title: EAC_024

tag: Patient #33782


title: EAC_021

status: Public on Jan 04 2011

type: RNA

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

country: USA

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48702 probes on the Human-6 beadChip ver.2 were used. Clinical data provided as a supplementary file on Series record:GSE13898_EAC_MDACC_DepSysB_ClinicalInformation.txt.gz

hyb_protocol: Labeled, amplified material (1,500 ng per array) was hybridized to a ver. 2 of the Illumina Human-6 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA). Array signals were developed by Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the BeadChip manual

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformation. To export to a data matrix, Sample Gene Profile option of this software was used.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Esophagus

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina?? TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

growth_protocol: Specimen from Primary Human esophageal Tumor biopsy

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer's protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

treatment_protocol: No treatment. Disease state only

tag: Patient #49711


title: EAC_026

tag: Patient #39370


title: EAC_023

tag: Patient #50984


title: EAC_025-2

tag: Patient #37023


title: EAC_020

tag: Patient #49434


title: EAC_014-1

tag: Patient #43134


title: EAC_017-1

tag: Patient #47226


title: EAC_017-2


title: EAC_014-2


title: EAC_016

tag: Patient #44526


title: EAC_013

tag: Patient #40982


title: EAC_012

tag: Patient #40590


title: EAC_027

tag: Patient #40768


title: EAC_011

tag: Patient #40550


title: EAC_009

tag: Patient #38461


title: EAC_018

tag: Patient #48424


title: EAC_007-2

tag: Patient #37910


title: EAC_008

tag: Patient #38198


title: EAC_010

tag: Patient #39839


title: EAC_007-1


title: EAC_006-2

tag: Patient #37199


title: EAC_005

tag: Patient #35033


title: deletion mutant 2 grown for 48 hours

city: Kundl

first: Ivo

last: Zadra

state: Tyrol

address: Biochemiestr. 10

department: Anti Infectives Microbiology

country: Austria

institute: SANDOZ GmbH

description: whole genome expression data

hyb_protocol: EukGE-WS2v4_450 (Affymetrix)

scan_protocol: GCS3000-Scanner (Affymetrix). Hybridized arrays were scanned and analysed using the Affymetrix GeneChip® Operating Software.

data_processing: Data was analyzed with Genespring 7.2

organism: Penicillium chrysogenum

source_name: mycelium from deletion mutant 2 grown for 48 hours

label_protocol: Affymetrix GeneChip® IVT Labeling Kit, according to manufacturer protocol

growth_protocol: solid production medium at 25 °C, 36, 48, 60, 72 and 96 hours

extract_protocol: Mycelia were ground to a fine powder under liquid nitrogen and total RNA was purified using Trizol reagent followed by an RNeasy® clean-up (Qiagen, Hilden, Germany) and DNAseI digestion. RNA quality was determined using an Agilent 2100 Bioanalyzer.

tag: tissue

value: vegetative mycelium

tag: strain

value: DstuA


title: EAC_003

tag: Patient #33579


title: deletion mutant 2 grown for 60 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 2 grown for 60 hours


title: EAC_004-2

tag: Patient #33986


title: EAC_006-1


title: EAC_004-1


title: deletion mutant 1 grown for 96 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 1 grown for 96 hours

value: DbrlA


title: deletion mutant 2 grown for 36 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 2 grown for 36 hours


title: deletion mutant 2 grown for 96 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 2 grown for 96 hours


title: EAC_001

tag: Patient #32321


title: deletion mutant 2 grown for 72 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 2 grown for 72 hours


title: deletion mutant 1 grown for 72 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 1 grown for 72 hours


title: BARRETT_013

tag: Patient #5319

tag: Pathology

value: high grade displasia


title: EAC_002

tag: Patient #33442


title: deletion mutant 1 grown for 48 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 1 grown for 48 hours


title: deletion mutant 1 grown for 60 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 1 grown for 60 hours


title: BARRETT_015

tag: Patient #5980

value: low grade displasia


title: BARRETT_014

tag: Patient #5421


title: BARRETT_012

tag: Patient #5307


title: deletion mutant 1 grown for 36 hours

description: whole genome expression data

source_name: mycelium from deletion mutant 1 grown for 36 hours


title: EAC_029

tag: Patient #42107


title: recipient strain grown for 72 hours

description: whole genome expression data

source_name: mycelium from recipient strain grown for 72 hours


title: recipient strain grown for 96 hours

description: whole genome expression data

source_name: mycelium from recipient strain grown for 96 hours


title: BARRETT_010

tag: Patient #5202


title: recipient strain grown for 60 hours

description: whole genome expression data

source_name: mycelium from recipient strain grown for 60 hours


title: BARRETT_011

tag: Patient #5293


title: recipient strain grown for 48 hours

description: whole genome expression data

source_name: mycelium from recipient strain grown for 48 hours


title: BARRETT_006

tag: Patient #2927


title: BARRETT_003

tag: Patient #3660


title: recipient strain grown for 36 hours

description: whole genome expression data

source_name: mycelium from recipient strain grown for 36 hours


title: BARRETT_005

tag: Patient #4055

value: no grade displasia


title: BARRETT_004

tag: Patient #3982


title: BARRETT_007

tag: Patient #3495


title: ESO_ST_028

tag: Patient #50984

value: normal


title: ESO_ST_026

tag: Patient #51064


title: BARRETT_001

tag: Patient #3136


title: ESO_ST_025


title: BARRETT_009

tag: Patient #4770


title: BARRETT_008

tag: Patient #4136

tag: Pathology


title: EAC_035

tag: Patient #49181


title: EAC_028

tag: Patient #41764


title: EAC_032

tag: Patient #47406


title: EAC_015

tag: Patient #44472


title: ESO_ST_019

tag: Patient #33413


title: ESO_ST_022

tag: Patient #42458


title: ESO_ST_021

tag: Patient #46663


title: JMJD2C shRNA - 96 hr - mAdbID:98062

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 98062

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1). Spot values were normalized using the default linear-lowess normalization.

source_name: Untreated (no DOX)

label_protocol:
Agilent Cy3 Labeling Protocol
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
Trizol Total RNA
Extraction method: Trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

tag: cell line

tag: cell type

value: Primary Mediastinal B-cell Lymphoma

tag: disease state

value: Primary Mediastinal B-cell Lymphoma Late Stage

source_name: JMJD2C shRNA - 96 hr

label_protocol:
Agilent Cy5 Labeling Protocol
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 96 hr
In-vitro treatment: Knockdown by JMJD2C shRNA after induction with doxycycline (20 ug/ml) for 96 hours.


title: ESO_ST_013

source_name: Esophagus

tag: Patient #50118


title: ESO_ST_016

tag: Patient #50492


title: ESO_ST_015

tag: Patient #50434


title: ESO_ST_023

tag: Patient #48174


title: ESO_ST_018

tag: Patient #50617


title: JAK2 shRNA - 24 hr - mAdbID:97878

description: mAdb experiment ID: 97878

source_name: JAK2 shRNA - 24 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hr
In-vitro treatment: Knockdown by JAK2 shRNA after induction with doxycycline (20 ug/ml) for 24 hours.


title: ESO_ST_012

tag: Patient #50046


title: JAK2 shRNA - 72 hr - mAdbID:97880

description: mAdb experiment ID: 97880

source_name: JAK2 shRNA - 72 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 72 hr
In-vitro treatment: Knockdown by JAK2 shRNA after induction with doxycycline (20 ug/ml) for 72 hours.


title: ESO_ST_011

tag: Patient #49793

tag: Pathology


title: BARRETT_002

tag: Patient #3437


title: ESO_ST_010

tag: Patient #33529


title: ESO_ST_008

tag: Patient #49764


title: JMJD2C shRNA - 24 hr - mAdbID:98059

description: mAdb experiment ID: 98059

source_name: JMJD2C shRNA - 24 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hr
In-vitro treatment: Knockdown by JMJD2C shRNA after induction with doxycycline (20 ug/ml) for 24 hours.


title: ESO_ST_009

tag: Patient #46682


title: ESO_ST_020

tag: Patient #48917


title: JMJD2C shRNA - 72 hr - mAdbID:98061

description: mAdb experiment ID: 98061

source_name: JMJD2C shRNA - 72 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 72 hr
In-vitro treatment: Knockdown by JMJD2C shRNA after induction with doxycycline (20 ug/ml) for 72 hours.


title: JAK2 shRNA - 48 hr - mAdbID:97879

description: mAdb experiment ID: 97879

source_name: JAK2 shRNA - 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hr
In-vitro treatment: Knockdown by JAK2 shRNA after induction with doxycycline (20 ug/ml) for 48 hours.


title: JAK2 inhibitor - 16 hr - mAdbID:102822

description: mAdb experiment ID: 102822

source_name: DMSO-treated Control

source_name: JAK2 inhibitor - 16 hr

treatment_protocol:
Treatment type: small molecule
Agent: JAK2 inhibitor TG101348
Treatment dose: 2 uM
Treatment time: 16 hr


title: ESO_ST_014

tag: Patient #50157


title: JAK2 inhibitor - 48 hr - mAdbID:102824

description: mAdb experiment ID: 102824

tag: cell line

source_name: JAK2 inhibitor - 48 hr

treatment_protocol:
Treatment type: small molecule
Agent: JAK2 inhibitor TG101348
Treatment dose: 2 uM
Treatment time: 48 hr


title: ESO_ST_027

tag: Patient #51393


title: ESO_ST_024

tag: Patient #48576


title: ESO_ST_017

tag: Patient #50512


title: JAK2 inhibitor - 6 hr - mAdbID:102820

description: mAdb experiment ID: 102820

tag: cell type

tag: disease state

source_name: JAK2 inhibitor - 6 hr

treatment_protocol:
Treatment type: small molecule
Agent: JAK2 inhibitor TG101348
Treatment dose: 2 uM
Treatment time: 6 hr


title: ESO_ST_006

tag: Patient #49256


title: JAK2 inhibitor - 8 hr - mAdbID:102821

description: mAdb experiment ID: 102821

source_name: JAK2 inhibitor - 8 hr

treatment_protocol:
Treatment type: small molecule
Agent: JAK2 inhibitor TG101348
Treatment dose: 2 uM
Treatment time: 8 hr


title: JAK2 shRNA - 96 hr - mAdbID:97881

description: mAdb experiment ID: 97881

source_name: JAK2 shRNA - 96 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 96 hr
In-vitro treatment: Knockdown by JAK2 shRNA after induction with doxycycline (20 ug/ml) for 96 hours.


