title: MTAP+, inhibitor, rep3

status: Public on Apr 30 2014

type: RNA

city: Philadelphia

first: warren

last: kruger

state: PA

address: 333 Cottman Ave.

country: USA

institute: Fox Chase Cancer Center

description: Gene Expression

hyb_protocol: The biotinylated cRNA samples were cleaned up, fragmented, and then hybridized to human GeneChip (Human Genome U133 plus 2.0, Affymetrix) in Affymetrix GeneChip Hybridization Oven 640 according to manufacturer’s protocols.  The washing procedures were carried out automatically in Affymetrix GeneChip Fluidics Station 450 .

scan_protocol: The processed GeneChip was scanned with Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were normalized with RMA. 6 additional arrays were included in the normalization, but these do not appear here. The data were filtered by including only probesets for which (1) at least three samples had expression intensities > 100, and (2) a valid Entrez identifier existed for the probeset (using Bioconductor annotations at the time of analysis). Probesets not passing the filters are given null values.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HT 1080 Cell Line

label_protocol: Ten μg of total RNA were reverse transcribed to cDNA by using One-Cycle cDNA Synthesis kit (Affymetrix, Santa Clara, CA).  Biotin-labeled cRNA synthesis was then carried out using the Affymetrix In Vitro Transcription Labeling Kit.

growth_protocol: Cells were grown in DMEM to 80% confluency.  The MT-DADMe-ImmA Inhibitor was added 48 hours before harvesting at a concentration of 10 micromolar.

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to manufacturer's instruction.

tag: cell line

tag: mtap

value: Positive

tag: treatment

value: 10 micromolar MT-DADMe-ImmA Inhibitor


title: MTAP- rep2

description: Gene Expression

value: Negative

value: NT


title: before patient5 with IVIG

city: Sagamihara Kanagawa

first: Yoshihito

last: Ogihara

address: 1-15-1 Kitasato Minami-ku

department: Pediatrics

country: Japan

institute: Kitasato University

description:
Gene expression data from whole blood cells before patient 5 with IVIG
Pre-IVIG-5

hyb_protocol: The biotinylated cRNA was fragmented and hybridized for 16 h at 45C with the Human Genome U133 plus 2.0 array (Affymetrix)(GPL9324), which contains the oligonucleotide probe set for 54,675 full-length transcripts and expressed sequence tags. The arrays were washed, stained with streptavidin-phycoerythrin, and scanned using an Affymetrix Model Fluidics Station 450

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

data_processing: For the expression analysis of gene chip microarray, the CEL files created from each gene chip were imported into Gene Spring GX 12.5 (Agilent Technologies, Santa Clara, US). Normalization and baseline approach was performed by robust multi-array average (RMA) and median of all samples

source_name: before patient5 with IVIG, whole blood cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Human whole blood cells

extract_protocol: PAX gene Blood RNA kit (QIAGEN) Next, α-globin and β-globin mRNA was removed from the total RNA using the globin reduction method (Affymetrix, Santa Clara, US).

treatment_protocol: Total RNA was isolated from 2.5ml of whole blood using a PAX gene tube (Becton Dickinson and Company, Plymouth, UK)

tag: nationality

value: Japanese

tag: disease state

value: Kawasaki disease

tag: individual

value: IVIG-responsive patient 5

value: untreated (pre-IVIG treatment)

tag: cell type

value: whole blood cells


title: MTAP+ rep1

description: Gene Expression


title: MTAP+, inhibitor, rep1

description: Gene Expression


title: MTAP+ rep3

description: Gene Expression


title: MTAP- rep3

description: Gene Expression


title: after patient1 with IVIG

description:
Gene expression data from whole blood cells after patient 1 with IVIG
Post-IVIG-1

source_name: after patient1 with IVIG, whole blood cells

value: IVIG-responsive patient 1

value: IVIG


title: MTAP+ rep2

description: Gene Expression


title: after patient8 with IFX

description:
Gene expression data from whole blood cells after patient 8 with IFX
Post-IFX-8

source_name: after patient8 with IFX, whole blood cells

value: IFX-responsive patient 8

value: IFX


title: after patient4 with IVIG

description:
Gene expression data from whole blood cells after patient 4 with IVIG
Post-IVIG-4

source_name: after patient4 with IVIG, whole blood cells

value: IVIG-responsive patient 4


title: after patient6 with IFX

description:
Gene expression data from whole blood cells after patient 6 with IFX
Post-IFX-6

source_name: after patient6 with IFX, whole blood cells

value: IFX-responsive patient 6


title: MTAP+, inhibitor, rep2

description: Gene Expression


title: after patient2 with IVIG

description:
Gene expression data from whole blood cells after patient 2 with IVIG
Post-IVIG-2

source_name: after patient2 with IVIG, whole blood cells

value: IVIG-responsive patient 2


title: before patient6 with IVIG

description:
Gene expression data from whole blood cells before patient 6 with IVIG
Pre-IVIG-6

source_name: before patient6 with IVIG, whole blood cells

value: IVIG-responsive patient 6


title: before patient3 with IVIG

description:
Gene expression data from whole blood cells before patient 3 with IVIG
Pre-IVIG-3

source_name: before patient3 with IVIG, whole blood cells

value: IVIG-responsive patient 3


title: after patient3 with IVIG

description:
Gene expression data from whole blood cells after patient 3 with IVIG
Post-IVIG-3

source_name: after patient3 with IVIG, whole blood cells


title: after patient5 with IVIG

description:
Gene expression data from whole blood cells after patient 5 with IVIG
Post-IVIG-5

source_name: after patient5 with IVIG, whole blood cells


title: after patient4 with IFX

description:
Gene expression data from whole blood cells after patient 4 with IFX
Post-IFX-4

