title: CEC#11P1

city: Berlin

first: Soroush

last: Sharbati

address: Oertzenweg 19b

department: Institute of Veterinary Biochemistry

institute: Freie Universitaet Berlin

hyb_protocol: Hybridisation was conducted as a two colour experiment in which cDNA of pooled samples from each treated group and time point was labelled with Alexa Fluor 647® (red emission), while a common reference was labelled with Alexa Fluor 555® (green emission) and hybridised on the same microarray. Hybridisation and washing was performed in the aHyb™ Hybridisation station (Miltenyi Biotec). First, slides were pre-hybridised at 45°C for 5 min in pre-hybridisation buffer (5×SSC, 0.1% SDS, 1% BSA). Prior to hybridisation fluorescently labelled samples were denatured for 5 min at 95°C and combined with 200 µl hybridisation buffer (37.5 mM sodium citrate, 375 mM NaCl, 20% formamide, 7% SDS and 200 µg/ml yeast RNA). Hybridisation was performed for 16 h at 50°C with a pump rate of 1 ml/min. The slides were washed in wash buffers with increased stringency as follows: first for 1 min at 50°C in wash buffer 1 (2×SSC, 0.5% SDS), then wash buffer 2 (0.5×SSC, 0.5% SDS), and wash buffer 3 (0.1%SSC, 0.2%SDS), each for 1 min at 25°C. Slides were removed from the hybridisation station, dipped several times in nuclease free water, and finally dried by brief centrifugation.

scan_protocol: The microarrays were scanned at 10 µm resolution using a GenePix 4000B scanner (Molecular Devices).

data_processing: Microarray image analysis and ratio-based normalisation of the microarray data was conducted using the software package GenePix Pro 6.1 (Molecular Devices). Replicate microarray data was combined by calculating the mean of respective log 2 ratios for subsequent analysis. Data analysis was performed using the Acuity 4.0 software package (Molecular Devices).

label: Alexa 647

organism: Sus scrofa

source_name: primary cell from pig number 11 passage 1

label_protocol: Total RNA was converted into cDNA and fluorescently labelled using the SuperScript Plus Indirect cDNA Labelling System (Life technologies) and the Alexa Fluor®Dyes (Life technologies).

growth_protocol: Animal materials: ascending colon from piglets aged between 11 and 33 days. Isolation protocol: after thourough washing, the intestinal lumen was filled with warm (37°C) medium containing 1mg/ml collagenase, and four successive incubation steps (30min each) were performed. Cell suspensions were collected after each incubation step (F1 – F4), centrifuged for 7 min at 100 x g, and resuspended in culture medium . The lumen was then gently squeezed and released cells were suspended in culture medium (F5). Finally, the lumen was opened and the mucosa was gently scraped off and suspended in culture medium (F6). Cell suspensions were plated and CEC cultures mainly arose from F6.

extract_protocol: Total RNA from cultured cells was isolated using the mirVana™ miRNA Isolation Kit (Ambion) and quality was controlled as described previously (Sharbati et al., 2010). For this purpose, intestinal cells (passage 1-4) originally isolated from ascending colon of 2 individual piglets were cultivated in 25 cm2 cell culture flasks until confluence. Additionally original colon tissues were used as the common reference.

treatment_protocol: Primary cell cultures were expanded and passages 1-4 were used for microarray analysis.

tag: subject

value: primary intestinal colonic cells

value: ascending colon, healthy

label: Alexa 555

source_name: common reference, pooled whole tissue sample


title: monocytes-NVAMD-12

status: Public on Feb 10 2017

type: RNA

city: Jerusalem

first: Michelle

last: Grunin

address: Hadassah Ein Kerem Medical Center

department: Ophthalmology

country: Israel

institute: Hadassah-Hebrew University Medical Center

description: gene expression data-Affymetrix Gene 1.0 ST array

hyb_protocol: Following fragmentation, 5.5µg of Biotinylated ssDNA were hybridized for 17 hrs at 45 degrees Celsius on the GeneChip Human 1.0 ST Array.

scan_protocol: The GeneChips were washed and stained in the Affymetrix Fluidic Station 450. GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Processing was performed with Partek, using RMA values, default analysis settings.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: total blood monocytes, neovascular AMD patient

label_protocol: Amplified and biotinylated sense-strand DNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

extract_protocol: Total monocyte mRNA was extracted via TriReagent (Sigma), and cleaned using MiniElute columns (Quiagen). RNA Integrity Number (RIN) was evaluated using the Agilent Bioanalzer (RIN>8).

treatment_protocol: Peripheral blood mononuclear cells were separated using Histopaque (Sigma) separation, and total blood monocytes including the CD16+ positive monocytes were separated using negative selection via magnetic beads (Stemcell Technologies).

tag: cell type

tag: disease state

value: macular degeneration


title: CEC#11P4

country: Germany

source_name: primary cell from pig number 11 passage 4

tag: tissue


title: B. subtilis PG479 Day 4

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

hyb_protocol: Hybridization, washing, and scanning was performed as described in the Two-Color Microarray-Based Gene Expression Analysis manual (Version 6.6, Agilent Technologies). Briefly, hybridization mixtures were made by combining 300 ng test (Cy3) and 300 ng common reference (Cy5) material and were subsequently hybridized to the Agilent SurePrint Custom 8x15k microarrays G2509F (Agilent Technologies).

scan_protocol: The slides were scanned with the Agilent G2505C scanner as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis guide (G4140-90050, Agilent technologies).

data_processing: Data were extracted with Feature Extraction software (Agilent Technologies). The data were analyzed in R-2.14.1 (http://cran.r-project.org/). All arrays were subjected to a set of quality control checks, such as visual inspection of the scans, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, density plots, ratio-intensity plots and principal component analysis. The data from B. subtilis strains PG479 and 168 were normalized, together with data from other strains, using the robust multi-array average (RMA) algorithm (Irizarry et al.).

organism: Bacillus subtilis

source_name: B. subtilis PG479 Day 4

label_protocol: Labeling was performed by reverse transcription using random octamers, incorporating Cy3 for the test samples and Cy5 for the common reference

growth_protocol: B. subtilis strains were grown in LB at 37°C in the presence of 1.5% xylose and 1 mM IPTG (inducers were added in all cultures because some of the strains tested in the same experiment required induction). Cells were harvested at O.D.600 0.4-0.6.

extract_protocol: To isolate RNA, cell pellets were flash frozen in liquid nitrogen immediately after harvesting and stored at -80°C. Frozen pellets were grounded and subjected to RNA extraction

treatment_protocol: To construct B. subtilis strain PG479 (kre::erm), kre was replaced with an erythromycin resistance cassette amplified from pMutin4. Competent B. subtilis cells were transformed directly with the ligation products and mutants were verified with PCR.

tag: strain

tag: time (day)

source_name: Pool of different samples of different B. subtilis strains

treatment_protocol: No specific treatment was applied.

tag: sample type


title: CEC#11P2 rep

source_name: primary cell from pig number 11 passage 2


title: monocytes-NVAMD-5


title: monocytes-NVAMD-6


title: CEC#11P3

source_name: primary cell from pig number 11 passage 3


title: monocytes-NVAMD-2


title: CEC#11P2


title: CEC#5P2

source_name: primary cell from pig number 5 passage 2


title: monocytes-NVAMD-1


title: CEC#5P3

source_name: primary cell from pig number 5 passage 3


title: CEC#5P1

source_name: primary cell from pig number 5 passage 1


title: CEC#5P4

source_name: primary cell from pig number 5 passage 4


title: PAXIP1-AS1-silenced cells using siRNA, biological rep1

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained in the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol.

data_processing: The data were analyzed using noncoder web interface (http://noncoder.mpi-bn.mpg.de). After the normalization by Robust Multi-array Average (RMA) and the application of moderate t-statitsics via the limma package, Transcript Cluster IDs that match that do not match to a gene or to multiple genes were discarded. Then, a standard deviation is calculated across samples. For a gene that matches to multiple Transcript Cluster IDs, the Transcript Cluster ID with the highest standard deviation was kept for further analysis.

source_name: HEK-293 cells

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

growth_protocol: HEK-293 cells were cultured in the growth medium containing 10% FBS (Life Technologies, #10270106) in DMEM with low glucose, pyruvate (Life Technologies, #31885-023) supplemented with antibiotics (penicillin and streptomycin, Sigma-Aldrich, #P4333). All cells were cultured at 37°C in a humidified atmosphere containing 5% CO2.

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

treatment_protocol: Transient transfection of siRNA duplexes (MISSION, Sigma-Aldrich) (10nM and 100nM final concentration for LOC440173 and PAXIP1-AS1, respectively) was carried out using RNAiMax (Life Technologies) according to the manufacturer’s protocol. The corresponding amount of control siRNA (Mission Negative control SIC-002, confidential sequence (Sigma-Aldrich)) was used. Forty-eight hours after the transfection of siRNAs, cells were exposed to TRIzol to extract RNAs.

tag: cell line

tag: transfection

value: 100nM siRNA duplexes for PAXIP1-AS1


title: siScramble-transfected cells (100nM), biological rep1

value: (100nM) control siRNA


title: siScramble-transfected cells (100nM), biological rep2


title: PAXIP1-AS1-silenced cells using siRNA, biological rep2


title: LOC440173-silenced cells using siRNA #2, biological rep1

value: 10nM siRNA duplexes for LOC440173


title: LOC440173-silenced cells using siRNA #2, biological rep2


title: LOC440173-silenced cells using siRNA #1, biological rep2


title: LOC440173-silenced cells using siRNA #1, biological rep1


title: siScramble-transfected cells (10nM), biological rep2

value: (10nM) control siRNA


title: Acetaldehyde treated

city: Torrance

first: Robert

last: Gelfand

state: CA

address: 1124 W. Carson St

department: surgery

country: USA

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

description: Acetaldehyde treated

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.
Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].
A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.
All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: MCF12A monolayer

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 2 µg total RNA sample, which was 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy5 dye staining.

growth_protocol: MCF12A cells obtained from the American Type Culture Collection (ATCC) were grown in 6 well plastic culture plates in DMEM/F12 plus antibiotic-antimycotic in the presence of 2.5% horse serum supplemented with epidermal growth factor, hydrocortisone, bovine insulin, and cholera toxin. Cells were passaged when they reached 80% confluence.

