source_name: Bone Marrow from WJH at diagnosis


title: M5 Leukimia patient QYY with DNMT3a R882 mutant

description: Gene expression data from bone marrow of QYY at diagnosis

source_name: Bone Marrow from QYY at diagnosis


title: M5 Leukimia patient SQM with DNMT3a R882 mutant

description: Gene expression data from bone marrow of SQM at diagnosis

source_name: Bone Marrow from SQM at diagnosis


title: M5 Leukimia patient WBL with DNMT3a R882 mutant

description: Gene expression data from bone marrow of WBL at diagnosis

source_name: Bone Marrow from WBL at diagnosis


title: Mammary_control_cyno 5810

description: post-menopausal;ovariectomized

source_name: Mammary tissue; no treatment


title: Case 533

source_name: Matched noncancerous liver tissue of hepatocellular carcinoma


title: OV90_RNA6_10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68697.gif

value: Stratagene Reference amplified with AA MessageAmp II kit from Ambion

source_name: OV90_RNA6_10  amplified with AA MessageAmp II from Ambion

value: Serous


title: Case 532


title: M5 Leukimia patient GXL with DNMT3a R882 mutant

description: Gene expression data from bone marrow of GXL at diagnosis

source_name: Bone Marrow from GXL at diagnosis


title: Calu3_NSt_2

city: Aurora

first: Holger

middle: K.

last: Eltzschig

state: Colorado

address: 19th Avenue

department: Anesthesiology

institute: University of Colorado Denver

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G with Autoloader (GCS3000).

data_processing: MAS 5

source_name: Human airway epithelial Calu-3 cells, non strained

growth_protocol: Calu-3 cells were grown to confluence on BioFlex® Cell Culture Plates (Flexcell) in a cell culture incubator.

extract_protocol: Extraction of total RNA was performed with the RNeasy Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Control cells, non strained. Kept in the same cell culture incubator at 5% CO2 at 37⁰C .

value: Human airway epithelial cell line, derived from a male caucasian patient with  adenocarcinoma of the lung

tag: age

value: passage number 8.

value: non-strained


title: Case 531


title: Case 528


title: Case 526


title: Calu3_NSt_3


title: OVCAR3 RNA6_33a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68793.gif

source_name: Stratagene Reference amplified with Ambion AA MessageAmp II kit

source_name: OVCAR3 RNA6_33a amplified with Ambion AA MessageAmp II kit


title: TOV112D RNA5_39a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68517.gif

value: Amplified Stratagene Reference using AA MessageAmp II kit

source_name: TOV112D RNA5_39a


title: TOV112D RNA6_41

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68588.gif

source_name: TOV112D RNA6_41


title: Calu3_24hSt_3

source_name: Human airway epithelial Calu-3 cells, strained for 24h at 30%

growth_protocol: Calu-3 cells were grown to confluence on BioFlex® Cell Culture Plates (Flexcell) in a cell culture incubator at 37⁰C and 5% CO2.

treatment_protocol: Cell culture plates were transferred to a BioFlex® Loading Station™  BioFlex® Culture Plates. 30% equibiaxial strain (uniform radial and circumferential strain) was applied for 24h.

value: strained


title: Calu3_NSt_1


title: OVCAR3 RNA6_2a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68505.gif

source_name: OVCAR3  RNA6_2a


title: Case 525

source_name: Hepatocellular carcinoma


title: primary tumor_T-GS-10

city: Hamburg

first: Hauke

middle: Simon

last: Guenther

address: Martinistraße 52

department: Neurochirurgie

country: Germany

institute: UKE

description: primary tumor, tumor tissue

hyb_protocol: standard Affymetrix protocols

scan_protocol: standard Affymetrix protocols

data_processing: background-adjusted, normalized intensities were computed using the gcRMA package. Gene detection was performed using the PANP package (http://bioconductor.org/packages/bioc/vignettes/panp/inst/doc/panp.pdf) for the R program.

source_name: tumor tissue corresponding cell line GS-10

label_protocol: standard Affymetrix protocols

growth_protocol: conventional glioma cell lines and self established glioma cell lines (ML lines) -->Dulbecco´s modified Eagle´s medium, supplemented with 10% fetal calf serum, 2 mM L-glutamine, and 1 mM sodium pyruvate / glioblastoma stem-like cell lines (GS lines) -->  neurobasal medium with B27 supplement (20 μl ml−1), Glutamax (10 μl ml−1), fibroblast growth factor-2 (20 ng ml−1), epidermal growth factor (20 ng ml−1) and heparin (32 IE ml−1)

extract_protocol: Total RNA was extracted from cells using the RNeasy Protect Mini Kit (Qiagen). Genomic DNA contamination was removed through an on-column DNase digestion step.

tag: sample name

value: glioblastoma (GBM), original tumor

tag: tumor grade

value: WHO IV


title: Calu3_24hSt_1


title: Calu3_24hSt_2


title: primary tumor_T-GS-12

description: primary tumor, tumor tissue

source_name: tumor tissue corresponding cell line GS-12


title: OVCAR3 RNA5_1a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68501.gif

source_name: Amplified Stratagene Reference using AA MessageAmp II kit

source_name: OVCAR3  RNA5_1a

tag: cell type

tag: phenotype (histology)


title: primary tumor_T-GS-8

description: primary tumor, tumor tissue

source_name: tumor tissue corresponding cell line GS-8


title: primary tumor_T-GS-7

description: primary tumor, tumor tissue

source_name: tumor tissue corresponding cell line GS-7


title: OVCAR5_RNA5_71

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68701.gif

source_name: Stratagene Reference amplified with Ambion AA MessageAmp II

source_name: OVCAR5_RNA5_71 amplified with Ambion AA MessageAmp II


title: A2780 RNA6_45

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68521.gif


title: A1847 RNA 6_18

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68713.gif

source_name: Stratagene Reference amplified with AA MessageAmp II kit from Ambion

source_name: A1847 RNA 6_18 mplified with AA MessageAmp II from Ambion


title: OVCAR3 RNA6_33

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68506.gif

source_name: OVCAR3  RNA6_33


title: Case 523

source_name: Matched noncancerous liver tissue of hepatocellular carcinoma


title: Case 520


title: Case 506


title: Case 505


title: TOV112D RNA5_5a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68516.gif

