title: parental line Green King at harvest [GK-0D 665490]

status: Public on May 01 2013

city: Taipei

first: Mao-Sen

last: Liu

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

institute: Institute of Plant and Microbial Biology, Academia Sinica, Taiwan

description: Analysis used RNA of Green King inbred line 104 as control sample for comparison to the experimental samples of ipt-transgenic line 102, 103 and parental line Green King as well as 10 ppm BA treated Green King.

hyb_protocol: After mixing and cleaning up the florescence labeled cDNA, the probes were hybridized with microarray chips at 55 °C for 16-18 hrs.

scan_protocol: The signals were detected and analyzed by use of Axon GenePix 4000B and GenePix6.0 (Axon Instruments, Inc., Union City, Ca, USA), respectively.

data_processing: The GenePix Result was analyzed with GeneSpring 7.3 (Silicon Genetics, Redwood, CA, USA) after LOWESS normalization. Normalised values were used to calculate the Alexa555/Alexa647 fluorescence ratios.

organism: Brassica oleracea var. italica

source_name: florets of Green King at harvest

label_protocol: The cDNA from the inbred control line 104 was Alexa555 labeled and others, transgenic lines 102, 103 and the GK parental line, were Alexa647 labeled.  Labeling was reversed for the dyeswaps.

growth_protocol: Brassica oleracea var. italica cv. Green King, its inbred line 104, ipt-transgenic inbred lines, 102 and 103, harboring a Agrobacterium tumefaciens ipt gene driven by the senescence-associated gene 13 promoter were grown in a field at Taiwan Agricultural Research Institute, Wufeng, Taichung, Taiwan

extract_protocol: RNA from control and each transgenic line with different treatments was extracted by the TRIzol Reagent method, Invitrogen, follow the instruction of user manual. DNA was eliminated by use of the TURBO DNA-free kit, Ambion and cDNA was obtained staring with 30 μg of total RNA by use of SuperScritp™ II Reverse Transcriptase, Invitrogen, following the instructions of user manual.

treatment_protocol: The broccoli heads were harvested and transported immediately to laboratory in a cold storage cabinet to preserve sample freshness. Florets from three individuals of each line were sampled at once for experimental control. Other aliquotes were dipped into water or 10 ppm of BA, removed and allowed to drain for about 15 min before entering storage at 25 C in the dark for 4 days.

tag: cultivar

value: Green King

value: florets

tag: line

value: parental line

tag: timepoint

value: at harvest

source_name: florets of Green King inbred line 104 at harvest

value: inbred line 104


title: parental line Green King after storage [GK-4D rep 685485]

type: RNA

country: Taiwan

molecule: total RNA

source_name: florets of Green King after storage at 25 centigrade in the dark for 4 days

tag: tissue

source_name: florets of Green King inbred line 104 after storage at 25 centigrade in the dark for 4 days


title: hESC_BMP4treated_HLAG-/TROP2+_rep1

status: Public on May 02 2013

city: Columbia

first: Laura

middle: Clamon

last: Schulz

state: MO

address: 1 Hospital Dr.

department: Obstetrics, Gynecology and Women's Health

country: USA

institute: University of Missouri

description: TROP2 hESC 1

hyb_protocol: Purified cRNA (1 µg) was fragmented to uniform size and applied to Agilent 4x44K v2 microarrays (Design ID 026655, Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 h on a rotating incubator and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).  Values are normalized to 75th percentile intensity for each array (=1).

organism: Homo sapiens

source_name: embryonic stem cells

label_protocol: First and second strand cDNA was prepared from the total RNA samples.  cRNA target was prepared from the DNA template and verified on the Bioanalyzer.

growth_protocol: Human ES H1 (NIH code WA01) was maintained on irradiated mouse embryonic fibroblast (MEF) cells in 80% DMEM/F12 supplemented with 20% KnockOut serum replacement, 1 mM L-glutamine/0.1 mM 2-mercaptoethanol/1% nonessential amino acids (Life Technologies) and 4 ng/ml FGF2 . Placentas were collected from women undergoing surgery at 8-12 weeks of gestation by LMP (last menstrual period) due to fetal demise at University of Missouri Women‘s and Children’s Hospital. Trophoblast were isolated by mincing villous tissue and then incubating in dissociation solution (4.2mM MgSO4, 0.25 % trypsin, 100 kU/ml DNase I inDPBS) for 30 min at 37C. Cells were passed through a 100 µm cell filter, washed in Medium 199 and layered on a 40%/25% Percoll gradient. The TB layer was collected at the interface then washed and resuspended in PBS/ 0.5%BSA/ 2mM EDTA (PBS/BSA/EDTA).

extract_protocol: Both placental cells and BMP4-treated hESC were incubated with an anti-HLA-G antibody, conjugated to phycoerythrin (PE) and an anti-TACSTD2 (TROP2) antibody, conjugated to biotin for 10 min at 4C. Cells were washed in PBS/BSA/EDTA (x 3), then incubated in a 1:5 dilution of anti-PE antibody -conjugated to magnetic beads (Miltenyi Biotec, Auburn CA) at 4C for 10 min to tag HLA-G+ cells..  Cells were then separated into HLA-G+ and – fractions by using MS columns and a MimiMACS Separator held by a Multistand (Miltenyi) to capture magnetic beads. HLA-G- cells that passed through the columns were incubated in a 1:5 dilution of streptavidin -conjugated magnetic beads (R&D Systems) at 4C for 10 min to tag HLAGHLA-G-/TACSTD2+ cells. A second MS column was used to collect the bead-bound (HLA-G-/TACSTD2+) cells.  Total RNA was obtained using Ribopure (Ambion).

treatment_protocol: hESC were cultured in irradiated MEF-conditioned medium supplemented with either 4ng/ml FGF2 or 10 ng/ml BMP4 (R&D Systems) under a standard gas atmosphere of humidified air/5% CO2 at 37°C.

tag: cell source

value: human embryonic stem cells

tag: treated with

value: 10 ng/ml BMP4 for 5 days

tag: cell surface marker

value: TROP2 (TACSTD2)


title: parental line Green King at harvest [GK-0D dye swap]


title: parental line Green King at harvest [GK-0D rep 780450]


title: 10 ppm BA treated Green King after storage [GK-BA-4D 655465]

source_name: florets of Green King treated with 10 ppm BA before storage at 25 centigrade in the dark for 4 days

tag: treatment

value: 10 ppm BA

value: after storage at 25 centigrade in the dark for 4 days


title: ipt transgenic line 103 after storage [ipt103-4D]

source_name: florets of ipt-transgenic broccoli line 103 after storage at 25 centigrade in the dark for 4 days

value: ipt-transgenic line 103


title: ipt transgenic line 103 at harvest [ipt103-0D dye swap 675450]

source_name: florets of ipt-transgenic broccoli line 103 at harvest


title: ipt transgenic line 103 after storage [ipt103-4D dye swap]


title: D. alaskensis str. G20 in syntrophic coculture with Methanococcus maripaludis (chemostat dilution rate 0.027h-1), C31

city: Berkeley

first: Jennifer

middle: V

last: Kuehl

state: California

address: 1 Cyclotron Road

department: Physical Biosciences

institute: Lawrence Berkeley National Laboratory

description: Coculture C31_G20+MM

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Standard NimbleGen protocol.

data_processing: Quantile normalized the probe intensities to match the G20 monoculture sample and averaged the log2 values for each gene and set the median log2 expression level in each sample to zero.

label: Alexa Fluor 555

organism: Oleidesulfovibrio alaskensis G20

source_name: Desulfovibrio alaskensis str. G20 in syntrophic coculture with Methanococcus maripaludis (chemostat dilution rate 0.027h-1)

label_protocol: Prepared first-strand labeled cDNA with SuperScript Plus Indirect cDNA Labeling Module (Invitrogen).

growth_protocol: We collected expression data for 2 growth conditions: syntrophic or respiratory growth of Desulfovibrio alaskensis str. G20 on lactate. Desulfovibrio alaskensis str. G20 was grown in monoculture under sulfate-limited conditions and in syntrophic coculture with the methanogen Methanococcus maripaludis or Methanospirillum hungatei in chemostats at constant dilution rate of 0.027h-1. The basal salt solution of the media is described in Walker et. al. (2009) and contained 30 mM sodium DL-lactate or sodium pyruvate, resazurin as redox indicator, and 10 mM Na2SO4 (chemostat monoculture media). The media were prepared in bioreactor glass vessels (2 liters) and medium reservoir bottles (10 liters) anoxically under a N2-CO2 (80:20, v/ v) gas atmosphere according to Widdel and Bak (1992). The media were buffered using 1.1 mM KH2PO4 and 30 mM NaHCO3. Nonchelated trace element mixture 1 and selenite-tungstate solution as well as vitamin mixture, riboflavin, vitamin B1 and B12 solutions and [1M] Na2S solution (79) were added aseptically in 1 ml aliquots per liter of medium. All stock solutions were prepared under anoxic conditions. After preparation, the bioreactor and medium reservoir bottles were connected to a N2-CO2 (90:10, v/ v) gas mixture tank. Cells were harvested from triplicate mono- and coculture chemostat runs after at least 3 volume turnovers at steady state in the chemostat at constant dilution rate of 0.027h-1, giving a total of six coculture and three monoculture gene expression data sets.

extract_protocol: Isolated total RNA with RNeasy mini kit (Qiagen).

treatment_protocol: Varying growth conditions: syntrophic growth at different growth rates and with different methanogenic partner on substrate lactate (relative to respiratory growth conditions).

tag: carbon source

value: lactate (30 mM)

tag: electron acceptor

tag: stressor

tag: culture type

tag: growth phase

value: growth rate 0.027h-1 (chemostat growth)


title: ipt transgenic line 102 at harvest [ipt102-0D dye swap 650465]

source_name: florets of ipt-transgenic broccoli line 102 at harvest

value: ipt-transgenic line 102


title: parental line Green King after storage [GK-4D]


title: ipt transgenic line 102 after storage [ipt102-4D dye swap]

source_name: florets of ipt-transgenic broccoli line 102 after storage at 25 centigrade in the dark for 4 days


title: ipt transgenic line 103 at harvest [ipt103-0D 665460]


title: ipt transgenic line 102 at harvest [ipt102-0D 715470]


title: Array 9 - Cy3 C vs Cy5 A

city: Palmerston North

first: Wayne

last: Young

address: Tennent Drive

country: New Zealand

institute: AgResearch

description: RNA extracted from Caco-2 cells grown alone (A), in presence of AGR1487 (B), or in presence of AGR1485 (C)

hyb_protocol: The labelled samples were hybridized onto Agilent Technologies 44k whole human genome oligonucleotide arrays (G4112A) in a loop design with dye-swap using the Agilent gene expression hybridisation kit (5188-5242-A). RNA (750 ng of each sample per array) was mixed with the control target, fragmented for 30 min at 60°C in the dark and hybridised onto arrays in a rotation oven at 60°C, at 4 rpm for 17 hrs.