extract_protocol: Cells were washed with phosphate buffered saline pH7.4 and total RNA was extracted using the miRVana kit. RNA was analyzed by the nanodrop apparatus and for quality by Bioanalyzer.

treatment_protocol: Cells were cultured for 4 weeks either in the presence of 2.5% ethanol or 1% acetaldehyde. In one experiment, cells were selected for their ability to grow in soft agar, following which a cellular clone was grown on 6 well plates for further experimental exposure to ethanol and RNA extraction.

value: human breast cultures

tag: exposed to

value: 1mM acetaldehyde for 4 wks


title: Ethanol treated

description: ethanol treated

value: 2.5mM ethanol  for 4 wks


title: control for ethanol and acetaldehyde

value: none (control)


title: Venous blood samples were obtained from healthy subjects_15

city: shanghai

first: chunmei

last: huang

address: No. 1665 Rd. Kongjiang

department: Department of Emergency

country: China

institute: Department of Emergency, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China

description: Gene expression in healthy subjects blood

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: healthy_venous blood

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

tag: subject diagnosed with

value: none (healthy subject)

tag: gender

value: female

tag: age

value: serum


title: Venous blood samples were obtained from healthy subjects_14


title: Venous blood samples obtained from a patient within 24 h from the first day of diagnosis with sepsis_8

description: Gene expression within 24 h in sepsis human blood

source_name: sepsis non-AKI_venous blood_within 24 h

value: sepsis (non AKI)


title: Venous blood samples obtained from a patient within 24 h from the first day of diagnosis with sepsis_10


title: Venous blood samples obtained from a patient within 24 h from the first day of diagnosis with sepsis_9

value: male


title: Venous blood samples obtained from a patient within 24 h from the first day of diagnosis with sepsis_11


title: Venous blood samples obtained from a patient within 24 h from the first day of diagnosis with sepsis_12


title: Venous blood samples obtained from a patient within 24 h from the first day of diagnosis with sepsis_7


title: Venous blood samples obtained from a patient within 24 h from the first day of diagnosis with septic AKI_5

description: Gene expression within 24 h in septic AKI human blood

source_name: sepsis-induced AKI_venous blood_within 24 h

value: sepsis-induced acute kidney injury (AKI)


title: Venous blood samples obtained from a patient within 24 h from the first day of diagnosis with septic AKI_3


title: Venous blood samples obtained from a patient within 24 h from the first day of diagnosis with septic AKI_6


title: Venous blood samples were obtained from healthy subjects_13


title: Venous blood samples obtained from a patient within 24 h from the first day of diagnosis with septic AKI_1


title: Venous blood samples obtained from a patient within 24 h from the first day of diagnosis with septic AKI_2


title: NKp46+ ILC3, replicate 2

city: St. Louis

first: Marco

last: Colonna

state: Missouri

address: 509 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

description: Gene expression from innate lymphoid cells, Nkp46+ ILC3 subset

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Mouse Gene 1.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Following fragmentation with NuGen Encore Biotin Module, 2.5 ug of cDNA were hybridized on Mouse Gene 1.0 ST Array in the GeneChip Hybridization Oven 640 for 18 hr at 45C. GeneChip were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were processed using the AffySTExpressionFileCreator function of GenePattern using default settings that RMA normalize and background correct data, generating a .gct file of gene expression. Log2 transformation was removed because data were analyzed using MultiplotStudio, which automatically log2 transforms data.

label: Biotin

organism: Mus musculus

source_name: NKp46+ ILC3

label_protocol: Biotinylated cDNA were prepared according to the standard NuGEN WT-Ovation PicoSL RNA Amplification system from 2 ng of total RNA.

growth_protocol: Mice were sacrified between 5:30-5:45 am and sorted from 10-11 am.

extract_protocol: RNA was extracted using the Rneasy Micro Kit according to the manufacturer instructions.

treatment_protocol: ILC3 subsets were sorted from 3 pooled donors of 8-week-old WT small intestine lamina propria dissociated using 2 EDTA washes and Collagenase 4 digestion. Subsets were sorted into Buffer RLT (Qiagen) from CD3–,CD19–, CD45lo, Thy1+ cells, that were subdivided using CCR6 and NKp46.

value: small intestine lamina propria

value: NKp46+ ILC3


title: CCR6+ ILC3, replicate 2

description: Gene expression from innate lymphoid cells, CCR6+ ILC3 subset

source_name: CCR6+ ILC3

value: CCR6+ ILC3


title: Venous blood samples obtained from a patient within 24 h from the first day of diagnosis with septic AKI_4


title: NKp46+ ILC3, replicate 1


title: CCR6-NKp46- ILC3, replicate 2

description: Gene expression from innate lymphoid cells, DN ILC3 subset

source_name: DN ILC3

value: DN ILC3


title: siScramble-transfected cells (10nM), biological rep1


title: CCR6-NKp46- ILC3, replicate 1


title: CCR6+ ILC3, replicate 1


title: Zebrafish_96h_ZnSO4-LC25_rep1

status: Public on Feb 09 2017

city: Jinju

first: June-Woo

last: Park

address: 17, Jegok-gil, Munsan-eup

department: Environmental Risk Research

country: South Korea

institute: Korea Institute of Toxicology

description: Gene expression after 96hr in ZnSO4-LC25-treated zebrafish

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Zebrafish Gene Expression Microarrays (G2519F) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then air-dried by slowly removing the slide rack minimizing droplets on the slides.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026437_D_F20130127) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Danio rerio

source_name: Zebrafish, 96h, ZnSO4-LC25, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The zebrafish embryo (96h) was exposed to LC25 concentration of ZnO NPs and ZnSO4 (2.64 and 7.75 mg/L, respectively)

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Whole body


title: Zebrafish_96h_ZnO-LC25_rep2

description: Gene expression after 96hr in ZnO-LC25-treated zebrafish

source_name: Zebrafish, 96h, ZnO-LC25, replicate 2


title: Zebrafish_96h_ZnSO4-LC25_rep3

source_name: Zebrafish, 96h, ZnSO4-LC25, replicate 3


title: Zebrafish_96h_ZnSO4-LC25_rep2

source_name: Zebrafish, 96h, ZnSO4-LC25, replicate 2


title: Zebrafish_96h_Control_rep2

description: Gene expression after 96hr in non-treated zebrafish

source_name: Zebrafish, 96h, no treatment, replicate 2


title: Zebrafish_96h_ZnO-LC25_rep1

source_name: Zebrafish, 96h, ZnO-LC25, replicate 1


title: Zebrafish_96h_ZnO-LC25_rep3

source_name: Zebrafish, 96h, ZnO-LC25, replicate 3


title: Lxn-/- MPP, biological rep2

city: Lexington

first: Ying

last: Liang

state: KY

address: Health Sciences Research Bldg. Rm. 340, 1095 V.A. Drive

department: Toxicology and Cancer Biology

institute: University of Kentucky

description: gene expression data in MPPs

hyb_protocol: Following fragmentation,  cRNA were hybridized  on Affymetrix Gene Chip MoGene-1-0-st-v1 arrays in Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 7G scanner.

data_processing: The data were processed by the RMA method using Partek (version 6.0)

source_name: Lxn-/- MPPs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA using the standard protocol in the Affymetrix GeneChip Expression Analysis Manual.

extract_protocol: Total RNA was extracted using RNeasy® Kit (QIAGEN, Valencia, CA) according to manufacturer's instruction

treatment_protocol: WT and Lxn-/- MPPs

tag: background strain

value: multipotent progenitor cells

value: bone marrow

tag: genotype

value: deletion of exons 2-4 of latexin gene, and lack of latexin protein

value: 8-12 weeks old


title: Lxn-/- LT-HSC, biological rep3

description: gene expression data in LT-HSCs

source_name: Lxn-/- LT-HSCs

treatment_protocol: WT and Lxn-/- LT_HSCs

value: long-term hematopoietic stem cells


title: Mouse clonal Tg MMTV/neu breast tumor cell line M1

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: gene expression data on clonal mesenchymal cell line M1 derived from a Tg MMTV/neu spontaneous breast tumor

hyb_protocol: The Affymetrix GeneChip Mouse Gene 1.0 ST Array was selected for these studies for its overall comprehensive coverage.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity.

source_name: Tg MMTV/neu spontaneous breast tumor

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: To produce primary mammary tumor cell lines, a spontaneous mammary tumor was harvested from a female Tg/neu mouse. The tumor was processed to generate a single cell suspension by compression through a 1.0 mm pore mesh screen. To subfractionate the isolated mammary epithelial tumor cells into epithelial and mesenchymal compartments, cells were stained with a fluorescein isothiocyanate (FITC)-conjugated CD24 specific monoclonal antibody (clone M1/69, eBioscience, San Diego,CA), a mouse anti-c-ErbB2/c-neu monoclonal antibody (Clone 7.16.4, Calbiochem-EMD Chemicals, Gibbstown, NJ) plus a phycoerythrin (PE)-conjugated goat anti-mouse secondary antibody (Jackson ImmunoResearch, West Grove, PA), and then sorted by flow cytometry based on neu and CD24 expression using a FACSAria III flow cytometer and FACSDiva software (Becton-Dickinson, Franklin Lakes, NJ). Sorted epithelial tumor cells with high CD24 and high neu expression were cultured in RPMI supplemented with 20% fetal bovine serum (FBS), 12 mM HEPES buffer, 2 mM L-glutamine, 10 μM non-essential amino acids, 1mM sodium pyruvate, 100 μg/ml streptomycin and 100 U/ml penicillin. Mesenchymal-like tumor cells with low CD24 and low neu expression were cultured in MEGM® (Lonza, Switzerland) supplemented with 2% FBS and proprietary concentrations of bovine pituitary extract, epidermal growth factor, insulin, hydrocortisone, gentamycin, and amphotericin [7]. Cells were cultured by limiting dilution to produce two epithelial (E1 and E2) and two mesenchymal-like clonal cell lines (M1 and M2).