source_name: TOV112D RNA5_5a


title: glioblastoma stem-like cell line, serum free, later passage_GS-11 p11

description: glioblastoma stem-like cell lines, serum free conditions, later passage

source_name: glioblastoma stem-like cell line

value: glioblastoma stem-like (GS) cell line


title: glioblastoma stem-like cell line, serum free, later passage_GS-12 p11


title: primary tumor_T-GS-2

description: primary tumor, tumor tissue

source_name: tumor tissue corresponding cell line GS-2


title: Case 503


title: primary tumor_T-GS-5

description: primary tumor, tumor tissue

source_name: tumor tissue corresponding cell line GS-5


title: primary tumor_T-GS-4

description: primary tumor, tumor tissue

source_name: tumor tissue corresponding cell line GS-4


title: primary tumor_T-GS-11

description: primary tumor, tumor tissue

source_name: tumor tissue corresponding cell line GS-11


title: glioblastoma stem-like cell line, serum free, later passage_GS-10 p12


title: primary tumor_T-GS-6

description: primary tumor, tumor tissue

source_name: tumor tissue corresponding cell line GS-6


title: glioblastoma stem-like cell line, serum free, later passage_GS-9 p13

source_name: glioblastoma stem-like cell line, GSf cell line (Günther HS et al.)


title: primary tumor_T-GS-3

description: primary tumor, tumor tissue

source_name: tumor tissue corresponding cell line GS-3


title: Case 502

source_name: Hepatocellular carcinoma


title: primary tumor_T-GS-1

description: primary tumor, tumor tissue

source_name: tumor tissue corresponding cell line GS-1


title: CAOV3 RNA5_61

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68525.gif

source_name: Amplified Stratagene Reference using AA MessageAmp II kit

source_name: CAOV3 RNA5_61


title: Case 496


title: glioblastoma stem-like cell line, serum free, later passage_GS-8 p18


title: SKOV3 RNA6_37a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68514.gif

source_name: SKOV3 RNA6_37a


title: glioblastoma stem-like cell line, serum free, early passage_GS-8 p8

description: glioblastoma stem-like cell lines, serum free conditions, early passage

value: GS-8 p8


title: Case 491


title: PEO1_RNA5_27

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68689.gif

source_name: Stratagene Reference amplified with AA MessageAmp II kit from Ambion

source_name: PEO1_RNA5_27 amplified with AA MessageAmp II from Ambion


title: Case 493

source_name: Matched noncancerous liver tissue of hepatocellular carcinoma


title: glioblastoma stem-like cell line, serum free, later passage_GS-5 p12


title: OVCAR3 RNA5_1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68500.gif

source_name: OVCAR3  RNA5_1


title: glioblastoma stem-like cell line, serum free_GS-3 clone  3

description: glioblastoma stem-like cell lines, serum free conditions

source_name: glioblastoma stem-like cell line, GSf cell line, clonal cell line from GS3

value: GS-3 clone  3

value: clonal subline derived from glioblastoma stem-like (GS) cell line


title: TOV112D RNA5_39

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68587.gif

source_name: TOV112D RNA5_39

value: Cell-line, Ovarian


title: glioblastoma stem-like cell line, serum free, early passage_GS-5 p9

value: GS-5 p9


title: glioblastoma stem-like cell line, serum free_GS-3 clone  2

value: GS-3 clone  2


title: glioblastoma stem-like cell line, serum free, later passage_GS-3 p23


title: glioblastoma stem-like cell line, serum free_GS-3 clone  4

value: GS-3 clone  4


title: Case 488

value: liver carcinoma

value: noncancerous liver tissue


title: glioblastoma stem-like cell line, serum free, early passage_GS-9 p6

value: GS-9 p6


title: glioblastoma stem-like cell line, serum free_GS-3 clone  1

value: GS-3 clone  1


title: Case 487


title: glioblastoma stem-like cell line, serum free, early passage_GS-3 p12


title: TOV112D RNA6_6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68518.gif

source_name: TOV112D RNA6_6

value: Endometrioid


title: glioblastoma stem-like cell line, serum free_GS-7 clone 3

source_name: glioblastoma stem-like cell line, GSr cell line, clonal cell line from GS7

value: GS-7 clone 3


title: A2780 RNA5_7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68520.gif

value: Amplified Stratagene Reference using AA MessageAmp II kit

value: Adenocarcinoma


title: OVCAR3 RNA5_31

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68502.gif

source_name: OVCAR3  RNA5_31

value: Serous


title: Case 484


title: Case 482


title: SKOV3 RNA6_4a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68512.gif

source_name: SKOV3 RNA6_4a


title: Case 480


title: Case 479


title: TOV112D RNA6_41_Repeat

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68795.gif

source_name: Stratagene Reference amplified with Ambion AA MessageAmp II kit

source_name: TOV112D RNA6_41 amplified with Ambion AA MessageAmp II kit


title: glioblastoma stem-like cell line, serum free, later passage_GS-4 p12

source_name: glioblastoma stem-like cell line, GSr cell line (Günther HS et al.)

value: glioblastoma stem-like (GS) cell line


title: glioblastoma stem-like cell line, serum free_GS-6 p10


title: glioblastoma stem-like cell line, serum free_GS-7 clone 1

value: GS-7 clone 1


title: glioblastoma stem-like cell line, serum free_GS-7 clone 2

value: GS-7 clone 2


title: glioblastoma stem-like cell line, serum free, early passage_GS-4 p11


title: glioblastoma stem-like cell line, serum free, early passage_GS-7 p11


title: Case 469

source_name: Hepatocellular carcinoma


title: PEO1_RNA6_28

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68688.gif

value: Stratagene Reference amplified with AA MessageAmp II kit from Ambion

source_name: PEO1_RNA6_28 amplified with AA MessageAmp II from Ambion


title: IGROVE1_RNA6_20

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68693.gif

source_name: IGROVE1_RNA6_20 amplified with AA MessageAmp II from Ambion

value: Cell-line, Ovarian


title: primary tumor_T-GS-9

description: primary tumor, tumor tissue

source_name: tumor tissue corresponding cell line GS-9

value: glioblastoma (GBM), original tumor

value: WHO IV


title: Case 467


title: glioblastoma stem-like cell line, serum free, later passage_GS-7 p25


title: glioblastoma stem-like cell line, serum free, early passage_GS-2 p10


title: TOV112D RNA5_39_Repeat

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68794.gif

value: Stratagene Reference amplified with Ambion AA MessageAmp II kit

source_name: TOV112D RNA5_39 amplified with Ambion AA MessageAmp II kit


title: Case 466

value: liver carcinoma


title: Case 463

value: noncancerous liver tissue


title: glioblastoma stem-like cell line, serum free, later passage_GS-1 p28


title: Case 462


title: conventional glioma cell line, serum, est. from GS line-generating tumors_ML-9 p6

