title: Human Limbus Donor 15 OS (Left Eye)

city: Los Angeles

first: Martin

last: Nakatsu

address: 200 Stein Plaza

institute: Jules Stein Eye Institute

hyb_protocol: Affymetrix GeneChip Hybridization Protocol

scan_protocol: Affymetrix GeneChip 3000 Scanner Protocol

data_processing: All Affymetrix data were normalized with Robust Multichip Average (RMA) algorithm using Affymetrix Expression Console.

source_name: limbus

label_protocol: Affymetrix Gene Expression Protocol for Biotin Labeling

extract_protocol: Each sample was resuspended in a Qiagen lysis buffer provided in w/ β-mercaptoethanol (1:100). In between homogenizations, the blade was rinsed subsequently twice in filtered ddI water, 70% ethanol, and twice again in fresh Millipore ddI water. All samples are kept on dry ice before homogenization. Total RNA was isolated using the Qiagen’s RNA easy mini columns.

value: limbus


title: LPJ021 CD20int B-cells

status: Public on Jan 01 2013

type: RNA

city: Houston

first: Michael

middle: R

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

country: USA

institute: MD Anderson Cancer Center

hyb_protocol: Hybridized overnight according to the manufacturer's protocol using an Affymetrix GeneChip Hybridization Oven 640

scan_protocol: Scanned according to the manufacturer's protocol using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were RMA normalized using the "ExpressionFileCreator" module of GenePattern with the default settings.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: CD20int Follicular Lymphoma B-cells

label_protocol: Labelled according to Affymetrix manufacturers protocol

extract_protocol: RNA and DNA were extracted using a Qiagen AllPrep kit

tag: patient identifier

tag: gender

value: Male

tag: age

tag: type

value: Follicular Lymphoma

tag: subset

value: CD20int B-cell


title: LPJ021 CD20hi B-cells

source_name: CD20hi Follicular Lymphoma B-cells

value: CD20hi B-cell


title: 4d_DRG_3

city: Shanghai

first: Guohui

last: Ding

address: 320 Yueyang Road

country: China

institute: Shanghai Institutes for Biological Sciences

description: Gene expression at 4d following sciatic nerve resection in DRG

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA) in Hybridization Oven (Agilent technologies, Santa Clara, CA), according to the manufacturer's instructions. After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA) with Gene Expression Wash Buffer Kit(Agilent technologies, Santa Clara, CA), followed the manufacturer's instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA) with default settings，Dye channel: Green, Scan resolution = 5μm, PMT 100%，10%，16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA).

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA).

organism: Rattus norvegicus

source_name: DRG_sciatic nerve resection_4d

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

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion, Austin, TX) according to the manufacturer’s instructions. The quality of the purified RNA was assessed using a BioAnalyzer 2100 (Agilent Technology, Santa Clara, CA). The purified RNA was quantified by determining the absorbance at 260nm using a Nanodrop ND-1000 spectrophotometer (Infinigen Biotechnology Inc., City of Industry, CA).

treatment_protocol: Thirty adult, male Sprague-Dawley (SD) rats (180-220g, supplied by the Experimental Animal Center of Nantong University) were randomly divided into five groups of six rats each. Each animal was anaesthetized by an intraperitoneal injection of complex narcotics (85mg/kg trichloroac etaldehyde monohydrate, 42mg/kg magnesium sulfate, 17mg/kg sodium pentobarbital), and the sciatic nerve was exposed and lifted through an incision on the lateral aspect of the mid-thigh of the left hind limb. A 1cm long segment of sciatic nerve was then resected at the site just proximal to the division of tibial and common peroneal nerves, and the incision sites were then closed. To minimize discomfort and possible painful mechanical stimulation, the rats were housed in large cages with sawdust bedding after surgery. L4-6 DRG tissues and SN tissues (0.5cm) were collected at different time points after injury, respectively. All the experimental procedures involving animals were conducted in accordance with Institutional Animal Care guidelines and ethically approved by the Administration Committee of Experimental Animals, Jiangsu Province, China (Approval ID: SYXK(SU)2007-0021).

tag: strain

value: Sprague-Dawley

tag: tissue

value: dorsal root ganglia (DRG)


title: 1d_DRG_3

description: Gene expression at 1d following sciatic nerve resection in DRG

source_name: DRG_sciatic nerve resection_1d


title: 4d_DRG_1


title: 4d_DRG_2


title: 1d_DRG_1


title: 14d_SN_2

description: Gene expression at 14d following sciatic nerve resection in SN

source_name: SN_sciatic nerve resection_14d

value: proximal sciatic nerve (SN)


title: HaCaT_Cytokines_Rep3

city: Berlin

first: Geo

last: Semini

address: Oudenarderstrasse 16

department: Institute for Biochemie

country: Germany

institute: Charité - Universitätmedizin

description: Gene expression after 24h HaCaT cells stimulated with cytokines (each 2 ng/ml)

hyb_protocol: All samples were hybridized to Agilent whole human genome microarray kit 8x60K (G4851A) according to the manufacturer´s instructions (One-Color Microarray-Based Gene Expression Analysis).

scan_protocol: Arrays were scanned at 5 µm resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent).

data_processing: The signal values were extracted using the Agilent Feature Extracting Software version 10.7.3.1 and protocol GE_107_Sep09.

source_name: HaCaT cells, with cytokines, 24h, replicate 3

label_protocol: 200 ng of total RNA were used for production of fluorescent (Cyanine-3) cRNA as described in the Agilent analysis instruction manual for One-Color Microarray-Based Gene Expression Analysis (Agilent Technologies, Palo Alto, USA). Amplified cRNA was purificated using RNAeasy mini spin columns and subsequently quantified using NanoDrop ND-1000 UV-VIS Spectrophotometer.

growth_protocol: HaCaT cells were grown in RPMI medium supplemented with heat-inactivated fetal bovine serum (10 %), penicillin (100 U/ml), streptomycin (0.1 mg/ml) and L-glutamine (440 mg/l). One day prior to experimentation, cells were adapted to defined keratinocyte serum-free medium with growth supplement (including insulin, EGF, and FGF).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit in accordance to the manufacturer instructions (Qiagen Hilden, Germany). The integrity of RNA was verified by the presence of the 28S and 18S rRNA on agarose gels and an A260/280 ratio in the range of 1.9–2.1.

treatment_protocol: The assay was performed in defined keratinocytes serum-free medium without growth supplement. Cells were treated with IL-1α, IL-17, IL-22, TNF-α and oncostatin-M (2 ng/ml each) in the presence or absence of 5 µM Ino-C2-PAF or left untreated (control) 24 h.

tag: cell line

value: HaCaT

tag: treatment protocol


title: 1d_DRG_2


title: HaCaT_Cytokines_Rep1

source_name: HaCaT cells, with cytokines, 24h, replicate 1

value: stimulated with cytokines (each 2 ng/ml)


title: HaCaT_Cyt+Ino_Rep3

description: Gene expression after 24h HaCaT cells stimulated with cytokines (each 2 ng/ml) and 5 µM Ino-C2-PAF

source_name: HaCaT cells, with cytokines and Ino-C2-PAF, 24h, replicate 3


title: Human Limbus Donor 2

state: CA


title: 14d_SN_3


title: Human Limbus Donor 1


title: Human Limbus Donor 15 OD (Right Eye)


title: N6

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

description: Gene expression data from colonic biopsy sample

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

scan_protocol: GeneChips were scanned using the GeneChip 3000 Scanner

data_processing: The data were preprocessed by the function mas5 from the Bioconductor affy package

label: biotin

source_name: Human colonic biopsy sample

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 microg total RNA

extract_protocol: Qiagen RNeasy Mini extraction of total RNA was performed according to the manufacturer instructions

tag: disease state

value: Normal colonic mucosa


title: N8


title: N5


title: HaCaT_Cyt+Ino_Rep1

source_name: HaCaT cells, with cytokines and Ino-C2-PAF, 24h, replicate 1

value: stimulated with cytokines (each 2 ng/ml) and 5 µM Ino-C2-PAF


title: N7


title: HaCaT_Cytokines_Rep2

source_name: HaCaT cells, with cytokines, 24h, replicate 2


title: RNA-UPPP-25

city: Baltimore

middle: F

last: Ochs

state: MD

address: 550 North Broadway, Ste 1103

department: Oncology Biostatistics

institute: Johns Hopkins University

hyb_protocol: The labeled sense strand DNA was hybridized to Affymetrix GeneChip miRNA 1.0 for 17hr at 45 C with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cDNA.  The staining was further amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 3.4 (AGCC v3.4) software from Affymetrix.

data_processing: Analysis was performed in R with the oligo package, RMA was used for normalization; only H.sapiens probesets were retained for analysis.

source_name: normal

label_protocol: RNA from control and experimental samples were labeled using the Whole Transcript Sense Target Labeling protocol described by Affymetrix and reagent from Ambion and Affymetrix. Briefly, 100ng of total RNA was used to synthesize first strand cDNA using random oligonucleotides with T7 promoter as primer and the SuperScript Choice System (Invitrogen, Carlsbad, California).  Following the double stranded cDNA synthesis, the double strand cDNA was purified using magnetic beads, and cRNA was generated through in vitro transcription.  10 ug of cRNA was then used to generate sense strand cDNA using random primer, dNTP-dUTP mix, and Superscript II reverse transcriptase (Invitrogen, Carlsbad, California).  The resulting sense strand cDNA was then purified, fragmented using UDG and APE at 37C for 60 minutes, and terminal labeled with biotinylated nucleotide and terminal DNA transferase at 37C for 60 minutes.

growth_protocol: human HNSCC and UPPP surgical samples

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

treatment_protocol: human surgical specimens, flash frozen

tag: sample identifier

value: Ctrl 125

tag: sample type

value: normal


title: RNA-UPPP-23

value: Ctrl 123


title: N9


title: RNA-UPPP-22

value: Ctrl 122


title: RNA-UPPP-24

value: Ctrl 124


title: HaCaT_Cyt+Ino_Rep2

source_name: HaCaT cells, with cytokines and Ino-C2-PAF, 24h, replicate 2


title: RNA-UPPP-21

value: Ctrl 121


title: HaCaT_Control_Rep2

description: Gene expression after 24h in unstimulated HaCaT cells

source_name: HaCaT cells, unstimulated, 24h, replicate 2

value: control


title: N38


title: 14d_SN_1


title: RNA-UPPP-14

value: Ctrl 114


title: RNA-UPPP-15

value: Ctrl 115


title: RNA-UPPP-16

value: Ctrl 116


title: RNA-UPPP-18

value: Ctrl 118


title: RNA-UPPP-17

value: Ctrl 117


title: RNA-UPPP-19

value: Ctrl 119


title: RNA-UPPP-20

value: Ctrl 120


title: HaCaT_Control_Rep1

source_name: HaCaT cells, unstimulated, 24h, replicate 1

value: HaCaT


title: N4

value: Normal colonic mucosa


title: amp1

first: Jiexin

last: Zhang

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

description: fresh-frozen resected, untreated periampullary adenocarcinomas pancreaticoduodenectomies were identified from The University of Texas MD Anderson Cancer Center (UTMDACC) frozen tumor bank from 2002 to 2009

hyb_protocol: Samples were amplified, labeled, and 10μg of cDNA was hybridized to the HG-U133 Plus 2.0 Affymetrix GeneChip array according the manufacturer’s protocol (Affymetrix, Santa Clara, CA).