scan_protocol: The slides were scanned using a GenePix Professional 4200A scanner (Molecular Devices, Sunnyvale, CA, USA). Spot identification and quantification was performed with GenePix 6.0 software (Molecular Devices). The images were also manually checked and any poor quality spots were removed before statistical analysis.

data_processing: Microarray data was processed using limma package in R 2.15.1.  Loess within array normalisation and Aquantile between array normalisation was applied, without background correction.

label_protocol: The RNA samples were labelled using the Agilent Low RNA Input Linear Amplification Kit PLUS (5183-3523). The total RNA (500 ng) was amplified and reverse transcribed to cDNA using T7-polymerase. The cDNA was labelled with either cyanine3 or cyaninine5 labelled CTP dye (Perkin-Elmer/NEN Life Sciences, Boston, MA, USA).

growth_protocol: Caco-2 cells were cultured in  Medium 199 (M199; Invitrogen) containing 10% (v/v) fetal bovine serum (GIBCO), 1% (v/v) nonessential amino acids (MEM nonessential amino acids 100x solution; Sigma-Aldrich) and 1% Penicillin-Streptomycin (10,000 U penicillin G sodium salt and 10,000 mg streptomycin sulphate in 0.85% (v/v) saline; GIBCO) at 37°C in 5% CO₂. The media was replaced every 3-4 days.

extract_protocol: Total RNA was extracted from the Caco-2 cells using TRIzol (Invitrogen, Auckland, New Zealand) according to the manufacturer’s instructions.  Extracted RNA was purified using RNeasy mini columns (QIAGEN, San Diego, CA, USA) and RNA quality was assessed using an RNA 6000 NanoLabChip kit with the Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA).  All RNA samples had RIN > 8.

treatment_protocol: After 18 days the media was removed from the Caco-2 monolayers and replaced with one of 1) cell culture media (M199 in 1% non-essential amino acids); 2), AGR1487 (OD 600 nm of 0.9) suspended in cell culture media; and 3), AGR1485 (OD 600 nm of 0.9) suspended in cell culture media. After 8 hours of exposure the treatment solutions were removed and the monolayers were rinsed with PBS prior to RNA extraction.

tag: cell line

tag: lactobacillus fermentum isolate

value: Control


title: parental line Green King after storage [GK-4D dye swap]


title: Array 12 - Cy3 B vs Cy5 C


title: ipt transgenic line 102 after storage [ipt102-4D]


title: Array 10 - Cy3 C vs Cy5 A


title: Array 11 - Cy3 A vs Cy5 B


title: Array 6 - Cy3 B vs Cy5 A


title: Array 7 - Cy3 A vs Cy5 B


title: Array 8 - Cy3 A vs Cy5 C


title: major HCC3

city: Kanazawa

first: Yuji

last: Hodo

address: 13-1 Takara-Machi

country: Japan

institute: Kanazawa University Graduate School of Medical Sciences

description:
HC-MA3
Gene expression data from resected liver tumor

hyb_protocol: The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).

scan_protocol: The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).

data_processing: Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.

label: Biotin

source_name: resected liver tumor

label_protocol: Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.

extract_protocol: Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)

value: resected liver tumor

tag: genotype

value: major [rs8099917 TT]


title: Array 4 - Cy3 A vs Cy5 C


title: Array 5 - Cy3 C vs Cy5 B


title: Array 3 - Cy3 B vs Cy5 C


title: PD18 sample MS5 cells series3

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description:
Sample name: MS5_PD18_3
Gene expression data from MS5 stromal cells with MEK inhibitor (PD184352)

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

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: the data were RMA normalized  and  analysed with Partek Genomic Suit

label: biotin

organism: Mus musculus

source_name: MS5 stromal cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: cells growth in alpha-MEM medium(Gibco) supplemented FBS(10%)

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

treatment_protocol: stromal cells line

value: stromal cell line MS-5

tag: agent

value: MEK inhibitor (PD184352)


title: PD18 sample MS5 cells series1

description:
Sample name: MS5_PD18_J7
Gene expression data from MS5 stromal cells with MEK inhibitor (PD184352)


title: Array 2 - Cy3 C vs Cy5 B


title: Array 1 - Cy3 B vs Cy5 A


title: Control sample MS5 cells series3

description:
Sample name: MS5_DMSO_3
Gene expression data from MS5 stromal cells with DMSO

value: control


title: Control sample MS5 cells series2

description:
Sample name: MS5_DMSO_2
Gene expression data from MS5 stromal cells with DMSO


title: PD18 sample MS5 cells series2

description:
Sample name: MS5_PD18_2
Gene expression data from MS5 stromal cells with MEK inhibitor (PD184352)


title: Control sample MS5 cells series1

description:
Sample name: MS5_DMSO_J7
Gene expression data from MS5 stromal cells with DMSO


title: Mut+/+ rep2

city: bethesda

first: abdel

last: elkahloun

state: MD

address: 50 south dr

institute: nih

description: CV10_10_(MoGene-1_0-st-v1).rma-gene-default-Signal

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Human GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC, v.3.2.4). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software (v.1.2.1) and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

source_name: MMA wild type

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

extract_protocol: Whole kidney tissue total RNA  was extracted by Qiagen RNAeazy kit

treatment_protocol: HP diet for 2 months

tag: strain background

tag: gender

value: female

tag: genotype/variation

value: MMA wild type

value: kidney

tag: diet

value: high protein diet for 2 months


title: Mut-/- rep4

description: CV04_4_(MoGene-1_0-st-v1).rma-gene-default-Signal

source_name: MMA mutant

value: Mut -/- ;TgINS-Alb-Mut (MMA mutant)

tag: tissue


title: Mut+/+ rep1

description: CV09_9_(MoGene-1_0-st-v1).rma-gene-default-Signal


title: TCL1-192 PtC- cells Spleen 2

city: Manhasset

first: ShihShih

last: Chen

address: 350 community dr

institute: Feinstein Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Spleen

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

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

tag: disease state

value: chronic lymphocytic leukemia

tag: cell type

value: PtC- CLL cells

tag: genetic background

value: C3H/C57BL/6 mixed background


title: Mut+/- rep3

description: CV07_7_(MoGene-1_0-st-v1).rma-gene-default-Signal

source_name: MMA heterozygote

value: MMA heterozygote


title: Mut+/+ rep3

description: CV11_11_(MoGene-1_0-st-v1).rma-gene-default-Signal


title: Young TCL1 PtC- cells Peritoneum cavity

description: YW-ve.

source_name: Peritoneum cavity

value: Young PtC- CLL cells


title: Mut-/- rep1

description: CV01_1_(MoGene-1_0-st-v1).rma-gene-default-Signal


title: Mut-/- rep3

description: CV03_3_(MoGene-1_0-st-v1).rma-gene-default-Signal


title: Mut+/- rep2

description: CV06_6_(MoGene-1_0-st-v1).rma-gene-default-Signal


title: Mut+/+ rep4

description: CV12_12_(MoGene-1_0-st-v1).rma-gene-default-Signal


title: TCL1-192 PtC+ cells Peritoneum cavity 2

value: PtC+ CLL cells


title: Mut-/- rep2

description: CV02_2_(MoGene-1_0-st-v1).rma-gene-default-Signal


title: TCL1-192 PtC- cells Peritoneum cavity 2


title: Mut+/- rep4

description: CV08_8_(MoGene-1_0-st-v1).rma-gene-default-Signal


title: Mut+/- rep1

description: CV05_5_(MoGene-1_0-st-v1).rma-gene-default-Signal


title: TCL1-192 PtC+ cells Spleen 1


title: TCL1-192 PtC+ cells Spleen 2


title: Young TCL1 PtC+ cells Peritoneum cavity

description: YW+ve.

value: Young PtC+ CLL cells


title: TCL1-192 PtC+ cells Peritoneum cavity 1


title: TCL1-192 PtC- cells Peritoneum cavity 1


title: Wild type PtC+ cells Peritoneum cavity

value: Wild type


title: Wild type PtC- cells Peritoneum cavity


title: TCL1-192 PtC- cells Spleen 1


title: 52C control batchB rep2

city: Toronto

first: Sam

last: Au

state: ON

address: 160 College St. Room 440

country: Canada

institute: University of Toronto

description:
6903016037_F
Batch B Replicate 2

scan_protocol: Standard Illumina scan protocol

data_processing: Data analysis was conducted using Genespring v.11.5.1. Two batches of microarray data were normalized using the Empirical Bayes ComBat accommodation of batch effects using an R script. Each array batch contained 3 untreated control biological replicates for cross-batch normalization. Normalization by standard quantile method followed by a “per probe” median centered normalization

label_protocol: RNA samples were labelled using Illumina TotalPrep-96 RNA Amplification Kit Lot #1108030 Ambion as per protocol. 1.5 ng cRNA randomized and hybridized

extract_protocol: Cells were lysed and total RNA extracted and purified using Arcturus Picopure RNA Isolation kits (Applied Biosystems) according to manufacturer protocols. Quality control by Agilent Bioanalyzer

treatment_protocol: Cells were either untreated (negative), heat shocked for 15 minutes at 42C, 47C or 52C or actuated continuously on device for 15 minutes at 400Vpp and either 1 kHz or 18 kHz sinusoidal frequencies

tag: treatment

value: heat shocked for 15 minutes at 52C


title: 47C control batchB rep3

description:
6903016035_F
Batch B Replicate 3

value: heat shocked for 15 minutes at 47C


title: 42C control batchB rep1

description:
6903016037_C
Batch B Replicate 1

value: heat shocked for 15 minutes at 42C


title: 52C control batchB rep1

description:
6903016037_A
Batch B Replicate 1


title: 52C control batchB rep3

description:
6903016035_A
Batch B Replicate 3


title: 42C control batchB rep3

description:
6903016037_E
Batch B Replicate 3


title: 47C control batchB rep1

description:
6903016035_D
Batch B Replicate 1


title: 47C control batchB rep2

description:
6903016037_D
Batch B Replicate 2


title: DMF 1 kHz batchA rep3

description:
5871833044_C
Batch A Replicate 3

value: actuated continuously on device for 15 minutes at 400Vpp and 1 kHz sinusoidal frequency


title: Untreated batchA rep2

description:
5871833050_D
Batch A Replicate 2

value: untreated


title: DMF 1 kHz batchA rep1

description:
5871833044_B
Batch A Replicate 1


title: Untreated batchA rep1

description:
5871833050_F
Batch A Replicate 1


title: DMF 18 kHz batchA rep3

description:
5871833050_E
Batch A Replicate 3

value: actuated continuously on device for 15 minutes at 400Vpp and 18 kHz sinusoidal frequency


title: 42C control batchB rep2

description:
6903016035_B
Batch B Replicate 2


title: DMF 1 kHz batchA rep2

description:
5871833050_B
Batch A Replicate 2


title: Untreated batchB rep2

description:
6903016035_E
Batch B Replicate 2


title: Untreated batchA rep3

description:
5871833050_A
Batch A Replicate 3


title: Untreated batchB rep1

description:
6903016037_B
Batch B Replicate 1


title: DMF 18 kHz batchA rep1

description:
5871833044_E
Batch A Replicate 1


title: Untreated batchB rep3

description:
6903016035_C
Batch B Replicate 3


title: DMF 18 kHz batchA rep2

description:
5871833050_C
Batch A Replicate 2


title: Gene expression in BAL after allergen challenge and 1 month after mepolizumab injection, asthmatic1

city: Madison

first: Stephane

last: Esnault

address: 600 Highland avenue

department: Medicine

institute: University of Wisconsin

hyb_protocol: The labeled cDNAs were hybridized to Human Gene ST 1.0 GeneChips (Affymetrix) according to the manufacturer’s protocols.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 (Affymetrix).