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

value: FVB Tg MMTV/neu

value: Tg MMTV/neu breast tumor

value: mesenchymal (M) primary clonal cell line


title: Zebrafish_96h_Control_rep1

source_name: Zebrafish, 96h, no treatment, replicate 1


title: Lxn-/- MPP, biological rep1

description: gene expression data in MPPs

source_name: Lxn-/-MPPs

value: female


title: WT MPP, biological rep2

description: gene expression data in MPPs

source_name: WT MPPs

value: intact latexin gene and protein


title: WT MPP, biological rep1

description: gene expression data in MPPs


title: Lxn-/- MPP, biological rep3

description: gene expression data in MPPs


title: WT MPP, biological rep3

description: gene expression data in MPPs


title: Lxn-/- LT-HSC, biological rep2

description: gene expression data in LT-HSCs


title: Mouse clonal Tg MMTV/neu breast tumor cell line E1

description: gene expression data on clonal epithelial cell line E1 derived from a Tg MMTV/neu spontaneous breast tumor

value: epithelial (E) primary clonal cell line


title: WT LT-HSC, biological rep3

description: gene expression data in LT-HSCs

source_name: WT LT-HSCs


title: WT LT-HSC, biological rep1

description: gene expression data in LT-HSCs


title: Mouse clonal Tg MMTV/neu breast tumor cell line E2

description: gene expression data on clonal epithelial cell line E2 derived from a Tg MMTV/neu spontaneous breast tumor


title: WT LT-HSC, biological rep2

description: gene expression data in LT-HSCs


title: Mouse clonal Tg MMTV/neu breast tumor cell line M2

description: gene expression data on clonal mesenchymal cell line M2 derived from a Tg MMTV/neu spontaneous breast tumor


title: Lxn-/- LT-HSC, biological rep1

description: gene expression data in LT-HSCs


title: CEC_2

city: Palo Alto

first: Jeffrey

middle: L

last: Goldberg

address: 2452 Watson Ct

institute: Stanford University

description: Differentiated

hyb_protocol: 100ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).

scan_protocol: Scanning was performed on a GeneChip® Scanner

data_processing: .CEL files were normalized using Genespring GX 12 software with RMA normalization

source_name: embryonic stem cell-derived corneal endothelial cells (hESC-CECs)

label_protocol: Biotin

extract_protocol: Total RNA was isolated using the RNEasy kit (Qiagen)

value: corneal endothelial cells


title: adult_1

description: Cultured

source_name: adult corneal endothelial cells

tag: developmental stage

value: adult


title: monocytes-NVAMD-8

source_name: total blood monocytes, neovascular AMD patient

value: macular degeneration


title: adult_3

description: Cultured


title: adult_2

description: Cultured


title: CEC_1

description: Differentiated


title: shCTRL, bio. replicate 1

city: Baltimore

first: Jiou

last: Wang

state: MD

address: 615 N. Wolfe St.

institute: Johns Hopkins University

description: SAMPLE 1

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.na32.hg19.transcript.csv

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: HEK293 cells grown in DMEM, 10%FBS, 37˚C, 5% CO2

extract_protocol: Cells were lysed using RNAeasy mini kit (Qiagen), according to manufacturer's instructions. Genomic DNA was first removed by DNAse treatment on the column, and then, additionally, after total RNA was isolated, using DNase Turbo kit (Ambion), followed by additional round of cleaning through RNAeasy columns.

treatment_protocol: Cells were transfected in 60mm dishes using 4µg DNA, 10µl Lipofectamine 2000, in total 4.5ml  Optimem-MEM1. Origene's pRS-RFP-C plasmids encoding shRNAs against UBE4B and LSD1, or non-targeting control (CTRL) were used for knockdown. Cells were knocked down for 78h before lysis.

tag: transfected with

value: non-targeting shRNA (control)

tag: time point

value: 78h after transfection


title: shLSD1, bio. replicate 2

description: SAMPLE 7

value: shRNAs against LSD1


title: shUBE4B, bio. replicate 1

description: SAMPLE 2

value: shRNAs against UBE4B


title: shCTRL, bio. replicate 3

description: SAMPLE 9


title: shUBE4B+shLSD1, bio. replicate 2

description: SAMPLE 8

value: shRNAs against UBE4B and LSD1


title: shUBE4B+shLSD1, bio. replicate 3

description: SAMPLE 12


title: CEC_3

description: Differentiated

tag: cell type


title: shUBE4B, bio. replicate 2

description: SAMPLE 6


title: shLSD1, bio. replicate 1

description: SAMPLE 3


title: shUBE4B-3, bio. replicate 3

description: SAMPLE 10


title: shUBE4B+shLSD1, bio. replicate 1

description: SAMPLE 4


title: shCTRL, bio. replicate 2

description: SAMPLE 5


title: U87 LXSN-pp71

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

description: Gene expression data from human ST array

hyb_protocol: The Affymetrix Genechip WT Terminal Labeling and Hybridization protocol was used

scan_protocol: Chips were scanned using the Affymetrix 7G Plus scanner and Command Console Software

data_processing: Data was processed by importing CEL files into Partek Software and RMA normalization was performed

source_name: U87 cells stably expressing pLXSN-pp71

label_protocol: The Ambion WT Expression Kit with accompanying protocol was used to label the samples

growth_protocol: Cells were grown in DMEM with 10% FBS

extract_protocol: Total RNA was isolated using the Qiagen RNEAsy kit according to the manufacturer's instructions and RNA quality was verified by spectroscopy and agarose gel electrophoresis.

treatment_protocol: Cells were transduced with retrovirus supernatants expressing pLXSN or pLXSN-pp71 with betaine and then selected in G418 for 10 days.  Antibiotic was withdrawn and then total RNA was extracted from both stable cell lines.

value: U87 GBM cells

tag: transduction


title: shLSD1-3, bio. replicate 3

description: SAMPLE 11


title: PBL from Normal 4

city: Nantes

first: Daniel

last: BARON

state: Loire-Atlantique (44)

address: 30 Bd Jean Monnet

department: UMR1064 - Centre de Recherche en Transplantation & Immunologie

country: France

institute: Institut national de la santé et de la recherche médicale-INSERM

description: Normal, Biological replicate 4 of 8

hyb_protocol: cDNA microarrays, containing ~32,000 cDNA clones (12,400 known unique genes), were processed using established protocols, using 2 μg RNA in each channel against a “common reference” RNA pool.

scan_protocol: Hybridized microarrays were scanned using GenePix 4000 (Axon Instruments, Union City, CA) and fluorescent images were analyzed with the GenePix Pro software package.

data_processing: Defective spots were flagged and removed. Defective spots were flagged and removed, generating a data file with 11,820 clones under low stringency retrieval settings (80% representative data, signal/noise ratio of expression measurements > 1.5, signal >200 in both channels and expression cut-off of 2-fold in one or more array). Data were centered prior to statistical analysis.

source_name: Total RNA from 20 pooled cell lines

label_protocol: Samples of total RNA were subjected to two successive rounds of amplification before hybridization using a modified protocol based on the method described by Wang et al. (Nat Biotechnol,  2000).

extract_protocol: Patient peripheral blood (10 ml) was harvested in EDTA tubes from a peripheral vein or arterio-venous fistula. Peripheral blood leukocytes (PBL) were separated on a Ficoll layer (Eurobio, Les Ulis, France) and 10 million cells were frozen in Trizol reagent (Invitrogen,Life Technologies, San Diego, CA) for RNA extraction.

value: pool of 20 cell lines from Pat Brown's lab

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), N4

value: PBL from N4

value: Peripheral blood leukocytes

tag: treatment

value: normal

tag: response

value: Normal


title: PBL from Normal 5

description: Normal, Biological replicate 5 of 8

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), N5

value: PBL from N5


title: PBL from Normal 3

description: Normal, Biological replicate 3 of 8

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), N3

value: PBL from N3


title: PBL from Normal 8

description: Normal, Biological replicate 8 of 8

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), N8

value: PBL from N8


title: PBL from Normal 1

description: Normal, Biological replicate 1 of 8

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), N1

value: PBL from N1


title: U87 LXSN

source_name: U87 cells stably expressing pLXSN

value: pLXSN


title: PBL from Normal 6

description: Normal, Biological replicate 6 of 8

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), N6

value: PBL from N6


title: PBL from Chronic Rejection 7

description: Chronic Rejection, Biological replicate 7 of 11

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), CR7

value: PBL from CR7

value: renal transplant

value: Chronic Rejection


title: PBL from Normal 2

description: Normal, Biological replicate 2 of 8

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), N2

value: PBL from N2


title: PBL from Chronic Rejection 8

description: Chronic Rejection, Biological replicate 8 of 11

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), CR8

value: PBL from CR8


title: PBL from Normal 7

description: Normal, Biological replicate 7 of 8

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), N7

value: PBL from N7


title: PBL from Chronic Rejection 10

description: Chronic Rejection, Biological replicate 10 of 11

value: pool of 20 cell lines from Pat Brown's lab

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), CR10

value: PBL from CR10


title: PBL from Chronic Rejection 11

description: Chronic Rejection, Biological replicate 11 of 11

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), CR11

value: PBL from CR11

value: Peripheral blood leukocytes


title: PBL from Chronic Rejection 5

description: Chronic Rejection, Biological replicate 5 of 11

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), CR5

value: PBL from CR5


title: PBL from Chronic Rejection 6

description: Chronic Rejection, Biological replicate 6 of 11

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), CR6

value: PBL from CR6


title: PBL from Chronic Rejection 2

description: Chronic Rejection, Biological replicate 2 of 11

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), CR2

value: PBL from CR2


title: PBL from Chronic Rejection 3

description: Chronic Rejection, Biological replicate 3 of 11

source_name: Total RNA from 20 pooled cell lines

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), CR3

value: PBL from CR3


title: PBL from Acute Rejection 13

description: Acute Rejection, Biological replicate 13 of 14

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR13

value: PBL from AR13

value: Acute Rejection


title: PBL from Acute Rejection 10

description: Acute Rejection, Biological replicate 10 of 14

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR10

value: PBL from AR10


title: PBL from Chronic Rejection 1

description: Chronic Rejection, Biological replicate 1 of 11

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), CR1

value: PBL from CR1


title: PBL from Chronic Rejection 9

description: Chronic Rejection, Biological replicate 9 of 11

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), CR9

value: PBL from CR9

value: renal transplant


title: PBL from Acute Rejection 6

description: Acute Rejection, Biological replicate 6 of 14

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR6

value: PBL from AR6


title: PBL from Acute Rejection 8

description: Acute Rejection, Biological replicate 8 of 14

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR8

value: PBL from AR8


title: PBL from Acute Rejection 7

description: Acute Rejection, Biological replicate 7 of 14

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR7

value: PBL from AR7


title: PBL from Chronic Rejection 4

description: Chronic Rejection, Biological replicate 4 of 11

value: pool of 20 cell lines from Pat Brown's lab

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), CR4

value: PBL from CR4

value: Chronic Rejection


title: PBL from Acute Rejection 14

description: Acute Rejection, Biological replicate 14 of 14

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR14

value: PBL from AR14

value: Peripheral blood leukocytes


title: PBL from Acute Rejection 12

description: Acute Rejection, Biological replicate 12 of 14

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR12

value: PBL from AR12


title: PBL from Acute Rejection 9

description: Acute Rejection, Biological replicate 9 of 14

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR9

value: PBL from AR9


title: PBL from Acute Rejection 4

description: Acute Rejection, Biological replicate 4 of 14

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR4

value: PBL from AR4


title: PBL from Stable 10

description: Stable, Biological replicate 10 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), STA10