description: conventional glioma cell line, serum conditions, established from GS line-generating tumors

source_name: conventional glioma cell line established from primary tumor GS.9T

value: ML-9 p6

value: conventional glioma cell line (monolayer culture established from the same tumors as GS-lines using standard serum conditions)


title: glioblastoma stem-like cell line, serum free, later passage_GS-2. p13

description: glioblastoma stem-like cell lines, serum free conditions, later passage


title: conventional glioma cell line, serum, est. from GS line-generating tumors_ML-4 p3

source_name: conventional glioma cell line established from primary tumor GS.4T

value: ML-4 p3


title: SKOV3 RNA6_4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68527.gif

source_name: Amplified Stratagene Reference using AA MessageAmp II kit

source_name: SKOV3 RNA6_4


title: Case 459

source_name: Matched noncancerous liver tissue of hepatocellular carcinoma


title: conventional glioma cell line, serum_LN18

description: conventional glioma cell line, serum conditions

source_name: conventional glioma cell line

value: conventional glioma cell line


title: conventional glioma cell line, serum_G140


title: OVCAR5_RNA6_73

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68702.gif

source_name: Stratagene Reference amplified with Ambion AA MessageAmp II

source_name: OVCAR5_RNA6_73 amplified with Ambion AA MessageAmp II kit


title: conventional glioma cell line, serum, est. from GS line-generating tumors_ML-8 p8

source_name: conventional glioma cell line established from primary tumor GS.8T

value: ML-8 p8


title: conventional glioma cell line, serum_G96


title: conventional glioma cell line, serum_SF539


title: conventional glioma cell line, serum, est. from GS line-generating tumors_ML-5 p7

source_name: conventional glioma cell line established from primary tumor GS.5T

value: ML-5 p7


title: 2008_RNA5_23

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68692.gif

source_name: Stratagene Reference amplified with AA MessageAmp II kit from Ambion

source_name: 2008_RNA5_23  amplified with AA MessageAmp II from Ambion

value: Serous


title: TOV112D RNA6_41a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68519.gif

value: Amplified Stratagene Reference using AA MessageAmp II kit

source_name: TOV112D RNA6_41a

value: Endometrioid


title: Case 450

source_name: Hepatocellular carcinoma


title: conventional glioma cell line, serum_HS683


title: OV90 RNA6_49

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68591.gif


title: OV90 RNA5_9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68522.gif

source_name: OV90 RNA5_9


title: OVCAR3 RNA6_2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68504.gif

source_name: OVCAR3  RNA6_2


title: Case 448


title: Case 446


title: Case 443


title: conventional glioma cell line, serum_T98G


title: conventional glioma cell line, serum_G63


title: conventional glioma cell line, serum_G59


title: Case 456


title: conventional glioma cell line, serum_G22


title: TOV21G RNA5_55

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68593.gif

source_name: TOV21G RNA5_55

value: Clear Cell


title: OV90 RNA5a_47a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68590.gif

source_name: OV90 RNA5a_47a


title: SKOV3 RNA5_35

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68510.gif

source_name: SKOV3 RNA5_35

value: Adenocarcinoma


title: OV90 RNA5_49_Repeat

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68796.gif

source_name: Stratagene Reference amplified with Ambion AA MessageAmp II kit

source_name: OV90 RNA5_49 amplified with Ambion AA MessageAmp II kit

value: Cell-line, Ovarian


title: conventional glioma cell line, serum_G111


title: conventional glioma cell line, serum_SW1783


title: OV90 RNA5_9a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68523.gif

source_name: Amplified Stratagene Reference using AA MessageAmp II kit

source_name: OV90 RNA5_9a


title: Case 453

source_name: Matched noncancerous liver tissue of hepatocellular carcinoma


title: Case 440


title: Case 439


title: Case 431


title: Case 424


title: S-T2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71423.gif

source_name: Amplified Stratagene reference

value: Amplified Stratagene reference

source_name: 10-3 primary tissue from Hutch

value: ovarian tumor tissue

value: 58 years

tag: elevated risk for patient

value: N

tag: disease state

value: stage IIIC

tag: tumor number


title: OVCAR3 RNA5_31a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68503.gif

source_name: OVCAR3  RNA5_31a

tag: cell line


title: conventional glioma cell line, serum_G142

source_name: conventional glioma cell line


title: SKOV3 RNA6_37

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68513.gif

source_name: SKOV3 RNA6_37


title: conventional glioma cell line, serum_G124


title: E-T4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71387.gif

value: Y

value: stage IIA


title: conventional glioma cell line, serum_G28T


title: conventional glioma cell line, serum_G44


title: conventional glioma cell line, serum_G118


title: S-T14

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71389.gif

value: 42 years


title: Case 428

value: liver carcinoma

value: noncancerous liver tissue


title: conventional glioma cell line, serum_SF268

description: conventional glioma cell line, serum conditions

value: conventional glioma cell line


title: CC-T2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71427.gif

source_name: 26-2 primary tissue from Hutch

value: stage IC


title: Case 422

source_name: Hepatocellular carcinoma


title: Case 1032


title: S-T15a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71424.gif

source_name: 8-4 primary tissue from Hutch

value: 49 years


title: E-T9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71429.gif

source_name: 9-4 primary tissue from Hutch

value: 51 years

value: stage IIIB


title: conventional glioma cell line, serum_G130


title: S-T5a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71419.gif

source_name: 16-1 primary tissue from Hutch

value: 43 years


title: conventional glioma cell line, serum_U118MG


title: conventional glioma cell line, serum_G84


title: Case 1016


title: Case 1021


title: Case 1011


title: glioblastoma stem-like cell line, serum free, early passage_GS-1 p19

description: glioblastoma stem-like cell lines, serum free conditions, early passage

source_name: glioblastoma stem-like cell line, GSr cell line (Günther HS et al.)