title: JAK2 inhibitor - 24 hr - mAdbID:102823

description: mAdb experiment ID: 102823

source_name: JAK2 inhibitor - 24 hr

treatment_protocol:
Treatment type: small molecule
Agent: JAK2 inhibitor TG101348
Treatment dose: 2 uM
Treatment time: 24 hr


title: JMJD2C shRNA - 48 hr - mAdbID:98060

description: mAdb experiment ID: 98060

source_name: JMJD2C shRNA - 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hr
In-vitro treatment: Knockdown by JMJD2C shRNA after induction with doxycycline (20 ug/ml) for 48 hours.


title: ESO_ST_005


title: ESO_ST_007

tag: Patient #49668


title: JAK2 inhibitor - 4 hr - mAdbID:102819

description: mAdb experiment ID: 102819

source_name: JAK2 inhibitor - 4 hr

treatment_protocol:
Treatment type: small molecule
Agent: JAK2 inhibitor TG101348
Treatment dose: 2 uM
Treatment time: 4 hr


title: ESO_ST_004

tag: Patient #33986


title: JAK2 inhibitor - 0.5 hr - mAdbID:102817

description: mAdb experiment ID: 102817

source_name: JAK2 inhibitor - 0.5 hr

treatment_protocol:
Treatment type: small molecule
Agent: JAK2 inhibitor TG101348
Treatment dose: 2 uM
Treatment time: 0.5 hr


title: ESO_ST_003

tag: Patient #42244


title: JAK2 inhibitor - 2 hr - mAdbID:102818

description: mAdb experiment ID: 102818

source_name: JAK2 inhibitor - 2 hr

treatment_protocol:
Treatment type: small molecule
Agent: JAK2 inhibitor TG101348
Treatment dose: 2 uM
Treatment time: 2 hr


title: ESO_ST_001

source_name: Esophagus

growth_protocol: Specimen from Primary Human esophageal surrounding tissue biopsy

treatment_protocol: No treatment. Disease state only

tag: Patient #44472

tag: Pathology


title: Rat 12, Stimulated vs. NonStimulated, Replicate 1

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description:
Biological replicate 12 of 12.
Rat12_rep1

hyb_protocol: Hybridization according to Agilent 60-mer oligo microarray processing protocol v2.1 with the following modifications: 2 micro gram labeled DNA per channel were mixed; no fractionation; probes were denatured for 3 min at 98 degree celcius; hybridization at 65 degree celcius; SSPE washes as recommended; slides were dipped in acetonitril (10 s) then dried.

scan_protocol: Slides were scanned using an Agilent G2505B scanner, and data were extracted using the Feature Extraction software version 9.1 (Agilent Technologies).

data_processing: Normalization of the log2(Cy5/Cy3)-ratios with non-linear loess regression; statistical software: R, package limma.

organism: Rattus norvegicus

source_name: control skin explants of BN origin cultured in the presence of syngeneic lymphocytes of BN origin

label_protocol: Total RNA was transcribed, amplified and labeled according to the BD Atlas SMART fluorescent probe amplification kit with the following modifications: RNA template was hydrolized after transcription (high pH, 30 min/70 degree celcius), and PCR amplification progress was monitored and stopped before reaching saturation.

growth_protocol: Mononuclear cells were obtained from rat spleens by density gradient centrifugation on Biocoll (Biochrom, Berlin, Germany). Responder and irradiated (25 Gy) stimulator splenocytes were co-cultured in a mixed lymphocyte reaction (MLR) and the proliferation of responder lymphocytes was tested by [methyl-3H]-thymidine (Amersham, Braunschweig, Germany) incorporation. The stimulation index (SI) was calculated (cpm responder cells and irradiated stimulator cells/cpm responder cells alone). After 7 days 1.000.000 responder lymphocytes were added to freshly obtained skin samples from the stimulator strain that were cultured in 200 µl in 10 ml NaHCO3-buffered Dulbecco’s modified Eagle’s medium (DMEM) (Biochrom) supplemented with 3 % normal rat serum, 2 mM L-glutamine, 1 mM sodium pyruvate, and antibiotics (100 U/ml penicillin, 100 µg/ml streptomycin) in round-bottomed microtitre plates (Sarstedt, Nümbrecht, Germany). The skin samples were excised from the paws of rats after washing with 70 % ethanol and collected in N-2-hydroxyethylpiperazine-N’-2-ethanesulfonic acid (HEPES)-buffered DMEM. The subcutaneous fat tissue was removed and the samples were trimmed to a size of 1.5 x 1.5 mm. Skin samples cultured in medium only and samples co-cultured with lymphocytes from a “syngeneic MLR” culture were used as controls. After three days the skin explants were washed with HEPES-buffered DMEM and snap frozen in liquid nitrogen and stored at -80°C for RNA preparation. Parallel samples were fixed in 10 % neutral-buffered formalin, sectioned, and stained with hematoxylin and eosin (H&E). The histological evaluation of the skin explants was performed blinded by an expert histopathologist (L.S.).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen, Gaithersburg, MD).

treatment_protocol: Transplantation experiments were approved by the Experimental Animal Board under the Ministry of Agriculture of Norway. Male PVG.7b rats served as bone marrow and lymph node donors. Mononuclear bone marrow cells were purified by density gradient centrifugation in Nycoprep 1.077A (Medinor ASA, Norway). The cells were depleted of T cells by magnetic separation using Ox19 (anti-CD5) and R73 (anti-αβ T cell receptor) antibodies conjugated to pan-mouse IgG coated Dynabeads (Dynal Biotech ASA, Norway). Male BN rats were used as recipients. They were irradiated (9 Gy) and received subsequently an intravenous injection of 30×1.000.000 PVG.7b T cell depleted bone marrow cells. 15 days post transplantation, 15×1.000.000 lymph node cells were injected to evoke GVHD. The rats were regularly monitored for GVHD symptoms. Rats suffering from irreversible GVHD were sacrificed and skin samples were processed for RNA preparation and histology as described above for skin explant samples.

tag: gender

value: male

tag: age

value: 15 weeks

tag: strain

value: BN

source_name: rat skin explants of BN origin cultured in the presence of pre-stimulated allogeneic lymphocytes of PVG origin


title: c3 - untreated mouse

city: Stockholm

first: Qiang

last: Pan-Hammarström

address: F79, Huddinge Hospital

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institute

description: untreated mouse

hyb_protocol: 15 μg the fragmented cRNA were then hybridized with the mouse Genome 430A 2.0 array (Affymetrix), using GeneChip Eukaryotic Hybridization Control Kit (Affymetrix, P/N 900454). Hybridization was allowed to proceed overnight (16h) at 45 ºC, followed by automate washing and staining in the Fluidics Station 450 (Affymetrix).

scan_protocol: The GeneChips were scanned with an Affymetrix GeneArray 3000 Scanner and data acquired via the Microarray Suite software MAS 5.0.

data_processing: Affymetrix Microarray Suite Version 5.0

label: Standard Affymetrix Protocol

organism: Mus musculus

source_name: stomach

label_protocol: Four mg of total RNA from each sample was used to synthesize double-stranded cDNA (One-Cycle cDNA Synthesis Kit, Affymetrix). The double-stranded cDNA samples were subsequently reverse transcribed, amplified, labeled according to the Affymetrix standard protocol.

extract_protocol: Total RNA was isolated from the antrum portion of the stomach using the RNeasy mini kit (Qiagen, Hilden, Germany). In addition to the standard procedure, DNase I (Qiagen) was used to remove trace amounts of genomic DNA. RNA quality was checked using an Agilent 2001 Bioanalyzer (Agilent Technologies, Wilmington DE) before cDNA synthesis

tag: mouse stomach


title: Rat 11, Stimulated vs. NonStimulated, Replicate 1

description:
Biological replicate 11 of 12.
Rat11_rep1


title: c4 - untreated mouse

description: untreated mouse

source_name: stoamch

extract_protocol: Total RNA was isolated from the antrum portion of the stomach using the RNeasy mini kit (Qiagen, Hilden, Germany). In addition to the standard procedure, DNase I (Qiagen) was used to remove trace amounts of genomic DNA. RNA quality was checked using an Agilent 2001 Bioanalyzer (Agilent Technologies, Wilmington DE) before cDNA synthesis.


title: ESO_ST_002

tag: Patient #42697


title: Rat 12, Stimulated vs. NonStimulated, Replicate 2

description:
Biological replicate 12 of 12.
Rat12_rep2


title: CACO-2-sorted CD133+ cells (sample3)

city: Roma

first: Nathalie

last: Saulnier

address: Largo Francesco Vito,1

country: Italy

institute: Università Cattolica del Sacro Cuore di Roma

hyb_protocol: Ten micrograms of labeled cRNA were purified, chemically fragmented and hybridized to oligonucleotide probes on an Affymetrix HG-U133 GeneChip at 45°C for 16 hours in a hybridization oven (Affymetrix) set at 60RPM.

scan_protocol: Scanning of the arrays was carried using the Agilent Gene Array Scanner 3000 7G (Agilent technologies, Santa Clara, CA, USA).

data_processing: Data were generated by using Affymetrix GCOS v1.2 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software.

source_name: CACO-2 cell line derived from a human colorectal carcinoma

label_protocol: Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification Two-Cycle target Labeling and Control Reagents (Affymetrix Inc.)

growth_protocol: CaCo-2 cells were cultured in high-glucose Dulbecco’s modified Eagle’s medium (DMEM), supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere of 5% CO2 in air. The medium was changed twice a week.

extract_protocol: Total RNA was be extracted from CD133+ and CD133- sorted cells using RNeasy Miny Kit (Qiagen, Hilden, Germany).