data_processing: Raw data (CEL files) were uploaded into ArrayStar software version 4.0 (DNASTAR Inc., Madison, WI, USA) for normalization and statistical analysis. The robust multichip analysis (RMA) algorithm was used for background correction, quantile normalization and median polish summarization.

label_protocol: cDNA were prepared using Ambion whole transcript target labelling kit according to the manufacturer's instructions. Fragmentation and labeling of the single-stranded cDNA was performed using the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: No growth, BAL cells are used immediately after broncoscopy

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

treatment_protocol: Atopic subjects underwent bronchoscopies before and 48 h after an allergen challenge. The same procedure was repeated on each donor, 1 month after an injection with mepolizumab (anti-IL-5) that decreases the amount of airway eosinophils after allergen challenge.

tag: sample type

value: Human Bronchoalveolar cells from a mild asthmatic, after allergen challenge after mepolizumab, subject1

value: Bronchoalveolar cells

value: mild asthma

tag: individual

value: subject 1


title: Gene expression in BAL before allergen challenge, asthmatic2

value: Human Bronchoalveolar cells from a mild asthmatic, before allergen challenge, subject2

value: before allergen challenge

value: subject 2


title: Gene expression in BAL 48 h after allergen challenge, asthmatic2

value: Human Bronchoalveolar cells from a mild asthmatic, after allergen challenge, subject2

value: after allergen challenge


title: Gene expression in BAL 48 h after allergen challenge, asthmatic1

value: Human Bronchoalveolar cells from a mild asthmatic, after allergen challenge, subject1


title: Gene expression in BAL before allergen challenge and 1 month after mepolizumab injection, asthmatic2

value: Human Bronchoalveolar cells from a mild asthmatic, before allergen challenge after mepolizumab, subject2


title: Gene expression in BAL before allergen challenge, asthmatic1

value: Human Bronchoalveolar cells from a mild asthmatic, before allergen challenge, subject1


title: Gene expression in BAL before allergen challenge and 1 month after mepolizumab injection, asthmatic1

value: Human Bronchoalveolar cells from a mild asthmatic, before allergen challenge after mepolizumab, subject1


title: Gene expression in BAL after allergen challenge and 1 month after mepolizumab injection, asthmatic2

value: Human Bronchoalveolar cells from a mild asthmatic, after allergen challenge after mepolizumab, subject2


title: Exossomes SB-KMS-KS1

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technische Universität München

description:
Exosomes, ultracentrifuged from the supernatant of human Ewing´s sarcoma cell line SB-KMS-KS1
S2375_Exos_SB_KMS_KS1

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: Affymetrix scanner 3000 7g.

data_processing: RMA normalization.

source_name: Ewing's sarcoma derived exosomes

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

growth_protocol: At 80% confluency, cells were incubated with exosome depleted medium for 48h. Then newly secreted exosomes were prepared from the supernantant and exosomal and cellular RNA were extracted.

extract_protocol: Cellular and exosomal RNA were extracted using the miRCURY RNA Isolation Kit - Cell and Plant (Exiqon, Vedbaek, Denmark) according to the manufacturer's protocol.

treatment_protocol: Exosomes were isolated from the cell culture supernatent by ultracentrifugation at 100,000xg.

value: human Ewing´s sarcoma

tag: passage

tag: molecule subtype

value: exosomal RNA


title: Exosomes SK-N-MC

description:
Exosomes, ultracentrifuged from the supernatant of human Ewing´s sarcoma cell line SK-N-MC
S2373_Exos_SK_N_MC

tag: cell line

value: SK-N-MC


title: Cells A673

description:
Human Ewing´s sarcoma cell line A673
S2316_Zellen_A673

source_name: parental cells

value: total cellular RNA


title: Cells SK-N-MC

description:
Human Ewing´s sarcoma cell line SK-N-MC
S2374_Cell_SK-N_MC


title: Cells SB-KMS-KS1

description:
Human Ewing´s sarcoma cell line SB-KMS-KS1
S2376_Cell_SB_KMS_KS1


title: PCL-035_GENE10_2

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-035

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45¡C on GeneChip¨ Gene 1.0 ST array according to the standard Affymetrix protocol.

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: Log2-transformed expression values were extracted from CEL files and normalized using NetAffx Transcript Cluster Annotations, Release 32 (June 2011) and robust multi-array average (RMA) procedure in Expression Console software (Affymetrix Inc.). Non-annotated transcript clusters were discarded. The expression values of transcript cluster ID specific for loci representing naturally occurring read-through transcriptions or mapped to more than one chromosomal location were summarized as median value for each sample.

source_name: Human primary plasma cell leukemia patient PCL-035

label_protocol: 5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip¨ Whole Transcript (WT) Sense Target Labeling Assay Manual).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).

treatment_protocol: Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.

value: Human primary plasma cell leukemia

tag: legend

value: main IgH chromosomal translocations:t(11;14), t(4;14), t(14;16), t(14;20), TC classification in MM patients:TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005).

tag: age

tag: Sex

value: F

tag: cm

value: k

tag: maf

tag: hb

tag: ldh

tag: creatinine

tag: asct

tag: response

value: VGPR

tag: pfs months

tag: os months

tag: pfs status

tag: OS status


title: PCL-032_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-032

source_name: Human primary plasma cell leukemia patient PCL-032

tag: tissue

tag: genotype/variation

value: Gk

value: nd


title: PCL-034_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-034

source_name: Human primary plasma cell leukemia patient PCL-034

value: Gl

value: PR


title: PCL-030_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-030

source_name: Human primary plasma cell leukemia patient PCL-030


title: Control - 72h - rep3

city: Brno

first: Jan

last: Vondracek

address: Kralovopolska 135

department: Department of Cytokinetics

country: Czech Republic

institute: Institute of Biophysics ASCR

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to manufacturer's protocol.

scan_protocol: Affymetrix Gene Chip Scanner

data_processing:
Affymetrix Power Tools 1.12.0 as implemented via FlexArray 1.6.1.1. Data were normalized using RMA algorithm.
Probe Group File: RaEx-1_0-st-v1.r2.pgf
Cel Layout File: RaEx-1_0-st-v1.r2.clf

organism: Rattus norvegicus

source_name: WB-F344 cell line

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Confluent WB-F344 cells (passages 14-16) were grown on 60 mm diameter dishes and treated with 100 nM PCB 126 or 0.1 % DMSO (control).

extract_protocol: Cells were lysed and total RNA was extracted by Quiagen RNeasy Plus Mini Kit according to protocol provided.

treatment_protocol: 18 Total samples were analyzed (3 independent repeats for each treatment and time point): Control or PCB 126 for 6 h, 24 h, 72 h.

tag: cell line

value: stem-like WB-F344 cells

tag: treatment

value: DMSO, 0.1% v/v

tag: time of exposure

value: 72 hours


title: Control - 6h - rep3

value: 6 hours


title: Control - 24h - rep3

value: 24 hours


title: PCB126 - 24h - rep3


title: PCL-028_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-028

source_name: Human primary plasma cell leukemia patient PCL-028

tag: legend

tag: age

tag: Sex

value: NR


title: Control - 24h - rep2


title: PCL-029_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-029

source_name: Human primary plasma cell leukemia patient PCL-029

value: M

tag: cm

value: Al

tag: maf

tag: hb


title: PCL-023_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-023

source_name: Human primary plasma cell leukemia patient PCL-023

value: Human primary plasma cell leukemia

tag: ldh

tag: creatinine

tag: asct


title: PCL-036_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-036

source_name: Human primary plasma cell leukemia patient PCL-036

value: main IgH chromosomal translocations:t(11;14), t(4;14), t(14;16), t(14;20), TC classification in MM patients:TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005).

tag: response

tag: pfs months

tag: os months


title: PCL-027_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-027

source_name: Human primary plasma cell leukemia patient PCL-027

tag: tissue

value: l

value: CR

tag: pfs status

tag: OS status


title: PCL-026_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-026

source_name: Human primary plasma cell leukemia patient PCL-026

tag: genotype/variation

value: VGPR


title: Control - 6h - rep2

tag: cell line

tag: treatment

tag: time of exposure


title: PCL-037_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-037

source_name: Human primary plasma cell leukemia patient PCL-037

tag: legend

tag: age

tag: Sex


title: PCB126 - 6h - rep2


title: Exosomes  A673

description:
Exosomes, ultracentrifuged from the supernatant of human Ewing´s sarcoma cell line A673
S2315_Exosomen_A673

tag: cell type

value: human Ewing´s sarcoma

tag: passage

tag: molecule subtype

value: exosomal RNA


title: PCB126 - 72h - rep2


title: PCL-021_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-021

source_name: Human primary plasma cell leukemia patient PCL-021

tag: cm

value: Gl

tag: maf

tag: hb

tag: ldh

tag: creatinine

tag: asct


title: Control - 72h - rep2


title: Control - 72h - rep1


title: PCB126 - 72h - rep1


title: PCL-017_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-017

source_name: Human primary plasma cell leukemia patient PCL-017

tag: tissue

value: F

value: Gk

tag: response

tag: pfs months

tag: os months

tag: pfs status

tag: OS status


title: PCL-015_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-015

source_name: Human primary plasma cell leukemia patient PCL-015

tag: legend

tag: genotype/variation

tag: age

value: k

value: PR


title: PCB126 - 24h - rep1

tag: cell line

value: stem-like WB-F344 cells

tag: treatment

tag: time of exposure


title: PCB126 - 6h - rep3

value: 6 hours


title: PCL-016_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-016

source_name: Human primary plasma cell leukemia patient PCL-016

tag: Sex

tag: cm

tag: maf


title: PCL-019_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-019

source_name: Human primary plasma cell leukemia patient PCL-019

value: Mk

tag: hb

tag: ldh

tag: creatinine

value: NR


title: PCB126 - 72h - rep3

value: 72 hours


title: Control - 24h - rep1

value: DMSO, 0.1% v/v

value: 24 hours


title: PCB126 - 24h - rep2


title: PCL-014_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-014

source_name: Human primary plasma cell leukemia patient PCL-014

tag: tissue

value: Human primary plasma cell leukemia

value: main IgH chromosomal translocations:t(11;14), t(4;14), t(14;16), t(14;20), TC classification in MM patients:TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005).