value: glioblastoma stem-like (GS) cell line


title: conventional glioma cell line, serum_U87MG


title: conventional glioma cell line, serum_G120


title: Case 437


title: CC-T3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71390.gif

value: Amplified Stratagene reference

value: 45 years


title: Case 1020


title: conventional glioma cell line, serum_G121


title: S-T2a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71420.gif

source_name: 10-4 primary tissue from Hutch

value: ovarian tumor tissue

value: 58 years


title: E-T6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71388.gif

value: 46 years

value: N

value: stage IB


title: conventional glioma cell line, serum_G61


title: conventional glioma cell line, serum_G112


title: Case 1009


title: Case 1000


title: Case 1004


title: S-T15

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71422.gif

source_name: 8-3 primary tissue from Hutch

value: stage IIIC


title: conventional glioma cell line, serum_A172


title: E-T5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71421.gif

source_name: 4-3 primary tissue from Hutch

value: 55 years

value: stage IA


title: E-T8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/73407.gif

source_name: Amplified Stratagene Reference

source_name: Primary tumor 7-3

value: 38 years

value: Y


title: TetR_induced_24h_replicate 3

city: Regensburg

last: Nevels

address: Franz-Josef-Strauss-Allee 11

department: Medical Microbiology

institute: University of Regensburg

description: Gene expression data

hyb_protocol: Standard reagents and protocols from Affymetrix were used for hybridization

scan_protocol: For image acquisition, an Agilent G2565BA Microarray Scanner was used

data_processing: The Robust Multi-Array Average (RMA) algorithm was used for creation of the summarized probe intensity signals, and data files were generated by the Affymetrix GeneChip Operating 1.4 Software

source_name: Cells with Tet repressor (hCMV IE1-negative), induced for 24 h

label_protocol: Biotinylated sense strand DNA was prepared from 100 ng total RNA using reagents and protocols specified in the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix, P/N 701880 Rev. 4)

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle’s Medium (Invitrogen) supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 µg/ml streptomycin at 37°C and 5% CO2 in a humidified incubator

extract_protocol: RNA was extracted with Trizol (Invitrogen) and Phase Lock Gel Heavy (Eppendorf) and further purified using the RNeasy Mini Kit (Qiagen) including on-column DNase digestion according to the manufacturers' instructions

treatment_protocol: Growth-arrested (confluent) cells were induced by addition of 1 µg/ml doxycycline to the culture media for 24 h or 72 h before RNA preparation

value: Human embryonic lung fibroblasts

tag: inducible protein


title: TetR_induced_72h_replicate 1

description: Gene expression data

source_name: Cells with Tet repressor (hCMV IE1-negative), induced for 72 h


title: conventional glioma cell line, serum_G141

value: conventional glioma cell line


title: conventional glioma cell line, serum_LN229


title: E-T7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71428.gif

source_name: Amplified Stratagene reference

source_name: 6-3 primary tissue from Hutch

value: 47 years


title: conventional glioma cell line, serum_M059J

source_name: conventional glioma cell line


title: TetR_induced_24h_replicate 1

description: Gene expression data


title: TetR_induced_72h_replicate 3

description: Gene expression data


title: conventional glioma cell line, serum_DBTRG05MG


title: E-T1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74111.gif

source_name: 12-3 primary tissue

value: 75 years


title: TetR_uninduced_replicate 3

description: Gene expression data

source_name: Cells with Tet repressor (hCMV IE1-negative), uninduced


title: S-T2b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74321.gif

source_name: 10 primary tissue

value: stage IVA


title: E-T4a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74319.gif

value: Amplified Stratagene reference

source_name: 25 primary tissue

value: stage IIA


title: S-T3a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74110.gif

source_name: 13-1 primary tissue

value: ovarian tumor tissue

value: 77 years


title: TetR_induced_72h_replicate 2

description: Gene expression data


title: Case 1031

source_name: Hepatocellular carcinoma

value: liver carcinoma

source_name: Matched noncancerous liver tissue of hepatocellular carcinoma

value: noncancerous liver tissue


title: TetR_uninduced_replicate 2

description: Gene expression data


title: conventional glioma cell line, serum_M059K

description: conventional glioma cell line, serum conditions


title: TetR_uninduced_replicate 1

description: Gene expression data


title: S-T4b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74109.gif

source_name: 14-4 primary tissue

value: 74 years

value: N


title: S-T9a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72873.gif

source_name: 21-2 primary tissue

value: 69 years

value: stage IIIC


title: CC-T1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74106.gif

source_name: 11-1 primary tissue

value: 51 years

value: stage IA


title: E-T2a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74112.gif

source_name: 18-2 primary tissue

value: 43 years

value: stage IIB


title: S-T6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74316.gif

source_name: 19 primary tissue

value: 70 years


title: E-T3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74318.gif

source_name: 22 primary tissue

value: 58 years

value: Y


title: S-T12

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74108.gif

value: Amplified Stratagene reference

source_name: 27-1 primary tissue

value: 68 years


title: TetR_induced_24h_replicate 2

description: Gene expression data

source_name: Cells with Tet repressor (hCMV IE1-negative), induced for 24 h

value: Human embryonic lung fibroblasts


title: S-T7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74315.gif

source_name: Amplified Stratagene reference

source_name: 2 primary tissue

value: ovarian tumor tissue


title: ard1 delete, biological rep1

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.

data_processing: Array intensities were processed using the RMA algorithm in R/bioconductor. We processed the microarrays using only the probes for cerevisiae to avoid normalization artifacts.