treatment_protocol: CD133+ and CD133-subpopulations from CACO-2 cells were identified and separated by FACS-sorter (FACSAria, Beckton Dikinson). Cells were detached with 0.25% trypsin, washed twice with calcium/magnesium–free PBS and stained using the AC133 mouse monoclonal antibody directly conjugated with phycoerythrin (PE) (Miltenyi Biotech) and the corresponding conjugated isotype-matched monoclonal antibody in order to establish monoclonal background fluorescence. After 30 min incubation, cells were washed and resuspended in a solution of DMEM with 2% FBS at a concentration of 2x106 cells / ml and analyzed by FACS-sorter. CD133 + and CD133- cells were separated and aseptically recovered. The purity of the two fractions was tested by flow cytometry (BD FACSCalibur system).

value: CD133+ cells

tag: cell line


title: CACO-2-sorted CD133+ cells (sample1)


title: b4 - Mice challenged with H. pylori

description: Mice challenged with H. pylori


title: CACO-2-sorted CD133- cells (sample4)

value: CD133- cells


title: Ketamine PFC  1

city: Hong Kong

first: sijie

last: tan

country: China

institute: Chinese university of Hong Kong

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with Affymetrix Mouse Gene 1.0 ST Arrays and scanned at the HKU Genome Research Centre.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Expression Console (Affymetrix) for background correction and normalization. Data was analyzed for fold changes and Gene Ontology (GO) analysis in the computer software GeneSpring GX 9 (Agilent Technologies, Palo Alto, CA, USA).

source_name: Saline treated mice

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

extract_protocol: Total RNA was isolated from brain tissues using RNeasy Lipid Tissue Mini Kits (Qiagen Inc., Valencia, CA, USA) according to the manufactures’ protocals.

treatment_protocol: Ketamine (Alfasan Inc., Utrecht, Holland) was given through intraperitoneal injection daily at a sub-anesthetic dose of Ketamine (Alfasan Inc., Utrecht,  Holland) was given through intraperitoneal injection daily at a sub-anesthetic dose of 30 mg/kg while normal saline was given as controls.

value: ICR

tag: tissue

value: prefrontal cortex

tag: Sex

value: female


title: c5 - untreated mouse

description: untreated mouse


title: Ketamine PFC  2


title: CACO-2-sorted CD133- cells (sample6)


title: c2 - untreated mouse

description: untreated mouse

label_protocol: Four mg of total RNA from each sample was used to synthesize double-stranded cDNA (One-Cycle cDNA Synthesis Kit, Affymetrix). The double-stranded cDNA samples were subsequently reverse transcribed, amplified, labeled according to the Affymetrix standard protocol


title: Saline PFC  1

source_name: Ketamine addicted mice


title: WT strain untreated versus WT strain treated for 60 minutes with MT02-replicate 2

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: S. aureus HG001 exposed or not exposed for 60 min to antimicrobial compound MT02

hyb_protocol: A mixture of RNA from WT and mutant strain was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the GeneSpring 7 default LOWESS (locally weighted linear regression) method.

label: cyanine 3

organism: Staphylococcus aureus

source_name: S. aureus HG001 w/o MT02, 60 min

label_protocol: Incorporation during reverse transcription

growth_protocol: mid-log phase at an optical density at 600 nm of 0.6 to 0.8 in Muller-Hinton

extract_protocol: RNAprotectTM Bacteria Reagent (Qiagen, Hilden, Germany) and immediately incubated on ice. After centrifugation for 10 min at 6.000 x g and 4°C, the supernatant was discarded and the pellet resuspended in 1 ml RLT-buffer (Qiagen) supplemented with 1 % (vol/vol) β-mercaptoethanol. Cells were disrupted in Lysing Matrix E (MP Biomedicals) using a FastPrep®-24 (MP Biomedicals, Solon, OH, USA), followed by cooling on ice for 2 min. After brief centrifugation, the supernatant was purified using RNeasy®Mini Kit. Final treatment with DNase for 1 h at 37°C and again purified with RNeasy®Mini Kit.

tag: agent

label: cyanine 5

source_name: S. aureus HG001 with MT02, 60 min

treatment_protocol: Exposition to MT02 for 60 minutes


title: Rat 11, Stimulated vs. NonStimulated, Replicate 2

description:
Biological replicate 11 of 12.
Rat11_rep2


title: CACO-2-sorted CD133+ cells (sample2)

tag: cell type


title: CACO-2-sorted CD133- cells (sample5)


title: WT strain untreated versus WT strain treated for 60 minutes with MT02-replicate 1


title: b1 - Mice challenged with H. pylori

description: Mice challenged with H. pylori


title: Saline PFC  2


title: b3 - Mice challenged with H. pylori

description: Mice challenged with H. pylori

scan_protocol: The GeneChips were scanned with an Affymetrix GeneArray 3000 Scanner and data acquired via the Microarray Suite software MAS 5.0


title: Rat 10, Stimulated vs. NonStimulated, Replicate 2

description:
Biological replicate 10 of 12.
Rat10_rep2


title: Rat 10, Stimulated vs. NonStimulated, Replicate 1

description:
Biological replicate 10 of 12.
Rat10_rep1


title: Rat 9, Stimulated vs. NonStimulated, Replicate 2

description:
Biological replicate 9 of 12.
Rat9_rep2


title: A 5 -  Immunized mice challenged with H. pylori

source_name: Stomach


title: S8_RloA2_Hy5

city: Boulder

first: liang

last: zhang

state: CO

address: University of Colorado at Boulder, Han lab, Department of MCD Biology, Campus box 0347

institute: university of colorado at boulder

description: miRNA expression data from FACS sorted cells

hyb_protocol: Standard Exiqon miRCURY™ LNA Array (v.11.0) hybridization protocol according to he manufacturer's instructions

scan_protocol: Standard Exiqon miRCURY™ LNA Array (v.11.0) scanning protocol according to he manufacturer's instructions

data_processing:
Analysis of the scanned slides showed that the labeling was successful as all capture probes for the control spike-in oligo nucleotides produced signals in the expected range. The quantified signals (background correction) were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
Background correction, refers to adjustments to the data intended to remove nonbiological contributions (background) to the measured signal.
Normalization method, refers to computational data transformations intended to remove certain systematic biases from microarray data, such as dye effects or intensity dependence. We have good experience with using the non-linear regression method (LOESS) to apply this transformation to the data. The positive effect from normalization is illustrated on each slide sheet (slide 1 - 8) with a MA plot before and after normalization. After normalization the spots appear symmetrically scattered around the horizontal line M=0. The difference between the two channels (M) is now independent of the average intensity level of the two channels (A).

source_name: FACS sorted P4 Matrix cells

label_protocol: Standard Exiqon miRCURY™ Hy3™/Hy5™ power labeling kit protocol according to he manufacturer's instructions

growth_protocol: Standard mouse growth protocol

extract_protocol: miRNeasy kit  (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Hair follicle cells were isolated from P4 Backskin (Dox since P3 for 24hrs) of DTG (K14-rtTA/TRE-miR-125b/K14-H2BGFP), TRE (TRE-miR-125b/K14-H2BGFP), KrtA (K14-rtTA/K14-H2BGFP) as following: interfollicular epidermis sheet was pealed from hair follicle & dermis after dispase treatment.The hair follicle & dermis were first digested by collagenase (Sigma). Intact hair follicles were separated from dermal cells by low speed spinning (20g). The hair follicles were then digested by Trypsin and filtered by 40 µm cell strainers. The isolated hair follicle cells were FACS sorted. During FACS, cells were first gated against CD34 (endothelial cells), CD45 (immune cells), CD114 (melanocytes) and DAPI (dead cells). ORS cells were sorted from the remaining cells as α6HiGFPHi

value: skin

tag: genotype


title: S9_Rall3_Hy5

source_name: FACS sorted P4 RFPall HF cells


title: S10_Rall3_Hy3


title: S10_RloA4_Hy5


title: A 6 - Immunized mice challenged with H. pylori


title: Rat 8, Stimulated vs. NonStimulated, Replicate 1

description:
Biological replicate 8 of 12.
Rat8_rep1


title: Rat 9, Stimulated vs. NonStimulated, Replicate 1

description:
Biological replicate 9 of 12.
Rat9_rep1


title: Rat 8, Stimulated vs. NonStimulated, Replicate 2

description:
Biological replicate 8 of 12.
Rat8_rep2


title: U133plus2 Array 12h EGF stimulation rep2

city: Lebanon

first: Mathieu

last: Lupien

state: NH

address: One Medical Center Drive

department: Genetics

institute: Norris Cotton Cancer Center/Dartmouth Medical School

data_processing: Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718. RMA data for the expression profile assays is provided. The file used to convert affy probe_ID number to refseq gene ID found in the RMA data is also provided (name: HGU133Plus2_Hs_REFSEQ_13.0.0)

tag: stimulation

value: 12h EGF stimulation

value: breast cancer cells


title: U133plus2 Array 12h EGF stimulation rep1

hyb_protocol: Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718


title: U133plus2 Array 12h EGF stimulation rep3

scan_protocol: Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718


title: U133plus2 Array 3h ICI pre-treatment 3hEGF treatment stimulation rep2

label_protocol: Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718


title: U133plus2 Array 3h ICI pre-treatment 3hEGF treatment stimulation rep1

growth_protocol: Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718


title: S8_Rall2_Hy3


title: S9_RloA3_Hy3


title: U133plus2 Array 3h ICI pre-treatment 3hEGF treatment stimulation rep3

extract_protocol: Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718


title: S7_Rall2_Hy5


title: A 3 - Immunized mice challenged with H. pylori


title: A 4 - Immunized mice challenged with H. pylori

tag: Mouse stomach


title: Rat 7, Stimulated vs. NonStimulated, Replicate 1

description:
Biological replicate 7 of 12.
Rat7_rep1


title: Rat 7, Stimulated vs. NonStimulated, Replicate 2

description:
Biological replicate 7 of 12.
Rat7_rep2


title: S6_Rall2_Hy3


title: S6_GRA2_Hy5

source_name: FACS sorted P4 Early Bulge cells


title: U133plus2 Array 3h EGF stimulation rep3

source_name: U133plus2 Array 3h EGF stimulation rep3

treatment_protocol: Described in method section: http://www.ncbi.nlm.nih.gov/pubmed/20889718

value: 3h EGF stimulation


title: Rat 5, Stimulated vs. NonStimulated, Replicate 2

description:
Biological replicate 5 of 12.
Rat5_rep2


title: S7_RhiA2_Hy3

source_name: FACS sorted P4 Non Bulge ORS cells


title: Rat 6, Stimulated vs. NonStimulated, Replicate 2

description:
Biological replicate 6 of 12.
Rat6_rep2


title: U133plus2 Array 3h EGF stimulation rep1

source_name: U133plus2 Array 3h EGF stimulation rep1


title: U133plus2 Array control rep3

source_name: U133plus2 Array control rep3

value: control


title: Rat 6, Stimulated vs. NonStimulated, Replicate 1

description:
Biological replicate 6 of 12.
Rat6_rep1

source_name: control skin explants of BN origin cultured in the presence of syngeneic lymphocytes of BN origin


title: Mouse Olfactory Bulb E17

city: Berkeley

first: Grodon

middle: Ross Orion

last: Campbell

state: California

address: 265 Life Science Addition

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: Gene expression data from developing olfactory bulb