value: nd

tag: asct

tag: response


title: MM-233_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-233

source_name: Human multiple myeloma patient MM-233

value: Human multiple myeloma

tag: classification


title: MM-253_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-253

source_name: Human multiple myeloma patient MM-253

value: no IgH translocation


title: MM-246_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-246

source_name: Human multiple myeloma patient MM-246


title: PCL-010_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-010

source_name: Human primary plasma cell leukemia patient PCL-010

tag: pfs months

tag: os months

tag: pfs status

tag: OS status


title: MM-295_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-295

source_name: Human multiple myeloma patient MM-295

tag: legend

tag: genotype/variation


title: PCL-022_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-022

source_name: Human primary plasma cell leukemia patient PCL-022

tag: age

value: M

value: CR


title: Control - 6h - rep1

source_name: WB-F344 cell line

tag: cell line

tag: treatment

tag: time of exposure


title: MM-243_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-243

source_name: Human multiple myeloma patient MM-243


title: MM-229_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-229

source_name: Human multiple myeloma patient MM-229


title: MM-212_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-212

source_name: Human multiple myeloma patient MM-212


title: PCL-018_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-018

source_name: Human primary plasma cell leukemia patient PCL-018

tag: Sex

value: F

tag: cm

tag: maf

tag: hb


title: MM-224_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-224

source_name: Human multiple myeloma patient MM-224

tag: tissue


title: MM-239_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-239

source_name: Human multiple myeloma patient MM-239


title: MM-179_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-179

source_name: Human multiple myeloma patient MM-179


title: MM-177_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-177

source_name: Human multiple myeloma patient MM-177


title: MM-195_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-195

source_name: Human multiple myeloma patient MM-195


title: MM-140_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-140

source_name: Human multiple myeloma patient MM-140


title: PCB126 - 6h - rep1


title: MM-154_GENE10_2

description: Gene expression profiling data from human multiple myeloma patientMM-154

source_name: Human multiple myeloma patient MM-154


title: MM-143_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-143

source_name: Human multiple myeloma patient MM-143


title: MM-206_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-206

source_name: Human multiple myeloma patient MM-206


title: MM-131_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-131

source_name: Human multiple myeloma patient MM-131


title: MM-335_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-335

source_name: Human multiple myeloma patient MM-335


title: MM-111_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-111

source_name: Human multiple myeloma patient MM-111


title: MM-126_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-126

source_name: Human multiple myeloma patient MM-126


title: MM-104_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-104

source_name: Human multiple myeloma patient MM-104


title: MM-151_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-151

source_name: Human multiple myeloma patient MM-151


title: MM-094_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-094

source_name: Human multiple myeloma patient MM-094


title: MM-074_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-074

source_name: Human multiple myeloma patient MM-074


title: MM-115_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-115

source_name: Human multiple myeloma patient MM-115


title: MM-066_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-066

source_name: Human multiple myeloma patient MM-066


title: MM-123_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-123

source_name: Human multiple myeloma patient MM-123


title: MM-081_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-081

source_name: Human multiple myeloma patient MM-081


title: MM-055_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-055

source_name: Human multiple myeloma patient MM-055


title: MM-208_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-208

source_name: Human multiple myeloma patient MM-208


title: MM-052_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-052

source_name: Human multiple myeloma patient MM-052


title: MM-069_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-069

source_name: Human multiple myeloma patient MM-069


title: MM-083_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-083

source_name: Human multiple myeloma patient MM-083


title: MM-056_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-056

source_name: Human multiple myeloma patient MM-056


title: MM-050_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-050

source_name: Human multiple myeloma patient MM-050


title: MM-087_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-087

source_name: Human multiple myeloma patient MM-087


title: MM-079_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-079

source_name: Human multiple myeloma patient MM-079


title: MM-049_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-049

source_name: Human multiple myeloma patient MM-049


title: MM-039_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-039

source_name: Human multiple myeloma patient MM-039


title: MM-035_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-035

source_name: Human multiple myeloma patient MM-035


title: MM-043_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-043

source_name: Human multiple myeloma patient MM-043


title: MM-042_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-042

source_name: Human multiple myeloma patient MM-042


title: MM-038_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-038

source_name: Human multiple myeloma patient MM-038


title: MM-036_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-036

source_name: Human multiple myeloma patient MM-036


title: MM-034_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-034

source_name: Human multiple myeloma patient MM-034


title: MM-027_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-027

source_name: Human multiple myeloma patient MM-027


title: MM-025_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-025

source_name: Human multiple myeloma patient MM-025


title: MM-030_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-030

source_name: Human multiple myeloma patient MM-030


title: MM-026_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-026

source_name: Human multiple myeloma patient MM-026


title: MM-031_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-031

source_name: Human multiple myeloma patient MM-031


title: MM-040_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-040

source_name: Human multiple myeloma patient MM-040


title: MM-015_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-015

source_name: Human multiple myeloma patient MM-015


title: PCL-020_GENE10_2

description: Gene expression profiling data from human primary plasma cell leukemia patient PCL-020

source_name: Human primary plasma cell leukemia patient PCL-020

value: Gl

tag: ldh

tag: creatinine

tag: asct

tag: response


title: MM-016_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-016

source_name: Human multiple myeloma patient MM-016

tag: classification


title: Stallion 6

city: College Station

first: Nancy

last: Ing

state: TX

department: Animal Science

institute: Texas A&M University

description: Total cellular RNA labeled and hybridized to human gene expression microarray

hyb_protocol: Codelink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

scan_protocol: Codelink Gene Expression System: Single-Assay Bioarray Hybridization and Detection according to manufacturer's instructions http://www.appliedmicroarrays.com/application_notes/63005079.pdf

data_processing: Median normalized values derived from Codelink Expression Analysis Version 5.0

organism: Equus caballus

source_name: testis

label_protocol: Codelink Gene Expression System: Manual Labelled cRNA Target Preparation according to manufacturer's instructions http://www.appliedmicroarrays.com/pdf/iexpress2006_web.pdf

growth_protocol: Adult stallions fed free choice hay and moderate amount of horse feed

extract_protocol: Tripure reagent was used to prepare total RNA from minced parenchymal samples of testes from each stallion

treatment_protocol: Three stallions were treated with 0.1 mg/kg dexamethasone i.v. while three control stallions received an equivalent volume of saline. Testes were collected 12 h post-injection and assessed for differential gene expression

tag: agent

value: control

value: testicular parenchymal tissue


title: My-bi clone, donor type+, Sca-1+, Lin- cells, rep2

city: La Jolla

first: Hans

last: Sieburg

state: CA

address: 10901 North Torrey Pines Road

department: Stem Cells and Regenerative Biology

institute: Sanford Burnham Medical Research Institute

hyb_protocol: Cy3-labeled probes were heated to 99°C for 5 min, room temperature for 5 min and applied to the slides. The slides were covered with glass coverslips, sealed with DPX (Fluka, Milwaukee, Wisconsin) and hybridized at 42 °C for 14–16 h. The slides were washed in 1X SSC, 0.2% SDS at 55 °C for 5 min, 0.1X SSC, 0.2% SDS at 55 °C for 5 min. After a quick rinse in 0.1X SSC, the slides were centrifugated briefly to dry.

scan_protocol: The arrays were scanned for Cy3 fluorescence using an Array Scanner (Molecular Dynamics) and analyzed using Autogene 2.5 software (BioDiscovery, Los Angeles, California).

data_processing: The Affymetrix proprietary probes (i.e. labeled with an AFFY prefix and the GNF probes by the prefix gnf1m) were filtered out prior to any analyses. The resulting  reduced data set (of 23189 ID_REF) was normalized and scaled using GCRMA (matchprobes_1.14.0 with R v.2.8.0 (2008-10-20)).

source_name: Bone marrow

label_protocol: To generate Cy3-labeled cDNA probes, aRNA (5ug) and random hexamers (5ug, Pharmacia) were mixed in a total volume of 26 ul (containing RNase-free H2O), heated to 70 °C for 10 min and chilled on ice. Then, 10ul 5X first-strand buffer (Life Technologies), 5ul 0.1 M DTT (Life Technologies), 1.5ul Rnase Block (Stratagene), 1ul 25 mM d(GAT)TP and 2ul 1mM dCTP (Pharmacia), 2ul Cy3-dCTP (Amersham) and 2.5ul Superscript RT II (Life Technologies) were added and incubated at room temperature for 10 min and then at 37 °C for 2 h. To degrade the aRNA template, 1ul RNaseA (Amersham) and 5ul RNaseH (Life Technologies) was added and incubated at 37 °C for 20 min.  The probes were purified with a Qiagen 96 PCR Purification kit. The probes were normalized by fluorescence, vacuum-dried and resuspended in 55ul of hybridization buffer containing 25% 4X hybridization buffer (Amersham), 50% formamide and 10% mouse Cot1 DNA (Life Technologies).

extract_protocol: Bone marrow from clonally repopulated hosts was harvested and donor type HSC were enriched for Donor type+, Sca-1+, and Lin- cells by flow cytometry.  Whole RNA was isolated from about 5x10^4 cells using RNeasy® (Qiagen, Valencia,CA, USA) and was linearly amplified as described (Bystrykh et. al., 2005, #391).