source_name: after patient4 with IFX, whole blood cells

value: IFX-responsive patient 4


title: after patient2 with IFX

description:
Gene expression data from whole blood cells after patient 2 with IFX
Post-IFX-2

source_name: after patient2 with IFX, whole blood cells

value: IFX-responsive patient 2


title: before patient2 with IVIG

description:
Gene expression data from whole blood cells before patient 2 with IVIG
Pre-IVIG-2

source_name: before patient2 with IVIG, whole blood cells


title: after patient1 with IFX

description:
Gene expression data from whole blood cells after patient 1 with IFX
Post-IFX-1

source_name: after patient1 with IFX, whole blood cells

value: IFX-responsive patient 1


title: after patient5 with IFX

description:
Gene expression data from whole blood cells after patient 5 with IFX
Post-IFX-5

source_name: after patient5 with IFX, whole blood cells

value: Japanese

value: IFX-responsive patient 5


title: after patient7 with IFX

description:
Gene expression data from whole blood cells after patient 7 with IFX
Post-IFX-7

source_name: after patient7 with IFX, whole blood cells

value: Kawasaki disease

value: IFX-responsive patient 7


title: after patient6 with IVIG

description:
Gene expression data from whole blood cells after patient 6 with IVIG
Post-IVIG-6

source_name: after patient6 with IVIG, whole blood cells

value: whole blood cells


title: before patient4 with IVIG

description:
Gene expression data from whole blood cells before patient 4 with IVIG
Pre-IVIG-4

source_name: before patient4 with IVIG, whole blood cells

value: untreated (pre-IVIG treatment)


title: MTAP- rep1

description: Gene Expression

source_name: HT 1080 Cell Line

value: Negative

value: NT


title: before patient1 with IVIG

description:
Gene expression data from whole blood cells before patient 1 with IVIG
Pre-IVIG-1

source_name: before patient1 with IVIG, whole blood cells

value: IVIG-responsive patient 1


title: before patient8 with IFX

description:
Gene expression data from whole blood cells before patient 8 with IFX
Pre-IFX-8

source_name: before patient8 with IFX, whole blood cells

value: IFX-responsive patient 8

value: untreated (pre-IFX treatment)


title: after patient3 with IFX

description:
Gene expression data from whole blood cells after patient 3 with IFX
Post-IFX-3

source_name: after patient3 with IFX, whole blood cells

value: IFX-responsive patient 3

value: IFX


title: before patient7 with IFX

description:
Gene expression data from whole blood cells before patient 7 with IFX
Pre-IFX-7

source_name: before patient7 with IFX, whole blood cells


title: High light reactor, t=0 min, replicate series 3

city: Potsdam

first: Samuel

last: Arvidsson

state: Brandenburg

address: Am Muehlenberg 1

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

description:
Gene expression at t=0, high light reactor
ID20_5_4_T_R3_TP2

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software (10.7.3.1; Agilent).

data_processing: Agilent Feature Extraction Software (10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Chlamydomonas reinhardtii

source_name: High light reactor, t=0 min

label_protocol: 1 µg of total RNA were labeld according to the Agilent quick amplification labeling kit

growth_protocol: C. reinhardtii CC1690 cells were grown continuously at 24°C, 5% CO2 and 41 µmol photons*m-2*s-1 for three days before the start of the experiment to assure steady-state conditions

extract_protocol: Total RNA extraction was performed using the RNeasy Plant Mini Kit (Qiagen, Germany). The frozen cell pellet was homogenized in 450 μl of lysis buffer and frozen again in liquid nitrogen for 3 min. Cells were completely lysed by incubating the frozen cell pellet at 56°C for 3 min. Further steps of the RNA extraction were performed as described by the manufacturer.

treatment_protocol: Shift to 145 µmol photons*m-2*s-1 for 8 hours, during which sampling was performed.

tag: strain

tag: light regime

value: High light

tag: time

value: 0 min


title: Low light reactor, t=0 min, replicate series 1

description:
Gene expression at t=0, low light reactor
ID15_4_3_C_R1_TP2

source_name: Low light reactor, t=0 min

value: Low light


title: High light reactor, t=40 min, replicate series 1, technical replicate 2

description:
Gene expression at t=40 min, high light reactor
ID10_3_2_T_R1_TP6

source_name: High light reactor, t=40 min

value: 40 min


title: High light reactor, t=40 min, replicate series 2

description:
Gene expression at t=40 min, high light reactor
ID19_5_3_T_R2_TP6


title: High light reactor, t=480 min, replicate series 2

description:
Gene expression at t=480 min, high light reactor
ID11_3_3_T_R2_TP10

source_name: High light reactor, t=480 min

value: 480 min


title: High light reactor, t=0 min, replicate series 1, technical replicate 2

description:
Gene expression at t=0, high light reactor
ID16_4_4_T_R1_TP2


title: High light reactor, t=0 min, replicate series 2

description:
Gene expression at t=0, high light reactor
ID9_3_1_T_R2_TP2


title: High light reactor, t=480 min, replicate series 3

description:
Gene expression at t=480 min, high light reactor
ID14_4_2_T_R3_TP10


title: Low light reactor, t=480 min, replicate series 3

description:
Gene expression at t=480 min, low light reactor
ID13_4_1_C_R3_TP10

source_name: Low light reactor, t=480 min


title: before patient6 with IFX

description:
Gene expression data from whole blood cells before patient 6 with IFX
Pre-IFX-6

source_name: before patient6 with IFX, whole blood cells

value: Japanese

value: IFX-responsive patient 6


title: High light reactor, t=480 min, replicate series 1

description:
Gene expression at t=480 min, high light reactor
ID5_2_1_T_R1_TP10


title: Slide233 Area4 092012

city: Québec

first: Audrey

last: BUNEL

state: Québec

address: 2425, Rue de l'agriculture

department: Sciences Animales

country: Canada

institute: Université Laval

description: This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: This is a place holder for the Tecan scanning protocol.