scan_protocol: GeneArray Scanne using Microarray Suit software.

data_processing: RMA (Robust Multichip Average) algorithm is used for quantification of the data.

extract_protocol: Total RNA was extracted using the TRIzol method (Invitrogen, Carlsbad, CA). RNA was purified using the RNeasy mini-kit (Qiagen, Alameda, CA) and the quality of RNA was assessed on an Agilent 2100 Bioanalyzer and quantified using Nano Drop ND-1000 (Nano Drop, Wilmington, DE).

treatment_protocol: untreated

value: ampullary adenocarcinomas


title: 14d_DRG_3

description: Gene expression at 14d following sciatic nerve resection in DRG

source_name: DRG_sciatic nerve resection_14d

value: Sprague-Dawley

value: dorsal root ganglia (DRG)


title: N36


title: N37


title: N34


title: RNA-UPPP-12

value: Ctrl 112

value: normal


title: RNA-UPPP-11

value: Ctrl 111


title: RNA-UPPP-13

value: Ctrl 113


title: RNA-UPPP-10

value: Ctrl 110


title: N32


title: N35


title: N33


title: 0d_SN_3

description: Gene expression at 0d following sciatic nerve resection in SN

source_name: SN_sciatic nerve resection_0d

value: proximal sciatic nerve (SN)


title: RNA-UPPP-09

value: Ctrl 109


title: 14d_DRG_2


title: 14d_DRG_1


title: RNA-UPPP-08

value: Ctrl 108


title: RNA-UPPP-07

value: Ctrl 107


title: 0d_SN_2


title: 0d_DRG_3

description: Gene expression at 0d following sciatic nerve resection in DRG

source_name: DRG_sciatic nerve resection_0d


title: 0d_DRG_2


title: RNA-UPPP-04

value: Ctrl 104


title: RNA-UPPP-05

value: Ctrl 105


title: RNA-UPPP-03

value: Ctrl 103


title: RNA-UPPP-06

value: Ctrl 106


title: RNA-UPPP-02

value: Ctrl 102


title: 0d_SN_1


title: N31

value: Normal colonic mucosa


title: N30


title: RNA-UPPP-01

value: Ctrl 101

value: normal (UPPP)


title: RNA-HNSCC-50

source_name: tumor

value: Pt 50

value: tumor

value: tumor (HNSCC)


title: N29


title: 0d_DRG_1

value: Sprague-Dawley

value: dorsal root ganglia (DRG)


title: RNA-HNSCC-48

value: Pt 48


title: RNA-HNSCC-45

value: Pt 45


title: RNA-HNSCC-46

value: Pt 46


title: BDE-3

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

description: Data were resolved from microarray images using Agilent Feature Extraction software (Agilent Technologies, Palo Alto, CA).

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 μm resolution.

data_processing: Microarray image processing and data pre-processing were performed Agilent's Feature Extraction software v 9.5 following the manufacturer’s protocol and recommendations.

organism: Danio rerio

source_name: Zebrafish embryo exposed to BDE-209

label_protocol: cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling kit; Agilent, Palo Alto, CA).

growth_protocol: At the time of sample collection, fish were humanely killed in a buffered (200 mg Na2HCO3/L) solution tricaine methanesulfonate (MS-222; Finquel; Argent, Redmond WA, USA). Tissue was transferred to a labeled microcentrifuge tube and snap-frozen in liquid nitrogen, then stored at -80o C until extracted.

extract_protocol: Total RNA was isolated using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and quantity was determined using a Nanodrop® ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). Total RNA was stored at -80oC until analyzed.

treatment_protocol: Zebrafish embryos from the BDE-209 treatment

tag: treatment

tag: concentration

value: 12,500 ng/g sediment

value: whole embryo


title: BDE-5


title: RNA-HNSCC-49

value: Pt 49


title: BDE-2


title: N27


title: N28


title: N26


title: RNA-HNSCC-42

value: Pt 42


title: N3


title: CONTROL-4

source_name: Zebrafish embryo control

treatment_protocol: Zebrafish embryos from the control treatment

value: control


title: RNA-HNSCC-39

value: Pt 39


title: RNA-HNSCC-40

value: Pt 40


title: RNA-HNSCC-37

value: Pt 37


title: CONTROL-5


title: N24

value: Normal colonic mucosa


title: CONTROL-3


title: N25


title: RNA-HNSCC-44

value: Pt 44


title: CONTROL-2


title: RNA-HNSCC-36

value: Pt 36

value: tumor


title: RNA-HNSCC-32

value: Pt 32

value: tumor (HNSCC)


title: RNA-HNSCC-43

value: Pt 43


title: RNA-HNSCC-29

value: Pt 29


title: RNA-HNSCC-31

value: Pt 31


title: RNA-HNSCC-30

value: Pt 30


title: RNA-HNSCC-34

value: Pt 34


title: BDE-1

value: 12,500 ng/g sediment

value: whole embryo


title: RNA-HNSCC-19

value: Pt 19


title: RNA-HNSCC-17

value: Pt 17


title: RNA-HNSCC-20

value: Pt 20


title: RNA-HNSCC-18

value: Pt 18


title: RNA-HNSCC-21

value: Pt 21


title: RNA-HNSCC-23

value: Pt 23


title: RNA-HNSCC-22

value: Pt 22


title: RNA-HNSCC-26

value: Pt 26

value: tumor


title: RNA-HNSCC-24

value: Pt 24

value: tumor (HNSCC)


title: RNA-HNSCC-16

value: Pt 16


title: RNA-HNSCC-28

value: Pt 28


title: RNA-HNSCC-25

value: Pt 25


title: N20

value: Normal colonic mucosa


title: N19


title: N21


title: N2


title: N16


title: N22


title: N23


title: N15


title: RNA-HNSCC-15

value: Pt 15


title: N17


title: N18


title: N14


title: het-R het-V  T4h_26°C_replicate B

city: Orsay

first: Frederique

last: Bidard

address: Bâtiment 400

department: SIGNAL TRANSDUCTION, REPRODUCTION & DEGENERATIVE PROCESSES

country: France

institute: Institut de Génétique et Microbiologie UMR 8621

description: Biological replicate 4 of 4.  Zone 3 of WT

hyb_protocol: Hybridization experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). 825 ng of each of the Cy3- and Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven at 10 rpm for a 4x44K array format, using an Agilent in situ hybridization kit. The slides were washed in Agilent’s Gene Expression Wash Buffers following manufacturer’s instructions, then, any traces of solution were removed by centrifugation at 800 rpm for 1 min.

scan_protocol: Microarrays were scanned using the Agilent DNA microarray Scanner model G2567AA at 5 microns resolution using the extended dynamic range (XDR) feature.

data_processing: Spot and background intensities were extracted with the Feature Extraction (FE, v9.5.3) software (Agilent) using the GE2-v4_95_Feb07 default protocol. Preliminary array quality was assessed through the use of Agilent control features as well as spike-in controls (Agilent 2-Color Spike-in Kit for RNA experiment). Subsequent flagging was done according to the GenePix Pro software (Molecular Devices Syunnyvale, CA, USA) nomenclature, including four levels of flags (good (100), bad (-100), not found (-50), moderate (0)). FE software normalized data (Local background was subtracted and LOWESS normalization) from arrays issued of GPL10116 platform were processed with the MAnGO. Moderate t-test with adjustment of p-values was computed to measure the significance with each expression difference.

organism: Podospora anserina

label_protocol: Labelling experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). One microgram aliquots of total RNA were amplified and Cy-labelled with the Agilent’s Low RNA input fluorescent linear amplification (LRILAK) PLUS kit (Agilent) along with Agilent's Two-Color RNA Spike-in Kit. The labelling efficiency and the product integrity were checked by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent)

growth_protocol: P. anserina strains used for the common reference are the wild type S strains of either mat+ or mat- mating type. P. anserina strains used for the experiment are the wild type s mat+ and the het-R het-V self-incompatible mat+ strains. The het-R het-V self-incompatible strain was obtained from the progeny of a cross between the het-r het-V and the het-R het-V1 parental strains. The het-R het-V strain grows normally at 32°C and undergoes cell death at 26°C. For RNA extraction, wild type and self-incompatible strains were grown on solid M2 medium overlaid with a cellophane sheet at 32°C for 44h. The growth medium was renewed 4h before the end of the culture at 32°C (transfer of the cellophane sheet on fresh prewarmed (32°C) M2 medium). After growth at 32°C the strains were either collected (time T0) or transferred to 26°C on prewarmed M2 medium for 30min (T30min), 1hour (T1h), 2 hours (T2h), 3 hours (T3h) and 4 hours (T4h). M2 is a minimal synthetic medium as described (Esser K.,1974; pp. 531-51 in Handbook of Genetics).

extract_protocol: Strains were grown on cellophane sheet (cat#1650193, BioRad, Marne la Coquette, France) or cheesecloth (Sefar Nitex 03-48/31, Dominique Dutscher, Brumath, France) placed on Petri-dishes. In order to collect sufficient amounts of biological materials (20 to 100 mg), 1 to 5 Petri-dishes were simultaneously inoculated. Biological material was scraped from cellophane sheets or cheesecloth and flash frozen with buffer RLT (Qiagen, Courtaboeuf, France) in liquid nitrogen. The biological material was grinded with a Mikro-Dismembrator (Sartorius, Aubagne, France) in nitrogen freezed vessels. After removing cell debris by centrifugation, nucleic acids were passed through a Qiashreddrer (Qiagen) for sharing DNA and total RNA was purified on RNeasy Plant Mini Kit columns (Qiagen), with an additional DNase treatment. The quality and quantity of the total RNA was determined by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent).

value: het-R het-V self-incompatible s

tag: time

tag: growth condition

value: harvested after 44h at 32°C and transfer to 26°C for 4h, M2 media covered with a sheet of cellophane

tag: mating type

value: mat+

source_name: Common reference (a pool of four biosources: M48h, M96h, C48h and C96h)

tag: biosource 1

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 1

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 2

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name biosource 3

tag: biosource 4

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.