tag: primary host

tag: secondary host strain

tag: gender of the clone

value: male

tag: strain of the clone

tag: age of the clone

value: 24 months

tag: cell type

value: myeloid-biased (My-bi) hematopoietic stem cells


title: My-bi clone, donor type+, Sca-1+, Lin- cells, rep1


title: Stallion 5

value: Dexamethasone


title: Stallion 7


title: Stallion 3


title: Ly-bi clone, donor type+, Sca-1+, Lin- cells, rep2

value: 29 months

value: lymphoid-biased (Ly-bi) hematopoietic stem cells


title: MM-004_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-004

source_name: Human multiple myeloma patient MM-004

tag: legend

tag: genotype/variation


title: HH1380_F_lung

city: chapel hill

first: Yunjung

last: Kim

state: North Carolina

address: 120 Mason farm road

institute: UNC at Chapel Hill

description: gene expression data

hyb_protocol: Total RNA were hybridized to Affymetrix Mouse Gene 1.1 ST 96-Array Plate arrays using a GeneTitan instrument from Affymetrix according to the manufacturer’s protocols

scan_protocol: Affymetrix GeneTitan Instrument

data_processing: Robust multiarray average method (RMA) implemented in the Affymetrix gene expression console with default settings (median polish and sketch-quantile normalization) to estimate normalized expression levels of transcripts

source_name: WSB(dam) x WSB(sire) inbred,lung

label_protocol: WT Terminal Labeling and Controls Kit (part #901525)

extract_protocol: Total RNA was extracted from ~25 mg of tissue powder using automated instrumentation (Maxwell 16 Tissue LEV Total RNA Purification Kit, Promega, Madison, WI).

treatment_protocol: All animals were bred at UNC from mice that were less than six generations removed from founders acquired from the Jackson Laboratory (Bar Harbor, ME).

value: lung

tag: age

value: 23 days old


title: HH1379_F_kidney

description: gene expression data

source_name: WSB(dam) x WSB(sire) inbred,kidney

value: kidney


title: HH1380_F_liver

description: gene expression data

source_name: WSB(dam) x WSB(sire) inbred,liver

value: liver


title: HH1379_F_brain

description: gene expression data

source_name: WSB(dam) x WSB(sire) inbred,brain

value: brain


title: HH1380_F_kidney

description: gene expression data


title: Ly-bi clone, donor type+, Sca-1+, Lin- cells, rep1


title: HH1380_F_brain

description: gene expression data


title: HH1378_M_lung

description: gene expression data


title: HH1361_F_kidney

description: gene expression data


title: HH1360_F_lung

description: gene expression data


title: HH1361_F_brain

description: gene expression data


title: HH1361_F_liver

description: gene expression data


title: HH1378_M_liver

description: gene expression data


title: HH1360_F_brain

description: gene expression data


title: HH1379_F_lung

description: gene expression data


title: HH1360_F_liver

description: gene expression data


title: HH1360_F_kidney

description: gene expression data


title: MM-021_GENE10_2

description: Gene expression profiling data from human multiple myeloma patient MM-021

source_name: Human multiple myeloma patient MM-021

value: Human multiple myeloma

value: main IgH chromosomal translocations:t(11;14), t(4;14), t(14;16), t(14;20), TC classification in MM patients:TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005).


title: HH1379_F_liver

description: gene expression data


title: HH1359_F_lung

description: gene expression data


title: HH1359_F_brain

description: gene expression data


title: Stallion 4


title: HH1349_M_lung

description: gene expression data


title: HH1348_M_lung

description: gene expression data


title: HH1348_M_liver

description: gene expression data


title: HH1359_F_liver

description: gene expression data


title: HH1349_M_kidney

description: gene expression data


title: HH1347_M_lung

description: gene expression data


title: HH1346_M_brain

description: gene expression data


title: HH1347_M_liver

description: gene expression data


title: HH1344_M_brain

description: gene expression data


title: HH1359_F_kidney

description: gene expression data


title: HH1346_M_lung

description: gene expression data


title: HH1348_M_brain

description: gene expression data


title: HH1346_M_liver

description: gene expression data


title: HH1345_M_liver

description: gene expression data


title: HH1345_M_kidney

description: gene expression data


title: HH1346_M_kidney

description: gene expression data


title: HH1347_M_kidney

description: gene expression data


title: HH1344_M_kidney

description: gene expression data


title: HH1344_M_lung

description: gene expression data


title: HH1345_M_lung

description: gene expression data


title: HH1349_M_liver

description: gene expression data


title: HH1345_M_brain

description: gene expression data


title: HH1347_M_brain

description: gene expression data


title: HH1322_F_liver

description: gene expression data


title: HH1344_M_liver

description: gene expression data


title: HG0284_F_brain

description: gene expression data

source_name: WSB(dam) x PWK(sire) F1,brain


title: HH1348_M_kidney

description: gene expression data


title: HG0282_F_lung

description: gene expression data

source_name: WSB(dam) x PWK(sire) F1,lung


title: HH1322_F_kidney

description: gene expression data


title: HH1322_F_lung

description: gene expression data


title: HG0282_F_kidney

description: gene expression data

source_name: WSB(dam) x PWK(sire) F1,kidney


title: HG0281_M_lung

description: gene expression data


title: HG0282_F_brain

description: gene expression data


title: HG0282_F_liver

description: gene expression data

source_name: WSB(dam) x PWK(sire) F1,liver


title: HG0281_M_liver

description: gene expression data


title: HG0280_M_lung

description: gene expression data


title: HG0278_F_liver

description: gene expression data


title: HG0280_M_brain

description: gene expression data


title: HG0277_F_kidney

description: gene expression data


title: HG0277_F_brain

description: gene expression data


title: HG0276_M_liver

description: gene expression data


title: HG0278_F_brain

description: gene expression data


title: HG0275_M_kidney

description: gene expression data


title: HG0280_M_kidney

description: gene expression data


title: HG0276_M_kidney

description: gene expression data


title: HG0277_F_lung

description: gene expression data


title: HG0280_M_liver

description: gene expression data


title: HG0276_M_brain

description: gene expression data


title: HG0274_M_lung

description: gene expression data


title: HG0278_F_lung

description: gene expression data


title: HG0275_M_brain

description: gene expression data


title: HG0281_M_brain

description: gene expression data


title: HG0274_M_liver

description: gene expression data


title: HG0277_F_liver

description: gene expression data


title: HG0276_M_lung

description: gene expression data


title: HG0278_F_kidney

description: gene expression data


title: HG0275_M_liver

description: gene expression data


title: HG0274_M_kidney

description: gene expression data


title: HG0273_M_kidney

description: gene expression data


title: HG0273_M_liver

description: gene expression data


title: HG0275_M_lung

description: gene expression data


title: HG0273_M_brain

description: gene expression data


title: HG0274_M_brain

description: gene expression data


title: HG0243_F_liver

description: gene expression data


title: HG0242_F_liver

description: gene expression data


title: HG0243_F_brain

description: gene expression data


title: HF0150_M_lung

description: gene expression data

source_name: WSB(dam) x CAST(sire) F1,lung


title: HF0152_F_brain

description: gene expression data

source_name: WSB(dam) x CAST(sire) F1,brain


title: HF0151_M_liver

description: gene expression data

source_name: WSB(dam) x CAST(sire) F1,liver


title: HG0243_F_lung

description: gene expression data


title: HG0241_F_liver

description: gene expression data


title: HG0242_F_brain

description: gene expression data


title: HF0150_M_kidney

description: gene expression data

source_name: WSB(dam) x CAST(sire) F1,kidney


title: HF0151_M_kidney

description: gene expression data


title: HG0242_F_kidney

description: gene expression data


title: HG0242_F_lung

description: gene expression data


title: HG0241_F_brain

description: gene expression data


title: HF0151_M_brain

description: gene expression data


title: HG0241_F_lung

description: gene expression data


title: HF0152_F_lung

description: gene expression data


title: HF0134_F_liver

description: gene expression data


title: HF0150_M_liver

description: gene expression data


title: HF0150_M_brain

description: gene expression data


title: HF0151_M_lung

description: gene expression data


title: HF0134_F_lung

description: gene expression data


title: HF0133_F_lung

description: gene expression data


title: HF0133_F_kidney

description: gene expression data


title: HF0152_F_kidney

description: gene expression data


title: HF0134_F_kidney

description: gene expression data


title: HG0241_F_kidney

description: gene expression data


title: HF0133_F_brain

description: gene expression data


title: HF0132_F_lung

description: gene expression data


title: HF0132_F_liver

description: gene expression data


title: HF0133_F_liver

description: gene expression data


title: HH1349_M_brain

description: gene expression data


title: HF0132_F_brain

description: gene expression data


title: HF0132_F_kidney

description: gene expression data


title: HF0130_M_liver

description: gene expression data


title: Stallion 8


title: HF0131_F_lung

description: gene expression data


title: HF0130_M_lung

description: gene expression data


title: HF0131_F_kidney

description: gene expression data


title: HF0130_M_brain

description: gene expression data


title: HF0129_F_lung

description: gene expression data


title: HF0131_F_brain

description: gene expression data


title: HF0131_F_liver

description: gene expression data


title: HF0128_M_brain

description: gene expression data


title: HF0129_F_kidney

description: gene expression data


title: HF0126_M_lung

description: gene expression data


title: HF0128_M_kidney

description: gene expression data


title: HF0128_M_lung

description: gene expression data


title: HF0127_M_liver

description: gene expression data


title: HF0126_M_liver

description: gene expression data


title: HF0126_M_brain

description: gene expression data


title: HF0127_M_brain

description: gene expression data


title: HF0129_F_liver

description: gene expression data


title: GH0104_F_lung

description: gene expression data

source_name: PWK(dam) x WSB(sire) F1,lung


title: HF0127_M_lung

description: gene expression data


title: HF0128_M_liver

description: gene expression data


title: GH0104_F_kidney

description: gene expression data

source_name: PWK(dam) x WSB(sire) F1,kidney


title: HF0130_M_kidney

description: gene expression data


title: GH0104_F_liver

description: gene expression data

source_name: PWK(dam) x WSB(sire) F1,liver


title: GH0103_M_liver

description: gene expression data


title: HF0129_F_brain

description: gene expression data


title: HF0126_M_kidney

description: gene expression data


title: GH0104_F_brain

description: gene expression data

source_name: PWK(dam) x WSB(sire) F1,brain


title: GH0103_M_brain

description: gene expression data


title: GH0102_M_lung

description: gene expression data


title: GH0087_F_lung

description: gene expression data


title: GH0102_M_liver

description: gene expression data


title: GH0087_F_liver

description: gene expression data


title: GH0103_M_kidney

description: gene expression data


title: GH0087_F_brain

description: gene expression data


title: GH0101_M_brain

description: gene expression data


title: GH0102_M_kidney

description: gene expression data


title: GH0086_F_brain

description: gene expression data


title: GH0102_M_brain

description: gene expression data


title: GH0101_M_kidney

description: gene expression data


title: GH0085_F_kidney

description: gene expression data


title: GH0101_M_liver

description: gene expression data


title: GH0100_M_kidney

description: gene expression data


title: GH0085_F_lung

description: gene expression data


title: GH0086_F_liver

description: gene expression data


title: GH0100_M_lung

description: gene expression data


title: GH0083_F_lung

description: gene expression data


title: GH0084_F_liver

description: gene expression data


title: GH0084_F_kidney

description: gene expression data


title: GH0100_M_liver

description: gene expression data


title: GH0087_F_kidney

description: gene expression data


title: GH0084_F_lung

description: gene expression data


title: GH0083_F_liver

description: gene expression data


title: GH0086_F_kidney

description: gene expression data


title: GH0086_F_lung

description: gene expression data


title: GH0083_F_kidney

description: gene expression data


title: GH0085_F_liver

description: gene expression data


title: GH0084_F_brain

description: gene expression data


title: GH0082_M_lung

description: gene expression data


title: GH0082_M_liver

description: gene expression data


title: GH0082_M_kidney

description: gene expression data


title: GH0081_M_lung

description: gene expression data


title: GH0082_M_brain

description: gene expression data


title: GG6211_F_liver

description: gene expression data

source_name: PWK(dam) x PWK(sire) inbred,liver


title: GG6209_F_lung

description: gene expression data

source_name: PWK(dam) x PWK(sire) inbred,lung


title: 15) e16.5 WT

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

description:
WT_E16.5-4
microRNA data from WT mouse adrenals at E16.5

data_processing:
The non-normalized_data.txt file contains the preprocessed data (CT values) exported from the OpenArray ® Real-Time qPCR Analysis Software.  Data were analyzed with the Applied Biosystems DataAssist ™ Software.
CT values normalized to U6 using the Applied Biosystems DataAssist ™ Software.
Fold change (KO/WT)

label: FAM

source_name: WT mouse adrenals at E16.5

label_protocol: Megaplex ™ RT Primers were used to label the cDNA.  Protocol specified in TaqMan(R) OpenArray(R) MicroRNA Panels User Guide June 2011.