organism: Saccharomyces cerevisiae

source_name: ard1 yeast at 30C in liquid culture at OD 0.7

label_protocol: Biotinylated cRNA was prepared from 1 ug Total RNA using the MessageAmp II one-cycle linear amplification protocol from Ambion (Austin, Tx)

growth_protocol: Yeast cells were grown in a rich liquid media (YPD) and harvested at an OD600 of 0.7 for RNA purification.

extract_protocol: Total RNA was extracted using the hot acid phenol method.

treatment_protocol: wt and each of the mutants were grown to midlog phase (OD600 of 0.7) and then harvested by centrifugation for analysis.

tag: genotype


title: TetR-IE1_induced_24h_replicate 3

description: Gene expression data

source_name: Cells with Tet repressor and Tet-inducible hCMV IE1, induced for 24 h

value: hCMV (Towne strain) 72-kDa IE1


title: ard1 delete, biological rep2


title: TetR-IE1_induced_72h_replicate 3

description: Gene expression data

source_name: Cells with Tet repressor and Tet-inducible hCMV IE1, induced for 72 h


title: TetR-IE1_induced_72h_replicate 2

description: Gene expression data


title: TetR-IE1_induced_72h_replicate 1

description: Gene expression data


title: CC-T2a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74320.gif

source_name: 26 primary tissue

value: stage IC


title: conventional glioma cell line, serum_G122

source_name: conventional glioma cell line

value: conventional glioma cell line


title: E-T1a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/73122.gif

source_name: 12-3 primary tissue

value: 75 years

value: N


title: swi4 delete, biological rep1

source_name: swi4 mutant yeast at 30C in liquid culture at OD 0.7


title: TetR-IE1_induced_24h_replicate 2

description: Gene expression data


title: S-T10a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/73491.gif

source_name: 23-3 primary tissue

value: 59 years

value: stage IIIC


title: S-T13a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/73445.gif

source_name: Pimary tumor 29-4

value: 49 years


title: S-T10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74180.gif


title: swi4 delete, biological rep2


title: S-T9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74055.gif

source_name: 21-2 primary tissue

value: 69 years


title: TetR-IE1_induced_24h_replicate 1

description: Gene expression data


title: TetR-IE1_uninduced_replicate 3

description: Gene expression data

source_name: Cells with Tet repressor and Tet-inducible hCMV IE1, uninduced


title: TetR-IE1_uninduced_replicate 2

description: Gene expression data


title: dot1 delete, biological rep2

source_name: dot1 mutant yeast at 30C in liquid culture at OD 0.7


title: S-T5c

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72874.gif

source_name: 16-1 primary tissue

value: 43 years


title: S-T12a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74260.gif

source_name: 27-1 primary tissue


title: S-T1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74314.gif

source_name: 1-2 primary tissue

value: 82 years


title: dot1 delete, biological rep1


title: wt, biological rep2

source_name: wt yeast at 30C in liquid culture at OD 0.7

value: wt


title: wt, biological rep1


title: S-T14a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72911.gif

source_name: Amplified Stratagene reference

source_name: 3-3 primary tissue from Hutch

value: 42 years


title: TetR-IE1_uninduced_replicate 1

description: Gene expression data


title: S-T13

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74107.gif

value: Amplified Stratagene reference

source_name: 29-4 primary tissue


title: Ferret whole blood with PBS  plus vaccine immunizonion on day 1, biological rep3

status: Public on Feb 11 2011

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

description: Gene expression data from ferret whole blood with PBS  plus vaccine immunizonion on day 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine Genome 2.0 Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with PLIER using Expression Console Version 1.1 (Affymetrix) default analysis settings.

organism: Mustela putorius furo

source_name: Ferret

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

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

treatment_protocol: Ferrets were immunized with each adjuvanted vaccine through intramuscular rout by 200ul total volume in one leg.  At day 0 and day 1 post immunization, whole blood was collected in Paxgene tube for later RNA extraction.

value: Whole Blood

tag: treatment group


title: Ferret whole blood with PBS plus vaccine immunizonion on day 1, biological rep1

description: Gene expression data from ferret whole blood with PBS plus vaccine immunizonion on day 1


title: Ferret whole blood with PBS plus vaccine immunizonion on day 1, biological rep2


title: S-T8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72871.gif

source_name: 20-3 primary tissue

value: 56 years


title: Ferret whole blood with pegyloned IFN-alpha plus vaccine immunizonion on day 1, biological rep1

description: Gene expression data from ferret whole blood with pegyloned IFN-alpha plus vaccine immunizonion on day 1


title: Ferret whole blood with pegyloned IFN-alpha  plus vaccine immunizonion on day 1, biological rep3

description: Gene expression data from ferret whole blood with pegyloned IFN-alpha  plus vaccine immunizonion on day 1


title: S-T12b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73535.gif

source_name: 27-1 primary tumor

value: ovarian tumor tissue

value: 68 years


title: Ferret whole blood with pegyloned IFN-alpha  plus vaccine immunizonion on day 1, biological rep2


title: Ferret whole blood with CpG plus vaccine immunizonion on day 1, biological rep2

description: Gene expression data from ferret whole blood with CpG plus vaccine immunizonion on day 1


title: Ferret whole blood with CpG plus vaccine immunizonion on day 1, biological rep1


title: Ferret whole blood with CFA plus vaccine immunizonion on day 1, biological rep2

description: Gene expression data from ferret whole blood with CFA plus vaccine immunizonion on day 1


title: S-T5b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74261.gif


title: Ferret whole blood with CFA plus vaccine immunizonion on day 1, biological rep1


title: CC-T1a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72869.gif

source_name: 11-1 primary tissue

value: 51 years

value: stage IA


title: S-T3b

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74259.gif

source_name: 13-3 primary tissue

value: 77 years


title: S-T11

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72870.gif

source_name: 24-2 primary tissue

value: 48 years

value: Y


title: Ferret whole blood, unvaccinated, on Day 1, biological rep1

description: Gene expression data from ferret whole blood, unvaccinated

value: unvaccinated


title: Ferret whole blood, unvaccinated, on Day 1, biological rep4


title: Ferret whole blood with CFA plus vaccine immunizonion on day 1, biological rep3


title: Ferret whole blood, unvaccinated, on Day 1, biological rep2


title: Ferret whole blood with CpG plus vaccine immunizonion on day 1, biological rep3


title: E-T8a

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-03/72959.gif

source_name: 7-3 primary tissue from Hutch

value: 38 years

value: stage IC


title: Ferret whole blood, unvaccinated, on Day 1, biological rep3


title: L997

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

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

hyb_protocol: As per manufacturer's instructions.