tag: name biosource 4


title: het-R het-V  T4h_26°C_replicate D

tag: strain


title: het-R het-V  T4h_26°C_replicate F


title: het-R het-V  T3h_26°C_replicate D

description: Biological replicate 3 of 4. Zone 3 of WT

value: harvested after 44h at 32°C and transfer to 26°C for 3h, M2 media covered with a sheet of cellophane


title: het-R het-V  T3h_26°C_replicate B


title: het-R het-V  T4h_26°C_replicate E


title: RNA-HNSCC-13

value: Pt 13

tag: disease state


title: RNA-HNSCC-14

tag: sample identifier

value: Pt 14

value: tumor


title: RNA-HNSCC-09

value: Pt 9

tag: sample type

value: tumor (HNSCC)


title: RNA-HNSCC-11

value: Pt 11


title: RNA-HNSCC-10

value: Pt 10


title: RNA-HNSCC-08

value: Pt 8


title: RNA-HNSCC-07

value: Pt 7


title: RNA-HNSCC-06

value: Pt 6


title: RNA-HNSCC-05

value: Pt 5


title: RNA-HNSCC-04

value: Pt 4


title: RNA-HNSCC-12

value: Pt 12


title: RNA-HNSCC-01

value: Pt 1


title: RNA-HNSCC-03

value: Pt 3


title: RNA-HNSCC-02

value: Pt 2


title: het-R het-V  T3h_26°C_replicate C

value: het-R het-V self-incompatible s

value: harvested after 44h at 32°C and transfer to 26°C for 3h, M2 media covered with a sheet of cellophane

value: mat+

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: het-R het-V  T2h_26°C_replicate C

description: Biological replicate 2 of 4. Zone 3 of WT

value: harvested after 44h at 32°C and transfer to 26°C for 2h, M2 media covered with a sheet of cellophane


title: het-R het-V  T2h_26°C_replicate B


title: N12

value: Normal colonic mucosa


title: het-R het-V  T3h_26°C_replicate E


title: N10


title: het-R het-V  T2h_26°C_replicate D


title: het-R het-V  T2h_26°C_replicate E


title: N11


title: CRC_CD9

tag: Stage

value: Dukes C/D


title: het-R het-V  T1h_26°C_replicate A

description: Biological replicate 1 of 4.  Zone 3 of WT

value: harvested after 44h at 32°C and transfer to 26°C for 1h, M2 media covered with a sheet of cellophane


title: N1


title: het-R het-V  T1h_26°C_replicate B


title: CRC_CD8


title: N13


title: CRC_CD6


title: het-R het-V  T1h_26°C_replicate D


title: CRC_CD4


title: CRC_CD7


title: het-R het-V  T1h_26°C_replicate E


title: CRC_CD5


title: het-R het-V  T30min_26°C_replicate A

description: Biological replicate 4 of 4.  Zone 2 of WT

value: harvested after 44h at 32°C and transfer to 26°C for 30min, M2 media covered with a sheet of cellophane


title: het-R het-V  T30min_26°C_replicate D


title: het-R het-V  T30min_26°C_replicate B


title: 221

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

department: Oncology

country: Canada

institute: University of Alberta

description: Gene expression in breast cancer, validation set.

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 manufacturer's 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 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 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-v5_95_Feb07 and Grid: 014850_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  The data was them imported into GeneSpring 7.3.1 and default normalization procedures were used. The 176 samples used in the training set were normalized as a group and the 23 validation samples were normalized independently.

source_name: primary breast cancer, ER negative

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 RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: A polytron was used to disrupt tissue in the pressence of Trizol (SigmaAldrich). The sample was then phenol/chloroform extracted, and the aqueous layer was adjusted to 30% ethanol and applied to an RNeasy column (Qiagen) according to the manufacturer's instructions.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: primary breast tumor

tag: er status

value: negative

tag: set

value: validation


title: 219

source_name: primary breast cancer, ER positive

value: positive


title: 213


title: 217


title: 215


title: 218


title: 211


title: 222


title: 214


title: 209


title: CRC_CD3


title: 220


title: 208


title: CRC_CD13


title: CRC_CD2


title: 212


title: 216


title: 210


title: 206


title: CRC_CD11


title: 207


title: het-R het-V  T0h_32°C_replicate E

description: Biological replicate 3 of 4.  Zone 2 of WT

tag: time

tag: growth condition

value: harvested after 44h at 32°C, on M2 media covered with a sheet of cellophane

tag: mating type


title: het-R het-V  T30min_26°C_replicate E

value: het-R het-V self-incompatible s

tag: biosource 1

tag: name biosource 1

tag: biosource 2


title: 202


title: 205


title: 201


title: 204


title: 200


title: 174.b

description: Gene expression in breast cancer, training set.

value: training


title: 175.b


title: 176.b


title: CRC_CD1


title: CRC_AB8

value: Colorectal adenocarcinoma

value: Dukes A/B


title: CRC_CD12


title: Wild Type T4h_26°C_replicate B

description: Biological replicate 2 of 4.  Zone 2 of WT

value: Wild type s

value: harvested after 44h at 32°C and transfer to 26°C for 4 hours, M2 media covered with a sheet of cellophane

value: mat+

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 2

tag: biosource 3

tag: name biosource 3


title: het-R het-V  T0h_32°C_replicate C

tag: strain

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: biosource 4

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.

tag: name biosource 4


title: 172.b


title: 170.b


title: Wild Type T3h_26°C_replicate E

description: Biological replicate 1 of 4.  Zone 2 of WT

value: harvested after 44h at 32°C and transfer to 26°C for 3 hours, M2 media covered with a sheet of cellophane


title: het-R het-V  T0h_32°C_replicate D


title: 171.b

value: primary breast tumor


title: CRC_CD10

description: Gene expression data from colonic biopsy sample

value: Dukes C/D


title: Wild Type T4h_26°C_replicate E


title: CRC_AB6

tag: disease state


title: Wild Type T4h_26°C_replicate C


title: CRC_AB9

tag: Stage


title: Wild Type T4h_26°C_replicate D


title: het-R het-V  T0h_32°C_replicate B


title: 173.b

tag: tissue


title: CRC_AB7


title: CRC_AB4


title: 169.b

tag: er status


title: Wild Type T3h_26°C_replicate C


title: 163.b

value: negative

tag: set


title: 168.b

value: positive


title: CRC_AB2


title: 203

value: validation


title: Wild Type T3h_26°C_replicate B

tag: time


title: CRC_AB5


title: Wild Type T2h_26°C_replicate F

description: Biological replicate 4 of 4. Zone 1 of WT

tag: growth condition

value: harvested after 44h at 32°C and transfer to 26°C for 2 hours, M2 media covered with a sheet of cellophane


title: 162.b

value: training


title: Wild Type T3h_26°C_replicate D

tag: mating type


title: 165.b


title: 164.b


title: 157.b


title: CRC_AB13

value: Colorectal adenocarcinoma


title: 160.b


title: CRC_AB3

value: Dukes A/B


title: 158.b


title: CRC_AB12


title: CRC_AB14


title: 156.b


title: 161.b


title: 166.b


title: 167.b


title: Wild Type T2h_26°C_replicate D

value: Wild type s

tag: biosource 1


title: Wild Type T2h_26°C_replicate B

tag: name biosource 1


title: 155.b


title: CRC_AB11


title: Wild Type T2h_26°C_replicate C

tag: biosource 2


title: 159.b


title: CRC_AB10


title: Wild Type T1h_26°C_replicate E

description: Biological replicate 3 of 4. Zone 1 of WT

value: harvested after 44h at 32°C and transfer to 26°C for 1 hour, M2 media covered with a sheet of cellophane

tag: name biosource 2


title: Wild Type T1h_26°C_replicate D

value: mat+

tag: biosource 3


title: 151.b


title: Wild Type T1h_26°C_replicate C

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: name biosource 3


title: CRC_AB1


title: 150.b


title: 149.b


title: AL9

value: Adenoma

value: low-grade dysplasia


title: Wild Type T1h_26°C_replicate B

tag: strain

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: 154.b

value: primary breast tumor


title: AL8


title: 146.b

value: negative


title: Wild Type T30min_26°C_replicate C

description: Biological replicate 2 of 4. Zone 1 of WT

value: harvested after 44h at 32°C and transfer to 26°C for 30min, M2 media covered with a sheet of cellophane

tag: biosource 4


title: 153.b

value: positive


title: 148.b


title: AL6


title: 144.b


title: Wild Type T30min_26°C_replicate E

tag: name biosource 4


title: 147.b


title: 152.b


title: 143.b


title: 145.b


title: AL7

tag: disease state


title: 140.b


title: 142.b


title: AL4

tag: Stage


title: 141.b

tag: tissue


title: Wild Type T30min_26°C_replicate D


title: Wild Type T30min_26°C_replicate B


title: 137.b

tag: er status


title: AL2


title: 139.b

tag: set


title: AL15


title: 136.b


title: Wild Type T0h_32°C_replicate F

description: Biological replicate 1 of 4. Zone 1 of WT

tag: time

value: harvested after 44h at 32°C, on M2 media covered with a sheet of cellophane


title: AL5


title: Wild Type T0h_32°C_replicate C

tag: growth condition


title: 132.b

value: training


title: Wild Type T0h_32°C_replicate B

tag: mating type


title: AL3


title: 138.b


title: Wild Type T0h_32°C_replicate D

tag: biosource 1


title: 133.b


title: AL16


title: 130.b


title: AL14


title: AL13


title: AICAR_24h_rep3

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

description: Gene expression after 24h in AICAR treated J1 mESCs

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=3μm, 20bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Mus musculus

source_name: J1 mESC, AICAR, 24h, replicate 3

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), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: The J1 mouse embryonic stem cell line purchased from ATCC (Manassas, VA, USA) was gelatin adapted and grown on 0.2% (w/v) gelatin coated tissue culture plates in Knockout DMEM supplemented with 15% (v/v) Knockout Serum Replacement, 1× non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM glutamine, 50 units/ml Penicillin, 50 μg/ml Streptomycin, 1000 U/ml LIF (ESGRO, Millipore, USA).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life  technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: J1 mESCs maintained in medium containing 1000 U/mL LIF and treated by 3 μΜ CHIR99021 or 1mM AICAR for 24h.