growth_protocol: Sf1-Cre/Dicerlox/lox  mice,  Sf1-Cre/Dicer+/lox  and  Dicerlox/lox  mice  were  mated  together.    Females  from  each mating  pair  were  monitored  for  seminal  plugs,  and  the  morning  of  detection  was  designated  as  E0.5.

extract_protocol: Total RNA was isolated using the RNAqueous Micro kit (Life Technologies, Carlsbad, CA) in accordance with the manufacturer’s protocol.

tag: strain

value: adrenals

tag: genotype

value: WT


title: 16) e16.5 KO

description:
KO_E16.5-4
microRNA data from KO mouse adrenals at E16.5

source_name: KO mouse adrenals at E16.5

tag: tissue

value: KO Sf1-Cre/Dicer lox/lox


title: GH0081_M_liver

description: gene expression data


title: GG6211_F_kidney

description: gene expression data

source_name: PWK(dam) x PWK(sire) inbred,kidney


title: GG6208_F_lung

description: gene expression data


title: GG6209_F_liver

description: gene expression data


title: GG6209_F_brain

description: gene expression data

source_name: PWK(dam) x PWK(sire) inbred,brain


title: GG6208_F_kidney

description: gene expression data


title: GH0081_M_kidney

description: gene expression data


title: GG1258_M_lung

description: gene expression data


title: GG1260_F_kidney

description: gene expression data


title: GG6211_F_lung

description: gene expression data


title: GG1260_F_liver

description: gene expression data


title: GG1260_F_brain

description: gene expression data


title: GG1258_M_liver

description: gene expression data


title: GG6208_F_brain

description: gene expression data


title: GG6209_F_kidney

description: gene expression data


title: GG1259_M_kidney

description: gene expression data


title: GG1259_M_lung

description: gene expression data


title: GG1258_M_kidney

description: gene expression data


title: GG1260_F_lung

description: gene expression data


title: 13) e16.5 WT

description:
WT_E16.5-3
microRNA data from WT mouse adrenals at E16.5


title: 14) e16.5 KO

description:
KO_E16.5-3
microRNA data from KO mouse adrenals at E16.5


title: GG6208_F_liver

description: gene expression data


title: 12) e16.5 KO

description:
KO_E16.5-2
microRNA data from KO mouse adrenals at E16.5


title: 11) e16.5 WT

description:
WT_E16.5-2
microRNA data from WT mouse adrenals at E16.5


title: 9) e16.5 WT

description:
WT_E16.5-1
microRNA data from WT mouse adrenals at E16.5


title: 10) e16.5 KO

description:
KO_E16.5-1
microRNA data from KO mouse adrenals at E16.5


title: 6) e15.5 KO

description:
KO_E15.5-3
microRNA data from KO mouse adrenals at E15.5

source_name: KO mouse adrenals at E15.5


title: 7) e15.5 WT

description:
WT_E15.5-4
microRNA data from WT mouse adrenals at E15.5

source_name: WT mouse adrenals at E15.5


title: 8) e15.5 KO

description:
KO_E15.5-4
microRNA data from KO mouse adrenals at E15.5


title: GG1259_M_liver

description: gene expression data


title: 4) e15.5 KO

description:
KO_E15.5-2
microRNA data from KO mouse adrenals at E15.5


title: 5) e15.5 WT

description:
WT_E15.5-3
microRNA data from WT mouse adrenals at E15.5


title: 2R) e15.5 KO

description:
KO_E15.5-1
microRNA data from KO mouse adrenals at E15.5


title: 3) e15.5 WT

description:
WT_E15.5-2
microRNA data from WT mouse adrenals at E15.5


title: GG1257_M_kidney

description: gene expression data


title: 1R) e15.5 WT

description:
WT_E15.5-1
microRNA data from WT mouse adrenals at E15.5


title: GG1238_M_kidney

description: gene expression data


title: GG1241_F_kidney

description: gene expression data


title: GG1238_M_lung

description: gene expression data


title: GG1240_F_brain

description: gene expression data


title: GG1241_F_lung

description: gene expression data


title: GG1240_F_lung

description: gene expression data


title: GG1257_M_liver

description: gene expression data


title: GG1238_M_liver

description: gene expression data


title: GG1240_F_kidney

description: gene expression data


title: GG1240_F_liver

description: gene expression data


title: GG1236_M_lung

description: gene expression data


title: GG1237_M_brain

description: gene expression data


title: GG1237_M_lung

description: gene expression data


title: GG1237_M_kidney

description: gene expression data


title: GG1236_M_kidney

description: gene expression data


title: GG1257_M_lung

description: gene expression data


title: GF0267_M_kidney

description: gene expression data

source_name: PWK(dam) x CAST(sire) F1,kidney


title: GF0267_M_liver

description: gene expression data

source_name: PWK(dam) x CAST(sire) F1,liver


title: GF0267_M_lung

description: gene expression data

source_name: PWK(dam) x CAST(sire) F1,lung


title: GF0237_M_kidney

description: gene expression data


title: GF0237_M_brain

description: gene expression data

source_name: PWK(dam) x CAST(sire) F1,brain


title: GF0237_M_lung

description: gene expression data


title: GF0236_M_liver

description: gene expression data


title: GF0237_M_liver

description: gene expression data


title: GF0236_M_kidney

description: gene expression data


title: GF0169_F_brain

description: gene expression data


title: MPM Biphasic_117

city: Boston

first: Assunta

last: De Rienzo

state: Massachusetts

address: 75 Francis Street

department: Surgery

institute: Brigham and Women's Hospi

description: SAMPLE 117

hyb_protocol: 0.75 ug of total RNA was amplified using Illumina TotalPrep RNA amplification kit (Applied Biosystems, Foster City, CA, USA).  cRNA was hybridized to Illumina Human-6 Expression BeadChip (Illumina, San Diego, CA, USA) as recommended by the manufacturer

scan_protocol: The arrys were scanned by the Bead Station (Illumina, San Diego, CA, USA) as recommended by the manufacturer

data_processing: Array data processing was performed with Illumina BeadStudio software.

source_name: Tumor

label_protocol: Cy3-streptavidin (Amersham Biosciences, Little Chalfont, United Kingdom) as recommended by the manufacturer

extract_protocol: RNA was extracted using Triazol reagent (Invitrogen Corporation, Carlsbad, CA, USA) according to the manufacturer’s instructions.  DNase I (Invitrogen Corporation, Carlsbad, CA, USA) treatment was performed according to the manufacturer’s instructions

value: MPM Biphasic


title: MPM Biphasic_116

description: SAMPLE 116


title: GF0168_F_brain

description: gene expression data


title: GF0167_M_lung

description: gene expression data


title: MPM Biphasic_114

description: SAMPLE 114


title: MPM Biphasic_115

description: SAMPLE 115


title: MPM Sarcomatoid_112

description: SAMPLE 112

value: MPM Sarcomatoid


title: GF0168_F_kidney

description: gene expression data


title: GF0166_F_liver

description: gene expression data


title: GF0167_M_kidney

description: gene expression data


title: GF0168_F_lung

description: gene expression data


title: GF0167_M_brain

description: gene expression data


title: GF0167_M_liver

description: gene expression data


title: Normal Pleura_111

description: SAMPLE 111

source_name: Normal

value: Normal Pleura


title: GF0168_F_liver

description: gene expression data


title: GF0166_F_lung

description: gene expression data


title: Normal Pleura_110

description: SAMPLE 110


title: GF0165_F_liver

description: gene expression data


title: GF0164_F_kidney

description: gene expression data


title: GF0166_F_kidney

description: gene expression data


title: GF0165_F_lung

description: gene expression data


title: Normal Pleura_108

description: SAMPLE 108


title: GF0164_F_brain

description: gene expression data


title: GF0163_F_liver

description: gene expression data


title: GF0163_F_brain

description: gene expression data


title: GF0166_F_brain

description: gene expression data


title: GF0163_F_kidney

description: gene expression data


title: Normal Pleura_109

description: SAMPLE 109


title: GF0163_F_lung

description: gene expression data


title: Normal Pleura_107

description: SAMPLE 107


title: GF0162_F_brain

description: gene expression data


title: 5713384048_C

city: Seoul

first: Yuyoung

last: Lee

address: 50 Irwon-Dong, Gangnam-Gu

country: South Korea

institute: SMC

description: SAMPLE 296

data_processing: The software package to extract raw data was Genomestudio. The intensity of the probes was transformed by binary logarithm and then was normalized using the quantile normalization method.

source_name: cervical cancer

label_protocol: RNA was labelled using the WG-DASL kit from Illumina.

extract_protocol: RNA was extracted using a High Pure RNA Paraffin Kit protocol - Roche.