scan_protocol: As per manufacturer's instructions.

data_processing: Data were analyzed using the statistical language R. As Illumina identifiers are not stable and consistent between different chip versions, raw oligonucleotide sequences were converted to nuIDs. Data were transformed using the variance stabilizing transformation (vst) algorithm and subsequently normalized using robust spline normalization. Conversion to nuIDs, variance stabilizing transformation, and normalization of the data were all carried out using the Bioconductor package lumi. Quality control was performed using the Bioconductor package arrayQualityMetrics. Two supplementary/raw files are present, because each array that represents one sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

source_name: Osteosarcoma pre-chemotherapy biopsy

label_protocol: As per manufacturer's instructions.

extract_protocol: Osteosarcoma tissue was snap-frozen in 2-Methylbutane (Sigma-Aldrich, Zwijndrecht, the Netherlands) and stored at -70°C. Using a cryostat, 20 µm sections from each block were cut and stained with hematoxylin and eosin to ensure at least 70% tumor content and viability. RNA was isolated using TRIzol reagent (Invitrogen), followed by RNA clean-up using the QIAGEN Rneasy mini kit (Venlo, the Netherlands) with on-column DNAse treatment, according to manufacturers instructions. RNA quality and concentration were measured using an Agilent 2100 Bioanalyzer (Santa Clara, CA, USA) and Nanodrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA), respectively.

value: 217 months

tag: gender

value: M

tag: histological subtype

value: Osteoblastic

tag: tumor location

value: Right proximal fibula

tag: huvos grade

tag: group

value: No metastases

tag: status

value: Alive at 87 months after diagnosis of the primary tumor


title: L436

tag: age

value: 37 months

value: F

value: Left proximal tibia

value: Alive at 194 months after diagnosis of the primary tumor


title: L428

value: 192 months

value: Right proximal tibia

value: Alive at 193 months after diagnosis of the primary tumor


title: L432

value: 111 months

value: Pleomorphic

value: Right distal femur

value: Alive at 184 months after diagnosis of the primary tumor


title: M5 Patient No.9, bone marrow sample

description: Genomic DNA extracted from leukemia bone marrow blast cells was genotyped using Human660W-Quad v1.0  Genotyping BeadChips (Illumina).

hyb_protocol: standard Illumina protocol  standard Illumina protocol

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from blood was genotyped using Genotyping BeadChips (Illumina). Image data was analyzed using Genomestudio v2010.2 with GT module 1.6.3 (Illumina).

source_name: Bone Marrow 9 at diagnosis

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37oC using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: tumor

value: Acute monocytic leukemia


title: L975

value: 244 months

value: Anaplastic

value: Alive at 94 months after diagnosis of the primary tumor


title: L2620

value: 217 months

value: M

value: Osteoblastic

value: Left distal femur

value: No metastases

value: Alive at 219 months after diagnosis of the primary tumor


title: L2614

value: 165 months

value: Metastases present at diagnosis

value: Deceased at 29 months after diagnosis of the primary tumor


title: L2618

value: 96 months

value: Alive at 31 months after diagnosis of the primary tumor


title: L2616

value: 218 months

value: Left proximal fibula

value: Metastases at 24 months after diagnosis of the primary tumor

value: Alive at 32 months after diagnosis of the primary tumor


title: L2611

value: 242 months

value: F

value: Right distal femur

value: Alive at 91 months after diagnosis of the primary tumor


title: M5 Patient No.7, bone marrow sample

source_name: Bone Marrow 7 at diagnosis

value: Acute monocytic leukemia


title: TJA

value: 192 months

value: M

value: Osteoblastic

value: Femur

value: Unknown

value: Alive at 60 months after diagnosis of the primary tumor


title: M5 Patient No.1, bone marrow sample

source_name: Bone Marrow 1 at diagnosis


title: pediatric acute lymphoblastic leukemia_6512 [Custom TaqMan Array]

city: Rotterdam

first: Monique

last: Den Boer

address: POBox 2060

department: Pediatric Oncology

country: Netherlands

institute: Erasmus MC-Sophia Children's Hospital

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: The ∆Ct value was calculated according to the following equation: Ct value of the specific miRNA minus the Ct value of the internal reference. In case of the TaqMan MicroRNA arrays the mean Ct values for snoR-13 and snoR-14 were used as reference whereas in case of the Custom Taqman arrays snoR-1 was used.

label: FAM

source_name: pediatric acute lymphoblastic leukemia

label_protocol: not applicable

extract_protocol: RNA from the cell samples was extracted using TRIzol reagents (firma). Only RNA with an RNA Integrity Number (RIN) of  ≥ 7.5 as measured by the 2100 Bioanalyzer (Agilent, Amstelveen, the Netherlands) was used as input for the RT-qPCR reactions.

tag: subtype

value: thymocytes

tag: patient id

tag: prednisolone-score

value: unknown

tag: vincristine-score

tag: daunorubicin-score

tag: l-asparaginase-score


title: M5 Patient No.8, bone marrow sample

source_name: Bone Marrow 8 at diagnosis


title: L2301

value: 304 months

value: Left proximal tibia

value: Metastases at 27 months after diagnosis of the primary tumor

value: Deceased at 47 months after diagnosis of the primary tumor


title: GenAu MB BCELL v5.0 Ctcf Rag2-/-

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

description:
Sample ID: 147888
Chip-chip Rag2-/- pro-B cells Ctcf

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
log2(Signal Cy5/Signal Cy3) - tukey.biweight(Signal Cy5/Signal Cy3)
Performed using custom R script.

source_name: Ctcf ChIP DNA from Rag2-/- pro-B cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells.