value: PBL from STA10

value: Stable 10


title: PBL from Acute Rejection 5

description: Acute Rejection, Biological replicate 5 of 14

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR5

value: PBL from AR5

value: Acute Rejection


title: PBL from Stable 8

description: Stable, Biological replicate 8 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), STA8

value: PBL from STA8

value: Stable 8


title: PBL from Stable 11

description: Stable, Biological replicate 11 of 12

source_name: Total RNA from 20 pooled cell lines

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), STA11

value: PBL from STA11

value: renal transplant

value: Stable 11


title: PBL from Acute Rejection 1

description: Acute Rejection, Biological replicate 1 of 14

value: pool of 20 cell lines from Pat Brown's lab

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR1

value: PBL from AR1


title: PBL from Stable 1

description: Stable, Biological replicate 1 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), STA1

value: PBL from STA1

value: Stable 1


title: PBL from Acute Rejection 3

description: Acute Rejection, Biological replicate 3 of 14

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR3

value: PBL from AR3

value: Peripheral blood leukocytes


title: PBL from Stable 6

description: Stable, Biological replicate 6 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), STA6

value: PBL from STA6

value: Stable 6


title: PBL from Stable 7

description: Stable, Biological replicate 7 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), STA7

value: PBL from STA7

value: Stable 7


title: PBL from Acute Rejection 2

description: Acute Rejection, Biological replicate 2 of 14

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR2

value: PBL from AR2


title: PBL from Stable 9

description: Stable, Biological replicate 9 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), STA9

value: PBL from STA9

value: Stable 9


title: PBL from Stable 5

description: Stable, Biological replicate 5 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), STA5

value: PBL from STA5

value: Stable 5


title: PBL from Stable 4

description: Stable, Biological replicate 4 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), STA4

value: PBL from STA4

value: renal transplant

value: Stable 4


title: PBL from Stable 2

description: Stable, Biological replicate 2 of 12

value: pool of 20 cell lines from Pat Brown's lab

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), STA2

value: PBL from STA2

value: Stable 2


title: PBL from Minimal ImmunoSuppression 10

description: Minimal ImmunoSuppression, Biological replicate 10 of 10

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), MIS10

value: PBL from MIS10

value: Minimal ImmunoSuppression


title: PBL from Stable 12

description: Stable, Biological replicate 12 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), STA12

value: PBL from STA12

value: Peripheral blood leukocytes

value: Stable 12


title: PBL from Acute Rejection 11

description: Acute Rejection, Biological replicate 11 of 14

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), AR11

value: PBL from AR11

value: Acute Rejection


title: PBL from Minimal ImmunoSuppression 6

description: Minimal ImmunoSuppression, Biological replicate 6 of 10

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), MIS6

value: PBL from MIS6


title: PBL from Minimal ImmunoSuppression 1

description: Minimal ImmunoSuppression, Biological replicate 1 of 10

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), MIS1

value: PBL from MIS1


title: PBL from Minimal ImmunoSuppression 5

description: Minimal ImmunoSuppression, Biological replicate 5 of 10

source_name: Total RNA from 20 pooled cell lines

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), MIS5

value: PBL from MIS5


title: PBL from Minimal ImmunoSuppression 2

description: Minimal ImmunoSuppression, Biological replicate 2 of 10

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), MIS2

value: PBL from MIS2


title: PBL from Minimal ImmunoSuppression 8

description: Minimal ImmunoSuppression, Biological replicate 8 of 10

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), MIS8

value: PBL from MIS8


title: PBL from Minimal ImmunoSuppression 9

description: Minimal ImmunoSuppression, Biological replicate 9 of 10

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), MIS9

value: PBL from MIS9

value: renal transplant


title: PBL from Tolerant 11

description: Tolerant, Biological replicate 11 of 12

value: pool of 20 cell lines from Pat Brown's lab

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), TOL11

value: PBL from TOL11

value: Tolerant


title: PBL from Minimal ImmunoSuppression 3

description: Minimal ImmunoSuppression, Biological replicate 3 of 10

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), MIS3

value: PBL from MIS3


title: PBL from Tolerant 8

description: Tolerant, Biological replicate 8 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), TOL8

value: PBL from TOL8


title: PBL from Stable 3

description: Stable, Biological replicate 3 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), STA3

value: PBL from STA3

value: Stable 3


title: PBL from Minimal ImmunoSuppression 4

description: Minimal ImmunoSuppression, Biological replicate 4 of 10

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), MIS4

value: PBL from MIS4

value: Peripheral blood leukocytes

value: Minimal ImmunoSuppression


title: PBL from Tolerant 9

description: Tolerant, Biological replicate 9 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), TOL9

value: PBL from TOL9


title: PBL from Tolerant 7

description: Tolerant, Biological replicate 7 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), TOL7

value: PBL from TOL7


title: PBL from Tolerant 12

description: Tolerant, Biological replicate 12 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), TOL12

value: PBL from TOL12


title: PBL from Tolerant 6

description: Tolerant, Biological replicate 6 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), TOL6

value: PBL from TOL6


title: PBL from Tolerant 5

description: Tolerant, Biological replicate 5 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), TOL5

value: PBL from TOL5


title: PBL from Tolerant 1

description: Tolerant, Biological replicate 1 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), TOL1

value: PBL from TOL1


title: PBL from Tolerant 2

description: Tolerant, Biological replicate 2 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), TOL2

value: PBL from TOL2

value: renal transplant


title: PBL from Minimal ImmunoSuppression 7

description: Minimal ImmunoSuppression, Biological replicate 7 of 10

source_name: Total RNA from 20 pooled cell lines

value: pool of 20 cell lines from Pat Brown's lab

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), MIS7

value: PBL from MIS7


title: PBL from Tolerant 10

description: Tolerant, Biological replicate 10 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), TOL10

value: PBL from TOL10

value: Tolerant


title: PBL from Tolerant 3

description: Tolerant, Biological replicate 3 of 12

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), TOL3

value: PBL from TOL3


title: WT-nl-SP [6903024068_A]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite 6.6 (6.13.0201)

source_name: murine spleen

label_protocol: Biotinylated cRNA were prepared with the TargetAmpTM Nano-gTM Biotin-aRNA Labeling Kit

extract_protocol: Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).

tag: strain

value: 10-15 months

tag: tissue

value: spleen

tag: genotyp

value: TCL1+/wt Mif+/+

tag: leukemia

value: no


title: WT-l-SP [6903024068_F]

description: replicate 3

value: 2-5 months

value: yes


title: WT-nl-SP [6903024055_D]

description: replicate 2


title: WT-nl-BM [6752326052_C]

description: replicate 1

source_name: murine bone marrow

value: bone marrow


title: WT-nl-BM [6752326057_E]

description: replicate 2


title: KO-nl-SP [6903024068_E]

description: replicate 6

value: TCL1+/wt Mif-/-


title: WT-l-BM [7911798017_C]

description: replicate 4


title: KO-nl-BM [6903024068_B]

description: replicate 3


title: WT-nl-SP [6752326057_A]

description: replicate 1


title: KO-l-SP [6752326057_D]

description: replicate 3


title: KO-l-SP [6903024023_E]

description: replicate 4


title: WT-l-BM [6752326057_F]

description: replicate 1


title: WT-l-BM [7911798017_A]

description: replicate 3


title: WT-l-BM [7911798017_E]

description: replicate 5


title: WT-nl-BM [6903024055_B]

description: replicate 3


title: KO-nl-BM [6752326052_D]

description: replicate 1


title: WT-l-SP [6903024023_D]

description: replicate 2


title: KO-nl-BM [6903024055_F]

description: replicate 2


title: KO-nl-SP [6903024055_C]

description: replicate 4


title: KO-l-BM [7911798017_D]

description: replicate 5


title: KO-l-SP [6752326052_E]

description: replicate 1


title: KO-l-SP [6752326057_B]

description: replicate 2


title: KO-l-BM [7911798017_F]

description: replicate 6


title: KO-l-BM [6903024023_F]

description: replicate 3


title: KO-l-BM [6752326057_C]

description: replicate 2


title: KO-l-BM [7911798017_B]

description: replicate 4


title: WT-l-BM [6903024055_E]

description: replicate 2


title: Borrelia turicatae in blood rep 2

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_Borrelia turicatae in blood rep 2

hyb_protocol: All cRNAs were hybridized to a custom Affymetrix GeneChip

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

data_processing: The data were analyzed with EC 1.4 using Affymetrix default RMA

organism: Borrelia turicatae 91E135

source_name: Borrelia turicatae in blood rep 2

label_protocol: 100 ng of input RNA with RIN values above 8.0 was used for a nonbiased amplification with Ambion’s MessageAmpTM II- Bacteria Prokaryotic RNA kit (Life Technologies, Foster City, CA, USA) following the manufacturer’s instructions.  In vitro transcription was performed to incorporate biotin-11-CTP (PerkinElmer Life Sciences, Waltham, MA, USA) into the cDNA, and 3 µg of the sample was subsequently fragmented using Ambion’s 10x Fragmentation Reagent (Life Technologies) and used for each Affymetrix (Affymetrix, Santa Clara, CA, USA) GeneChip

growth_protocol: B. turicatae 91E135 cultured at 22 oC and 35 oC, infected and uninfected ticks, and murine blood five days after tick bite