tag: Stage

tag: largest diameter


title: Metastatic Leiomyosarcoma_104

description: SAMPLE 104

value: Metastatic Leiomyosarcoma


title: GF0162_F_kidney

description: gene expression data


title: Normal Pleura_106

description: SAMPLE 106


title: GF0161_M_lung

description: gene expression data


title: GF0162_F_lung

description: gene expression data


title: 5713384048_I

description: SAMPLE 298


title: 5713384048_K

description: SAMPLE 300


title: GF0162_F_liver

description: gene expression data


title: 5713384048_J

description: SAMPLE 299


title: 5713384048_H

description: SAMPLE 297

value: IIA


title: Normal Pleura_105

description: SAMPLE 105


title: MPM Biphasic_113

description: SAMPLE 113


title: GF0161_M_liver

description: gene expression data


title: GF0161_M_brain

description: gene expression data


title: Metastatic Chondrosarcoma_102

description: SAMPLE 102

value: Metastatic Chondrosarcoma


title: 5713384048_B

description: SAMPLE 295


title: Thymoma_101

description: SAMPLE 101

value: Thymoma


title: GF0160_M_lung

description: gene expression data

value: lung


title: GG1257_M_brain

description: gene expression data

value: 23 days old


title: 5713384048_A

description: SAMPLE 294


title: 5713384026_K

description: SAMPLE 292


title: GF0160_M_liver

description: gene expression data


title: Metastatic Angiosarcoma_103

description: SAMPLE 103

value: Metastatic Angiosarcoma


title: FH0168_F_lung

description: gene expression data

source_name: CAST(dam) x WSB(sire) F1,lung


title: Colon Normal_99

description: SAMPLE 99

value: Colon Normal


title: FH0168_F_liver

description: gene expression data

source_name: CAST(dam) x WSB(sire) F1,liver

value: liver


title: 5713384026_H

description: SAMPLE 291


title: 5713384026_L

description: SAMPLE 293


title: GF0160_M_brain

description: gene expression data

value: brain


title: GF0161_M_kidney

description: gene expression data

value: kidney


title: FH0167_F_liver

description: gene expression data


title: Metastatic Leiomyosarcoma_98

description: SAMPLE 98


title: 5713384026_E

description: SAMPLE 289


title: FH0168_F_kidney

description: gene expression data

source_name: CAST(dam) x WSB(sire) F1,kidney


title: Lung  Adenocarcinoma_97

description: SAMPLE 97

value: Lung  Adenocarcinoma


title: FH0167_F_lung

description: gene expression data


title: GF0160_M_kidney

description: gene expression data


title: FH0168_F_brain

description: gene expression data

source_name: CAST(dam) x WSB(sire) F1,brain


title: FH0167_F_kidney

description: gene expression data


title: 5713384026_D

description: SAMPLE 288


title: MPM Epithelioid_96

description: SAMPLE 96

value: MPM Epithelioid


title: FH0113_F_lung

description: gene expression data


title: K2/E5 met.prostate_100

description: SAMPLE 100

value: K2/E5 met.prostate


title: 5713384026_F

description: SAMPLE 290


title: MPM Epithelioid_95

description: SAMPLE 95


title: 5713384026_A

description: SAMPLE 285


title: FH0113_F_kidney

description: gene expression data


title: MPM Biphasic_93

description: SAMPLE 93

value: MPM Biphasic


title: 5713384026_C

description: SAMPLE 287


title: 5713384018_K

description: SAMPLE 284


title: 5713384026_B

description: SAMPLE 286


title: FH0113_F_liver

description: gene expression data


title: FH0112_F_brain

description: gene expression data


title: FH0111_M_lung

description: gene expression data


title: 5713384018_J

description: SAMPLE 283


title: FH0112_F_lung

description: gene expression data


title: FH0112_F_liver

description: gene expression data


title: FH0111_M_liver

description: gene expression data


title: MPM Epithelioid_91

description: SAMPLE 91


title: FH0113_F_brain

description: gene expression data


title: FH0100_F_liver

description: gene expression data


title: Normal Lung_94

description: SAMPLE 94

value: Normal Lung


title: 5713384018_I

description: SAMPLE 282


title: FH0110_M_brain

description: gene expression data


title: FH0100_F_lung

description: gene expression data


title: FH0100_F_kidney

description: gene expression data


title: 5713384018_G

description: SAMPLE 280


title: FH0100_F_brain

description: gene expression data


title: FH0110_M_liver

description: gene expression data


title: 5713384018_F

description: SAMPLE 279


title: 5713384018_H

description: SAMPLE 281


title: 5713384018_E

description: SAMPLE 278


title: FH0099_F_lung

description: gene expression data


title: FH0099_F_liver

description: gene expression data


title: FH0099_F_brain

description: gene expression data


title: 5713384018_D

description: SAMPLE 277


title: Normal Lung_92

description: SAMPLE 92


title: FH0111_M_kidney

description: gene expression data


title: 5713384018_C

description: SAMPLE 276


title: FH0097_M_lung

description: gene expression data


title: FH0098_M_lung

description: gene expression data


title: FH0097_M_liver

description: gene expression data


title: 5713384018_B

description: SAMPLE 275


title: 5713384017_L

description: SAMPLE 273


title: FH0097_M_kidney

description: gene expression data


title: 5713384018_A

description: SAMPLE 274


title: FH0096_M_brain

description: gene expression data


title: FH0096_M_kidney

description: gene expression data


title: FH0098_M_liver

description: gene expression data


title: FH0097_M_brain

description: gene expression data


title: FH0099_F_kidney

description: gene expression data


title: FH0096_M_liver

description: gene expression data


title: FH0095_M_lung

description: gene expression data


title: FH0096_M_lung

description: gene expression data


title: FH0098_M_kidney

description: gene expression data


title: 5713384017_J

description: SAMPLE 272


title: FG0168_F_lung

description: gene expression data

source_name: CAST(dam) x PWK(sire) F1,lung


title: FG0168_F_liver

description: gene expression data

source_name: CAST(dam) x PWK(sire) F1,liver


title: FG0168_F_kidney

description: gene expression data

source_name: CAST(dam) x PWK(sire) F1,kidney


title: FH0095_M_liver

description: gene expression data


title: 5713384017_G

description: SAMPLE 270


title: FG0168_F_brain

description: gene expression data

source_name: CAST(dam) x PWK(sire) F1,brain


title: FG0167_F_liver

description: gene expression data


title: FH0095_M_kidney

description: gene expression data


title: FG0167_F_kidney

description: gene expression data


title: 5713384017_H

description: SAMPLE 271


title: 5713384017_E

description: SAMPLE 268


title: 5713384017_D

description: SAMPLE 267


title: FG0167_F_lung

description: gene expression data


title: FG0164_F_kidney

description: gene expression data


title: 5713384017_F

description: SAMPLE 269


title: FG0162_F_liver

description: gene expression data


title: 5713384017_B

description: SAMPLE 265


title: FG0163_F_lung

description: gene expression data


title: 5713384017_C

description: SAMPLE 266


title: FG0162_F_lung

description: gene expression data


title: FG0164_F_lung

description: gene expression data


title: FG0163_F_brain

description: gene expression data


title: FG0162_F_kidney

description: gene expression data


title: FG0163_F_kidney

description: gene expression data


title: 5713384017_A

description: SAMPLE 264


title: 5713384016_L

description: SAMPLE 263


title: FG0167_F_brain

description: gene expression data


title: FG0164_F_liver

description: gene expression data


title: FG0160_M_liver

description: gene expression data


title: 5713384016_K

description: SAMPLE 262


title: 5713384016_J

description: SAMPLE 261


title: FG0159_M_kidney

description: gene expression data


title: FG0159_M_brain

description: gene expression data


title: FG0161_M_brain

description: gene expression data


title: 5713384016_I

description: SAMPLE 260


title: FG0160_M_lung

description: gene expression data


title: 5713384016_D

description: SAMPLE 256


title: FH0112_F_kidney

description: gene expression data


title: FG0125_F_brain

description: gene expression data


title: 5713384016_E

description: SAMPLE 257


title: 5713384016_G

description: SAMPLE 259


title: FG0125_F_kidney

description: gene expression data


title: 5713384016_B

description: SAMPLE 254


title: FG0159_M_lung

description: gene expression data


title: 5713384016_C

description: SAMPLE 255


title: FG0160_M_kidney

description: gene expression data


title: FG0125_F_lung

description: gene expression data


title: FG0123_M_liver

description: gene expression data


title: FG0123_M_kidney

description: gene expression data


title: 5713384016_F

description: SAMPLE 258


title: FG0160_M_brain

description: gene expression data


title: FG0162_F_brain

description: gene expression data


title: 5713384012_L

description: SAMPLE 253


title: FG0122_M_liver

description: gene expression data


title: FG0122_M_kidney

description: gene expression data


title: FG0125_F_liver

description: gene expression data


title: FG0123_M_brain

description: gene expression data


title: FG0122_M_lung

description: gene expression data


title: FG0121_M_kidney

description: gene expression data


title: FG0121_M_liver

description: gene expression data


title: FG0120_M_lung

description: gene expression data


title: FG0120_M_liver

description: gene expression data


title: FF0760_M_kidney

description: gene expression data

source_name: CAST(dam) x CAST(sire) inbred,kidney


title: 5713384012_K

description: SAMPLE 252


title: 5713384012_G

description: SAMPLE 249


title: FG0120_M_brain

description: gene expression data


title: 5713384012_C

description: SAMPLE 247


title: 5713384012_J

description: SAMPLE 251


title: FG0120_M_kidney

description: gene expression data


title: FF0760_M_liver

description: gene expression data

source_name: CAST(dam) x CAST(sire) inbred,liver


title: FF0760_M_brain

description: gene expression data

source_name: CAST(dam) x CAST(sire) inbred,brain


title: 5713384012_H

description: SAMPLE 250


title: FF0759_M_liver

description: gene expression data


title: FF0760_M_lung

description: gene expression data

source_name: CAST(dam) x CAST(sire) inbred,lung


title: ChIP-DNA of SKOV-3, replicate-3

type: genomic

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: About 1.5 x 10^7 number of healthy SKOV-3 cells were used to immunoprecipitate the DNA with PITX2 antibody to identify its global target genes.

hyb_protocol: Using Agilent’s In situ Hybridzation kit 5184-3568. As per Manufacturer's instructions.

scan_protocol: Post-hybridization, the slides were washed as per Agilent protocol and scanned at 5 micron resolution using Agilent Technologies Scanner G2505C.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1) with linear normalization.

molecule: genomic DNA

source_name: Input DNA from Human ovarian adenocarcinoma cells SKOV-3

label_protocol: The DNA was blunted at 12°C for 20 minutes using T4 DNA polymerase as per the Mammalian Chip on Chip Protocol Version 10.0, May 2008 of Agilent Technologies. The blunted DNA was cleaned by phenol:chloroform extraction and the precipitated DNA was resuspended in 25 microlitres of water and the entire DNA was ligated to linkers overnight. The linker-ligated DNA was subjected to two rounds of LMPCR as per protocol and resuspended in 25 microliters of water. DNA Concentration and Purity of amplified samples estimated using Nanodrop Spectrophotometer. Two micrograms of each sample was labeled using Agilent Genomic DNA Labeling Kit PLUS and Cy3 or Cy5 dUTP from Agilent. DNA yield and incorporation of label (specific activity) was measured using NanoDrop spectrophotometer.