data_processing: Background subtracted, Loess and Quantile normalized data obtained from log2 of processed Red signal/processed Green signal. Flexarray software used.

organism: Bos taurus

source_name: CC-Blast

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: A little piece of cumulus is cut from each COC and frozen individually. COC are further individually matured, fertilized and cultured umtil day 8.

extract_protocol: This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.

treatment_protocol: CC biopsies obtained from COCs of 2-6mm follicles from slaughterhouse ovaries before individual in vitro maturation, fertilization and culture until day 8 post-fertilization. Each COC was individually tracked and categorized based on his fate: embryo at blastocyst stage (CC-Blast) or embryo arrested at 2- to 8-cell stage (CC-2-8-cells).

value: CC-Blast

tag: number per pool

tag: in vitro production

value: Yes

tag: biopsy

tag: cryopreservation

value: No


title: Low light reactor, t=0 min, replicate series 3

description:
Gene expression at t=0, low light reactor
ID17_5_1_C_R3_TP2


title: High light reactor, t=40 min, replicate series 3

description:
Gene expression at t=40 min, high light reactor
ID6_2_2_T_R3_TP6


title: Low light reactor, t=480 min, replicate series 2

description:
Gene expression at t=480 min, low light reactor
ID7_2_3_C_R2_TP10


title: High light reactor, t=120 min, replicate series 3

description:
Gene expression at t=120 min, high light reactor
ID4_1_4_T_R3_TP8

source_name: High light reactor, t=120 min

value: 120 min


title: Low light reactor, t=0 min, replicate series 2

description:
Gene expression at t=0, low light reactor
ID12_3_4_C_R2_TP2


title: Slide233 Area2 092012


title: Slide232 Area4 092012


title: before patient4 with IFX

description:
Gene expression data from whole blood cells before patient 4 with IFX
Pre-IFX-4

source_name: before patient4 with IFX, whole blood cells

value: Kawasaki disease

value: IFX-responsive patient 4

value: whole blood cells


title: Slide232 Area3 092012


title: before patient2 with IFX

description:
Gene expression data from whole blood cells before patient 2 with IFX
Pre-IFX-2

source_name: before patient2 with IFX, whole blood cells

value: IFX-responsive patient 2

value: untreated (pre-IFX treatment)


title: Slide233 Area3 092012


title: before patient3 with IFX

description:
Gene expression data from whole blood cells before patient 3 with IFX
Pre-IFX-3

source_name: before patient3 with IFX, whole blood cells

value: IFX-responsive patient 3


title: before patient1 with IFX

description:
Gene expression data from whole blood cells before patient 1 with IFX
Pre-IFX-1

source_name: before patient1 with IFX, whole blood cells

value: IFX-responsive patient 1


title: 100µM EMD at 72hr, biological rep3 (human)

city: Nottingham

first: John

last: Okyere

address: BioCity Nottingham

country: United Kingdom

institute: CrossGen Limited

description:
H45
Gene expression data from human primary hypatocytes.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with the Affymetrix Console using RMA summarization.

label: Biotin

source_name: Primary hypatocytes

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

growth_protocol: Hepatocytes were plated in 60-mm dishes at a density of 3.5 X 10^6 cell/dish or in 6-well BD BioCoat plated (BD Biosciences, San Jose, CA) at a density of 1.5 X 10^6 cells/well in attachment medium and cultured under a CO2/air (5%/95%) humidified atmosphere at 37oC.

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

treatment_protocol: After a 24h attachment period, the medium was discarded and replaced by incubation medium, consisting of Dulbecco's Modified Eagle's medium, supplemented with 50 mg/l gentamicin, 4 mg/l insulin, and 10-5 M hydrocortisone and containing 0 [vehicle control, 0.1% (v/v) dimethyl sulfoxide], 30, or 100 µM EMD.

tag: tissue

value: liver

value: 100µM EMD at 72hr


title: High light reactor, t=120 min, replicate series 2

description:
Gene expression at t=120 min, high light reactor
ID8_2_4_T_R2_TP8

value: High light


title: High light reactor, t=40 min, replicate series 1, technical replicate 1

description:
Gene expression at t=40 min, high light reactor
ID2_1_2_T_R1_TP6

value: 40 min


title: High light reactor, t=0 min, replicate series 1, technical replicate 1

description:
Gene expression at t=0, high light reactor
ID1_1_1_T_R1_TP2

value: 0 min


title: Low light reactor, t=480 min, replicate series 1

description:
Gene expression at t=480 min, low light reactor
ID3_1_3_C_R1_TP10

value: Low light

value: 480 min


title: 30µM EMD at 72hr, biological rep3 (human)

description:
H43
Gene expression data from human primary hypatocytes.

value: 30µM EMD at 72hr


title: Slide232 Area2 092012

value: Yes

value: CC-Blast


title: 30µM EMD at 24hr, biological rep3 (human)

description:
H35
Gene expression data from human primary hypatocytes.

value: 30µM EMD at 24hr


title: before patient5 with IFX

description:
Gene expression data from whole blood cells before patient 5 with IFX
Pre-IFX-5

source_name: before patient5 with IFX, whole blood cells

value: Japanese

value: Kawasaki disease

value: IFX-responsive patient 5


title: 100µM EMD at 24hr, biological rep3 (human)

description:
H36
Gene expression data from human primary hypatocytes.

value: 100µM EMD at 24hr


title: 0.1% DMSO at 72hr, vehicle control, rep3 (human)

description:
H41
Gene expression data from human primary hypatocytes.