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array 430.2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G

data_processing: The data were analyzed with GCRMA package from Bioconductor, version 2.0.

label: Biotin

source_name: Developing mouse olfactory bulb at embryonic day 17

label_protocol: RNA was purified with TRIzol reagent, subjected to two rounds of amplification, and Biotinylated, using Affymetrix reagents and protocols (http://www.affymetrix.com).

growth_protocol: Embryos were removed at appropriate age from pregnant females or collected at birth

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

treatment_protocol: Olfactory bulbs were accutely dissected

value: Embryonic olfactory bulb

tag: developmental stage

value: embryonic day 17


title: Mouse Olfactory Bulb P0

source_name: Developing mouse olfactory bulb at postnatal day 0

value: Postnatal olfactory bulb

value: postnatal day 0


title: Mouse Olfactory Bulb E16

source_name: Developing mouse olfactory bulb at embryonic day 16

value: embryonic day 16


title: Mouse Olfactory Bulb E14

source_name: Developing mouse olfactory bulb at embryonic day 14

value: embryonic day 14


title: U133plus2 Array 3h EGF stimulation rep2

source_name: U133plus2 Array 3h EGF stimulation rep2


title: S5_Bas2_Hy5

source_name: FACS sorted P4 Basal Epidermal cells


title: Rat 5, Stimulated vs. NonStimulated, Replicate 1

description:
Biological replicate 5 of 12.
Rat5_rep1

value: male

value: 15 weeks

value: BN

source_name: rat skin explants of BN origin cultured in the presence of pre-stimulated allogeneic lymphocytes of PVG origin


title: S3_Rall1_Hy5


title: Rat 4, Stimulated vs. NonStimulated, Replicate 2

description:
Biological replicate 4 of 12.
Rat4_rep2


title: Mouse Olfactory Bulb E18

source_name: Developing mouse olfactory bulb at embryonic day 18

value: embryonic day 18


title: Mouse Olfactory Bulb E13

source_name: Developing mouse olfactory bulb at embryonic day 13

value: embryonic day 13


title: Rat 4, Stimulated vs. NonStimulated, Replicate 1

description:
Biological replicate 4 of 12.
Rat4_rep1


title: Mouse Olfactory Bulb E12

source_name: Developing mouse olfactory bulb at embryonic day 12

value: embryonic day 12


title: Mouse Olfactory Bulb E15

source_name: Developing mouse olfactory bulb at embryonic day 15

value: embryonic day 15


title: U133plus2 Array control rep2

source_name: U133plus2 Array control rep2


title: S3_RhiA1_Hy3

value: skin


title: U133plus2 Array control rep1

source_name: U133plus2 Array control rep1

value: breast cancer cells


title: Rat 3, Stimulated vs. NonStimulated, Replicate 2

description:
Biological replicate 3 of 12.
Rat3_rep2


title: S5_Rall2_Hy3

source_name: FACS sorted P4 RFPall HF cells


title: Rat 3, Stimulated vs. NonStimulated, Replicate 1

description:
Biological replicate 3 of 12.
Rat3_rep1


title: S2_Rall1_Hy5


title: S2_GRA1_Hy3

source_name: FACS sorted P4 Early Bulge cells


title: S1_Rall1_Hy5


title: Rat 2, Stimulated vs. NonStimulated, Replicate 2

description:
Biological replicate 2 of 12.
Rat2_rep2


title: Rat 2, Stimulated vs. NonStimulated, Replicate 1

description:
Biological replicate 2 of 12.
Rat2_rep1


title: S1_Bas1_Hy3


title: Female10_DTG_log2

description: Gene expression data from FACS sorted P4 ORS

hyb_protocol: Labeled cRNA samples were hybridized to MOE 430 2.0 mouse expression arrays which were processed and analyzed according to standard Affymetrix protocols.

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with RMA using Affymetrix expression console default analysis settings. All displayed signals were log2 transformed

source_name: FACS sorted P4 ORS cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: FVB/N

value: female

tag: treatment

value: Dox 24hrs


title: Rat 1, Stimulated vs. NonStimulated, Replicate 2

description:
Biological replicate 1 of 12.
Rat1_rep2

source_name: control skin explants of BN origin cultured in the presence of syngeneic lymphocytes of BN origin


title: Mouse Olfactory Bulb E11

source_name: Developing mouse olfactory bulb at embryonic day 11

value: Embryonic olfactory bulb

value: embryonic day 11


title: Male2_DTG_log2


title: JN_Rhi

description: Gene expression data from FACS sorted P4 non-bulge ORS cells

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix expression console default analysis settings

source_name: FACS sorted P4 non-bulge ORS cells from K14-RFP/Sox9-EGFP mice

treatment_protocol: Hair follicle cells were isolated from P4 Backskin of K14-RFP/Sox9-EGFP double transgenic mice as following: interfollicular epidermis sheet was pealed from hair follicle & dermis after dispase treatment. The hair follicle & dermis were first digested by collagenase (Sigma). Intact hair follicles were separated from dermal cells by low speed spinning (20g). The hair follicles were then digested by Trypsin and filtered by 40 µm cell strainers.   The isolated hair follicle cells were FACS sorted. Dead cells and large differentiated cells were excluded based on DAPI and side scattering. Early bulge cells were gated as GFPHi,RFPHi. Non-bulge ORS cells were gated as GFP-, RFPHi.


title: Female2_KrtA_log2


title: Rat 1, Stimulated vs. NonStimulated, Replicate 1

description:
Biological replicate 1 of 12.
Rat1_rep1


title: DNA packaging in mouse spermatozoal chromatin investigated by micrococcal nuclease digestion (MND); biol rep.

type: genomic

city: Leeds

first: David

last: Miller

address: Clarendon Way

department: Leeds Institute for Genetics and Health Therapeutics

country: United Kingdom

institute: Leeds University

description: Spermatozoal chromatin from mouse was digested with micrococcal nuclease (MN) to profile soluble and insoluble DNA.

hyb_protocol: For hybridisation, equal quantities of labelled DNA (500 - 1000 ng) were mixed with Cot-1 DNA (1 mg/ml) and incubated at 95°C for 3 minutes and then re-incubated at 37°C for 30 minutes. The DNAs were applied to either Agilent's 44K (100 µl) or 244K (490 µl) arrays, sealed and then incubated for 40 hours (244K arrays) or 24 hours (44K arrays) at 65°C with constant rotation (20 rpm).

scan_protocol: Scanning was conducted an accordance with the Agilent protocol.

data_processing: Data was processed for feature extraction, background subtraction and normalized in the Agilent CGH analytics software package. The default settings for the Agilent Analytics CGH v9.1 protocols were used (selection of a subset of rank invariant probes and using these for a linear median normalization between channels).

molecule: genomic DNA

source_name: Spermatozoal DNA digested with micrococcal nuclease (MNDI; insoluble fraction)

label_protocol: Labelling with cy3 or cy5 (GE Healthcare, Amersham UK) was accomplished using a random priming method in the presence of Klenow DNA polymerase (Invitrogen, Paisley, UK) according to the suggested Agilent protocol. Unincorporated nucleotides were removed by passing the reaction mixture through a sephadex G50 column.

tag: fraction

value: MNDI (insoluble fraction)

source_name: Spermatozoal DNA digested with micrococcal nuclease (MNDS; soluble Fraction)

extract_protocol:
DNA obtained from spermatozoa released into HEPES buffered synthetic oviduct fluid from the dissected epididymides of CD1 mice
Prior to processing, all DNA samples (including those pre-digested with EcoR1 and BamH1 or MNase were double re-digested with 10 units each of Alu1 and Rsa1 (New England Biolabs, Hitchin, UK) that generates fragments of 500 bp or less.

treatment_protocol: Semen was washed free of seminal plasma in HSOF buffer and pellets resuspended in 10mM Tris-Cl pH 8.0 containing 0.05% w/v PMSF and 1% w/v CTAB to detach principal pieces. Following centrifugation, pellets were resuspended in Mg2+ and Ca2+ free phosphate buffered saline (PBS) containing 0.5% v/v Triton X-100 and incubated for 10 minutes at 4°C. Following centrifugation, the pellets were resuspended in 1 ml PBS containing 0.5% PMSF, 10 mM DTT and incubated for 30 minutes at 37°C. CaCl2 was added to a final concentration of 0.6 mM and 5 units of micrococcal nuclease (Fermentas,, York, UK) added. Digestion was stopped after 3 minutes incubation at 37°C by the addition of EDTA to 5 mM. Following centrifugation at 5000g for 10 minutes, the supernatants (representing the soluble, histone-enriched fraction) and pellets (protamine-enriched) were processed.

value: MNDS (soluble fraction)


title: Male8_TRE_log2


title: Biopsy_CD_024

city: New Delhi

first: Vineet

last: Ahuja

state: delhi

address: Department of Gastroenterology, All India Institute of Medical Sciences

country: India

institute: AIIMS

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using Average normalization with IlluminaGUI in Bead Studio Software.

source_name: Colonic biopsies, Crohn's disease

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.