growth_protocol: SKOV-3 cells were maintained in McCoy’s 5A (Sigma, St Louis, USA) supplemented with 10% FBS (SIGMA), 100 U/ml penicillin/streptomycin at humidified atmosphere at 37°C.

extract_protocol: The immunoprecipitated DNA and the input DNA was reverse crosslinked and then extracted and purified with PCR Purification kit (QIAGEN).

treatment_protocol: About 1.5 x 10^7 number of cells were crosslinked with formaldehyde, sonicated and immunoprecipitated with PITX2 antibody (cat no. sc8748X. Lot no.E0206. Santa cruz)

tag: cell line

value: Adherent in nature and human ovarian epithelial cells

source_name: IP DNA from Human ovarian adenocarcinoma cells SKOV-3


title: 5713384012_D

description: SAMPLE 248


title: ChIP-DNA of SKOV-3, replicate-4


title: FF0758_M_liver

description: gene expression data


title: FF0759_M_brain

description: gene expression data


title: FF0754_M_lung

description: gene expression data


title: FF0759_M_kidney

description: gene expression data


title: ChIP-DNA of SKOV-3, replicate-1


title: FF0759_M_lung

description: gene expression data


title: 5713384012_B

description: SAMPLE 246


title: 5713384012_A

description: SAMPLE 245


title: FF0758_M_lung

description: gene expression data


title: FF0754_M_kidney

description: gene expression data


title: 5713384045_J

description: SAMPLE 243


title: FF0758_M_brain

description: gene expression data


title: 5713384045_I

description: SAMPLE 242


title: FF0754_M_liver

description: gene expression data


title: FF0758_M_kidney

description: gene expression data


title: FF0754_M_brain

description: gene expression data


title: FF0743_M_lung

description: gene expression data


title: E13.5PGCs_rep3

city: Sendai

first: Ikuma

last: Maeda

state: Miyagi

address: 4-1 Seiryomachi, Aoba-ku

institute: Institute of Development, Aging and Cancer, Tohoku University

description: Gene expression of PGCs from mouse E13.5 embryo genital ridges.

hyb_protocol: 1.65ug of Cy3-labelled cRNAs from each sample were fragmented and hybridized to microarrays according to the manufacturer's instructions using the Gene Expression Hybridization kit (Agilent 5188-5242) and Agilent hybridization oven. After hybridization, microarrays were washed using the Gene Expression Wash Pack (Agilent 5188-5327).

scan_protocol: The microarrays were scanned using the Agilent DNA microarray scanner (Agilent G2505C); the spot signals were quantified using Feature Extraction software.

data_processing: Data was normalized and analyzed by GeneSpring GX (Agilent).

source_name: PGCs derived from mouse E13.5 embryo genital ridges

label_protocol: Cy3-labeled cRNA samples were prepared using the Agilent Low Input Quick Amp Labeling Kit (one-color) (5190-2305) and RNA Spike-In Kit (one-color) (5188-5282) according to the manufacturer's instructions. Input was 100 ng of total RNA from each sample.

extract_protocol: Total RNA was purified using the RNeasy micro kit according to the manufacturer's instructions.

treatment_protocol: The genital ridges were dissected from mouse E13.5 embryos. After trypsin treatment, live, single and GFP-positive cells were purified using FACS from the dissociated cells.

tag: strain/background

value: MCH x C57BL6/J (Oct4ΔPE-GFP Tg)

tag: gender

value: male

value: primordial germ cells (PGCs)


title: E13.5PGCs_rep1


title: ESCs_Max_rep4

description: Gene expression of Max siRNA-transfected VV3 mouse ESCs.

source_name: VV3 ESCs, Max siRNA transfected

growth_protocol: Cells were cultured with ESCs medium with 14% KSR, 1% FBS and LIF at 37 ºC in a humidified incubator with 5% CO2.

treatment_protocol: ESCs were transfected with siRNA against the Max gene using Lipofectamine RNAiMAX. After 3 days culture, live, single and Vasa::Venus positive cells were purified using FACS from the ESCs.

value: embryonic stem cells (ESCs)

tag: sirna

value: Max


title: 5713384045_L

description: SAMPLE 244

source_name: cervical cancer


title: 5713384045_G

description: SAMPLE 240


title: 5713384045_F

description: SAMPLE 239


title: E13.5PGCs_rep2


title: FF0743_M_liver

description: gene expression data

value: 23 days old


title: ESCs_AllStars_rep3

description: Gene expression of negative control siRNA-transfected VV3 mouse ESCs.

source_name: VV3 ESCs, control siRNA transfected

treatment_protocol: ESCs were transfected with non-silencing negative control siRNA (AllStars) using Lipofectamine RNAiMAX. After 3 days culture, the live and single cells were purified using FACS from the ESCs.

value: non-silencing negative control


title: FF0742_M_kidney

description: gene expression data


title: FF0742_M_lung

description: gene expression data

value: lung


title: ESCs_AllStars_rep2


title: 5713384045_C

description: SAMPLE 237


title: 5713384045_D

description: SAMPLE 238


title: FF0742_M_liver

description: gene expression data

value: liver


title: FF0743_M_kidney

description: gene expression data


title: D73-1

city: Seattle

first: Pradipsinh

middle: K

last: Rathod

state: WA

address: Campus Box 351700

department: Chemistry

institute: University of Washington

hyb_protocol: Hybridization was performed for 16-18h in a 42C waterbath (sample was loaded under a glass coverslip and array was placed in a water-tight hybridization chamber).

scan_protocol: Arrays were scanned using an Axon GenePix 4000B at 5uM resolution according to the NimbleGen Users Guide v 8.0.

data_processing: Qspline normalization and SegMNT CGH analysis were performed using NimbleScan v2.6 and plotted for figures using GraphPad PRISM.

organism: Plasmodium falciparum

source_name: D73-1 clone

label_protocol: Genomic DNA was labeled with Cy3 and Cy5 random nanomers per the NimbleGen Users Guide v 8.0.

growth_protocol: Parasites were grown in RPMI 1640 plus 20% human plasma, human erythrocytes (A+), and DSM1 at 37C and 5% oxygen and 5% CO2.

extract_protocol: Clonal asynchronous P. falciparum blood-stage parasites were lysed with saponin, and genomic DNA was extracted using the Qiagen DNeasy kit.

treatment_protocol: Round 1 D clone parasites were selected in 3uM DSM1 and cloned by limiting dilution.

value: whole body

tag: parasite stage

value: erythrocytic

tag: round of selection

tag: array identifier

source_name: Clonal Dd2 P. falciparum

growth_protocol: Parasites were grown in RPMI 1640 plus 20% human plasma, human erythrocytes (A+) at 37C and 5% oxygen and 5% CO2.

treatment_protocol: Cloned by limiting dilution.

tag: sample type

value: reference


title: 5713384045_H

description: SAMPLE 241


title: ESCs_Max_rep2

tag: cell type


title: C53-1

source_name: C53-1 clone

treatment_protocol: Round 1 C clone parasites were selected in 3uM DSM1 and cloned by limiting dilution.


title: C710-1a

source_name: C710-1a clone


title: 5713384045_B

description: SAMPLE 236


title: 5713384044_K

description: SAMPLE 234


title: D53-1

source_name: D53-1 clone


title: FF0685_F_brain

description: gene expression data

value: brain


title: ESCs_AllStars_rep1


title: FF0742_M_brain

description: gene expression data


title: FF0685_F_lung

description: gene expression data


title: FF0684_F_liver

description: gene expression data


title: 5713384045_A

description: SAMPLE 235


title: ESCs_Max_rep1


title: FF0728_F_liver

description: gene expression data


title: FF0727_F_lung

description: gene expression data


title: FF0685_F_liver

description: gene expression data


title: FF0684_F_lung

description: gene expression data


title: FF0727_F_kidney

description: gene expression data

value: kidney


title: FF0728_F_brain

description: gene expression data


title: FF0683_F_liver

description: gene expression data


title: FF0683_F_kidney

description: gene expression data


title: FF0684_F_kidney

description: gene expression data


title: 5713384044_D

description: SAMPLE 231


title: FF0683_F_lung

description: gene expression data


title: 5713384044_H

description: SAMPLE 232

value: IIA


title: FF0685_F_kidney

description: gene expression data


title: 5713384044_J

description: SAMPLE 233


title: ChIP-DNA of SKOV-3, replicate-2


title: FF0727_F_liver

description: gene expression data


title: FF0728_F_kidney

description: gene expression data


title: PCL-036_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-036

hyb_protocol: Sample was hybridized on an Agilent microarray (G4470B) at 55¡C for 17 hr in a rotating oven.

scan_protocol: Image at 5 um resolution was generated using an Agilent scanner G2505B and the Agilent Feature Extraction Software version 10.7.3.1 (Agilent Technologies) was used to obtain the microarray raw-data.

data_processing: The raw gTotalGeneSignal has been recalculated using the procedures described in Agilent Feature Extraction Software version 10.1 manual. Non-human probes, miRNAs flagged as absent (i.e. expressed below background levels) throughout the whole dataset and miRNAs expired according to Sanger miRBase Release 15 (April 2010) were discarded, and a quantile normalization was applied on raw data using the aroma.light package for Bioconducor. The data were then converted to obtain positive values throughout the dataset, at a minimum value of 1, and log2 transformed.

source_name: Primary plasma cell leukemia patient PCL-036

label_protocol: Labeled miRNAs were obtained from 500 ng of total RNA by ligating 5'-cytidine bisphosphate-Cy3 (pCp-Cy3, Agilent Technologies) in their 3'-ends. To enhance the ligation efficiency of the pCp-Cy3 T4 RNA ligase (Promega, Madison, WI), the total RNA was previously treated with alkaline phosphatase (Amersham, GE Healthcare, Buckinghamshire, UK) at 37¡C for 30 min. The labeled RNA was purified on chromatography columns (Micro Biospin 6, Bio-Rad, Hercules, CA)

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

value: Primary plasma cell leukemia

tag: igh translocation


title: 5713384044_B

description: SAMPLE 230


title: PCL-035_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-035

source_name: Primary plasma cell leukemia patient PCL-035


title: PCL-037_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-037

source_name: Primary plasma cell leukemia patient PCL-037


title: PCL-032_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-032

source_name: Primary plasma cell leukemia patient PCL-032


title: PCL-034_miRNA_1

description: MicroRNA profiling data from primary plasma cell leukemia patient PCL-034

source_name: Primary plasma cell leukemia patient PCL-034


title: FF0683_F_brain

description: gene expression data

source_name: CAST(dam) x CAST(sire) inbred,brain