value: 0.1% DMSO at 72hr


title: 0.1% DMSO at 24hr, vehicle control, rep3 (human)

description:
H33
Gene expression data from human primary hypatocytes.

value: 0.1% DMSO at 24hr


title: myr-SetB_3, biological rep3

city: Farmington

first: Ephraim

middle: F

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

institute: University of Connecticut School of Medicine

description: Transfected cells FACS-isolated

hyb_protocol: The labeled product was hybridized to whole genome GeneChip Rat Gene 2.0 ST Arrays (Affymetrix).

scan_protocol: The staining, washing and scanning of the arrays was carried out using a Fluidics 450 station, GeneChip Operating Software and GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Image intensities were analyzed with Expression Console (Affymetrix) from CEL files for quality control using standard GeneChip Rat Gene 2.0 ST Array control probes (Affymetrix), and to determine the RMA expression signal intensity values and for annotations.

organism: Rattus norvegicus

source_name: myr-SetB-transfected RGCs

label_protocol: 5 µg of cDNA product from each sample was used as input for fragmentation and labeling using the Encore Biotin Module kit (4200-12, NuGEN).

growth_protocol: Postnatal rat retinal ganglion cells were purified by immunopanning and cultured in defined growth medium “full-sato” prior to isolation of RNA.

extract_protocol: The Quick-RNA MicroPrep kit (R1050, Zymo Research) was used for RNA extraction according to the manufacturer's instructions.

treatment_protocol: Postnatal rat retinal ganglion cells (RGC) were electroporated with constructs immediately after isolation by immunopanning and then plated in glass bottom dishes uncoated with any substrate. Transfected RGCs were FACS-isolated next day and cultured two more days on laminin prior to isolation of RNA.

value: Sprague Dawley

tag: age

value: postnatal day 4 (P4)

value: purified retinal ganglion cells (RGC)

tag: transfected with

value: myr-Set-β (w/ pMAX-GFP)

tag: cell subtype

value: FACS-isolated, GFP positive RGCs


title: SCCNC2 cell line

type: mixed

city: Oviedo

first: Mario

middle: A

last: Hermsen

state: Asturias

address: Celestino Villamil s/n

department: Otolaryngology

country: Spain

institute: Hospital Universitario Central de Asturias

description: Cell line vs normal XY DNA pooled from 18 males

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Images were acquired using a Microarray scanner G2505B (Agilent Technologies, Palo Alto CA, USA). Analysis and data extraction were quantified using feature extraction software (version 9.1, Agilent Technologies, Palo Alto CA, USA).

data_processing: Log2ratios of signal intensities between tumor and reference for every probe were median-normalized and after segmentation mode normalization was performed (van de Wiel et al., Brief Bioinform 2011). aCGH quality was assessed by means of the MAD of the log2ratios.

molecule: genomic DNA

source_name: SCCNC2 squamous carcinoma cells

label_protocol: 500 ng genomic DNA was combined with a mixture of primers and reaction buffer to a final volume of 39 ul. The DNA was denatured at 99ºC for 10 min, and placed on ice. While on ice, 10 ul cyanine 3-dUTP and cyanine 5-dUTP nucleotide mixture was added to the test and reference DNA, respectively, and finally 1 ul Klenow DNA polymerase was added to each sample to extend the primers. After 4 hr incubation at 37ºC, 5 ul stop buffer was added to stop the reaction. Label was purified using the QIAquick PCR Purification Kit.

growth_protocol: The cell lines were cultured in MEM culture medium, supplemented with 10% FBS, 100 U/ml penicillin, 200 μg/ml streptomycin, 2 mM L-Glutamine and non-essential amino acids 100 μM (PAA Laboratories GmbH, Pasching, Austria) and incubated in 5% C02 at 37ºC.

extract_protocol: DNA was extracted with Qiagen extraction kits (Qiagen GmbH, Hilden, Germany) from the primary tumor, the cell line and from peripheral blood lymphocytes of the same patient. DNA from the cell lines was obtained at passages bewteen 6 and 10.

tag: cell line

value: SCCNC2 cell line

tag: gender

value: male

tag: Stage

tag: grade

value: moderately differentiated

tag: tobacco smoker

value: no

source_name: pooled XY normal blood lymphocytes

tag: reference

value: pooled XY normal blood lymphocytes


title: myr-SetB_1, biological rep1

description: Transfected cells FACS-isolated

tag: strain

tag: cell type


title: wt-SetB_3, biological rep3

description: Transfected cells FACS-isolated

source_name: wt-SetB-transfected RGCs

value: wild-type Set-β (w/ pMAX-GFP)


title: SCCNC2 primary tumor

source_name: SCCNC2 squamous carcinoma tissue

value: SCCNC2 primary tumor


title: wt-SetB_1, biological rep1

description: Transfected cells FACS-isolated


title: SCCNC1 cell line

source_name: SCCNC1 squamous carcinoma cells

value: SCCNC1 cell line


title: mCherry_2, biological rep2

description: Transfected cells FACS-isolated

source_name: mCherry-transfected RGCs

value: mCherry (w/ pMAX-GFP)


title: mCherry_1, biological rep1

description: Transfected cells FACS-isolated


title: mCherry_3, biological rep3

description: Transfected cells FACS-isolated


title: 100µM EMD at 72hr, biological rep2 (human)

description:
H28
Gene expression data from human primary hypatocytes.

value: liver

tag: treatment

value: 100µM EMD at 72hr


title: wt-SetB_2, biological rep2

description: Transfected cells FACS-isolated


title: SCCNC1 primary tumor

source_name: SCCNC1 squamous carcinoma tissue

value: SCCNC1 primary tumor


title: myr-SetB_2, biological rep2

description: Transfected cells FACS-isolated

value: Sprague Dawley


title: 100µM EMD at 24hr, biological rep2 (human)

description:
H20
Gene expression data from human primary hypatocytes.