value: 40 years

tag: disease state

value: Crohn's disease

value: colonic biopsy


title: Biopsy_ITB_026

source_name: Colonic biopsies, intestinal tuberculosis disease

tag: gender

value: intestinal tuberculosis disease


title: Biopsy_Control_030

source_name: Colonic biopsies, control

tag: age

value: 65 years

tag: sample type

value: control


title: JN_RG

description: Gene expression data from FACS sorted P4 early bulge stem cells

source_name: FACS sorted P4 early bulge stem cells from K14-RFP/Sox9-EGFP mice

tag: strain


title: Biopsy_CD_017

value: 29 years

value: male


title: Biopsy_ITB_012

value: 26 years


title: Biopsy_Control_015

value: 23 years


title: Mpl-/- LSK_GFP_3

status: Public on Jan 03 2011

city: Leiden

first: Martijn

last: Brugman

address: PO Box 9600

department: Immunohematology and Bloodtransfusion

country: Netherlands

institute: LUMC

hyb_protocol: Following fragmentation, 3.75 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Summarized probeset data was compiled using RMA (as implemented in the 'affy' package) in R-2.10 using bioconductor packages.

source_name: LSK cells

label_protocol: Biotin labeled cRNA generated by amplification of the > 50 ng of RNA using the Nugen Ovation v2 system (Nugen Technologies, AC Bemmel, Netherlands), followed by biotin labeling and fragmentation using the Nugen FL-Ovation Biotin v2 module following the manufacturer's guidelines.

extract_protocol: RNA was isolated using RNeasy Micro Kit (Qiagen GmbH, Hilden, Germany)

treatment_protocol: LSK cells were isolated using flow cytometry on freshly harvested mouse bone marrow of gene therapy treated mice.

tag: genotype/variation

value: Mpl-/-

value: LSK cells

tag: protocol


title: Mpl-/- LSK_GFP_1


title: Mpl-/- LSK_Mpl_1

value: Mpl transduction


title: Mpl-/- LSK_GFP_2


title: Mpl-/- LSK_Mpl_2


title: Lg17 (M-)_infectedBMMf_vs._Lg13 (M+)_infectedBMMf_24hrs_rep.2

city: Lausanne

first: Frédéric

last: Schütz

address: Batiment Amphipole

institute: Swiss Institute of Bioinformatics

description: biological replicate 2

hyb_protocol: Cy3 and Cy5 labeled cDNA were mixed together, and loaded onto the glass-slides. Glass-slides were then scanned using an Agilent Technologies microarray scanner. The resulting TIF images were analyzed using GenePix Pro software (Axon Instruments, USA). For each labeling reaction, reference control RNA (2μl Alien spikes pool and 2μl Arabidopsis spikes pool obtained from the DAFL) was added for data normalization

data_processing:
Data analysis was performed using R statistics software (http://www.r-project.org/), Cy5 (red) and Cy3 (green) signal intensities were used to calculate M and A values for the array spots. In order to normalize the data, the log ratios were centered by lowess in each subarray (without scaling correction).
Genes that were at least 1.5 fold over or under-expressed and with a p-value <0.05 being considered as differentially expressed.

label_protocol: cDNA was synthesized from 5 μg of RNA by direct incorporation of Cy3 or Cy5 fluorophore-labeled DCTP using random primers (Invitrogen) mediated by the Superscript II reverse transcriptase.The labeled cDNA probes were then purified using the MiniElute PCR Purification kit (Qiagen), and mixed then concentrated using Millipore Microcon YM-30 columns.

growth_protocol: BMMf were differentiated from bone marrow precursor cells for 5 days at 370C in Dulbecco's Modified Eagle Medium supplemented with 1% penicillin/strepamycin(penstrep), 10% Fetal bovine serum (FBS) and 1% HEPES (cDMEM). Leishmania guyanensis (L.g.) parasites were grown to stationary phaze in Medium M199 supplemented with 10% FBS, 1% penstrep, and 5% HEPES (cM199).

extract_protocol: RNA was purified by RNAeasy Mini Kit (Qiagen™), and the quality and quantity were verified by Agilent Technologies (Germany) 2100 bioanalyzer and RNA 6000 Nano Assay LabChip® kit.

treatment_protocol: BMMf were infected 1:10 with L.g. parasites Lg13(M+) or Lg17(M-) with an uninfected control in cDMEM for 24hrs. Infectivity was verified using small scale infections on microscope culture slides stained with Diff-Quick to visualize infected BMMf . For the experiment to be use there had to be at least 80% infectivity with an average of 5 parasites per BMMf.

value: BALB/c


title: MEFdox0Div_rep1

city: Boston

first: Richard

last: Koche

state: MA

address: 185 Cambridge St.

institute: Broad Institute of Harvard and MIT

description: Gene expression from 96 hours of doxycycline-induced MEFs with an average of zero cell divisions.

hyb_protocol: Standard Affymetrix protocol

data_processing: Preprocessing, normalization, and analysis were all performed using GenePattern (http://www.broadinstitute.org/cancer/software/genepattern/).

source_name: Doxycycline-induced MEFs

label_protocol: Standard Affymetrix protocol

growth_protocol: Standard 10% Fetal Bovine Serum containing growth medium

extract_protocol: Extraction of total RNA was done using TRIzol (Invitrogen) followed by cleanup using the RNeasy(R) Mini column system (Qiagen).

treatment_protocol: Either 15% FBS containing medium supplemented with 2 ug/ul Doxycyline or 0.5% FBS containing Serum Starvation medium

value: Doxycycline

tag: replicate

value: secondary, inducible MEFs

value: 129/SvJ x C57/B6 hybrid

tag: cell division cohort

value: average of zero cell divisions


title: Lg17 (M-)_infectedBMMf_vs._Lg13 (M+)_infectedBMMf_24hrs_rep.1

description: biological replicate 1

scan_protocol: Glass-slides were then scanned using an Agilent Technologies microarray scanner. The resulting TIF images were analyzed using GenePix Pro software (Axon Instruments, USA).


title: MEFdox1Div_rep1

description: Gene expression from 96 hours of doxycycline-induced MEFs with an average of one cell division.

tag: agent

value: average of one cell division


title: MEFdox0Div_rep2

tag: cell type


title: Lg13 (M+)_infectedBMMf_vs._Lg17 (M-)_infectedBMMf_24hrs_rep.3

description: biological replicate 3


title: EBIO-treated differentiated ES cells sample 1

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

description: BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).

hyb_protocol: Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: ES cells were induced to differentiated in embryoid body (EB) assay for 5 days and then treated with EBIO for 10 days (EBIO_day5+10)

label_protocol: Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.

extract_protocol: Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

tag: cell line

tag: tissue

value: embryo

tag: morphology

value: small, tightly packed

value: differentiated embryonic stem cell (ES cells)


title: MEFdox2Div_rep2

description: Gene expression from 96 hours of doxycycline-induced MEFs with an average of two cell divisions.

value: average of two cell divisions


title: MEFdox2Div_rep1


title: MEFdox1Div_rep2


title: EBIO-treated differentiatedES cells sample 2


title: EBIO-treated ES cells sample 2

source_name: Embryonic stem cells, CGR8, passage 26, treated with EBIO (1mM) for 3 days

value: embryonic stem cell (ES cells)


title: Lg13 (M+)_infectedBMMf_vs._Lg17 (M-)_infectedBMMf_24hrs_rep.2

description: biological replicate 2


title: Lg13 (M+)_infectedBMMf_vs._Lg17 (M-)_infectedBMMf_24hrs_rep.1

description: biological replicate 1


title: EBIO-treated ES cells sample 1

source_name: Embryonic stem cells, CGR8, passage 25, treated with EBIO (1mM) for 3 days


title: Lg17 (M-)_infectedBMMf_vs._Lg13 (M+)_infectedBMMf_24hrs_rep.3

description: biological replicate 3


title: Mpl-/- LSK_Mpl_3


title: Untreated control differentiated ES cells sample 2

source_name: ES cells were induced to differentiated in embryoid body (EB) assay for 5 days and then cultured without EBIO for 10 days (Con_day5+10)


title: EBIO-treated ES cells sample 3

source_name: Embryonic stem cells, CGR8, passage 27, treated with EBIO (1mM) for 3 days


title: uninfected_BMMf_vs._Lg17(M-)_infectedBMMf_24hrs_rep.2

description: biological replicate 2


title: Untreated control ES cells sample 3

source_name: Embryonic stem cells, CGR8, passage 27


title: Untreated control differentiated ES cells sample 1


title: Lg17 (M-)_infectedBMMf_vs._uninfected_BMMf_24hrs_rep.3

description: biological replicate 3


title: Lg17 (M-)_infectedBMMf_vs._uninfected_BMMf_24hrs_rep.1

description: biological replicate 1


title: uninfected_BMMf_vs._Lg17(M-)_infectedBMMf_24hrs_rep.3

description: biological replicate 3


title: Lg17 (M-)_infectedBMMf_vs._uninfected_BMMf_24hrs_rep.2

description: biological replicate 2


title: Lg13 (M+)_infectedBMMf_vs._uninfected_BMMf_24hrs_rep.2

description: biological replicate 2


title: Lg13 (M+)_infectedBMMf_vs._uninfected_BMMf_24hrs_rep.3

description: biological replicate 3


title: Untreated control ES cells sample 1

source_name: Embryonic stem cells, CGR8, passage 25


title: uninfected_BMMf_vs._Lg17(M-)_infectedBMMf_24hrs_rep.1

description: biological replicate 1


title: Untreated control ES cells sample 2

source_name: Embryonic stem cells, CGR8, passage 26


title: CYD3_donor7

city: Marcy l'Etoile

first: Bruno

last: Guy

address: 1541 Av M Mérieux

department: Discovery

country: France

institute: sanofi pasteur

description: Analysis used non-infected cells RNA as control samples for comparison to the cells infected by Dengue virus type 3, chimeric dengue vaccine type 3 or live-attenuated dengue virus type 3

hyb_protocol: Slides were hybridized according to the manufacturer’s instructions (Agilent)

scan_protocol: Slides were scanned with a GenePix Personal 4100A scanner (Axon Instruments). The signal intensities were measured with the GenePix PRO v6.1 software.

data_processing: Data analysis were carried out with Rosetta Resolver software v4 (Rosetta biosoftware). Data normalisation and transformation was performed with Axon/Genepix error model (version 5.1; using a simplified version of the algorithm described in Schadt EE et al J. Cell. Biochemistry 2002;84:120-125) when loading data into Rosetta Resolver. All oligochip experiments were performed in dye swap.