value: Inner Cell Mass

tag: cell type

value: Embryonic Stem Cell

tag: treatment

value: 24h in 1mM AICAR


title: 135.b


title: 128.b


title: AICAR_24h_rep1

source_name: J1 mESC, AICAR, 24h, replicate 1


title: 127.b


title: 131.b


title: 125.b


title: 129.b


title: AICAR_24h_rep2

source_name: J1 mESC, AICAR, 24h, replicate 2


title: AL11

source_name: Human colonic biopsy sample


title: 123.b


title: 134.b


title: AL12


title: 126.b


title: AL1


title: 119.b


title: CHIR_24h_rep3

description: Gene expression after 24h in CHIR treated J1 mESCs

source_name: J1 mESC, CHIR, 24h, replicate 3

value: 24h in 3 uM CHIR99021


title: 122.b


title: 121.b


title: CHIR_24h_rep2

source_name: J1 mESC, CHIR, 24h, replicate 2


title: DMSO_24h_rep3

description: Gene expression after 24h in DMSO(control) treated J1 mESCs

source_name: J1 mESC, DMSO, 24h, replicate 3

value: 24h in DMSO


title: AH9

value: high-grade dysplasia


title: AL10

value: Adenoma


title: 117.b


title: 116.b


title: DMSO_24h_rep2

source_name: J1 mESC, DMSO, 24h, replicate 2


title: AH6


title: 118.b


title: AH7


title: CHIR_24h_rep1

source_name: J1 mESC, CHIR, 24h, replicate 1


title: 124.b


title: AH8


title: 114.b


title: 115.b


title: 112.b


title: 120.b


title: 108.b


title: 111.b


title: DMSO_24h_rep1

source_name: J1 mESC, DMSO, 24h, replicate 1


title: AH4


title: Metastatic osteosarcomic MSCs (S1d/s) injected, mouse array

city: Leiden

first: Alex

middle: B

last: Mohseny

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: LUMC

description: Cells isolated from lung metastases of osteosarcomas produced in mouse after injection of sample 5, injected in zebrafish

hyb_protocol: Each zebrafish 4x44k array (Design ID: 021626) was hybridized with 825 ng Cy5-labelled pooled material which was mixed by samples of all injected zebrafish (common reference channel) and 825 ng Cy3-labelled material (test channel). Each mouse 4x44k array (Design ID: 026687) was hybridized with 825 ng Cy5-labelled pooled material which was mixed by samples of different mouse MSCs (common reference channel) and 825 ng Cy3-labelled material for cultured cells or 5x825 ng Cy3-labelled material for zebrafish injected with mouse cells (test channel) because of the low amounts of mouse cells in the injected zebrafish. Hybridization and washing were performed according to the manufacturer’s instruction (Two-Colour Microarray-Based Gene Expression Protocol Manual version 5.5, Agilent Technologies).

scan_protocol: Slides were scanned with an Agilent G2505C scanner at 2 µm resolution and 20 bit scan-depth. Data were extracted with Feature Extraction version 10.7.3.1.

data_processing: Data analysis was performed using Agilent GeneSpring 11.0 software (Agilent Technologies) for fold change analysis.

organism:
Danio rerio
Mus musculus

source_name: S1d/s in zebrafish

label_protocol: From each sample 500 ng of total RNA was amplified with the Quick Amp Labeling Kit (Agilent Technologies) after adding spike-ins (Two-Colour RNAS Spike-In Kit, Agilent Technologies). After column purification the yield and quality were assessed with Nanodrop ND-1000 (Isogen) and a 2100 Bioanalyzer (Agilent Technologies).

growth_protocol:
Zebrafish embryos were kept for a maximum of 5 days in egg water at 28.5 degrees celcius.
Cells were cultured in Alpha-MEM supplemented with 10% FBS, 2% Glutamax and 2% Penicillin/Streptomycin.

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen) following manufacturer's instructions

tag: cell line

tag: passage

value: Cells isolated from metastasis of osteosarcoma produced by TmMSC cells in mouse

source_name: Total RNA from pooled in vitro cultured mouse MSCs

value: Mixed

value: Pooled cell lines


title: Cross-hybridization control uninjected zebrafish, mouse array

description: Uninjected zebrafish on mouse array to check cross-hybridization

source_name: Uninjected zebrafish

value: Not Applicable


title: 110.b

value: primary breast tumor


title: 106.b


title: 104.b


title: 113.b


title: AH5


title: 109.b


title: 105.b


title: BC-BMMSC high-passage injected, mouse array

description: Biological replicate of sample GSM802536

source_name: BC-BMMSC high in zebrafish

value: BC-BMMSC

value: Mesenchymal stem cells

value: BALB/C


title: 107.b

value: negative


title: AH3


title: Tumorigenic mous MSCs (TmMSC) injected, mouse array

description: MSCs that produce osteosarcoma after injection in mouse, injected in zebrafish

source_name: TmMSC in zebrafish

value: TmMSC

value: Osteosarcoma producing mesenchymal stem cells in mouse


title: AH2


title: 102.b

value: positive

value: training


title: 103.b


title: B6-BMMSC high-passage injected, mouse array

description: Transformed MSCs injected in zebrafish

source_name: B6-BMMSC high in zebrafish


title: AH12


title: 101.b

source_name: primary breast cancer, ER positive


title: 99.b


title: BC-BMMSC low-passage injected, mouse array

description: Biological replicate of sample GSM802535

source_name: BC-BMMSC low in zebrafish


title: 100.b


title: 97.b


title: 96.b

source_name: primary breast cancer, ER negative


title: B6-BMMSC low-passage injected, mouse array

description: Normal MSCs, injected in zebrafish

source_name: B6-BMMSC low in zebrafish


title: AH11

source_name: Human colonic biopsy sample


title: Metastatic osteosarcomic MSCs (S1d/s) cultured, mouse array

description: Cells isolated from lung metastases of osteosarcomas produced in mouse after injection of sample 5, in vitro

source_name: S1d/s cultured


title: AH1


title: AH13


title: 95.b

description: Gene expression in breast cancer, training set.


title: BC-BMMSC high-passage cultured, mouse array

description: Biological replicate of sample GSM802530

source_name: BC-BMMSC high cultured


title: 98.b


title: 93.b


title: 92.b


title: BC-BMMSC low-passage cultured, mouse array

description: Biological replicate of sample GSM802529

source_name: BC-BMMSC low cultured


title: 94.b


title: Tumorigenic mouse MSCs (TmMSC) cultured, mouse array

description: MSCs that produce osteosarcoma after injection in mouse, in vitro

source_name: TmMSC cultured


title: B6-BMMSC high-passage cultured, mouse array

description: Transformed MSCs in vitro

source_name: B6-BMMSC high cultured


title: 91.b


title: 89.b


title: B6-BMMSC low-passage cultured, mouse array

description: Normal MSCs, in vitro

source_name: B6-BMMSC low cultured


title: gyerek28

description: Gene expression data from colonic biopsy sample

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 3 microg total RNA

tag: gender

value: Female

tag: age

value: Normal colonic mucosa


title: 88.b


title: 90.b


title: gyerek18

value: Male


title: AH10

value: Adenoma

value: high-grade dysplasia


title: 86.b


title: 87.b


title: Cross-hybridization control mouse MSCs, zebrafish array

description: Sample 4 hybridized to zebrafish arrays to check for cross-hybridization

tag: strain

source_name: Total RNA from pooled zebrafish embryos injected with mouse MSCs

value: Mixed

value: Pooled embryos and cell lines


title: gyerek20


title: 82.b


title: gyerek12


title: gyerek13


title: 85.b


title: Tumorigenic mous MSCs (TmMSC) injected, zebrafish array

description: MSCs that produce osteosarcoma after injection in mouse, injected in zebrafish, on zebrafish arrays


title: 81.b


title: Metastatic osteosarcomic MSCs (S1d/s) injected, zebrafish array

description: Cells isolated from lung metastases of osteosarcomas produced in mouse after injection of sample 5, injected in zebrafish, on zebrafish arrays

source_name: S1d/s in zebrafish

value: Cells isolated from metastasis of osteosarcoma produced by TmMSC cells in mouse


title: gyerek11


title: 78.b

value: primary breast tumor


title: Negative control PVP injected zebrafish, zebrafish array

description: Embryos injected only by PVP as a control for the host response

source_name: PVP injected zebrafish

value: Not Applicable


title: B6-BMMSC high-passage injected, zebrafish array

description: Transformed MSCs injected in zebrafishon, on zebrafish arrays

value: Mesenchymal stem cells


title: BC-BMMSC low-passage injected, zebrafish array

description: Biological replicate of sample GSM802542

value: BC-BMMSC

value: BALB/C


title: 79.b


title: S_N

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: Normal

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 133 plus 2.0  arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station FS 400.

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

data_processing: The data were analyzed using RMA as implemented in Partek Genomics Suite 6.6, background adjustment, quantile normalization and finally summarization.

source_name: Normal

label_protocol: 200ng Total RNA was labeled using Affymetrix IVT Express Kit according to the manufacturer's instructions.

growth_protocol: Biopsy specimens from patient volunteers

extract_protocol: Tissues were stabilized in RNAlater-ice and RNA extracted using Qiagen RNEASY fibrous tissue according to the manufacturer's recommendations.

treatment_protocol: Tissues were snap frozen immediately in a cryovial, placed in -80C until laboratory analysis.

tag: condition

value: Normal

tag: patient

value: S


title: 76.b

value: positive


title: 84.b

value: negative

value: training


title: B6-BMMSC low-passage injected, zebrafish array

description: Normal MSCs, injected in zebrafish, on zebrafish arrays


title: 80.b


title: 77.b


title: BC-BMMSC high-passage injected, zebrafish array

description: Biological replicate of sample GSM802543

source_name: BC-BMMSC high in zebrafish


title: 83.b


title: 72.b


title: S_U

description: Ulcer

source_name: Ulcer

value: Ulcer


title: 69.b


title: 74.b


title: 73.b


title: 67.b


title: R_U

description: Ulcer

value: R


title: 70.b

source_name: primary breast cancer, ER positive


title: 75.b


title: Q_U

description: Ulcer

value: Q


title: shPKCz2

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: Gene expression from SW480 cell infected with lentivirus expressing PKCz RNA interference

hyb_protocol: Used Affymetrix GeneChip hybridization and stain kit following the manufacturer’s instructions

scan_protocol: The GeneChips are scanned with Affymetrix GeneChip Scanner 3000 7G Plus using Affymetrix GeneChip Command Console 3.2.3.1515 software and Affymetrix preset settings.

data_processing: Microarray data was preprocessed using RMA implemented in R with BrainArray custom CDF (Entrez Gene, version 13)

source_name: SW480 cell shPKCz

label_protocol: Ovation Pico WTA System (NuGEN, San Carlos, CA) following the manufacturer’s instructions

growth_protocol: SW480 cells were cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% glutamine and 1% penicillin-streptomycin, in an atmosphere of 95% air and 5% CO2.

extract_protocol: Total RNA was extracted using Tri-Zol according to the manufacturer's instructions.

treatment_protocol: Lentivirus for the different target genes were made as follow: shRNA encoding plasmids were co-transfected with psPAX2 and pMD2.G packaging plasmids into actively growing HEK-293T cells by using FuGENE 6 transfection reagent.

value: shPKCz


title: shPKCz3


title: Q_N

description: Normal


title: R_N

description: Normal


title: 71.b


title: 65.b


title: 66.b


title: 68.b

source_name: primary breast cancer, ER negative


title: 64.b


title: shPKCz1


title: shNT3

description: Gene expression from SW480 cell infected with a control lentivirus

source_name: SW480 cell shNT

value: shNT


title: P_U

description: Ulcer

value: P


title: shNT2


title: 63.b


title: 60.b


title: P_N

description: Normal


title: O_U

description: Ulcer

value: O


title: 61.b

value: primary breast tumor


title: 59.b


title: shNT1


title: UCD 543  6h 3

city: Davis

first: Douglas

middle: D

last: Risser

state: California

address: One Shields Ave

department: Microbiology

institute: UC Davis

description: SAMPLE 39

hyb_protocol: Two micrograms of labled cDNA were prepared for hybridization using the Nimblegen hybridization kit and sample tracking controls and hybridized to a Nimblegen 12x135k slide fitted with an HX12 mixer at 42C on a Nimblegen Hybridization System 4 hybridizer for 16-20h.