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer(500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

treatment_protocol: pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice.

value: 5 days in culture

tag: cell type

value: pro-B cells

tag: strain

tag: antibody

value: Ctcf

tag: antibody vendor

value: Upstate

tag: antibody lot#

tag: antibody catalog#

tag: type

value: ChIP

source_name: Input DNA from Rag2-/- pro-B cells

growth_protocol: see channel 1

extract_protocol: see channel 1

treatment_protocol: see channel 1

value: Input


title: L2297

value: 137 months

tag: gender

value: F

tag: histological subtype

tag: tumor location

tag: huvos grade

tag: group

value: No metastases

value: Alive at 77 months after diagnosis of the primary tumor


title: GenAu MB BCELL v5.0 H3K4me3 Rag2-/-

description:
Sample ID: 142355
Chip-chip Rag2-/- pro-B cells H3K4me3

source_name: H3K4me3 ChIP DNA from Rag2-/- pro-B cells

tag: genotype

tag: age


title: L2302

value: 229 months

value: Chondroblastic

value: Right proximal humerus

tag: status

value: Alive at 120 months after diagnosis of the primary tumor


title: M5 Patient No.5, bone marrow sample

source_name: Bone Marrow 5 at diagnosis

tag: tumor

value: Acute monocytic leukemia


title: GenAu MB BCELL v5.0 Pax-bio Pax5bio/bio Rag2-/-

description:
Sample ID: 226775
Chip-chip Pax5bio/bio Rag2-/- pro-B cells Pax-bio

source_name: Pax-bio ChIP DNA from Pax5bio/bio Rag2-/- pro-B cells

value: Pax5bio/bio Rag2-/-

tag: antibody-like reagent

value: streptavidin pulldown of in-vivo bio-tagged protein (Pax-bio)

source_name: Input DNA from Pax5bio/bio Rag2-/- pro-B cells


title: M5 Patient No.3, bone marrow sample

description: Genomic DNA extracted from leukemia bone marrow blast cells was genotyped using Human610-Quad v1.0  Genotyping BeadChips (Illumina).

source_name: Bone Marrow 3 at diagnosis


title: GenAu MB BCELL v5.0 H3K9ac Rag2-/-

description:
Sample ID: 141262
Chip-chip Rag2-/- pro-B cells H3K9ac

source_name: H3K9ac ChIP DNA from Rag2-/- pro-B cells

value: 5 days in culture

tag: cell type


title: GenAu MB BCELL v5.0 H3K4me3 Pax5-/- Rag2-/-

description:
Sample ID: 142343
Chip-chip Pax5-/- Rag2-/- pro-B cells H3K4me3

source_name: H3K4me3 ChIP DNA from Pax5-/- Rag2-/- pro-B cells

value: pro-B cells

tag: strain

source_name: Input DNA from Pax5-/- Rag2-/- pro-B cells


title: GenAu MB BCELL v5.0 Pax5 Rag2-/-

description:
Sample ID: 147460
Chip-chip Rag2-/- pro-B cells Pax5

source_name: Pax5 ChIP DNA from Rag2-/- pro-B cells

tag: antibody

value: Pax5 (IgG purified)

tag: antibody provider

value: M. Busslinger


title: pediatric acute lymphoblastic leukemia_6210 [Custom TaqMan Array]

tag: subtype

value: thymocytes

tag: patient id

tag: prednisolone-score

value: unknown

tag: vincristine-score

tag: daunorubicin-score

tag: l-asparaginase-score


title: GenAu MB BCELL v5.0 Ctcf Pax5-/- Rag2-/-

description:
Sample ID: 182394
Chip-chip Pax5-/- Rag2-/- pro-B cells Ctcf

source_name: Ctcf ChIP DNA from Pax5-/- Rag2-/- pro-B cells

value: Ctcf

tag: antibody vendor

value: Upstate

tag: antibody lot#

tag: antibody catalog#

tag: type

value: ChIP

value: Input


title: GenAu MB BCELL v5.0 H3K4me2 Pax5-/- Rag2-/-

description:
Sample ID: 141263
Chip-chip Pax5-/- Rag2-/- pro-B cells H3K4me2

source_name: H3K4me2 ChIP DNA from Pax5-/- Rag2-/- pro-B cells

tag: genotype

tag: age


title: GenAu MB BCELL v5.0 H3K27me3 Rag2-/-

description:
Sample ID: 181972
Chip-chip Rag2-/- pro-B cells H3K27me3

source_name: H3K27me3 ChIP DNA from Rag2-/- pro-B cells

value: T. Jenuwein


title: pediatric acute lymphoblastic leukemia_4182 [Custom TaqMan Array]


title: L2296

source_name: Osteosarcoma pre-chemotherapy biopsy

value: 198 months

tag: gender

value: M

tag: histological subtype

value: Osteoblastic

tag: tumor location

value: Left proximal tibia

tag: huvos grade

tag: group

value: Metastases at 10 months after diagnosis of the primary tumor

tag: status

value: Deceased at 33 months after diagnosis of the primary tumor


title: GenAu MB BCELL v5.0 H3K9ac Pax5-/- Rag2-/-

description:
Sample ID: 141193
Chip-chip Pax5-/- Rag2-/- pro-B cells H3K9ac

source_name: H3K9ac ChIP DNA from Pax5-/- Rag2-/- pro-B cells

value: 5 days in culture

tag: cell type

tag: strain

tag: antibody


title: pediatric acute lymphoblastic leukemia_4181 [Custom TaqMan Array]

source_name: pediatric acute lymphoblastic leukemia

tag: subtype

tag: patient id

tag: prednisolone-score

tag: vincristine-score

tag: daunorubicin-score


title: M5 Patient No.6, bone marrow sample

source_name: Bone Marrow 6 at diagnosis

tag: tumor

value: Acute monocytic leukemia


title: pediatric acute lymphoblastic leukemia_4179 [Custom TaqMan Array]

tag: l-asparaginase-score


title: GenAu MB BCELL v5.0 H3K36me3 Rag2-/-

description:
Sample ID: 226556
Chip-chip Rag2-/- pro-B cells H3K36me3

source_name: H3K36me3 ChIP DNA from Rag2-/- pro-B cells

tag: genotype

tag: age

value: pro-B cells

tag: antibody vendor

value: Abcam

tag: antibody catalog#

tag: type

source_name: Input DNA from Rag2-/- pro-B cells


title: M5 Patient No.2, bone marrow sample

source_name: Bone Marrow 2 at diagnosis


title: M5 Patient No.4, bone marrow sample

source_name: Bone Marrow 4 at diagnosis


title: L2295

value: 487 months

tag: gender

value: F

tag: histological subtype

value: Anaplastic

tag: tumor location

value: Left proximal femur

tag: huvos grade

tag: group

value: No metastases

value: Alive at 97 months after diagnosis of the primary tumor


title: organism part name: 24DAP_Embryo - rep2

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

hyb_protocol: NimbleGen protocol for sample hybridization

scan_protocol: NimbleGen protocol for scanning one-color arrays

data_processing: RMA normalization was performed using the rma() function in the oligo package of Bioconductor (www.bioconductor.org), modified to handle possible many-to-many relationships between probes and source sequences (summarization groups). The normalization scripts are available from the PLEXdb team by request.