source_name: Human monocyte derived dendritic cells non-infected

label_protocol: The labeled RNA were prepared using a Low RNA input fluorescence linear amplification kit (Agilent technology, Palo Alto, CA) according to the manufacturer’s instructions

extract_protocol: Total RNA are extracted with Nucleospin RNA II kit from Macherey Nagel, according to the manufacturer’s instructions

value: monocyte derived dendritic cells

source_name: Human monocyte derived dendritic cells infected with chimeric dengue 3 vaccine


title: uninfected_BMMf_vs._Lg13(M+)_infectedBMMf_24hrs_rep.1

description: biological replicate 1


title: TV_donor4

description: Analysis used non-infected cells RNA as control samples for comparison to the cells infected by tetravalent chimeric dengue vaccine

data_processing: Data analysis were carried out with Rosetta Resolver software v5 (Rosetta biosoftware). Data normalisation and transformation was performed with Axon/Genepix error model (version 6; using a simplified version of the algorithm described in Schadt EE et al J. Cell. Biochemistry 2002;84:120-125) when loading data into Rosetta Resolver. All oligochip experiments were performed in dye swap.

source_name: Human monocyte derived dendritic cells infected with tetravalent chimeric dengue vaccine


title: VDV3_donor7

source_name: Human monocyte derived dendritic cells infected with live-attenuated dengue virus 3


title: wtDEN3_donor3

source_name: Human monocyte derived dendritic cells infected with dengue virus type 3


title: CL1-5 cells treated DMSO

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: Gene expression data from CL1-5 treated with DMSO

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome 133 plus 2.0 GeneChip on Affymetrix Hybridization Oven 645, 60 RPM, then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were processed by GeneSpring GX software version 11 GC-RMA preprocessor to use on the CEL files

source_name: human lung cancer cell line treated DMSO as control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)(Santa Clara, CA, USA, http://www.affymetrix.com).

growth_protocol: Human lung adenocarcinoma CL1-5 cells were grown in DMEM with 10% fetal bovine serum at 37°C, 20% O2, 5% CO2.

treatment_protocol: 2.5 × 105 CL1-5 cells were treated for 24 h with 0.11 microM Analogue 3 or DMSO at a concentration of 0.05 µg/mL

value: control


title: EV8, biological rep3

description: The mRNA profiles from RD cells infected with/without EV71 were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).

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

scan_protocol: GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.

data_processing: The data were processed by GeneSpring GX software version 7.3.1 GC-RMA preprocessor to use on the CEL files

source_name: Human rhabdomyosarcoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Human rhabdomyosarcoma cells (RD) were cultured in MEM medium with 1 mM L-glutamate, 100 units/mL penicillin, 100 £gg/mL streptomycin and 10% fetal bovine serum (Gibco) at 37¢XC, 20% O2 and 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).

value: female

value: rhabdomyosarcoma cell

tag: infection

tag: time

value: 8 h


title: uninfected_BMMf_vs._Lg13(M+)_infectedBMMf_24hrs_rep.3

description: biological replicate 3


title: Leaves_MeOH_1day_rep2

city: Gwangju

first: Young Soon

last: Kim

address: 300 Youngbong-dong

department: Bioenergy Research Center

country: South Korea

institute: Chonnam National University

hyb_protocol: The amplified RNA was fragmented using 8 ㎕ of 5X fragmentation buffer (Sample cleanup Module; Affymetrix). Fragmentation was checked on 1 % agarose gel stained with EtBr and hybridized to the gene containing over 22,500 probe sets, as described in the Gene Chip Expression Analysis Technical Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing:
After the final wash & staining step, Affymetrix GeneChip® Rice Genome arrays was scanned using Affymetrix Model 3000 G7 scanner and the image data was extracted through Affymetrix Commnad Console software1.1. The raw .cel file generated through above procedure meant expression intensity data and was used for the next step.
For the normalization, Affymetrix microarray suite 5(MAS5) algorithm implemented in Affymetrix Expression Console software(version1.1) was used. To reduce noise for the significance analysis, probe sets that were not called Present by the MAS5 detection call in over 50% of the samples were filtered out. Highly expressed genes that showed over 2 fold difference comparing the signal value of control and test sample, were selected for the further study. The web-based tool, DAVID (the Database for Annotation, Visualization, and Integrated Discovery) was used to perform the biological interpretation of differentially expressed genes. Then, these genes were classified based on the information of gene function in Gene ontology, KEGG pathway database.
Ratio data and significance analysis results are available as supplementary files on the Series record.

organism: Oryza sativa

source_name: leaves, detached, MeOH, 1day

label_protocol: Per RNAsample, 6 ㎍ were used as input into the Affymetrix procedure as recommended by protocol (http://www.affymetrix.com). Briefly, 6 ㎍ of total RNA from each sample was converted to double-strand cDNA Using oligo(dT) primer incorporating a T7 promoter. Biotin-labeled RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module.

growth_protocol: Seeds of wild-type and transgenic rice were immersed in tap water for 2 d to induce germination and then potted in a tray filled with glasshouse compost (Boonong Soil, Seoul, Korea). Seedlings were grown in a plant growth room at 28°C and 70% humidity on a 14-h light/10-h dark cycle at 150 μmol m–2 s–1 4 photosynthetic photon flux density for 4 weeks. The apical 15 cm of the third leaf was used in all experiments.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit columns as described by the manufacturer (Qiagen, Hilden, Germany). RNA quality was assessed by Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., DE, USA).

treatment_protocol: A group of ten segments was floated into a 50-ml polypropylene conical tube containing 20 ml of water with or without various chemicals, and incubated under the same growth conditions described above for indicated time periods. Rice leaves were harvested, frozen in liquid nitrogen and stored at –80°C until used for the analysis

tag: cultivar

value: Japonica cultiva

tag: developmental stage

value: 4weeks-old rice

value: leaves


title: CYD4_donor4

description: Analysis used non-infected cells RNA as control samples for comparison to the cells infected by chimeric dengue vaccine type 4

source_name: Human monocyte derived dendritic cells infected with chimeric dengue 4 vaccine


title: uninfected_BMMf_vs._Lg13(M+)_infectedBMMf_24hrs_rep.2

description: biological replicate 2

value: BALB/c


title: Leaves_MeOH_1day_rep1


title: EV8, biological rep1

tag: gender


title: VDV3_donor3


title: wtDEN3_donor7


title: CYD3_donor4

description: Analysis used non-infected cells RNA as control samples for comparison to the cells infected by chimeric dengue vaccine type 3


title: CL1-5 cells treated Analogue 3, 4′-iodo-3,3,5-tripropyl-4-methoxy

description: Gene expression data from CL1-5 treated with Analogue 3

source_name: human lung cancer cell line treated Analogue 3 as test

tag: treatment


title: NOS sarcoma sample from patient 9

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

hyb_protocol: Following fragmentation, 7.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133A_2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner  300 with G7 update.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: NOS sarcoma sample from patient 9

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual_v2, 2004, Affymetrix).

extract_protocol:
Tumor samples were harvested intraoperatively and preserved in RNAlater and frozen at -20°C. Probes were then processed as suggested by the Quiagen RNAlater manual.
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: tumor type

value: NOS, primary

tag: grading

tag: age

tag: Neoadjuvant radiation

value: no

tag: Distant metastasis

tag: Local recurrence

tag: Status at follow up

value: NED


title: Leaves_DW_1day

source_name: leaves, detached, DW, 1day


title: EV8, biological rep2

tag: cell type


title: NOS sarcoma sample from patient 10

source_name: NOS sarcoma sample from patient 10

value: yes

value: died of disseminated disease


title: TV_donor3


title: NOS sarcoma sample from patient 8

source_name: NOS sarcoma sample from patient 8

value: NOS, recurrent


title: EV4, biological rep2

value: 4 h


title: CYD3_donor3


title: EV4, biological rep3


title: CYD1_donor4

description: Analysis used non-infected cells RNA as control samples for comparison to the cells infected by chimeric dengue vaccine type 1

source_name: Human monocyte derived dendritic cells infected with chimeric dengue 1 vaccine


title: CYD2_donor3

description: Analysis used non-infected cells RNA as control samples for comparison to the cells infected by chimeric dengue vaccine type 2

source_name: Human monocyte derived dendritic cells infected with chimeric dengue 2 vaccine


title: NOS sarcoma sample from patient 7

source_name: NOS sarcoma sample from patient 7

value: died of MI with NED after local recurrence


title: CYD4_donor3

source_name: Human monocyte derived dendritic cells non-infected

value: monocyte derived dendritic cells


title: EV0, biological rep2

value: uninfected

value: 0 h


title: EV4, biological rep1

value: female

value: rhabdomyosarcoma cell


title: BMDM stimulated with dexa+IL4, rep2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: mouse bone marrow cells after a total of 7 days cultivation in vitro  stimulated with dexa+IL4, rep2

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 3.2, from SAS. A custom CDF (Mouse4302_Mm_UG, Brainarray Version 9) was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: BMDM stimulated with dexa+IL4

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

growth_protocol: Bone marrow cells were isolated from the tibias and femurs of C57BL/6 mice. M-CSF at a concentration of 30 ng/ml was added to the culture medium [DMEM, 10% FCS, and penicillin/streptomycin].

extract_protocol: Total RNA extraction was carried out with a RNeasy RNA-extraction Kit (Qiagen) according to the manufacturers protocols

treatment_protocol: At day 4  the culture medium was replaced by stimulation medium as indicated and cells were cultured for 3 more days.