scan_protocol: Following hybridization slides were washed with Nimblegen wash buffer and scanned using a GenePix 4000B scanner using GenePix Pro-6.0 software (Molecular Devices)

data_processing: Scanned images (.tif) were imported into NimbleScan software (NimbleGen) where the image containing all 12 arrays on each slide was separated into 12 individual image files.  An automatic alignment was performed for each individual array and X, Y, and Signal files (.xys) were generated.  Normalization of .xys files was performed using the R package oligo (Carvalho et al, 2007).

organism: Nostoc punctiforme PCC 73102

label_protocol: Ten micrograms  of total RNA were used for cDNA synthesis using SuperScript Double Stranded cDNA Synthesis Kit (Invitrogen). 0.5 ug of cDNA was labled with Cy3 dye using the Nimblegen One-color DNA labeling kit.

growth_protocol: Nostoc punctiforme strains were cultured in Allan and Arnon medium diluted four fould (AA/4), as previously described (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256) with the exception that cultures were supplemented with 30mM fructose

extract_protocol: RNA extractions were performed as previously described with a bead beater and phenol (Campbell et al. 2007. Global gene expression patterns of Nostoc punctiforme in steady-state dinitrogen-grown heterocyst containing cultures and at single time points during the differentiation of akinetes and hormogonia. J. Bacteriol 189:5247-5256)

treatment_protocol: For hormogonium induction culutres supplemented with 2.5 mM NH4Cl at a chlorophyl a concentration of 2-3 ug/ml were harvested at 1000xg for 5 min, washed 3x with AA/4 and resuspended in AA/4 supplemented with 2.5 mM NH4Cl and containing the Anthoceros punctatus derived hormogonium inducing factor (HIF) (see materials and methods of above indicated manuscript for more detailed protocol)

tag: genotype/variation

value: hmpD-deletion


title: UCD 543  12h 3

description: SAMPLE 40


title: O_N

description: Normal


title: 56.b

tag: tissue


title: UCD 543  24h 3

description: SAMPLE 42


title: N_U

description: Ulcer

value: N


title: 58.b

tag: er status


title: UCD 543  18h 3

description: SAMPLE 41


title: 51.b

tag: set


title: M_U

description: Ulcer

value: M


title: 57.b


title: 54.b


title: N_N

description: Normal


title: 55.b


title: M_N

description: Normal


title: UCD 543  24h 2

description: SAMPLE 38

tag: time


title: 50.b


title: 62.b


title: 53.b


title: L_CTL

description: Control

source_name: Control

value: Control

value: L


title: K_CTL

description: Control

value: K


title: 52.b

value: positive


title: 49.b


title: UCD 543  18h 2

description: SAMPLE 37


title: J_CTL

description: Control

value: J


title: 46.b

value: negative

value: training


title: UCD 543  24h 1

description: SAMPLE 34


title: 45.b


title: UCD 543  12h 2

description: SAMPLE 36


title: UCD 543  6h 2

description: SAMPLE 35


title: 43.b


title: 47.b


title: UCD 543  18h 1

description: SAMPLE 33


title: G_U

description: Ulcer

value: Ulcer

value: G


title: H_CTL

description: Control

value: H


title: 48.b


title: 41.b


title: 40.b


title: 42.b


title: 44.b


title: I_CTL

description: Control

value: I


title: 39.b


title: G_N

description: Normal

value: Normal


title: UCD 543  12h 1

description: SAMPLE 32


title: UCD 543  6h 1

description: SAMPLE 31


title: F_N

description: Normal

value: F


title: F_U

description: Ulcer


title: 38.b

value: primary breast tumor


title: 37.b


title: 34.b


title: 35.b


title: UCD 543  3h 1

description: SAMPLE 28

value: hmpD-deletion


title: UCD 543  3h 3

description: SAMPLE 30


title: 36.b


title: 33.b


title: E_U

description: Ulcer

value: E


title: UCD 543  1h 3

description: SAMPLE 27


title: UCD 543  1h 2

description: SAMPLE 26


title: 31.b


title: 28.b


title: 32.b


title: UCD 543  0h 3

description: SAMPLE 24


title: UCD 543  1h 1

description: SAMPLE 25


title: D_U

description: Ulcer

value: D


title: 22.b


title: D_N

description: Normal


title: 27.b


title: 26.b


title: 24.b


title: 23.b


title: E_N

description: Normal


title: 21.b


title: 29.b


title: UCD 543  0h 2

description: SAMPLE 23


title: 30.b


title: 20.b


title: C_N

description: Normal

value: C


title: 18.b


title: 25.b


title: UCD 543  3h 2

description: SAMPLE 29


title: C_U

description: Ulcer


title: ATCC 29133  18h3

description: SAMPLE 20

value: wild type


title: B_U

description: Ulcer

value: B


title: 19.b

value: positive


title: 15.b


title: ATCC 29133  24h 3

description: SAMPLE 21


title: ATCC 29133  12h 3

description: SAMPLE 19


title: B_N

description: Normal


title: 17.b


title: A_N

description: Normal

value: A


title: ATCC 29133  3h 3

description: SAMPLE 17


title: 14.b

value: negative


title: 13.b

value: training


title: ATCC 29133  6h 3

description: SAMPLE 18


title: ATCC 29133  1h 3

description: SAMPLE 16


title: A_U

description: Ulcer

value: Ulcer


title: 10.b


title: 11.b


title: 9.b


title: 16.b


title: UCD 543  0h 1

description: SAMPLE 22


title: 8.b


title: 12.b


title: ATCC 29133  24h 2

description: SAMPLE 14


title: 5.b


title: ATCC 29133  0h 3

description: SAMPLE 15


title: 6.b


title: U87MG cells expressing high level EGFRvIII, biological rep 2

city: New York

first: Shao-shan

middle: Carol

last: Huang

state: NY

address: 12 Waverly Pl

department: Biology

institute: New York University

description: Gene expression data from U87MG cells with constitutively active EGFR pathway.

hyb_protocol: The arrays were hybridized in an Affymetrix GeneChip Hybridization Oven 640 at 45 degree Celsius at 60 rpm for 16 hours, washed and stained in Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with the GCRMA package in the R BioConductor library.  Quantile normalization was used as the normalization method.

source_name: U87MG cell line, 2 million EGFRvIII

label_protocol: Labeling was performed following the standard Affymetrix GeneChip protocol.

growth_protocol: Cell were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 100 units/mL penicillin,  100 mg/mL streptomycin, 4 mM L-glutamine and in a 95% air/5% carbon dioxide humidified atmosphere at 37 degree Celsius.  Expression of EGFRvIII and DK receptors were selected by 400 mg/mL G418.

extract_protocol: Total RNA was prepared by the RNeasy Plus Mini Kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Cells were washed with PBS and grown in serum free media for 24 hours before harvesting.

value: glioblastoma

value: 2 million copies of EGFRvIII receptor per cell


title: ATCC 29133  18h 2

description: SAMPLE 13


title: U87MG cells expressing high level EGFRvIII, biological rep 1


title: U87MG cells expressing super-high level EGFRvIII, biological rep 1

source_name: U87MG cell line, 2.5 million EGFRvIII

value: 2.5 million copies of EGFRvIII receptor per cell


title: 2.b


title: 3.b


title: 1.b


title: 4.b


title: 7.b


title: U87MG cells expressing super-high level EGFRvIII, biological rep 2


title: U87MG cells expressing kinase dead EGFRvIII, biological rep 2

description: Gene expression data from U87MG cells with EGFRvIII unable to signal.

source_name: U87MG cell line, kinase dead EGFRvIII

value: kinase dead EGFRvIII


title: ATCC 29133  3h 2

description: SAMPLE 10


title: ATCC 29133  6h 2

description: SAMPLE 11


title: U87MG cells expressing medium level EGFRvIII, biological rep 2

source_name: U87MG cell line, 1.5 million EGFRvIII

value: 1.5 million copies of EGFRvIII receptor per cell


title: U87MG cells expressing medium level EGFRvIII, biological rep 1


title: ATCC 29133  12h 2

description: SAMPLE 12


title: SCF and CCL28 biological rep3

first: Mattias

last: Magnusson

address: 621 Charles E Young Drive South, 2204

department: MCDB

institute: UCLA

description:
Gene expression from cord blood HSPC cultured for 18 hrs with SCF and CCL28
SCF_CCL28 3.CEL

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files were normalised using d-chip (inveriant)

source_name: Cord blood  CD45RAlow+CD34+CD38-CD90+ cells cultured for 18 hrs with SCF and CCL28

label_protocol: standard Affymetrix protocol

growth_protocol: 50000 CB-derived CD34hiCD38loCD90+CD45RA- cells were grown for 18 hours in StemSpan® Serum-Free Expansion Medium (SFEM; Stem Cell Technologies) supplemented with  (SCF; 10 ng/mL) or (SCF; 10 ng/mL and CCL28  500 ng/mL ).

extract_protocol: Total RNA were extracted with RNeasy Mini Kit (Qiagen) after processing cell lysates through QIAshredder columns. The RNA was amplified using the NuGen FFPE amplification kit (Roche)

value: Cord blood

value: HSPC

tag: agent

value: SCF and CCL28


title: SCF and CCL28 biological rep2

description:
Gene expression from cord blood HSPC cultured for 18 hrs with SCF and CCL28
SCF_CCL28 2.CEL


title: ATCC 29133  24h 1

description: SAMPLE 7


title: SCF and CCL28 biological rep1

description:
Gene expression from cord blood HSPC cultured for 18 hrs with SCF and CCL28
SCF_CCL28 1.CEL


title: U87MG cells expressing kinase dead EGFRvIII, biological rep 1


title: ATCC 29133  18h 1

description: SAMPLE 6


title: ATCC 29133  12h 1

description: SAMPLE 5


title: SCF biological rep2

description:
Gene expression from cord blood HSPC cultured for 18 hrs with SCF
SCF 2.CEL

source_name: Cord blood  CD45RAlow+CD34+CD38-CD90+ cells cultured for 18 hrs with SCF

value: SCF


title: SCF biological rep1

description:
Gene expression from cord blood HSPC cultured for 18 hrs with SCF
SCF 1.CEL


title: ATCC 29133  0h 2

description: SAMPLE 8


title: ATCC 29133  1h 2

description: SAMPLE 9


title: ATCC 29133  6h 1

description: SAMPLE 4


title: HMVEC SC siRNA biological rep2

city: Kansas City

first: Shui

last: Ye

state: MO

address: 2401 Gillham Road

department: Medical Genetics Research

institute: Children's Mercy Hospital

data_processing: RMA

source_name: HMVEC-LBI RNA treated with scrambled siRNA

extract_protocol: Trizol

value: primary HMVEC-LBI

tag: knockdown

value: scramble


title: ATCC 29133  0h 1

description: SAMPLE 1

value: wild type


title: HMVEC SC siRNA biological rep3


title: ATCC 29133  1h 1

description: SAMPLE 2


title: SCF biological rep3

description:
Gene expression from cord blood HSPC cultured for 18 hrs with SCF
SCF 3.CEL


title: HMVEC SC siRNA biological rep1


title: ATCC 29133  3h 1

description: SAMPLE 3


title: pstA1regX3KO_rep4

city: Aurora

first: Martin

middle: I

last: Voskuil

state: CO

institute: University of Colorado Denver

hyb_protocol: Arrays were prehybridized in water, SSC, BSA, and SDS. Labeling reaction was concentrated to 5ul in a microcon 10 filter tube, added to tRNA, SSC, formamide, and SDS, and heated to 98 C for two minutes. Samples were hybridzed overnight at 50 C.