value: 100µM EMD at 24hr


title: 30µM EMD at 72hr, biological rep2 (human)

description:
H27
Gene expression data from human primary hypatocytes.

value: 30µM EMD at 72hr


title: cyano4

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

description: Replicate 4 of 4, London-CYANO vs London

hyb_protocol: Cy3- and Cy5-labeled cRNA were pooled and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies) for 17h in a rotating hybridization oven at 20 r.p.m. and 65 °C; Slides were washed using the Gene Expression Wash Buffer Kit (also provided by Agilent Technologies)

scan_protocol: Hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 10.5 with default parameter settings for gene expression two-color microarrays (GE2_107_Sep09). The data was transferred to GeneSpring GX 11.0 software (Agilent Technologies) for further statistical analysis. Probes were flag filtered (only probes that had flag-value “present” in 50% of all replicates were retained) and linked to T. urticae genes using the “Create New Gene-Level Experiment” option. Differentially expressed genes were identified by a Student’s t test with the cut off of Fold Change (FC) and corrected P-value (Benjamini-Hochberg correction) at 2 and 0.05, respectively.

organism: Tetranychus urticae

source_name: London-CYANO, whole organism

label_protocol: 100 ng of total RNA (+ RNA-spike in control) was used to generate Cy3- or Cy5-labeled cRNAs, using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies)

growth_protocol: Both the London and London-CYANO strain were maintained in climatically controlled rooms at 26 °C, 60% RH and 16:8 h light:dark photoperiod

extract_protocol: Total RNA samples were isolated using the RNeasy minikit (Qiagen) and were subsequently treated with DNase (Turbo DNA-free kit, Ambion). RNA was extracted from 100-120 young adult female mites in four replicates from each strain (London, London-CYANO)

value: adult

value: female

tag: host

value: London-CYANO

source_name: London, whole organism

value: London


title: cyano1

description: Replicate 1 of 4, London-CYANO vs London


title: 0.1% DMSO at 72hr, vehicle control, rep2 (human)

description:
H25
Gene expression data from human primary hypatocytes.

value: 0.1% DMSO at 72hr


title: Smarca5-cKO-P10 replicate 3

city: Ottawa

first: Alan

last: Mears

state: ON

address: 401 Smyth Rd

department: Research Institute

institute: Children's Hospital of Eastern Ontario

description: Replicate 3 (of 3). Dissected cerebellum at P10. Dye flip.

hyb_protocol: Hybridization protocols were followed according to manufacturers guidelines (Genisphere) using the formamide-based buffer.

scan_protocol: Slides were scanned with a ScanArray Express (Perkin Elmer) scanner for the Cy5 and Cy3 channels

data_processing: Raw signal values were obtained using a ProScan array express scanner (Perkin Elmer). Background subtracted values were then processed using GLOBAL LOESS (intra-array) and QUANTILE (inter-array) normalization via the online WEBARRAY tool.(http://www.webarraydb.org/webarray/index.html).

organism: Mus musculus

source_name: P10 cerebellum

label_protocol: cDNA synthesis and labeling was performed with the 3DNA Array 900 kit (Genisphere).

extract_protocol: RNA was isolated from brain tissue (cerebella) with Trizol reagent (Invitrogen) according to manufacturers protocols.

tag: genotype

value: wild type

value: Smarca5 cKO


title: 30µM EMD at 72hr, biological rep1 (human)

description:
H11
Gene expression data from human primary hypatocytes.


title: 30µM EMD at 24hr, biological rep2 (human)

description:
H19
Gene expression data from human primary hypatocytes.

value: 30µM EMD at 24hr


title: cyano3

description: Replicate 3 of 4, London-CYANO vs London


title: 0.1% DMSO at 72hr, vehicle control, rep1 (human)

description:
H9
Gene expression data from human primary hypatocytes.


title: cyano2

description: Replicate 2 of 4, London-CYANO vs London


title: Smarca5-cKO-P0 replicate 3

description: Replicate 3 (of 4). Dissected cerebellum at P0.

source_name: P0 cerebellum

tag: sample #

value: sample #230

value: sample #231


title: 30µM EMD at 24hr, biological rep1 (human)

description:
H3
Gene expression data from human primary hypatocytes.


title: Smarca5-cKO-P10 replicate 1

description: Replicate 1 (of 3). Dissected cerebellum at P10.


title: 100µM EMD at 24hr, biological rep1 (human)

description:
H4
Gene expression data from human primary hypatocytes.


title: 100µM EMD at 72hr, biological rep1 (human)

description:
H12
Gene expression data from human primary hypatocytes.


title: Pooled_P. falciparum_complicated malaria samples and Pooled_un-complicated malaria samples (Cy3/background intensity)

city: Pilani

first: Ashis

middle: Kumar

last: Das

state: Rajasthan

address: Vidya Vihar

department: Biological Sciences

country: India

institute: Birla Institute of Technology & Science,Pilani (Pilani Campus)

description: Pooled_P. falciparum_complicated malaria samples and Pooled_P. falciparum_un-complicated malaria samples (Cy3/background intensity)

hyb_protocol: The labeled cRNA samples were hybridized to Plasmodium falciparum Custom 244k Array designed by Genotypic Technology Private Limited and Prof.Ashis K Das (AMADID:19056) with Gene Expression Hybridization Kit (Agilent Technologies, part number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Gene Expression wash buffers (Agilent Technologies, Part No: 5188-5327).