tag: strain

tag: stimulation


title: CYD4_donor1


title: BMDM stimulated with cmB16F1, rep2

description: mouse bone marrow cells after a total of 7 days cultivation in vitro  stimulated with cmB16F1, rep2

source_name: BMDM stimulated with cmB16F1

tag: tissue


title: BMDM stimulated with cmB16F1 and dexa+IL4, rep2

description: mouse bone marrow cells after a total of 7 days cultivation in vitro  stimulated with cmB16F1 and dexa+IL4, rep2


title: BMDM stimulated with cmB16F1, rep1

description: mouse bone marrow cells after a total of 7 days cultivation in vitro  stimulated with cmB16F1, rep1


title: BMDM stimulated with cmB16F1, rep3

description: mouse bone marrow cells after a total of 7 days cultivation in vitro  stimulated with cmB16F1, rep3


title: TV_donor1

source_name: Human monocyte derived dendritic cells infected with tetravalent chimeric dengue vaccine


title: CYD3_donor1

source_name: Human monocyte derived dendritic cells infected with chimeric dengue 3 vaccine


title: NOS sarcoma sample from patient 3

source_name: NOS sarcoma sample from patient 3

value: male


title: BMDM stimulated with dexa+IL4, rep3

description: mouse bone marrow cells after a total of 7 days cultivation in vitro  stimulated with dexa+IL4, rep3


title: BMDM stimulated with cmB16F1 and dexa+IL4, rep3

description: mouse bone marrow cells after a total of 7 days cultivation in vitro  stimulated with cmB16F1 and dexa+IL4, rep3


title: EV0, biological rep1

source_name: Human rhabdomyosarcoma cell line

tag: infection


title: NOS sarcoma sample from patient 6

source_name: NOS sarcoma sample from patient 6

value: died of pulmonary metastasis


title: CYD1_donor1


title: NOS sarcoma sample from patient 5

source_name: NOS sarcoma sample from patient 5

value: died of recurrent disease


title: CYD1_donor3


title: NOS sarcoma sample from patient 1

source_name: NOS sarcoma sample from patient 1


title: BMDM stimulated with cmB16F1 and dexa+IL4, rep1

description: mouse bone marrow cells after a total of 7 days cultivation in vitro  stimulated with cmB16F1 and dexa+IL4, rep1


title: NOS sarcoma sample from patient 4

source_name: NOS sarcoma sample from patient 4


title: BMDM stimulated with dexa+IL4, rep1

description: mouse bone marrow cells after a total of 7 days cultivation in vitro  stimulated with dexa+IL4, rep1


title: NOS sarcoma sample from patient 2

source_name: NOS sarcoma sample from patient 2

value: NED after pulmonary metastasis and local recurrence


title: EV0, biological rep3

tag: time


title: CYD2_donor1


title: Lg13 (M+)_infectedBMMf_vs._uninfected_BMMf_24hrs_rep.1

description: biological replicate 1

value: BALB/c


title: Anaplastic meningioma, NCH_T_133

status: Public on Jan 02 2011

city: Lecce

first: Oscar

middle: Fernando

last: D'Urso

state: Lecce

address: provinciale Monteroni

department: Department of biological science

institute: Salento University

description: Primary meningioma vs. non-neoplastic adult meningeal tissue.

hyb_protocol: Purified tagged miRNA was hybridized to an epoxy-coated glass slide printed with miRNA probes in the antisense orientation. Purified tagged miRNA was diluted 1:1 in 2X Hybridization solution. The so-obtained mix was held at the hybridization temperature (52°C) until loading the array. After loading the array the chamber was sealed. Maintaining controlled humidity during hybridization is crucial for successful microarray experiments to prevent the slide from drying out. The hybridization chamber was placed in an incubator at 52°C, and incubated overnight (16–20 hours). Washing steps was performed as follows: array was washed in wash solution 1 (2X SSC/0.2% SDS) for 15 minutes at 50°C, in wash solution 2 (2X SSC) for 15 minutes at room temperature, and finally in wash solution 3 (0.2X SSC). Finally array was dried by centrifugation.

scan_protocol: After hybridization, arrays were scanned using a confocal laser scanner (Affymetrix 428 scanner) at a resolution of 10 um. Data from the laser scans were collected as graphics (.tiff format) for each channel. To maximize the dynamic range of microarrays, the same arrays were scanned using different photo-multiplier settings (PMT). The use of different intensities allows the quantification of both the high and low copy expressed genes.

data_processing: The images were combined and processed using the ScanAnalyze program (written by Michael Eisen, http://rana.Stanford.EDU/software/) and the positions on the images were assigned to grid coordinates for the matching of spot identity with average pixel intensity at that region. Background corrected, log converted intensity ratios were determined for each element of the array. The image processing analysis also extracted information regarding spot quality and assigned a quality score to each ratio measurement. The definition of the quality metric was based on the notion that unreliable data points usually result from weak target intensity, high local background, small target area, and inconsistent target intensity within a given target. Implementation of the quality metric enabled unified and universally applicable data filtering before downstream higher-level data analysis. ScanAlyze data was imported in GeneSpring and GenePattern for further elaboration (Silicon Genetics, Redwood City, CA). To import data a file for each sample containing information about its gene name, signal and detection for each gene, was created. After importing data several experiments defining parameters and normalization were tested. Parameters are not numerical but define the sample nature or tissue type. The normalization of each sample was performed dividing each signal intensity by the 50th- percentile of all genes in that array. The normalization of each gene between samples was performed on the median of signal intensity of that gene in the reference sample. Genes were also analyzed using GeneSpring for differential expression between sample classes. The software allow the data filtering upon signal intensity and detection value. To select differentially expressed genes we used several approaches: for two class matching we utilized the Scatter Plot selecting the genes with an expression fold >2. To identify differentially expressed genes in a multi class match we calculated the log2 of normalized data. In this way over-expressed genes was the ones with a value >0, while the down-expressed was the ones with a value <0. For statistical validation we used t-test with a p-value of 0.01.

source_name: meningioma tissue, anaplastic

label_protocol: The labelling protocol consisted of two steps: a prehybridization target tagging and a post hybridization incubation with capture labelled reagents. The target was tagged with the following steps: 1. miRNAs were added of a poly(A) tail using a polyA polymerase; 2. a short  highly specific tag was ligated to each tailed miRNA using a bridging oligo. Following a purification, tagged miRNAs could be hybridized to the microarray.

extract_protocol: Total RNA was extracted from tissue using TRIZOL, after pulverizing the tissue in a stainless steel mortar and pestle that was chilled on liquid nitrogen. miRNA was isolated by PureLink™ miRNA Isolation Kit (Invitrogen) following manufacturer’s instructions.

value: meningioma

tag: meningioma type

value: anaplastic

tag: tumor location

value: convexity

tag: survival (years)

tag: sample

source_name: non-neoplastic adult meningeal tissue

value: meningeal

value: adult


title: Anaplastic meningioma, NCH_T_132

value: supresellar

tag: developmental stage


title: Anaplastic meningioma, NCH_T_130

value: falx


title: Anaplastic meningioma, NCH_T_131


title: GB 9 65A NO LPA

city: Dublin

last: MURRAY

address: 123 St Stephens Green

country: Ireland

institute: RCSI

description:
Gene expression in NET1 knockdown AGS cells.
GB 9 65A NO LPA.CEL

hyb_protocol: Following fragmentation,  cRNA was hybridized for 16 hr at 45C on Affymetrix U133 plus 2.0 genechips. GeneChips were washed and stained in the Automated fluidics 450 station.

scan_protocol: Genechips were scanned using the GeneChip 3000 7G scanner

data_processing: Scanned images, obtained using Affymetrix Software (MAS5), were normalized using robust multichip average (RMA) express analysis

source_name: NET1 knockdown AGS cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix) using the Affymetrix IVT labeling kit.

growth_protocol: Human Caucasian gastric adenocarcinoma cells (AGS cells) were purchased from the European Collection of Cell Cultures (ECACC) and cultured in Hams F12 medium (Sigma Aldrich), supplemented with 10% fetal bovine serum, L-glutamine and Penicillin-Streptomycin (Sigma Aldrich), as per ECACC recommendations and incubated at 37ºC and 5%CO2.

extract_protocol: RNA was extraction by Trizol™ (Sigma Aldrich) following the manufacturers instructions.

treatment_protocol: MISSION™ shRNA Lentiviral Transduction Particles (Sigma Aldrich) were used to achieve stable NET1 knockdown. 5 NET1 specific shRNA constructs, and one non target construct were transduced separately into AGS cells. Briefly, AGS cells were incubated with the Net1-specific shRNA lentiviral particles at a ratio of 2 particles : 1 cell, in the presence of hexadimethrine bromide to improve transduction efficiency. Non-target shRNA lentiviral particles were used to control for the effects of the transduction process itself. Successfully transduced cells included a puromycin resistance tag, and these cells were selected using 1μg/ml puromycin.    Net 1 knockdown was confirmed using quantitative RTPCR and western blot analysis.  For the remainder of this study, two distinct cell types were used: NET1 knockdown cells and non-target shRNA cells.

tag: cell line

value: gastric adenocarcinoma AGS cells

tag: shRNA

value: 65 shRNA

tag: replicate

value: A

tag: genotype/variation

value: NET1 knockdown

tag: agent

value: no LPA (control)


title: GB 8 63B NO LPA

description:
Gene expression in NET1 knockdown AGS cells.
GB 8 63B NO LPA.CEL

value: 63 shRNA

value: B


title: GB 7 63A NO LPA

description:
Gene expression in NET1 knockdown AGS cells.
GB 7 63A NO LPA.CEL


title: GB 10 65B NO LPA

description:
Gene expression in NET1 knockdown AGS cells.
GB 10 65B NO LPA.CEL


title: GB 3 65A +LPA

description:
Gene expression in NET1 knockdown AGS cells treated with LPA.
GB 3 65A +LPA.CEL

source_name: NET1 knockdown AGS cells treated with 10 microM LPA for 4 hr

value: LPA


title: GB 6 NTB +LPA

description:
Gene expression in AGS cells treated with LPA
GB 6 NTB +LPA.CEL

source_name: Control AGS cells (transduced with non targetting shRNA) treated with 10 microM LPA for 4 hr

value: non targetting shRNA (control)

value: NET1 present


title: GB 12 NTB NO LPA

description:
Gene expression in AGS cells.
GB 12 NTB NO LPA.CEL

source_name: Control AGS cells (transduced with non targetting shRNA)