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer’s instructions.  RNA integrity numbers (RIN) were calculated using the Agilent RNA 6000 Pico kit and the 2100 Bioanalyzer (Agilent Technologies, Waldbroon, Germany).


title: Borrelia turicatae in blood rep 1

description: Gene expression data from_Borrelia turicatae in blood rep 1

source_name: Borrelia turicatae in blood rep 1


title: Borrelia turicatae at 22ºC rep 3

description: Gene expression data from_Borrelia turicatae at 22ºC rep 3

source_name: Borrelia turicatae at 22ºC rep 3


title: Borrelia turicatae at 22ºC rep 2

description: Gene expression data from_Borrelia turicatae at 22ºC rep 2

source_name: Borrelia turicatae at 22ºC rep 2


title: Borrelia turicatae at 35ºC rep 1

description: Gene expression data from_Borrelia turicatae at 35ºC rep 1

source_name: Borrelia turicatae at 35ºC rep 1


title: Borrelia turicatae at 35ºC rep 2

description: Gene expression data from_Borrelia turicatae at 35ºC rep 2

source_name: Borrelia turicatae at 35ºC rep 2


title: Borrelia turicatae at 35ºC rep 3

description: Gene expression data from_Borrelia turicatae at 35ºC rep 3

source_name: Borrelia turicatae at 35ºC rep 3


title: Gfp_rep3

first: hao

last: zhen

address: The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, 225 Changhai Road, Shanghai 200438, China

description: Gene expression in HCC cell

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).  Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: Normal HCC Cell

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit(Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: HCC


title: Gfp_rep2

institute: The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University

description: Gene expression in HCC cell


title: KO-l-BM [6752326052_A]

description: replicate 1


title: Gfp_rep1

description: Gene expression in HCC cell


title: Borrelia turicatae in blood rep 3

description: Gene expression data from_Borrelia turicatae in blood rep 3

source_name: Borrelia turicatae in blood rep 3


title: shTMED3_rep2

description: Gene expression after TMED3 knocked down in HCC cell

source_name: TMED3 knocked down HCC Cell

tag: knockdown


title: shTMED3_rep3


title: Borrelia turicatae at 22ºC rep 1

description: Gene expression data from_Borrelia turicatae at 22ºC rep 1

source_name: Borrelia turicatae at 22ºC rep 1


title: shTMED3_rep1


title: Colorectal_Cancer_Survival_Patient52

city: Beijing

first: Kaitai

last: Zhang

state: Beijing

address: NO. 17, Pan Jiayuan South, Chao Yang District

department: Department of Etiology and Carcinogenesis

institute: Peking Union Medical College & Cancer Institute (Hospital), Chinese Academy of Medical Sciences

description:
Gene expression of colorectal cancer survival patient
R9D10

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Colorectal Cancer survival tissue

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

extract_protocol: Total RNA was extracted from frozen tissues using the TRIzol RNA isolation reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s specifications. RNA integrity was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). If the RNA integrity number was greater than or equal to 5, the total RNA was purified using the RNeasy Mini Kit (Cat No.74106, Qiagen, Germany). The RNA concentration was determined with a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, USA).

value: Cancer survival tissue

value: Male

tag: location

tag: Stage

tag: survival (year)

tag: events (death = 1, alive = 0)


title: Colorectal_Cancer_Survival_Patient51

description:
Gene expression of colorectal cancer survival patient
R9B9

tag: gender

tag: age


title: Colorectal_Cancer_Survival_Patient46

description:
Gene expression of colorectal cancer survival patient
Q4A12

value: Female


title: Colorectal_Cancer_Survival_Patient49

description:
Gene expression of colorectal cancer survival patient
R4E10


title: Colorectal_Cancer_Survival_Patient50

description:
Gene expression of colorectal cancer survival patient
R8F9


title: PBL from Tolerant 4

description: Tolerant, Biological replicate 4 of 12

source_name: Total RNA from 20 pooled cell lines

tag: sample type

value: pool of 20 cell lines from Pat Brown's lab

source_name: Total RNA from Peripheral Blood Leukocytes (PBL), TOL4

value: PBL from TOL4

value: Peripheral blood leukocytes

value: renal transplant


title: Colorectal_Cancer_Survival_Patient33

description:
Gene expression of colorectal cancer survival patient
H6A2


title: WT-l-SP [6752326052_F]