scan_protocol: Scanning was performed using the Agilent Microarray Scanner (Agilent, Palo Alto, CA, G Model G2565BA) at 5 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software (Agilent Technologies). Channel split Analysis was performed. Data was analyzed separately for complicated (Cy5) and un-complicated (Cy3) samples. The raw signal intensities and back ground intensities were obtained from the raw data files for each channel. Based on the annotation and probe orientation the probes were classified as sense and antisense probes. Ratio was calculated by taking the raw signal intensity vs. background signal intensity for each of the probes.

organism: Plasmodium falciparum

source_name: P. falciparum parasites from patients peripheral blood

label_protocol: Nine complicated and two un-complicated malaria parasite RNA samples were pooled separately in equimolar amounts. The two pooled RNA samples were labeled using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technolgies). 500ng each of the pooled un-complicated (control) and complicated malaria (test) samples were incubated with reverse transcription mix at 40°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The double stranded cDNA was used as template for cRNA generation. This was performed by in vitro transcription and during this process Cy3 and Cy5 CTP dyes (Agilent) were incorporated for un-complicated and complicated malaria samples respectively. The cDNA synthesis and in vitro transcription steps were carried out at 40°C.

growth_protocol: P. falciparum isolates collected directly from infected patients with differing clinical symptoms

extract_protocol: Total RNA extracted using Tri-Reagent (Sigma Aldrich, USA) following manufacturer's instructions

treatment_protocol: Blood was immediately (Within 15 minutes of collection) subjected to density gradient based separation (Histopaque 1077, Sigma Aldrich, USA) to separate the Peripheral Blood Mononuclear Cells (PBMCs) from the infected and uninfected erythrocytes following manufacturer’s instructions. Both fractions were washed with Phosphate buffered saline (PBS) twice and lysed using 4 volumes of Tri-Reagent (Sigma Aldrich, USA) and stored at -80°C.

tag: clinical presentation

value: un-complicated malaria (pooled 2 samples)

tag: age (1#pfu_1)

tag: gender (1#pfu_1)

value: M

tag: age (1#pfu_2)

tag: gender (1#pfu_2)

tag: age (1#pfc_1)

tag: gender (1#pfc_1)

tag: age (2#pfc_2)

tag: gender (2#pfc_2)

tag: age (3#pfc_3)

tag: gender (3#pfc_3)

tag: age (4#pfc_4)

tag: gender (4#pfc_4)

tag: age (5#pfc_5)

tag: gender (5#pfc_5)

value: F

tag: age (6#pfc_6)

tag: gender (6#pfc_6)

tag: age (7#pfc_7)

tag: gender (7#pfc_7)

tag: age (8#pfc_8)

tag: gender (8#pfc_8)

tag: age (9#pfc_9)

tag: gender (9#pfc_9)


title: NBS11356_97128227_08_V2

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

description:
NBS11356_97128227_08_V2
A_4x44k_252665217112-1_V2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-143

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Human Reference B

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-138

extract_protocol: Qiagen Rneasy Mini

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

source_name: Normal Tissue Adjacent to Breast Tumor

tag: distance to tumor

value: Peritumoral

tag: er status


title: Smarca5-cKO-P0 replicate 4

description: Replicate 4 (of 4). Dissected cerebellum at P0. Dye flip.

tag: strain

tag: genotype

tag: sample #

value: sample #224


title: RNA from skin MSC donor 2

city: Stanford

first: Andreas

last: Reinisch

state: CA

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

hyb_protocol: Fragmented and labeled targets were hybridized overnight at 45C, 60rpm in an Affymetrix GeneChip Hybridization Oven 645.

scan_protocol: Genechips weres scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: Arrays were normalized in R using oligolibrary. The script  (R) used  to generate the matrix is provided (data_processing_script.txt).

source_name: skin-derived MSC

label_protocol: Bioting-labeling using standard Afymetrix WT Terminal Labeling Kit

extract_protocol: RNA was isolated from 5x10E6 cells using the Qiagen RNeasy PlusMini Kit.

tag: donor id

value: donor 2

tag: tisse source for mscs

value: skin

tag: cell type

value: Mesenchymal Stromal Cells (MSC)

tag: sample isolation method

value: plastic adherence

tag: passage

value: passage 2


title: NBS10116_99556326_01_V2

description:
NBS10116_99556326_01_V2
A_4x44k_252665217098-4

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-148

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-143


title: 0.1% DMSO at 24hr, vehicle control, rep1 (human)

description:
H1
Gene expression data from human primary hypatocytes.

source_name: Primary hypatocytes

tag: tissue

value: liver

tag: treatment

value: 0.1% DMSO at 24hr


title: Smarca5-cKO-P10 replicate 2

description: Replicate 2 (of 3). Dissected cerebellum at P10.

value: wild type

value: Smarca5 cKO


title: NBS10136_91970970_02_V2

description:
NBS10136_91970970_02_V2
A_4x44k_252665217097-1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: RNA from skin MSC donor 1

value: donor 1


title: NBS10181_94349438_08_V2

description:
NBS10181_94349438_08_V2
A_4x44k_252665217097-2

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-161

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-156

value: Remote


title: sh_c

city: Würzburg

first: Katrin

last: Schlegelmilch

address: Brettreichstr. 11

department: Orthopedic Centre for Musculoskeletal Research

institute: University of Würzburg

description: shRNA5 knock-down C

hyb_protocol: Samples were fragmented and hybridized onto the GeneChip for 16h.

scan_protocol: The arrays were washed and stained according to the manufacturer's recommendation, and finally scanned in a GeneChip scanner 3000 (Affymetrix).

data_processing: R/Bioconductor, RMA normalization with expresso

source_name: human MSCs

label_protocol: Genome-wide gene expression profiling was performed using Affymetrix GeneChips HG-U133Plus_2.0 (High Wycombe, United Kingdom) and reagents according to the Affymetrix ExpressKit protocol (www.affymetrix.com). Therefore, total RNA samples were used to generate biotin-labelled, single-stranded cRNA samples.