scan_protocol: Scanned on Molecular Device's Genepix 4000B

data_processing: ArrayStar software was used for microarray analysis. Experiments performed in triplicate or quadruplicate were loaded into ArrayStar and normalized using RMA.  Statistical significance was determined using the Students t-test.

organism: Mycobacterium tuberculosis str. Erdman = ATCC 35801

source_name: total RNA from aerobic cultures

label_protocol: 1.5 ug of RNA was primed with N6 primers, heated for two minutes at 98 C, then incubated 10 minutes at 25 C followed by 90 minutes at 42 C. 5mM A,G,C and 0.2mM T dNTP mix was used.

extract_protocol: Cell pellets were flash frozen on dry ice, resuspended in Trizol, and bead-beaten 3 x 30 seconds. Resulting cell lysate was added to chloroform and nucleic acids were then precipitated in isopropanol, rehydrated in 75% ethanol, then DNAse treated. Fur further purification, Quiagen RNeasy kit was used according to the manufacturer's instructions.

value: wildtype

tag: growth phase

value: logarithmic phase aerobic cultures, OD600 of 0.2


title: pstA1regX3KO_rep3


title: pstA1regX3KO_rep2


title: regX3KO_rep4


title: pstA1regX3KO_rep1


title: HMVEC 116 PBEF siRNA biological rep1

source_name: HMVEC-LBI RNA treated with PBEF siRNA

tag: cell type

value: PBEF


title: HMVEC 116 PBEF siRNA biological rep3


title: CL1-5_EF stimulation_biological rep3

city: Taipei

first: Ji-Yen

last: Cheng

address: 128 Academia Road, Section 2, Nankang

department: Research Center for Applied Sciences

country: Taiwan

institute: Academia Sinica

description: Gene expression data from the cultured CL1-5 cells with dcEF stimulation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on GeneChip Human Genome U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidic Station-450.

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

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. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: lung cancer CL1-5 cell line, EF stimulation, 300mV/mm, 2hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual rev5, Affymetrix).

growth_protocol: Before the treatment of dcEF, the cells were cultured in a home-made microfluidic chip overnight at 37C with fresh medium flow. The microfluidic chip was made for applying stable dcEF in cell culture region. The culture medium was Dulbecco's Modified Eagle's medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Invitrogen).

extract_protocol: Total RNA was extracted by using RNaqueous kit (Ambion, Applied Biosystems) according to the manufacturer's instructions.

treatment_protocol: The cultured cells were stimulated with the EF strength of 0 or 300mV/mm for 2 hours in serum-free medium (DMEM, Gibco). Then the cells were trypsinized and collected from the microfluidic chip. The cells were preserved in RNAlater (Ambion, Applied Biosystems) at 4C before RNA isolation.

tag: tumor type

value: non-small cell lung cancer, adenocarcinoma


title: CL1-5_EF stimulation_biological rep2


title: CL1-0_EF stimulation_biological rep3

description: Gene expression data from the cultured CL1-0 cells with dcEF stimulation.

source_name: lung cancer CL1-0 cell line, EF stimulation, 300mV/mm, 2hr


title: RB626-SI

city: Duarte

first: Ravi

last: Bhatia

address: 1500 E Duarte Road

department: Hematopoietic Stem Cell and Leukemia Research

institute: City of Hope Beckman Research Institute

description: Gene expression data from CML CD34+ cells

hyb_protocol: ~5.5ug of labeled cDNA was hybridized to Affymetrix Gene Array ST-1.0

scan_protocol: Arrays were scanned at 5um resolution with Affymetrix scanner 3000 7G

data_processing: Microarray data analysis was performed using R (version 2.9) with genomic analysis packages from Bioconductor (version 2.4). The 33297 probes represented on the microarray were filtered by cross-sample mean, and for standard deviation of greater than the 25% quantile, yielding 18624 probes representing 12553 genes. Linear regression was used to model the gene expression with the consideration of a 2x2 factorial design and matched samples. Differentially expressed genes were identified by calculating empirical Bayes moderated t-statistic, and p-values were adjusted by FDR using the “LIMMA” package. Gene Set Enrichment Analysis (GSEA) was performed using GSEA software version 2.04 [http://www.broadinstitute.org/gsea/] to detect enrichment of predetermined gene sets using t-scores from all genes for 1263 gene sets in the C2 (curated gene sets) category from the Molecular Signature Database (MsigDB)41. For significant gene sets related to the Wnt/β-catenin and Cadherin pathways, leading edge genes commonly enriched in these sets were analyzed. Heatmaps were plotted to show contrasts amongst the different treatment groups.

source_name: CML CD34+

label_protocol: 100ng total RNA for each sample was linear amplified and labeled with Biotin

growth_protocol: CML CD34+ cells were cultured in the presence or absence of irradiated MSC at 37°C with 5% CO2 in serum-free expansion medium (SFEM, Stem Cell Technologies, Vancouver, BC,) supplemented with GFs at concentrations similar to those found in stroma-conditioned medium from long-term bone marrow cultures [granulocyte-macrophage colony-stimulating factor (200pg/mL), granulocyte colony-stimulating factor (1ng/mL), stem cell factor (200pg/mL), leukemia inhibitory factor (50pg/mL), macrophage inflammatory protein-1 (200pg/mL), and interleukin-6 (1ng/mL)].

extract_protocol: Total RNA was extracted using the RNAeasy Mini Kit (Qiagen, Valencia, CA), amplified, labeled  and hybridized to GeneChip 1.0 arrays (Affymetrix, Santa Clara, CA).

treatment_protocol: CML CD34+ cells  were treated with or without IM (5μM) in the presence or absence of MSC for 96 hours (n=3 each).

value: PB

tag: msc treatment

value: MSC

tag: imatinib treatment

value: IM


title: HMVEC 116 PBEF siRNA biological rep2


title: regX3KO_rep2


title: regX3KO_rep3


title: RB611-SI


title: RB611-SN

value: No IM


title: CL1-0_EF stimulation_biological rep1


title: CL1-5_EF stimulation_biological rep1


title: CL1-0_EF stimulation_biological rep2


title: CL1-5_no EF stimulation_biological rep2

description: Gene expression data from the cultured CL1-5 cells without dcEF stimulation.

source_name: lung cancer CL1-5 cell line, no EF stimulation


title: RB626-NN

value: No MSC


title: regX3KO_rep1


title: pstA1KO_rep3


title: Parent no pH C

city: Tampa

first: Olivier

last: Lucas

address: 3720 spectrum blvd

institute: University of South Florida

data_processing: Genespring and R/bioconductor

organism: Toxoplasma gondii

source_name: tachyzoite

label_protocol: Ambion messageAmp premier

growth_protocol: parasites were grown in T175 flasks in human foreskin fibroblasts

extract_protocol: Qiagen RNA easy, double DNAse digestion

treatment_protocol: pH8.2 and/or shield-1 treatment

value: type III CTG

tag: Stage

value: tachyzoite

tag: drug treatment

value: 200nM shield-1


title: pstA1KO_rep1


title: RB611-NI


title: RB626-NI


title: CL1-5_no EF stimulation_biological rep3


title: pstA1KO_rep2


title: RB611-NN


title: RB585-SN

value: bone marrow


title: RB626-SN


title: RB585-SI


title: CL1-0_no EF stimulation_biological rep3

description: Gene expression data from the cultured CL1-0 cells without dcEF stimulation.

source_name: lung cancer CL1-0 cell line, no EF stimulation


title: RB585-NI


title: CL1-5_no EF stimulation_biological rep1


title: RB585-NN


title: Parent pH + Sh repA

source_name: pH induced parasite

tag: treatment

value: alkaline

tag: strain

value: in vitro pH induced bradyzoite


title: Parent pH repB


title: CL1-0_no EF stimulation_biological rep1


title: Parent pH + Sh repB


title: Parent no pH B


title: Parent pH repA


title: CL1-0_no EF stimulation_biological rep2


title: Parent no pH A


title: Human corneal epithelial cells, siEhf, rep3

city: Irvine

first: Denise

last: Stephens

address: 250 Sprague Hall

department: Biological Chemistry

institute: University of California, Irvine

description: hCEC Ehf si expt - E3

hyb_protocol: 2ug of the labeled, fragmented single-stranded cDNA is hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 1.0 ST array. The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing: The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files. The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

source_name: human corneal epithelial cells, siEhf

label_protocol: The Ambion WT expression kit (Life Technologies, Carlsbad, CA) was used to prepare RNA samples for whole transcriptome microarray analysis. Briefly, random hexamers that are tagged with a T7 promoter are used in first strand synthesis of cDNA. Then, using the T7 promoter, second strand synthesis is performed and the double-stranded cDNA is subsequently used as a template in an in vitro transcription reaction to generate many copies of antisense cRNA. 10ug of antisense cRNA is input into a second cycle cDNA reaction using reverse transcriptase and random hexamers to produce single-stranded DNA in the sense orientation. The single-stranded DNA is fragmented to an average length of 70 bases and then labeled using a recombinant terminal deoxynucleotidyl transferase (TdT) and an Affymetrix proprietary DNA labeling reagent that is covalently linked to biotin.

growth_protocol: Primary human corneal epithelial cells (HCEPs) from CELLnTEC Inc. were grown in CnT-20 medium as directed by the manufacturer.

extract_protocol: RNA were extracted from the plated cells with the Purelink RNA miniprep kit (Ambion) 72 hours after transfection.

treatment_protocol: P3 HCEP cells were trypsinized and plated 100,000 cells/well into a 12-well dish containing 1ul lipofectamine RNAiMAX and 30nM EHF or scramble siRNA pre-mixed 20 prior to cell plating. The EHF siRNA were pooled from 3 individual siRNA targeting EHF (Ambion, ID s25397, s25398, s25399) in the same concentration.