description: replicate 1


title: Colorectal_Cancer_Survival_Patient41

description:
Gene expression of colorectal cancer survival patient
L7F3


title: Colorectal_Cancer_Survival_Patient45

description:
Gene expression of colorectal cancer survival patient
Q2B1


title: Colorectal_Cancer_Survival_Patient48

description:
Gene expression of colorectal cancer survival patient
R3A2


title: Colorectal_Cancer_Survival_Patient47

description:
Gene expression of colorectal cancer survival patient
R1A2


title: Colorectal_Cancer_Survival_Patient42

description:
Gene expression of colorectal cancer survival patient
L8E7


title: Colorectal_Cancer_Survival_Patient44

description:
Gene expression of colorectal cancer survival patient
N5F1


title: Colorectal_Cancer_Survival_Patient39

description:
Gene expression of colorectal cancer survival patient
L3B11


title: Colorectal_Cancer_Survival_Patient35

description:
Gene expression of colorectal cancer survival patient
H9E6


title: Colorectal_Cancer_Survival_Patient43

description:
Gene expression of colorectal cancer survival patient
M4F5


title: Colorectal_Cancer_Survival_Patient38

description:
Gene expression of colorectal cancer survival patient
K3A5


title: Colorectal_Cancer_Survival_Patient40

description:
Gene expression of colorectal cancer survival patient
L4D3


title: Colorectal_Cancer_Survival_Patient32

description:
Gene expression of colorectal cancer survival patient
H2A8


title: Colorectal_Cancer_Survival_Patient37

description:
Gene expression of colorectal cancer survival patient
J7A3


title: Colorectal_Cancer_Survival_Patient29

description:
Gene expression of colorectal cancer survival patient
E7C10


title: Colorectal_Cancer_Survival_Patient34

description:
Gene expression of colorectal cancer survival patient
H6F8


title: Colorectal_Cancer_Survival_Patient30

description:
Gene expression of colorectal cancer survival patient
F5C3


title: Colorectal_Cancer_Survival_Patient36

description:
Gene expression of colorectal cancer survival patient
J1A3


title: Colorectal_Cancer_Survival_Patient31

description:
Gene expression of colorectal cancer survival patient
G8A6


title: Colorectal_Cancer_Survival_Patient26

description:
Gene expression of colorectal cancer survival patient
R4D10


title: Colorectal_Cancer_Survival_Patient27

description:
Gene expression of colorectal cancer survival patient
B1F6


title: Colorectal_Cancer_Survival_Patient28

description:
Gene expression of colorectal cancer survival patient
E5A3


title: Colorectal_Cancer_Survival_Patient23

description:
Gene expression of colorectal cancer survival patient
J9A2


title: Colorectal_Cancer_Survival_Patient16

description:
Gene expression of colorectal cancer survival patient
F2E9


title: Colorectal_Cancer_Survival_Patient12

description:
Gene expression of colorectal cancer survival patient
D6A3


title: Colorectal_Cancer_Survival_Patient21

description:
Gene expression of colorectal cancer survival patient
G9D2


title: Colorectal_Cancer_Survival_Patient25

description:
Gene expression of colorectal cancer survival patient
R4C4


title: Colorectal_Cancer_Survival_Patient22

description:
Gene expression of colorectal cancer survival patient
J1B2


title: Colorectal_Cancer_Survival_Patient15

description:
Gene expression of colorectal cancer survival patient
E8D11


title: Colorectal_Cancer_Survival_Patient19

description:
Gene expression of colorectal cancer survival patient
F7E9


title: Colorectal_Cancer_Survival_Patient5

description:
Gene expression of colorectal cancer survival patient
B5B6


title: Colorectal_Cancer_Survival_Patient18

description:
Gene expression of colorectal cancer survival patient
F4E12


title: Colorectal_Cancer_Survival_Patient8

description:
Gene expression of colorectal cancer survival patient
C2D4


title: Colorectal_Cancer_Survival_Patient1

description:
Gene expression of colorectal cancer survival patient
14B23


title: Colorectal_Cancer_Survival_Patient20

description:
Gene expression of colorectal cancer survival patient
G6A12


title: Colorectal_Cancer_Survival_Patient4

description:
Gene expression of colorectal cancer survival patient
A1B3


title: Colorectal Cancer_tissue_rep47

description:
Gene expression of colorectal cancer tissue
89C

source_name: Colorectal Cancer_tissue

value: cancer tissue

value: rectum


title: Colorectal_Cancer_Survival_Patient7

description:
Gene expression of colorectal cancer survival patient
B9E1


title: Colorectal Cancer_tissue_rep46

description:
Gene expression of colorectal cancer tissue
86C


title: Colorectal_Cancer_Survival_Patient11

description:
Gene expression of colorectal cancer survival patient
C7B7


title: Colorectal_Cancer_Survival_Patient9

description:
Gene expression of colorectal cancer survival patient
C6D5


title: Colorectal_Cancer_Survival_Patient3

description:
Gene expression of colorectal cancer survival patient
17B16


title: Colorectal_Cancer_Survival_Patient10

description:
Gene expression of colorectal cancer survival patient
C7A2


title: Colorectal_Cancer_Survival_Patient6

description:
Gene expression of colorectal cancer survival patient
B9A9


title: Colorectal_Cancer_Survival_Patient14

description:
Gene expression of colorectal cancer survival patient
E2F11


title: Colorectal_Cancer_Survival_Patient2

description:
Gene expression of colorectal cancer survival patient
16B18


title: Colorectal Cancer_tissue_rep44

description:
Gene expression of colorectal cancer tissue
76C

value: colon


title: Colorectal_Cancer_Survival_Patient24

description:
Gene expression of colorectal cancer survival patient
R4B11


title: Colorectal_Cancer_Survival_Patient13

description:
Gene expression of colorectal cancer survival patient
E1F1


title: Colorectal Cancer_tissue_rep45

description:
Gene expression of colorectal cancer tissue
77C


title: Colorectal Cancer_tissue_rep43

description:
Gene expression of colorectal cancer tissue
60C


title: Colorectal Cancer_tissue_rep42

description:
Gene expression of colorectal cancer tissue
56C


title: Colorectal Cancer_tissue_rep41

description:
Gene expression of colorectal cancer tissue
54C


title: Colorectal Cancer_tissue_rep34

description:
Gene expression of colorectal cancer tissue
39C


title: Colorectal Cancer_tissue_rep39

description:
Gene expression of colorectal cancer tissue
49C


title: Colorectal Cancer_tissue_rep36

description:
Gene expression of colorectal cancer tissue
42C


title: Colorectal Cancer_tissue_rep32

description:
Gene expression of colorectal cancer tissue
37C


title: Colorectal Cancer_tissue_rep28

description:
Gene expression of colorectal cancer tissue
31C


title: Colorectal Cancer_tissue_rep33

description:
Gene expression of colorectal cancer tissue
38C


title: Colorectal Cancer_tissue_rep38

description:
Gene expression of colorectal cancer tissue
45C


title: Colorectal Cancer_tissue_rep30

description:
Gene expression of colorectal cancer tissue
35C


title: Colorectal Cancer_tissue_rep35

description:
Gene expression of colorectal cancer tissue
40C


title: Colorectal Cancer_tissue_rep23

description:
Gene expression of colorectal cancer tissue
25C


title: Colorectal Cancer_tissue_rep37

description:
Gene expression of colorectal cancer tissue
44C


title: Colorectal Cancer_tissue_rep40

description:
Gene expression of colorectal cancer tissue
53C


title: Colorectal Cancer_tissue_rep19

description:
Gene expression of colorectal cancer tissue
231C


title: Colorectal Cancer_tissue_rep25

description:
Gene expression of colorectal cancer tissue
267C


title: Colorectal Cancer_tissue_rep21

description:
Gene expression of colorectal cancer tissue
241C


title: Colorectal Cancer_tissue_rep29

description:
Gene expression of colorectal cancer tissue
33C


title: Colorectal Cancer_tissue_rep27

description:
Gene expression of colorectal cancer tissue
29C


title: Colorectal Cancer_tissue_rep18

description:
Gene expression of colorectal cancer tissue
22C


title: KO-nl-SP [6903024068_C]