growth_protocol: Primary hMSCs from trabecular bone were isolated from the femoral heads. These were obtained from patients undergoing total hip arthroplasty and cultivated as described in other studies. Experiments were performed with the approval of the Local Ethics Committee of the University of Würzburg. Each patient was informed and provided a written consent. MSCs from four individuals were used for this study, ranging between 45 and 80 years of both genders. Seeded cells were cultivated in passage zero in DMEM/Ham’s F-12 with L-glutamine supplemented with 10% FCS, 1% penicillin- streptomycin and 50 mg/ml L-ascorbic acid 2-phosphate (Sigma-Aldrich Chemie GmbH, Schnelldorf, Germany) and incubated at 37°C in a humidified atmosphere enriched with 5% CO2. Cells were trypsinized and splitted into passage one for experimental settings.

extract_protocol: RNA isolation of WISP1 down-regulated and control cells took place simultaneously and sequentially to investigate the gradient of WISP1 gene silencing. Total RNA from cultured cells was isolated following the manufacturer’s instruction of the NucleoSpin® RNA II kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany). Finally, RNA samples were analyzed using a BioPhotometer (Eppendorf AG, Hamburg, Germany) to measure the final RNA quality and integrity.

treatment_protocol: In this study, shRNA constructs integrated into the lentiviral expression vector pLKO.1, were used to generate stable siRNA expression against WISP1 in hMSCS. A set of five different shRNA constructs and one shRNA scrambled negative control were commercially supplied from the RNAi Consortium (TRC) of Thermo Fisher Scientific (Open Biosystems Inc., Fisher Scientific GmbH, Schwerte, Germany). These constructs were designed to include a 21bp hairpin stem (sense and antisense) flanking a loop of 6bp. Due to the fact that all CCN family members share several conserved sequence homologies, gene silencing experiments were performed with two different effective shRNA constructs (further referenced as shRNA2 and shRNA5) to exclude the observations of so called “off-target effects”. Furthermore, appropriate shRNA constructs were selected according to their ability to target different domains existing in WISP1-T1 and -T2 (shRNA2 - TSP domain; shRNA5 - CT domain).  Hairpin sequences the effective constructs were for shRNA2: 5’-CCGGCCACTCGGATCTCCAATGTTACTCGAGTAACATTGGAGATCCGAGTGGTTTTTG-3’ and respectively for shRNA5: 5’-CCGGGCTTCTGTAACCTGAGCTGTACTCGAGTACAGCTCAGGTTACAGAAGCTTTTTG-3’. The shRNA scrambled negative control sequence was 5’-CCGGCCTAAGGTTAAGTCGCCCTCGCTCGAGCGAGGGCGACTTAACCTTAGGTTTTTG- 3’.

value: mesenchymal stem cells

value: WISP1 knock-down


title: High light reactor, t=120 min, replicate series 1

description:
Gene expression at t=120 min, high light reactor
ID18_5_2_T_R1_TP8

source_name: High light reactor, t=120 min

tag: light regime

value: High light

tag: time

value: 120 min


title: 0.1% DMSO at 24hr, vehicle control, rep2 (human)

description:
H17
Gene expression data from human primary hypatocytes.


title: NBS11245_93859536_02_V2

description:
NBS11245_93859536_02_V2
A_4x44k_252665217097-3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-136

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-131

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

value: Peritumoral


title: Pooled_P. falciparum_complicated malaria samples and Pooled_un-complicated malaria samples (Cy5/background intensity)

description: Pooled_P. falciparum_complicated malaria samples and Pooled_P. falciparum_un-complicated malaria samples (Cy5/background intensity)

tag: clinical presentation

value: un-complicated malaria (pooled 2 samples)

tag: age (1#pfu_1)

tag: gender (1#pfu_1)

value: M

tag: age (1#pfu_2)

tag: gender (1#pfu_2)

value: complicated malaria  (pooled 9 samples)

tag: age (1#pfc_1)

tag: gender (1#pfc_1)

tag: age (2#pfc_2)

tag: gender (2#pfc_2)

tag: age (3#pfc_3)

tag: gender (3#pfc_3)

tag: age (4#pfc_4)

tag: gender (4#pfc_4)

tag: age (5#pfc_5)

tag: gender (5#pfc_5)

value: F

tag: age (6#pfc_6)

tag: gender (6#pfc_6)

tag: age (7#pfc_7)

tag: gender (7#pfc_7)

tag: age (8#pfc_8)

tag: gender (8#pfc_8)

tag: age (9#pfc_9)


title: RNA from UC MSC donor 3

source_name: UC-derived MSC

tag: donor id

value: donor 3

tag: tisse source for mscs

value: umbilical cord (UC)

tag: cell type

value: Mesenchymal Stromal Cells (MSC)

tag: sample isolation method

value: plastic adherence

tag: passage

value: passage 2


title: Smarca5-cKO-P0 replicate 2

description: Replicate 2 (of 4). Dissected cerebellum at P0. Dye flip.

tag: strain

tag: genotype

value: wild type

tag: sample #

value: sample #229

value: Smarca5 cKO

value: sample #225


title: Lung 129 IFNAR1-/- X31 infected, rep4

city: London

first: Stefania

last: Crotta

address: The Ridgeway

department: IR

institute: The Crick- Mill Hill Laboratories

description:
Sample 24
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A

hyb_protocol: 1.5µg of sample hybridised using standard illumina Protocol (55ºC High Stringency wash 100%EtOHFix Illumina BlockBuffer Block Cy3Streptavidin Staining).