value: corneal epithelial cells

tag: sirna

value: Ehf


title: Human corneal epithelial cells, siEhf, rep1

description: hCEC Ehf si expt - E1


title: CD2- expressing HMC1 cells

city: Vienna

last: Bilban

country: Austria

institute: Medical University of Vienna

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: RMA normalization (Affymetrix Expression Console version 1.1)

source_name: HMC1 subclone negative for CD2 surface expression

label_protocol: Affymetrix

extract_protocol: RNeasy mini kit (Qiagen)

treatment_protocol: This HMC1 cell line subclone was obtained from HMC1 cells after FACS sortong with an anti-CD2 antibody. This subclone represents HMC1 cells devoid of CD2 surface receptor expression

tag: cell line

tag: hmc1 subclone


title: Human corneal epithelial cells, siEhf, rep2

description: hCEC Ehf si expt - E2


title: Human corneal epithelial cells, siRNA control, rep3

description: hCEC Ehf si expt - C3

source_name: human corneal epithelial cells, siRNA control

value: scramble


title: DDIX-9pH + Sh repB

tag: overexpression


title: DDIX-9pH repA


title: DDIX-9pH + Sh repA


title: Endothelial Cells siRNA KLF2 rep2

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

country: Japan

institute: LSBM, RCAST

description: KLF2 siRNA with 4h statin treatment

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45 degrees CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix Microarray Suite v5.0 with target intensity=100

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: Human umbilical vein endothelial cells (HUVECs) (Lonza, Basel, Switzerland) were cultured in EGM2MV medium (Lonza).  HUVECs were used within the first 6 passages.

extract_protocol: Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix.

treatment_protocol: 1.5x105 HUVEC cells were plated in 6 well culture plate.  Next day before statin treatment siRNA KLF2 or KLF4 were transfected for 1day, and then HUVECs were stimulated with pitavastatin at a concentration of 1 micromolar for 4 hours.

value: KLF2 siRNA with 4h statin

value: Human umbilical vein cells


title: Endothelial Cells siRNA KLF4

description: KLF4 siRNA with 4h statin treatment

value: KLF4 siRNA with 4h statin


title: DDIX-9pH repB


title: Endothelial Cells siRNA KLF4 rep 2

description: KLF4 siRNA with 4h statin treatment


title: EcfO maltose Inducible vector control

city: Greenville

first: Charles

middle: Jeffrey

last: Smith

state: NC

address: 600 Moye Blvd.

department: Microbiology & Immunology

institute: East Carolina University

description: EcfO/anti-EcfO mutant with empty vector control for maltose induced expression of EcfO experiment

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., using standard protocol as described on their website.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., using standard protocol as described on their website.

data_processing: Raw data (pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction by NimbleGen Systems as described on their web site.

organism: Bacteroides fragilis 638R

source_name: Bacteroides fragilis, 638R, EcfO/anti-EcfO null, empty vector

label_protocol: Labeling was performed by NimbleGen Systems Inc., using standard protocol as described on their website.

growth_protocol:
Overnight cultures of the vector control or maltose inducible strain were diluted 1/50 into complex media with maltose as carbon source.  Cultures were grown under anaerobic conditions at 37C
to mid-logarithmic phase at A550 of 0.3

extract_protocol: Total RNA was isolated by the hot phenol method and treated as described by Sund et al, 2008, Mol. Microbiol.67:129-142.

tag: transformation construct

value: EcfO/anti-EcfO null mutation with empty vector control


title: Human corneal epithelial cells, siRNA control, rep1

description: hCEC Ehf si expt - C1


title: CD2+ HMC1 subclone

source_name: CD2 expressing HMC1 subclone

treatment_protocol: This HMC1 cell line subclone was obtained from HMC1 cells after FACS sortong with an anti-CD2 antibody. This subclone represents HMC1 cells expressing CD2 surface receptor.

value: expressing CD2 surface receptor


title: EcfO IPTG Inducible vector control

description: EcfO mutant with empty vector control for IPTG induced expression of EcfO experiment

source_name: Bacteroides fragilis, 638R, EcfO null, empty vector

growth_protocol:
Overnight cultures of the vector control or IPTG inducible strain were diluted 1/50 into complex media.  IPTG was added and cultures were grown under anaerobic conditions at 37C
to mid-logarithmic phase at A550 of 0.3

value: EcfO null mutation with empty vector control


title: EcfO maltose Induced expression

description: EcfO/anti-EcfO mutant with maltose induced expression of EcfO experiment

source_name: Bacteroides fragilis, 638R, EcfO/anti-EcfO null, with pFD1045EcfO

value: EcfO/anti-EcfO null mutation with pFD1045EcfO


title: Endothelial Cells siRNA KLF2

description: KLF2 siRNA with 4h statin treatment


title: EcfO IPTG Induced expression

description: anti-EcfO mutant with IPTG induced expression of EcfO experiment

source_name: Bacteroides fragilis, 638R, anti-EcfO null, IPTG induced expression of EcfO

value: anti-EcfO mutant with IPTG induced expression of EcfO from pFD1146


title: LCL. PA 5y female, GM22030, normal

city: Washington

first: Kimberly

last: Chapman

state: DC

address: 111 Michigan Ave NW

department: Genetics and Metabolism

institute: Children's National Medical Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 1.0 ST array

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and Primary Component anylsis, Partek

source_name: LCL, normal glucose

label_protocol: Biotinylated cRNA were created using GeneChip Whole transcripts sense target Labeling assay (Affymetrix) according to manufacturer's instructions

growth_protocol: Cells maintained in RPMI 1640 with 15% FBS, 2 mmol/L L-glutamine, 100 units/mL penicukkub-streptomycin

extract_protocol: Cells lysed using Quiashredder and total RNA isolated using Rneasy Purification kits

treatment_protocol: Cells switch to low glucose (RPMI 1640 with no glucose) +15% FBS +2 mM glutamine or RPMI 1640 +15%FBS +2 mM glutamine  24 hours prior to harvest and extraction

tag: gender

value: female

tag: age

value: 5 y

tag: disease state

value: Propionic acidemia

value: normal glucose


title: Endothelial Cells control 4h rep 9

description: 4h after DMSO treatment

treatment_protocol: 1.5x105 HUVEC cells were plated in 6 well culture plate, and cultivated for 2 days. They were stimulated with pitavastatin at a concentration of 1 μM for 4 hours, and same concentration of DMSO was used as a control sample.

value: DMSO treatment for 4h


title: LCL, PA 9 y male, GM22025, low glucose

source_name: LCL, low glucose

value: male

value: 9 y

value: low glucose


title: LCL, PA 7 yo female, GM22113, low glucose

value: 7  y


title: Human corneal epithelial cells, siRNA control, rep2

description: hCEC Ehf si expt - C2

value: corneal epithelial cells

value: scramble


title: Endothelial Cells statin 4h rep 7

description: 4h after statin treatment

value: Human umbilical vein cells

value: statin treatment for 4h


title: LCL, PA 7 yo female, GM22113, normal


title: Endothelial Cells control 4h rep 8

description: 4h after DMSO treatment


title: Endothelial Cells statin 4h rep 8

description: 4h after statin treatment


title: LCL, PA 9 y male, GM22025, normal


title: Endothelial Cells statin 4h rep 9

description: 4h after statin treatment


title: LCL, carrier mother, GM22019, low glucose

value: carrier mother


title: Endothelial Cells control 4h rep 7

description: 4h after DMSO treatment


title: LCL, carrier mother, GM22014, normal


title: Endothelial Cells statin 4h rep 6

description: 4h after statin treatment


title: 528h_lwp_rep3

city: Dresden

first: Dunja

last: Knapp

address: Fetscherstraße 105

institute: DFG-Center for Regenerative Therapies Dresden

description: Gene expression in wound-healing limb, 524h after lateral injury

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner (G2505C US45102998) using one color scan setting for 1x44k array slides, 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 from Agilent using default parameters (protocol GE1-v5_95_Feb07 and Grid: 019788_D_F_20080327 ) to obtain background subtracted and spatially detrended Processed Signal intensities.  Thus obtained values are termed raw [attached to the Series record as a supplementary file]. For expression analysis arrays have been quantile normalized using GeneSpring 10 and displayed as log2 values.

organism: Ambystoma mexicanum

source_name: wound-healing limb, 524h after lateral injury, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug total RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol.

extract_protocol: Total RNA was purified using Qiagen RNeasy midi kit.  RNA was then DNase-treated and then repurified using Qiagen RNeasy mini kit. RNA quality was confirmed using Agilent Bioanalyzer-  The RIN values were at least  9.4.

treatment_protocol: For both, amputation and lateral injury samples the first cut was done at ¼ stylopod length behind the wrist using animals at the size  40-50 mm from nose to cloaca. In amputated stumps protruding bones were trimmed (≈ 0.5 mm ).  For regenerating samples, for each timepoint all tissue between 2mm behind the amputation plane and the tip of the blastema was collected. For lateral wound samples an incision was made using scalpel through the posterior half of the lower arm such that ulna was cut through but radius was not. No tissue was removed. At the appropriate timepoint all tissue between 2mm proximal to the cut plane and 0.5 mm distal to the cut plane was collected. Collected tissue was frozen immediately in liquid nitrogen, for each sample tissue from four limbs was pooled together and kept at -80°C until further processing.   Limb bud samples were collected at mid-bud and notch stage from 1.5-1.7 cm long animals 6 and 12 days after hatching, respectively. 40-50 buds were collected per sample.

tag: time after injury (hours)

tag: type of injury

value: lateral wound

tag: tissue type

value: limb

tag: biological replicate


title: Endothelial Cells statin 4h rep5

description: 4h after statin treatment

tag: cell type


title: LCL. PA 5y female, GM22030, low glucose


title: LCL, carrier mother, GM22014, low glucose


title: LCL, control, GM07020 repeat,low glucose

value: control


title: 288h_lwp_rep3

description: Gene expression in wound-healing limb, 288h after lateral injury

hyb_protocol: according to the manufacturer's protocol

source_name: wound-healing limb, 288h after lateral injury, replicate 3


title: LCL, carrier mother, GM22019, normal

value: female


title: Endothelial Cells control 4h rep 6

description: 4h after DMSO treatment


title: 72h_lwp_rep3

description: Gene expression in wound-healing limb, 72h after lateral injury

source_name: wound-healing limb, 72h after lateral injury, replicate 3


title: 168h_lwp_rep3

description: Gene expression in wound-healing limb, 168h after lateral injury

source_name: wound-healing limb, 168h after lateral injury, replicate 3


title: Endothelial Cells statin 4h rep 4

description: 4h after statin treatment


title: 120h_lwp_rep3

description: Gene expression in wound-healing limb, 120h after lateral injury

source_name: wound-healing limb, 120h after lateral injury, replicate 3


title: 36h_lwp_rep3

description: Gene expression in wound-healing limb, 36h after lateral injury

source_name: wound-healing limb, 36h after lateral injury, replicate 3


title: Endothelial Cells control 4h rep 4

description: 4h after DMSO treatment


title: 52h_lwp_rep3

description: Gene expression in wound-healing limb, 52h after lateral injury

source_name: wound-healing limb, 52h after lateral injury, replicate 3


title: LCL, control, GM07020 repeat, normal


title: LCL, control, GM12042 repeat low glucose.


title: Endothelial Cells statin 4h rep 3

description: 4h after statin treatment


title: LCL, control GM10859 repeat, low glucose


title: 24h_lwp_rep3

description: Gene expression in wound-healing limb, 24h after lateral injury

source_name: wound-healing limb, 24h after lateral injury, replicate 3


title: LCL, control, GM12042 repeat normal.