description: replicate 5

source_name: murine spleen

value: 10-15 months

value: spleen


title: Colorectal Cancer_tissue_rep22

description:
Gene expression of colorectal cancer tissue
257C


title: Colorectal Cancer_tissue_rep26

description:
Gene expression of colorectal cancer tissue
28C


title: Colorectal Cancer_tissue_rep20

description:
Gene expression of colorectal cancer tissue
23C


title: Colorectal Cancer_tissue_rep24

description:
Gene expression of colorectal cancer tissue
261C


title: Colorectal Cancer_tissue_rep17

description:
Gene expression of colorectal cancer tissue
228C


title: Colorectal Cancer_tissue_rep31

description:
Gene expression of colorectal cancer tissue
36C


title: Colorectal Cancer_tissue_rep16

description:
Gene expression of colorectal cancer tissue
225C


title: Colorectal Cancer_tissue_rep15

description:
Gene expression of colorectal cancer tissue
221C


title: Colorectal Cancer_tissue_rep13

description:
Gene expression of colorectal cancer tissue
212C


title: Colorectal_Cancer_Survival_Patient17

description:
Gene expression of colorectal cancer survival patient
F3B9


title: Colorectal Cancer_tissue_rep12

description:
Gene expression of colorectal cancer tissue
201C


title: Colorectal Cancer_tissue_rep9

description:
Gene expression of colorectal cancer tissue
183C


title: Colorectal Cancer_tissue_rep6

description:
Gene expression of colorectal cancer tissue
164C


title: Colorectal Adenoma tissue_rep58

description:
Gene expression of colorectal adenoma tissue
70A

source_name: Colorectal Adenoma tissue

value: adenoma tissue


title: Colorectal Cancer_tissue_rep2

description:
Gene expression of colorectal cancer tissue
127C


title: Colorectal Adenoma tissue_rep48

description:
Gene expression of colorectal adenoma tissue
181


title: Colorectal Cancer_tissue_rep14

description:
Gene expression of colorectal cancer tissue
217C


title: Colorectal Cancer_tissue_rep11

description:
Gene expression of colorectal cancer tissue
198C


title: Colorectal Adenoma tissue_rep55

description:
Gene expression of colorectal adenoma tissue
50C


title: Colorectal Adenoma tissue_rep57

description:
Gene expression of colorectal adenoma tissue
57A


title: Colorectal Adenoma tissue_rep51

description:
Gene expression of colorectal adenoma tissue
223


title: Colorectal Adenoma tissue_rep47

description:
Gene expression of colorectal adenoma tissue
175


title: Colorectal Cancer_tissue_rep7

description:
Gene expression of colorectal cancer tissue
167C


title: Colorectal Cancer_tissue_rep4

description:
Gene expression of colorectal cancer tissue
151C


title: Colorectal Adenoma tissue_rep52

description:
Gene expression of colorectal adenoma tissue
226


title: Colorectal Cancer_tissue_rep3

description:
Gene expression of colorectal cancer tissue
13C


title: Colorectal Cancer_tissue_rep8

description:
Gene expression of colorectal cancer tissue
172A


title: Colorectal Cancer_tissue_rep1

description:
Gene expression of colorectal cancer tissue
119C


title: Colorectal Cancer_tissue_rep5

description:
Gene expression of colorectal cancer tissue
154C


title: Colorectal Adenoma tissue_rep53

description:
Gene expression of colorectal adenoma tissue
237


title: Colorectal Adenoma tissue_rep54

description:
Gene expression of colorectal adenoma tissue
43C


title: Colorectal Adenoma tissue_rep49

description:
Gene expression of colorectal adenoma tissue
182


title: Colorectal Adenoma tissue_rep46

description:
Gene expression of colorectal adenoma tissue
173


title: Colorectal Cancer_tissue_rep10

description:
Gene expression of colorectal cancer tissue
197


title: Colorectal Adenoma tissue_rep56

description:
Gene expression of colorectal adenoma tissue
52C


title: Colorectal Adenoma tissue_rep50

description:
Gene expression of colorectal adenoma tissue
203


title: Colorectal Adenoma tissue_rep45

description:
Gene expression of colorectal adenoma tissue
17


title: Colorectal Adenoma tissue_rep42

description:
Gene expression of colorectal adenoma tissue
16


title: Colorectal Adenoma tissue_rep39

description:
Gene expression of colorectal adenoma tissue
114A


title: Colorectal Adenoma tissue_rep44

description:
Gene expression of colorectal adenoma tissue
169


title: Colorectal Adenoma tissue_rep37

description:
Gene expression of colorectal adenoma tissue
88A


title: Colorectal Adenoma tissue_rep29

description:
Gene expression of colorectal adenoma tissue
259


title: Colorectal Adenoma tissue_rep32

description:
Gene expression of colorectal adenoma tissue
65A


title: Colorectal Adenoma tissue_rep26

description:
Gene expression of colorectal adenoma tissue
246


title: Colorectal Adenoma tissue_rep23

description:
Gene expression of colorectal adenoma tissue
235


title: Colorectal Adenoma tissue_rep43

description:
Gene expression of colorectal adenoma tissue
165


title: Colorectal Adenoma tissue_rep19

description:
Gene expression of colorectal adenoma tissue
216


title: Colorectal Adenoma tissue_rep20

description:
Gene expression of colorectal adenoma tissue
229


title: Colorectal Adenoma tissue_rep41

description:
Gene expression of colorectal adenoma tissue
155


title: Colorectal Adenoma tissue_rep34

description:
Gene expression of colorectal adenoma tissue
69A


title: Colorectal Adenoma tissue_rep33

description:
Gene expression of colorectal adenoma tissue
68A


title: Colorectal Adenoma tissue_rep24

description:
Gene expression of colorectal adenoma tissue
236


title: Colorectal Adenoma tissue_rep30

description:
Gene expression of colorectal adenoma tissue
260


title: Colorectal Adenoma tissue_rep21

description:
Gene expression of colorectal adenoma tissue
233


title: Colorectal Adenoma tissue_rep36

description:
Gene expression of colorectal adenoma tissue
87A


title: Colorectal Adenoma tissue_rep18

description:
Gene expression of colorectal adenoma tissue
210


title: Colorectal Adenoma tissue_rep31

description:
Gene expression of colorectal adenoma tissue
263


title: Colorectal Adenoma tissue_rep38

description:
Gene expression of colorectal adenoma tissue
91A


title: Colorectal Adenoma tissue_rep40

description:
Gene expression of colorectal adenoma tissue
14


title: Colorectal Adenoma tissue_rep22

description:
Gene expression of colorectal adenoma tissue
234


title: Colorectal Adenoma tissue_rep27

description:
Gene expression of colorectal adenoma tissue
248


title: Colorectal Adenoma tissue_rep17

description:
Gene expression of colorectal adenoma tissue
209


title: Colorectal Adenoma tissue_rep28

description:
Gene expression of colorectal adenoma tissue
253


title: Colorectal Adenoma tissue_rep25

description:
Gene expression of colorectal adenoma tissue
238


title: Colorectal Adenoma tissue_rep35

description:
Gene expression of colorectal adenoma tissue
79A


title: Colorectal Adenoma tissue_rep14

description:
Gene expression of colorectal adenoma tissue
199


title: Colorectal Adenoma tissue_rep16

description:
Gene expression of colorectal adenoma tissue
208


title: Colorectal Adenoma tissue_rep13

description:
Gene expression of colorectal adenoma tissue
196


title: Colorectal Adenoma tissue_rep15

description:
Gene expression of colorectal adenoma tissue
200


title: Colorectal Adenoma tissue_rep10

description:
Gene expression of colorectal adenoma tissue
190


title: Colorectal Adenoma tissue_rep4

description:
Gene expression of colorectal adenoma tissue
166


title: Normal rectum mucosa_rep9

description:
Gene expression of normal colorectal tissue
N27

source_name: Normal colorectal tissue

value: normal tissue


title: Colorectal Adenoma tissue_rep5

description:
Gene expression of colorectal adenoma tissue
176


title: Normal rectum mucosa_rep12

description:
Gene expression of normal colorectal tissue
N32


title: Colorectal Adenoma tissue_rep1

description:
Gene expression of colorectal adenoma tissue
101A


title: Normal rectum mucosa_rep10

description:
Gene expression of normal colorectal tissue
N28


title: Colorectal Adenoma tissue_rep2

description:
Gene expression of colorectal adenoma tissue
103A


title: Colorectal Adenoma tissue_rep9

description:
Gene expression of colorectal adenoma tissue
188


title: Colorectal Adenoma tissue_rep11

description:
Gene expression of colorectal adenoma tissue
194


title: Colorectal Adenoma tissue_rep7

description:
Gene expression of colorectal adenoma tissue
179


title: Colorectal Adenoma tissue_rep8

description:
Gene expression of colorectal adenoma tissue
180


title: Normal rectum mucosa_rep4

description:
Gene expression of normal colorectal tissue
N15


title: Normal rectum mucosa_rep7

description:
Gene expression of normal colorectal tissue
N23


title: Colorectal Adenoma tissue_rep6

description:
Gene expression of colorectal adenoma tissue
177


title: Normal rectum mucosa_rep8

description:
Gene expression of normal colorectal tissue
N24


title: Colorectal Adenoma tissue_rep12

description:
Gene expression of colorectal adenoma tissue
195


title: Normal rectum mucosa_rep11

description:
Gene expression of normal colorectal tissue
N29


title: Middle_embryonic_colon_rep6

description:
Gene expression of middle embryonic colon tissue
MF04

source_name: Middle embryonic colon tissue

value: embryonic tissue


title: Normal rectum mucosa_rep3

description:
Gene expression of normal colorectal tissue
N12


title: Normal rectum mucosa_rep5

description:
Gene expression of normal colorectal tissue
N17


title: Colorectal Adenoma tissue_rep3

description:
Gene expression of colorectal adenoma tissue
148


title: Normal rectum mucosa_rep6

description:
Gene expression of normal colorectal tissue
N22


title: Normal rectum mucosa_rep1

description:
Gene expression of normal colorectal tissue
N10


title: Middle_embryonic_colon_rep5

description:
Gene expression of middle embryonic colon tissue
MF03


title: Normal rectum mucosa_rep2

description:
Gene expression of normal colorectal tissue
N11


title: Middle_embryonic_colon_rep7

description:
Gene expression of middle embryonic colon tissue
MF05


title: Middle_embryonic_colon_rep4

description:
Gene expression of middle embryonic colon tissue
EF04


title: Middle_embryonic_colon_rep3

description:
Gene expression of middle embryonic colon tissue
EF03


title: Middle_embryonic_colon_rep2

description:
Gene expression of middle embryonic colon tissue
EF02


title: Middle_embryonic_colon_rep1

description:
Gene expression of middle embryonic colon tissue
EF01


title: Early_embryonic_colon_rep6

description:
Gene expression of early embryonic colon tissue
EF27

source_name: Early embryonic colon tissue


title: Early_embryonic_colon_rep4

description:
Gene expression of early embryonic colon tissue
EF24


title: cell line of human uterine leiomyosarcoma SK-UT1B

city: Fukuoka

first: Tomoko

last: Miyata

state: Fukuoka

address: 3-1-1 Maedashi, Higashi-ku

department: Gynecology and Obstetrics

country: Japan

institute: Kyushu University

hyb_protocol: The resultant cRNAs were fragmented for 30 min at 60oC in dark. The fragmented cRNAs (600 ng) were hybridized on the microarray at 65oC for 17 h.

scan_protocol: After washing, slides were scanned with the Agilent microarray scanner G2505B.

data_processing: Feature extraction software (version 10.7.3.1) was used to calculate signal intensities from the scanned images.

source_name: cell line

label_protocol: Total RNA samples (100 ng) were amplified and labelled with Cy3 using the Low Input QuickAmp Labeling Kit (Agilent).

growth_protocol: All specimens were isolated during the primary uterus surgery at the Department of Obstetrics and Gynecology in the Kyushu University Hospital, immediately frozen in liquid nigrogen, and stored at -80C˚. SKN (RBRC-RCB0513) obtained from RIKEN BRC, and SK-UT1 (HTB-114TM) and SK-UT1B (HTB-115TM) obtained from American Type Culture Collection. All cells were cultured under standard culture conditions (at 37°C, 5% CO2 in air) in a medium supplemented with 15% fetal bovine serum and Penicillin-Streptomycin-Glutamine Liquid (final 1x, GIBCO 10378-016). HamF12 medium was used for SKN cells, and Eagle medium was used for SK-UT1 and SK-UT1B cells.

extract_protocol: Total RNA was isolated using All Prep DNA/RNA Mini kit (Qiagen) according to the manufacturer’s instruction.

tag: cell line

value: female


title: Early_embryonic_colon_rep3

description:
Gene expression of early embryonic colon tissue
EF23


title: Early_embryonic_colon_rep1

description:
Gene expression of early embryonic colon tissue
EF18


title: Whole_embryo_rep6

description:
Gene expression of early whole embryo tissue
SWE21

source_name: Whole embryonic tissue


title: Whole_embryo_rep3

description:
Gene expression of early whole embryo tissue
SWE09


title: Early_embryonic_colon_rep5

description:
Gene expression of early embryonic colon tissue
EF25


title: Whole_embryo_rep2

description:
Gene expression of early whole embryo tissue
SWE08


title: Whole_embryo_rep5

description:
Gene expression of early whole embryo tissue
SWE19


title: Early_embryonic_colon_rep2

description:
Gene expression of early embryonic colon tissue
EF21


title: uterine leiomyoma tissue from case 6

source_name: uterine leiomyoma

value: uterine leiomyoma


title: uterine leiomyoma tissue from case 5


title: uterine leiomyosarcoma tissue from case 8

source_name: uterine leiomyosarcoma

value: uterine leiomyosarcoma


title: Whole_embryo_rep4

description:
Gene expression of early whole embryo tissue
SWE11


title: cell line of human uterine leiomyosarcoma SK-UT1


title: uterine normal myometrium tissue from case 2

source_name: normal uterine myometrium

value: normal uterine myometrium


title: Whole_embryo_rep1

description:
Gene expression of early whole embryo tissue
SWE04


title: cell line of human uterine leiomyosarcoma SKN

value: SKN


title: uterine normal myometrium tissue from case 3


title: uterine normal myometrium tissue from case 1


title: uterine leiomyoma tissue from case 4


title: uterine leiomyosarcoma tissue from case 7


title: hippocampus_CA3_late_L47

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: Gene expression from CA3 explant

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent). The normalization method used was Lowess and we used Log (base 2).

source_name: hippocampus, CA3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Brain tissue explants from GD (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen)

treatment_protocol: Fresh ex-vivo explants of patients were obtained at the surgery room and immediately preserved with 600 uL of RNAlater (Qiagen).

tag: age of ipi (yr/mo)

tag: age of epilepsy onset (yr)

tag: age at surgery (yr)

tag: side

value: right


title: hippocampus_CA3_late_L28

description: Gene expression from CA3 explant


title: hippocampus_CA3_late_L60

description: Gene expression from CA3 explant

value: left


title: hippocampus_CA3_late_L17

description: Gene expression from CA3 explant

value: male


title: hippocampus_CA3_late_L18

description: Gene expression from CA3 explant


title: hippocampus_CA3_early_E81

description: Gene expression from CA3 explant


title: hippocampus_CA3_early_E30

description: Gene expression from CA3 explant


title: hippocampus_CA3_late_L46

description: Gene expression from CA3 explant


title: hippocampus_CA3_early_E69

description: Gene expression from CA3 explant


title: hippocampus_CA3_late_L19

description: Gene expression from CA3 explant


title: hippocampus_CA3_early_E12

description: Gene expression from CA3 explant


title: NHEK-Empty Vector

city: Bethesda

first: Hong-wei

last: Sun

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

description: Gene expression data in DLX3-transduced human keratinocytes - Biological replicates

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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

label_protocol: RNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: NHEK were grown in KGM (Keratinocyte Growth Media) (Lonza).

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

treatment_protocol: Cells were transduced with Empty Vector (VECTOR) or Dlx3/Flag (DLX3) retroviruses (Morasso Lab). No transfected cells were used as control.

tag: cell type

value: primary human keratinocytes


title: hippocampus_CA3_early_E03

description: Gene expression from CA3 explant


title: BC8

city: Miaoli County

first: Ya-Wen

last: Chen

address: 35, Keyan Rd, Zhunan Town

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Quantile normalization.

source_name: Malignant breast diseases

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano-G Bioti- aRNA Labeling kit (Epicentre) for Illumina arrays.

growth_protocol: Peripheral blood mononuclear cells were isolated by density-gradient centrifugation with Ficoll-Hypaue (GE Healthcare, Little Chalfont, UK) from 10-ml whole blood with ethylenediaminetetraacetic acid (EDTA). One million of mononuclear cells were suspended in CFU-Hill Liquid medium (#5900, Stemcell Technologies, Vancouver, British Columbia, Canada) in fibronectin-coating 24-well plate (BD Biosciences). After 5-7 day culture, the endothelial cell colony forming units (EC-CFU) were collected.