organism: Zea mays

source_name: embryo (organism part name: 24DAP_Embryo)

label_protocol: NimbleGen One-Color DNA Labeling Kit

extract_protocol: TRIZOL RNA extraction

tag: germplasm name

value: Inbred line B73

tag: organism part

value: PO:0009009 embryo

tag: development stage

value: PO:0007631 embryo development stages


title: pediatric acute lymphoblastic leukemia_2044 [Custom TaqMan Array]

tag: subtype

value: nBM

tag: patient id

tag: prednisolone-score

value: unknown

tag: vincristine-score


title: L2619

value: 128 months

value: Osteoblastic

value: Right distal femur

value: Metastases present at diagnosis

tag: status

value: Deceased at 25 months after diagnosis of the primary tumor


title: organism part name: 24DAP_Embryo - rep1


title: organism part name: 24DAP_Endosperm - rep3

source_name: endosperm (organism part name: 24DAP_Endosperm)

value: PO:0009089 endosperm

value: PO:0007633 endosperm development stages


title: pediatric acute lymphoblastic leukemia_3564 [Custom TaqMan Array]

tag: daunorubicin-score

tag: l-asparaginase-score


title: organism part name: 24DAP_Endosperm - rep2


title: L2292

tag: age

value: 136 months

value: M

value: Left proximal tibia

value: Alive at 78 months after diagnosis of the primary tumor


title: pediatric acute lymphoblastic leukemia_2557 [Custom TaqMan Array]


title: organism part name: 24DAP_Endosperm - rep1


title: organism part name: 24DAP_Whole Seed - rep2

description: 24DAP_Whole Seed

source_name: fruit (organism part name: 24DAP_Whole Seed)

value: PO:0007042 5 fruit formation


title: organism part name: 24DAP_Whole Seed - rep3

description: 24DAP_Whole Seed

value: Inbred line B73


title: pediatric acute lymphoblastic leukemia_1601 [Custom TaqMan Array]


title: L1386

value: 101 months

value: Diaphysis of left femur

value: No metastases

value: Alive at 105 months after diagnosis of the primary tumor


title: pediatric acute lymphoblastic leukemia_1253 [Custom TaqMan Array]

value: nBM

value: unknown


title: GenAu MB BCELL v5.0 H3K4me2 Rag2-/-

description:
Sample ID: 142171
Chip-chip Rag2-/- pro-B cells H3K4me2

source_name: H3K4me2 ChIP DNA from Rag2-/- pro-B cells

tag: genotype

value: 5 days in culture

tag: cell type

value: pro-B cells

tag: strain

tag: antibody

tag: antibody vendor

value: Upstate

tag: antibody lot#

tag: antibody catalog#

tag: type

value: ChIP

value: Input


title: L1382

value: 175 months

tag: gender

tag: histological subtype

value: Osteoblastic

tag: tumor location

value: Right distal tibia

tag: huvos grade

tag: group

value: Alive at 143 months after diagnosis of the primary tumor


title: organism part name: 24DAP_Whole Seed - rep1

description: 24DAP_Whole Seed

tag: germplasm name

tag: organism part

tag: development stage

value: PO:0007042 5 fruit formation


title: pediatric acute lymphoblastic leukemia_6485 [Custom TaqMan Array]

tag: subtype

value: thymocytes

tag: patient id

tag: prednisolone-score

tag: vincristine-score

tag: daunorubicin-score

tag: l-asparaginase-score


title: L1385

tag: age

value: 200 months

value: M

value: Left proximal humerus

value: Unknown

value: Metastases present at diagnosis

tag: status

value: Deceased at 11 months after diagnosis of the primary tumor


title: organism part name: 22DAP_Embryo - rep3

source_name: embryo (organism part name: 22DAP_Embryo)

value: Inbred line B73

value: PO:0009009 embryo

value: PO:0007631 embryo development stages


title: L1376

value: 164 months

value: F

value: Telangiectatic

value: Right proximal tibia

value: Metastases at 18 months after diagnosis of the primary tumor

value: Deceased at 40 months after diagnosis of the primary tumor


title: organism part name: 22DAP_Embryo - rep1


title: L1372

value: Right distal femur

value: Deceased at 25 months after diagnosis of the primary tumor


title: organism part name: 22DAP_Whole Seed - rep3

description: 22DAP_Whole Seed

source_name: fruit (organism part name: 22DAP_Whole Seed)

value: PO:0007042 5 fruit formation


title: organism part name: 22DAP_Endosperm - rep3

source_name: endosperm (organism part name: 22DAP_Endosperm)

value: PO:0009089 endosperm

value: PO:0007633 endosperm development stages


title: organism part name: 22DAP_Whole Seed - rep1

description: 22DAP_Whole Seed


title: organism part name: 22DAP_Endosperm - rep2


title: organism part name: 24DAP_Embryo - rep3


title: organism part name: 20DAP_Embryo - rep3

source_name: embryo (organism part name: 20DAP_Embryo)


title: organism part name: 22DAP_Whole Seed - rep2

description: 22DAP_Whole Seed


title: organism part name: 22DAP_Embryo - rep2


title: L1370

value: 216 months

value: M

value: Osteoblastic

value: Left distal femur

value: No metastases

value: Alive at 246 months after diagnosis of the primary tumor