title: Atypical meningioma, NCH_T_72

source_name: meningioma tissue, atypical

value: meningioma

value: atypical


title: GB 11 NTA NO LPA

description:
Gene expression in AGS cells.
GB 11 NTA NO LPA.CEL


title: Atypical meningioma, NCH_T_73

value: sphenoid wing


title: Anaplastic meningioma, NCH_T_128

value: anaplastic

value: convexity

value: meningeal


title: Atypical meningioma, NCH_T_68

value: posterior fossa

value: adult


title: Atypical meningioma, NCH_T_69


title: Atypical meningioma, NCH_T_65


title: Anaplastic meningioma, NCH_T_127

value: supresellar


title: GB 4 65B +LPA

description:
Gene expression in NET1 knockdown AGS cells treated with LPA.
GB 4 65B +LPA.CEL

value: gastric adenocarcinoma AGS cells

value: 65 shRNA


title: Typical meningioma, NCH_T_63

source_name: meningioma tissue, typical

value: typical


title: GB 5 NTA +LPA

description:
Gene expression in AGS cells treated with LPA
GB 5 NTA +LPA.CEL

value: A


title: Typical meningioma, NCH_T_62


title: GB 2 63B +LPA

description:
Gene expression in NET1 knockdown AGS cells treated with LPA.
GB 2 63B +LPA.CEL

value: 63 shRNA

value: B

value: NET1 knockdown


title: Typical meningioma, NCH_T_59

value: optic nerve


title: Typical meningioma, NCH_T_57

value: meningioma

value: parasagittal


title: Anaplastic meningioma, NCH_T_129

value: sphenoid wing


title: Typical meningioma, NCH_T_54


title: Typical meningioma, NCH_T_5

value: olfactory groove


title: GB 1 63A +LPA

description:
Gene expression in NET1 knockdown AGS cells treated with LPA.
GB 1 63A +LPA.CEL

value: LPA


title: Typical meningioma, NCH_T_48

value: meningeal


title: CYD2_donor4

description: Analysis used non-infected cells RNA as control samples for comparison to the cells infected by chimeric dengue vaccine type 2

source_name: Human monocyte derived dendritic cells non-infected

value: monocyte derived dendritic cells

source_name: Human monocyte derived dendritic cells infected with chimeric dengue 2 vaccine


title: Typical meningioma, NCH_T_45

value: posterior fossa

value: adult


title: Typical meningioma, NCH_T_39


title: Typical meningioma, NCH_T_36

value: convexity


title: Typical meningioma, NCH_T_43


title: Typical meningioma, NCH_T_6

value: falx


title: Typical meningioma, NCH_T_14

value: typical


title: Typical meningioma, NCH_T_17


title: Typical meningioma, NCH_T_18


title: Typical meningioma, NCH_T_23


title: Typical meningioma, NCH_T_26


title: Typical meningioma, NCH_T_34


title: Typical meningioma, NCH_T_27

value: supresellar


title: Typical meningioma, NCH_T_33


title: Typical meningioma, NCH_T_2


title: Typical meningioma, NCH_T_1


title: 120 minutes bile exposure replicate D

status: Public on Jan 01 2011

city: Helsinki

first: Kati

last: Laakso

address: Meijeritie 4

department: R&D

country: Finland

institute: Valio Ltd

hyb_protocol: The labeled cDNA samples were hybridized to microarrays following Agilent’s procedure titled “Two-Color Microarray-Based Gene Expression Analysis.” For each microarray, 825 ng of cyanine 3-labeled cDNA and 825 ng of cyanine 5-labeled cDNA were mixed with 11 µl of 10X GE Blocking Agent and 2.2 µl of 25X Fragmentation Buffer. Volume of this fragmentation mix was brought to 55 µl with nuclease-free water and mix was incubated at 60 °C for exactly 30 minutes. After incubation, fragmentation reaction was stopped by adding 55 µl of 2X Hi-RPM Hybridization Buffer, mixed gently and centrifuged for one minute at RT at 15800 × g. 100 µl of hybridization sample was loaded onto an array and hybridized at 65 °C for 17 hours at 10 rpm with Agilent hybridization oven. Microarrays were washed twice with GE Wash Buffer 1 for one minute at RT and once with prewarmed (37 °C) GE Wash Buffer 2 for one minute.

scan_protocol: Immediately after washing, microarrays were scanned at 5 µm resolution with a GenePix 4200 AL scanner (Axon Instruments) and stored as TIFF images. The fluorescence intensities were quantified and addressed to genomic ORFs with GenePix Pro 6.0 software (Axon Instruments / Molecular Devices Corp.). Microarray image analysis and feature detection were performed using GenePix Pro 6.0 software with default parameters, and results were further improved manually.

data_processing: Data analysis was performed using Bioconductor for the R statistical software. Background correction and normalization were done using the limma package, and the statistical significance was assessed using cyberT. The data set contained 12 two-color microarrays, with each condition measured four times, and was analyzed as an entity. The foreground and background median intensity estimates were used, and the data were background corrected using the normexp-function (offset set to 50), normalized within arrays using loess (100 iterations, suspicious spots and probe sequences deleted, matching multiple hits or borders of the coding regions downweighted to zero and intergenic probe sequences downweighted to 0.1) and normalized between arrays using quantile normalization. Expression ratios for genes were obtained by taking the averages of the log2-transformed expression ratios of probes describing the same gene and matching a single genetic coding region locus. The gene expression ratios were calculated for 2798 genes out of the total 2944 (95% coverage) genes in the genome. The statistical significance of the expression ratio of a gene between two conditions was analyzed using a paired t-test method implemented in CyberT (Bayesian prior estimate of within-treatment variance was set to five, and the window size was set to 101). P-values were Bonferroni adjusted by the number of performed t-tests in total (8394). The analysis showed that 248, 133, and 9 genes had significant differences in expression between the zero and 10 min conditions, the zero and 30 min conditions, and zero and 120 min conditions, respectively, when using 0.01 as the threshold for statistical significance and when requiring at least two-fold changes in expression ratio.

organism: Lacticaseibacillus rhamnosus

source_name: Total RNA 120 minutes after bile exposure

label_protocol: Five micrograms of RNA were reverse transcribed to cDNA with the SuperScript Indirect cDNA Labeling System (Invitrogen) according to the manufacturer’s protocol except that 6 µg of random primers (Invitrogen, 48190-011) were used instead of anchored oligo(dT)20 primers and random hexamers. The cDNA was fluorescently labeled using Cy3 or Cy5 mono-reactive dyes (Amersham Biosciences) and purified with a column included in the SuperScript Indirect cDNA Labeling System kit.

growth_protocol: Bacterial cells were grown in MRS broth at bioreactor at 37 °C. pH was maintained constant at 6.0.

extract_protocol: One to three milliliters of bacterial culture were mixed with 2–6 mL of RNAprotect Bacteria reagent (Qiagen) and handled according to the manufacturer’s instructions. The cell pellets were stored at –70 °C for subsequent RNA extraction. Cells were lysed with 10 mg/mL lysozyme (Amresco), 3 mg/mL proteinase K (Sigma-Aldrich), and 100 U of mutanolysin (Sigma-Aldrich) at 37 °C for 30 minutes. The suspension was supplemented with 1 mL of preheated (65 °C) TRIzol reagent (Invitrogen) and vortexed for 3 minutes. After incubation at RT for 5 minutes, the cell lysate was homogenized in a MagNA Lyser instrument (Roche) with <106 µm glass beads (Sigma-Aldrich) for four 30 s cycles at 6000 rpm. Between each cycle, the cells were chilled on ice for 1 minute. Cell debris was removed by centrifugation (12000 × g at 4 °C for 15 min), and the lysate was extracted with 200 µl of chloroform by vortexing for 15 s. After incubation at RT for 3 min, the phases were separated by centrifugation (12000 × g at 4 °C for 15 min). The aqueous phase was mixed with 500 µl of 80% ethanol for total RNA purification with an RNeasy Mini Kit (Qiagen). During RNA purification, DNA was removed using RNase-Free DNase (Qiagen) as described in the manual.

value: GG

source_name: Total RNA before bile exposure


title: Typical meningioma, NCH_T_12


title: CYD3_donor3

description: Analysis used non-infected cells RNA as control samples for comparison to the cells infected by Dengue virus type 3, chimeric dengue vaccine type 3 or live-attenuated dengue virus type 3

source_name: Human monocyte derived dendritic cells infected with chimeric dengue 3 vaccine


title: Typical meningioma, NCH_T_31


title: Typical meningioma, NCH_T_9


title: 120 minutes bile exposure replicate C


title: J2-null trypomastigotes sample 3

city: Athens

first: Dilrukshi

middle: K

last: Ekanayake

state: GA

address: 120, Green Street

department: Biochemistry and Molecular Biology

institute: University of Georgia

hyb_protocol: Microarrays were obtained from the Pathogen Functional Genomic resource center, and contained an array of 12,288 70mer oligonuclotides, each with complementarity to an individual T. cruzi open reading frame. Microarray was prehybridized immediately before hybridization. Three hybridizations were performed for each life stages as previously

scan_protocol: Arrays were scanned on a ScanArray 4000(GSI Lumonics, Wilmington, MA) to obtain tagged Image File format (TIFF) images.

data_processing: Background subtracted intensities were normalized by lowess, log2 transformed ratio of medians (ProScanArray Express version 4.0 (Perkin Elmer)).

organism: Trypanosoma cruzi

source_name: wild type

label_protocol: cDNA was synthesis using superscript II reverse transcriptase (Life technologies, Grand Island, NY) and Cy3 or Cy5-dUTP (Amersham Phamacia Biotech) included in the reaction mix. Unincorporated fluorescence nucleotide was removed using GFX columns per manufacture’s instructions

growth_protocol: Trypomasigotes were then grown in monolayer of Vero cells/myoblast in Modified Eagle’s Media containing 20% fetal bovine serum. Emergent trypomastigotes were harvested daily and examined by light microscopy. Preparations containing >95% of trypomasigotes were used in the subsequent assays.

extract_protocol: Briefly, total RNA was isolated using TRIZOL and cleaned up with RNAeasy kit (QIAGEN, Valencia, CA) per the manufacture’s instruction

tag: stage

value: trypomastigotes

value: Y

value: J2-null Y


title: J2-null trypomastigotes sample 2


title: J2-null trypomastigotes sample 1


title: J1-null trypomastigotes sample 3

value: J1-null Y