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit according to  protocol provided in the kit by the  manufacturer. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatment

tag: tissue

value: endothelial cell colony forming unit cells


title: BC3


title: hippocampus_CA3_early_E33

description: Gene expression from CA3 explant


title: BC2


title: NHEK-Control


title: C2

source_name: Healthy control


title: BC7


title: NHEK-DLX3/Flag Vector


title: Middle_embryonic_colon_rep8

description:
Gene expression of middle embryonic colon tissue
MF08


title: BC6


title: hippocampus_CA3_early_E80

description: Gene expression from CA3 explant


title: BC9


title: BC10


title: BC5


title: C6


title: KLF12 overexpression effect in colorectal cancer cells [LS174T_Con_3]

city: Seoul

first: YUNYONG

last: PARK

address: 84 Heukseok-ro

institute: ChuangAng University

description: control

hyb_protocol: Hyb was done at 58 degree for 18 hrs

scan_protocol: HighScan was used

data_processing: GenomeStudio was used for data processing and quantile normalization method was used.

source_name: Colon cancer cell

label_protocol: Extracted RNA was amplified and labeled with Amplification kit (AMIL1797; Ambion)

growth_protocol: The cells were grown in McCoy 5A medium containing 10% FBS

extract_protocol: miRvana kit was used for RNA extraction

treatment_protocol: Cells were treated with indicated lenti-viral vector

tag: genotype/variation

value: Control


title: KLF12 overexpression effect in colorectal cancer cells [LS174T_KLF12_Over_3]

description: Over-expression in Colon cancer cell

value: KLF12 Over-expression


title: C4


title: C3


title: KLF12 overexpression effect in colorectal cancer cells [LS174T_KLF12_Over_1]

description: Over-expression in Colon cancer cell


title: KLF12 overexpression effect in colorectal cancer cells [LS174T_Con_1]

description: control


title: C5


title: BC4


title: HaCaT_With_AMP18_2hrs_rep3

city: SYRACUSE

first: Mira

last: Krendel

state: New York

address: 505 Irving Ave

institute: Upstate Medical University

description:
Triplicate 3
GT24

data_processing: Average signal intensities were background-subtracted, log2 transformed, and quantile normalization using Illumina Genome Studio v2011.1

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

growth_protocol: SCC-61 cells were grown in a 1:1 mixture of DMEM/F12 medium containing 1.2 g/L sodium bicarbonate, 2.5 mM L-glutamine, 15 mM HEPES and 0.5 mM sodium pyruvate, and supplemented with 400 ng/ml hydrocortisone, 10% FBS, penicillin (50 U/mL) and streptomycin (50 µg/mL), at 37ºC in a humidified incubator supplemented with 5% CO2. HaCaT were grown in DMEM with FBS, penicillin and streptomycin.

extract_protocol: Total RNA was extracted from SCC-61 and HaCaT cells using the RNeasy kit (Quiagen) according to the manufacturer’s specifications.

treatment_protocol: Cells were starved in medium with 1% FBS, and were then left untreated, or treated with 2 ug/ml AMP-18.

value: HaCaT

value: an immortal keratinocyte cell line

tag: treated with

value: 2 ug/ml AMP-18 for 2hrs


title: KLF12 overexpression effect in colorectal cancer cells [LS174T_Con_2]

description: control


title: HaCaT_Without_AMP18_2hrs_rep3

description:
Triplicate 3
GT21

value: none for 2hrs (untreated control)


title: SCC61_With_AMP18_2hrs_rep3

description:
Triplicate 3
GT18

value: Head and neck cancer cell line


title: SCC61_Without_AMP18_2hrs_rep3

description:
Triplicate 3
GT15


title: SCC61_Without_AMP18_2hrs_rep2

description:
Triplicate 2
GT14


title: SCC61_Without_AMP18_2hrs_rep1

description:
Triplicate 1
GT13


title: KLF12 overexpression effect in colorectal cancer cells [LS174T_KLF12_Over_2]

description: Over-expression in Colon cancer cell


title: BC1

value: female


title: HaCaT_Without_AMP18_2hrs_rep1

description:
Triplicate 1
GT19


title: SCC61_With_AMP18_2hrs_rep1

description:
Triplicate 1
GT16


title: SCC61_With_AMP18_2hrs_rep2

description:
Triplicate 2
GT17


title: HaCaT_Without_AMP18_24hrs_rep3

description:
Triplicate 3
GT9

value: none for 24hrs (untreated control)


title: HaCaT_With_AMP18_24hrs_rep2

description:
Triplicate 2
GT11

value: 2 ug/ml AMP-18 for 24hrs


title: HaCaT_With_AMP18_2hrs_rep1

description:
Triplicate 1
GT22


title: HaCaT_With_AMP18_24hrs_rep3

description:
Triplicate 3
GT12


title: HaCaT_With_AMP18_24hrs_rep1

description:
Triplicate 1
GT10


title: HaCaT_Without_AMP18_2hrs_rep2

description:
Triplicate 2
GT20


title: C1


title: HaCaT_With_AMP18_2hrs_rep2

description:
Triplicate 2
GT23


title: HaCaT_Without_AMP18_24hrs_rep2

description:
Triplicate 2
GT8


title: HaCaT_Without_AMP18_24hrs_rep1

description:
Triplicate 1
GT7


title: SCC61_With_AMP18_24hrs_rep3

description:
Triplicate 3
GT6


title: SCC61_With_AMP18_24hrs_rep1

description:
Triplicate 1
GT4


title: SCC61_Without_AMP18_24hrs_rep3

description:
Triplicate 3
GT3


title: MDA-MB-231 rep2

city: Montreal

first: David

last: Cheishvili

state: Quebec

address: 3655 Sir William Osler

country: Canada

institute: McGill

description: replicate 2

data_processing: The data were normalised using quantile normalisation with Genome Studio expression module

source_name: MDA-MB-231 cell line

label_protocol: biotin-labeled cRNA using Illumina® TotalPrep RNA Amplification Kit, according to manufacturer’s instructions (Life Technologies)

growth_protocol: HepG2, SKHep1 and MCF-7 cells were maintained in MEM medium (Gibco, Invitrogen, Life Technologies). MCF7 cells were cultured with 0.01 mg/ml of insulin (Invitrogen, Carlsbad, California). MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (Invitrogen). PC3 and LNCaP were cultured in RPMI1640 media (Gibco, Invitrogen, Life Technologies). All media were supplemented with 2 mmol/L glutamine (Sigma-Aldrich), 10% FBS (Gibco), 1 U/mL penicillin and 1 mg/mL streptomycin (Gibco).

extract_protocol: RNA was

value: cell line

tag: disease state

value: cancer

value: MDA-MB-231 cell line


title: SKHep1 rep2

description: replicate 2

source_name: SKHep1 cell line

value: SKHep1 cell line


title: MDA-MB-231 rep1

description: replicate 1


title: MDA-MB-231 rep3

description: replicate 3


title: SCC61_Without_AMP18_24hrs_rep2

description:
Triplicate 2
GT2


title: HepG2 rep3

description: replicate 3

source_name: HepG2 cell line

value: male

value: HepG2 cell line


title: SKHep1 rep1

description: replicate 1


title: MCF7 rep2

description: replicate 2

source_name: MCF7 cell line

value: MCF7 cell line


title: HepG2 rep2

description: replicate 2


title: SKHep1 rep3

description: replicate 3


title: NO_982_CN-AML

city: Taipei

first: Wen-Chien

last: Chou

address: No. 7, Chung-Shan S. Rd.

department: Department of Laboratory Medicine

institute: National Taiwan University Hospital

hyb_protocol: cRNA was hybridized to Illumina HumanHT-12 v4 Expression BeadChip according to the manufacturer’s instructions.

scan_protocol: After 14–20 hours hybridization, the BeadChips were stained by Cy3 and were then washed. Intensities of bead fluorescence were detected by Illumina BeadArray Reader, and the results were transformed to numeric values using GenomeStudio v2010.1 software (Illumina).

data_processing: Expression values were processed with log2 transformation and quantile normalization.  The raw data file (Non-normalized_data_.txt) includes instances of null (~100 or fewer per sample ) where the raw signal is not available.  The 104 samples were analyzed in ~10 batches. The raw dataset for each batch was obtained from the service provider with values for a range of 47,219-47,317 probes. When raw data for a specific probe was missing from one of the batches, it was annotated with null.

source_name: de novo acute myeloid leukemia

label_protocol: cDNA was amplified (in vitro transcription) to generate biotin labeled cRNA (Ambion) according to manufacturer's instructions.

extract_protocol: RNA was extracted by TriZol reagent according to manufacturer's instructions.

tag: disease

value: CN-AML

value: bone marrow

tag: overall survival (months)

tag: event (1

value: dead, 0:alive):1


title: SCC61_With_AMP18_24hrs_rep2

description:
Triplicate 2
GT5


title: NO_960_CN-AML

value: dead, 0:alive):0


title: NO_959_CN-AML


title: HepG2 rep1

description: replicate 1


title: NO_965_CN-AML


title: NO_976_CN-AML


title: NO_975_CN-AML


title: MCF7 rep3

description: replicate 3


title: MCF7 rep1

description: replicate 1


title: SCC61_Without_AMP18_24hrs_rep1

description:
Triplicate 1
GT1


title: NO_968_CN-AML


title: NO_949_CN-AML


title: NO_974_CN-AML


title: NO_927_CN-AML


title: uterine leiomyosarcoma tissue from case 9

value: uterine leiomyosarcoma


title: NO_860_CN-AML


title: NO_873_CN-AML


title: NO_914_CN-AML


title: NO_868_CN-AML


title: NO_874_CN-AML


title: NO_861_CN-AML


title: NO_915_CN-AML


title: NO_871_CN-AML


title: NO_848_CN-AML


title: NO_923_CN-AML


title: NO_852_CN-AML


title: NO_939_CN-AML


title: NO_857_CN-AML


title: NO_846_CN-AML


title: NO_921_CN-AML


title: NO_840_CN-AML


title: NO_903_CN-AML


title: NO_858_CN-AML


title: NO_780_CN-AML


title: NO_890_CN-AML


title: NO_879_CN-AML


title: NO_807_CN-AML


title: NO_761_CN-AML


title: NO_181_CN-AML


title: NO_189_CN-AML


title: NO_140_CN-AML


title: NO_864_CN-AML


title: NO_856_CN-AML


title: NO_138_CN-AML


title: NO_837_CN-AML


title: NO_129_CN-AML


title: NO_121_CN-AML


title: NO_128_CN-AML


title: NO_118_CN-AML


title: NO_104_CN-AML


title: NO_114_CN-AML


title: NO_134_CN-AML


title: NO_126_CN-AML


title: NO_103_CN-AML


title: NO_102_CN-AML


title: NO_96_CN-AML


title: NO_137_CN-AML


title: NO_135_CN-AML


title: NO_98_CN-AML


title: NO_106_CN-AML


title: NO_112_CN-AML


title: NO_108_CN-AML


title: NO_124_CN-AML


title: NO_92_CN-AML


title: NO_100_CN-AML


title: NO_89_CN-AML


title: NO_93_CN-AML


title: NO_94_CN-AML


title: NO_87_CN-AML


title: NO_88_CN-AML


title: NO_83_CN-AML


title: NO_82_CN-AML


title: NO_79_CN-AML