title: Endothelial Cells control 4h rep 5

description: 4h after DMSO treatment


title: Endothelial Cells control 4h rep 3

description: 4h after DMSO treatment


title: LCL, control GM10859 repeat, normal


title: LCL,carrier father, GM22015, normal

value: carrier father


title: Endothelial Cells control 4h rep 2

description: 4h after DMSO treatment


title: Endothelial Cells statin 4h rep 2

description: 4h after statin treatment


title: Endothelial Cells statin 4h

description: 4h after statin treatment


title: LCL, carrier father, GM22498, low glucose


title: Endothelial Cells control 4h

description: 4h after DMSO treatment


title: LCL, carrier father, GM22498, normal


title: 528h_amp_rep3

description: Gene expression in regenerating limb, 524h after amputation

source_name: regenerating limb, 524h after amputation, replicate 3

value: amputation


title: 12h_lwp_rep3

description: Gene expression in wound-healing limb, 12h after lateral injury

source_name: wound-healing limb, 12h after lateral injury, replicate 3


title: 168h_amp_rep3

description: Gene expression in regenerating limb, 168h after amputation

source_name: regenerating limb, 168h after amputation, replicate 3


title: 6h_lwp_rep3

description: Gene expression in wound-healing limb, 6h after lateral injury

source_name: wound-healing limb, 6h after lateral injury, replicate 3


title: LCL,carrier father, GM22015, low glucose


title: 9h_lwp_rep3

description: Gene expression in wound-healing limb, 9h after lateral injury

source_name: wound-healing limb, 9h after lateral injury, replicate 3


title: 3h_lwp_rep3

description: Gene expression in wound-healing limb, 3h after lateral injury

source_name: wound-healing limb, 3h after lateral injury, replicate 3


title: LCL, carrier mother, GM22497, low glucose


title: 288h_amp_rep3

description: Gene expression in regenerating limb, 288h after amputation

source_name: regenerating limb, 288h after amputation, replicate 3


title: fibroblastic meningioma

city: Shanghai

first: Xuanchun

last: Wang

address: 12 Wulumuqi Road (Middle)

institute: Huashan Hospital

description: Gene expression data from fibroblastic meningioma tissue

hyb_protocol: Hybridization was performed according to the manufacturer's instruction at the Expression Analysis, Inc. (http://www.expressionanalysis.com)

scan_protocol: Scanning was performed at the Expression Analysis, Inc. (http://www.expressionanalysis.com)

data_processing: Scanned raw data images were processed with GeneChip Operating Software (GCOS) 1.4; Algorithm: ExpressionSta 5.0

source_name: fibroblastic meningioma tissue

label_protocol: Biotinylated cRNA were prepared using Affymetrix one cycle kit according to the standard Affymetrix protocol at the Expression Analysis, Inc. (http://www.expressionanalysis.com)

growth_protocol: Human brain arachnoidal tissue and meningioma tissues were snap-frozen in liquid nitrogen at the time of surgery and stored at -80 °C until used.

extract_protocol: Total RNA was extracted by Trizol. At the final step of purification, RNA was loaded onto an RNeasy column (Qiagen) and treated with RNAse free DNAse I.

tag: tissue

value: fibroblastic meningioma tissue


title: anaplastic meningioma

description: Gene expression data from anaplastic meningioma tissue

source_name: anaplastic meningioma tissue

treatment_protocol: Human brain arachnoidal tissue and meningioma tissues were snap-frozen in liquid nitrogen at the time of surgery and stored at -80 °C until used.

value: anaplastic meningioma tissue


title: 72h_amp_rep3

description: Gene expression in regenerating limb, 72h after amputation

source_name: regenerating limb, 72h after amputation, replicate 3


title: 36h_amp_rep3

description: Gene expression in regenerating limb, 36h after amputation

source_name: regenerating limb, 36h after amputation, replicate 3


title: 120h_amp_rep3

description: Gene expression in regenerating limb, 120h after amputation

source_name: regenerating limb, 120h after amputation, replicate 3


title: FADU-citric buffer

first: Muh-Hwa

last: Yang

address: No.155, Sec.2, Li-Nong Street

department: Institute of Clinical Medicine

institute: National Yang-Ming University

description: Human hypopharyngeal cancer cell line FADU transfected treated with citric buffer were grown to near confluence and collected total RNA for array analysis.

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

scan_protocol: Arrays were scanned with the Affymetrix GeneChip® Scanner 3000 7G and the data was extracted using Microarray Analysis Suite 5.0 (Affymetrix).

data_processing: We used the Affymetrix GeneChip Suite 5.0 software (MAS 5.0) to calculate raw expression values for each probe sets on the U133 2.0 oligonucleotide arrays.

source_name: human hypopharyngeal squamous cell carcinoma cell line FADU treat citric buffer

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

growth_protocol: cultivated in RPMI + 10% fetal bovine serum

extract_protocol: Cells were lysed by adding 2 ml of trizol reagent (Invitrogen) and homogenized by passing through a syringe with a needle (26G). RNA was picked up in the aqueous phase following phase separation by chloroform. The RNA was then precipitate with isopropanol, washed with ethanol (75%), dissolved in DEPC-treated RNAse/DNAse free water and quantified by spectrophotometry.

value: hypopharyngeal cancer cell line FADU

tag: cell line source ethnicity

value: Caucasian

tag: cell line source gender

value: Male

tag: cell line source age

tag: cell line source tissue

value: primary human hypopharyngeal squamous cell carcinoma

tag: agent

value: citric buffer


title: FADU-rCTGF

description: Human hypopharyngeal cancer cell line FADU transfected treated with rCTGF 100 ng/mL for 24 hours and collected total RNA for array analysis.

source_name: human hypopharyngeal squamous cell carcinoma cell line FADU treated with rCTGF

treatment_protocol: treated rCTGF 100 ng/mL for 24 hours

tag: cell line

value: rCTGF


title: LCL, carrier mother, GM22497, normal

source_name: LCL, normal glucose

tag: treatment

value: normal glucose


title: LCL, control, GM11997, normal


title: LCL, PA 8 week male, GM22496, low glucose

source_name: LCL, low glucose

value: male

value: 8 wk

value: Propionic acidemia

value: low glucose


title: LCL, control, GM11997, low glucose

value: control


title: 24h_amp_rep3

description: Gene expression in regenerating limb, 24h after amputation

source_name: regenerating limb, 24h after amputation, replicate 3

value: limb


title: LCL control, GM11916 low glucose


title: LCL, PA 4yo male, GM22083, low glucose

value: 4 y


title: brain arachnoidal tissue

description: Gene expression data from brain arachnoidal tissues

source_name: brain arachnoidal tissue

value: brain arachnoidal tissue


title: 12h_amp_rep3

description: Gene expression in regenerating limb, 12h after amputation

source_name: regenerating limb, 12h after amputation, replicate 3

value: amputation


title: 52h_amp_rep3

description: Gene expression in regenerating limb, 52h after amputation

source_name: regenerating limb, 52h after amputation, replicate 3


title: LCL control, GM11916 normal


title: LCL, PA 8 week male, GM22496, normal


title: 9h_amp_rep3

description: Gene expression in regenerating limb, 9h after amputation

source_name: regenerating limb, 9h after amputation, replicate 3


title: 3h_amp_rep3

description: Gene expression in regenerating limb, 3h after amputation

source_name: regenerating limb, 3h after amputation, replicate 3


title: 6h_amp_rep3

description: Gene expression in regenerating limb, 6h after amputation

source_name: regenerating limb, 6h after amputation, replicate 3


title: LCL, control, GM07020, low glucose


title: mat-2_rep3

description: Gene expression in the mature limb

source_name: mature limb, replicate 3


title: LCL, PA 4yo male, GM22083, normal


title: mat-1_rep3

description: Gene expression in the mature limb


title: LCL, control, GM07021,low glucose


title: 528h_lwp_rep2

description: Gene expression in wound-healing limb, 524h after lateral injury

source_name: wound-healing limb, 524h after lateral injury, replicate 2

value: lateral wound


title: LCL, control, GM07021, normal


title: limb.bud_rep3

description: Gene expression in the developing limb bud

source_name: developing limb bud, replicate 3

value: limb bud


title: MOCK_6h_MDP_biological replicate 2

city: Kiel

first: Susanne

last: Billmann

address: Schittenhelmstraße 12

institute: Institute of Clinical Molecular Biology Christian-Albrechts-Universität Kiel

description: RNA from cell culture with different NOD2 genotypes

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array in a Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station.

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

data_processing: The data were analyzed with Gene Chip Operating Software 1.1. Represents the relative level of expression of a transcript. The median of the data is identified and each datum is weighted by how far it is from the median using One-step Tukey's Biweight Algorithm. A weighted mean is then calculated.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: NOD2wt and NOD2-L1007fsinsC expressing cells were generated with the FLP-IN system (Invitrogen, Carlsbad, CA, USA). HEK 293 cells containing the recombination site were purchased from Invitrogen. Wildtype and mutated NOD2 were inserted to the genomic recombination site by FLP-recombinase enzyme. A control cell line was generated by transfecting an empty mock vector. All stable cell lines were selected for Hygromycin B resistance and consequently cultured in MEM + 10 % FCS + 1% Penicillin/Streptomycin + 50 μg/ml Hygromycin B (Invitrogen).

extract_protocol: RNA was isolated using the RNeasy Kit (Qiagen)

treatment_protocol: FLP-IN HEK 293-NOD2wt, HEK 293-NOD2L1007fsinsC and HEK 293mock cells were cultivated in medium without FCS for 7 h before stimulation with 10 µg/ml MDP for 0h, 2h and 6h. Cells were harvested simultaneously.

tag: genotype

value: control mock

tag: stimulation

value: Muramyl-dipeptide (MDP) 10 µg/ml

tag: time point

value: 6 h


title: LCL, control, GM07020, normal

tag: disease state


title: uninvolved skin from patient C

city: Seoul

first: Eun Young

last: Seo

address: Yongon-dong 28, Chongno-gu

department: Department of Dermatology

country: South Korea

institute: Seoul National University College of Medicine

hyb_protocol: Affymetrix protocol

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

data_processing: The data were analyzed with Robust Multi-array Analysis (RMA) as normalization method using Affymetrix Expression Console 1.1 software. The trimmed mean intensity of each array was arbitrarily set to 100.

source_name: skin with seborrheic keratosis

label_protocol: Affymetrix protocol

extract_protocol: Full thickness excisional skin biopsy was performed from skin with seborrheic keratosis and uninvolved skin. RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions.

value: skin

tag: patient identification

value: C

tag: condition

value: seborrheic keratosis


title: LCl, PA 9 yo female, GM22018, normal

tag: gender

value: female

tag: age

value: 9  y

value: normal glucose


title: LCL, Sibling, GM22020, low glucose

value: Sibling

value: low glucose


title: uninvolved skin from patient D

value: D


title: seborrheic keratosis from patient C

source_name: control skin

value: control skin


title: uninvolved skin from patient A

value: A