scan_protocol: Scanner: Illumina iScan. Data acquisition software: Illumina iScan Control Software-V3. Intensity .idat files for use in downstream analysis software Genome Studio.

data_processing: The data were normalised using 75th percentile normalisation in GeneSpring 11.5.

source_name: lung from 129 IFNAR1-/-, influenza A (X31) infected

label_protocol: Ambion Illumina Total Prep 96RNAAmplification Kit.

extract_protocol: Lung samples were homogenized in 10 volumes of TRI Reagent and then processed using the RiboPure kit (Ambion) according to the manufacturer's instructions.

treatment_protocol: Mock- or 5 day influenza A (X31)-infected total lungs from mice with the indicated genotypes were collected and processed for expression profiling.

tag: strain/background

tag: genotype/variation

tag: tissue

value: lung

tag: treatment

value: influenza A (X31) infection


title: Smarca5-cKO-P0 replicate 1

description: Replicate 1 (of 4). Dissected cerebellum at P0.

value: sample #224

value: sample #227


title: RNA from UC MSC donor 2

value: donor 2


title: sh_b

description: shRNA5 knock-down B

value: mesenchymal stem cells

value: WISP1 knock-down


title: Lung 129 IFNAR1-/- X31 infected, rep3

description:
Sample 23
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: Lung 129 IFNAR1-/- X31 infected, rep2

description:
Sample 22
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: RNA from UC MSC donor 1

value: donor 1


title: scr_b

description: Scrambled Control B

value: scrambled oligo


title: Lung 129 X31 infected, rep1

description:
Sample 17
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A

source_name: lung from 129, influenza A (X31) infected


title: Lung C57BL/6 X31 infected, rep3

description:
Sample 15
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A

source_name: lung from C57BL/6, influenza A (X31) infected


title: RNA from WAT MSC donor 3

source_name: WAT-derived MSC

value: donor 3

value: white adipose tissue (WAT)


title: RNA from WAT MSC donor 1

value: Mesenchymal Stromal Cells (MSC)

value: plastic adherence


title: sh_a

description: shRNA5 knock-down A


title: Lung 129 X31 infected, rep2

description:
Sample 18
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A

value: wild type


title: RNA from WAT MSC donor 2

value: passage 2


title: scr_c

description: Scrambled Control C


title: Lung 129 IFNAR1-/- X31 infected, rep1

description:
Sample 21
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: Lung C57BL/6 X31 infected, rep2

description:
Sample 14
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: Lung 129 X31 infected, rep3

description:
Sample 19
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: Lung 129 X31 infected, rep4

description:
Sample 20
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: CN-11

type: genomic

city: Adelaide

first: Naiara

middle: G

last: Bediaga

state: South Australia

address: 4 North Terrace

department: Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences

country: Australia

institute: The University of Adelaide

hyb_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Quality control and data pre-processisng was performed using lumi package (Bioconductor).Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor).

source_name: Oral rinse

label_protocol: standard as recommended by illumina

extract_protocol: genomic DNA was extracted and purified from oral rinse samples using using Gentra Puregene Buccal Cell Kit according to standard instructions

tag: gender

value: Female

tag: age

tag: disease

value: Control


title: scr_a

description: Scrambled Control A


title: Lung C57BL/6 X31 infected, rep4

description:
Sample 16
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A

value: lung


title: CN-12

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting


title: RNA from BM MSC donor 2

source_name: BM-derived MSC

value: bone marrow (BM)


title: Lung 129 IFNAR1-/- mock infected, rep3

description:
Sample 11
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A

source_name: lung from 129 IFNAR1-/-, mock infected

value: mock infection


title: Lung C57BL/6 X31 infected, rep1

description:
Sample 13
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A

value: influenza A (X31) infection


title: Lung 129 IFNAR1-/- mock infected, rep1

description:
Sample 9
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: RNA from BM MSC donor 1


title: Lung 129 IFNAR1-/- mock infected, rep4

description:
Sample 12
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: RNA from BM MSC donor 3


title: Lung 129 IFNAR1-/- mock infected, rep2

description:
Sample 10
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: LQ-90

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: Quality control and data pre-processing was performed using lumi package (Bioconductor). Samples were background adjusted, processed for the colour channel adjustment and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor).

source_name: Oral rinse, oral lichenoid disease

label_protocol: Standard as recommended by Illumina.

extract_protocol: Genomic DNA was extracted and purified from oral rinse samples using the Gentra Puregene Buccal Cell Kit according to standard instructions.

tag: disease state

value: oral lichenoid disease

tag: Sex

value: female

value: buccal cells

tag: tobacco

tag: alcohol


title: Lung 129 mock infected, rep4

description:
Sample 8
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A

source_name: lung from 129, mock infected


title: CN-09


title: LQ-93

tag: cell type


title: LQ-99


title: LQ-89


title: LQ-88


title: CN-08


title: Lung 129 mock infected, rep3

description:
Sample 7
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: CN-01

value: Male


title: LQ-85


title: LQ-143

value: Oral Lichenoid disease


title: Lung C57BL/6 mock infected, rep4

description:
Sample 4
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A

source_name: lung from C57BL/6, mock infected


title: LQ-116


title: maternal lowp.+fol. diet 1 day pup rep 4

first: Gioia

last: Altobelli

address: 5 University Street

institute: UCL

description: replicate 4

hyb_protocol: Standard Illumina

scan_protocol: Standard Illumina

data_processing: R-Bioconductor, Limma and Beadarray packages

source_name: Rat liver

label_protocol: MessageAmp for Illumina arrays (Ambiogen)

growth_protocol: liver tissue snap-frozen in liquid nitrogen, stored at -80 C

extract_protocol: Rneasy mini kit (QIAGEN)

treatment_protocol: TurboDNaseI (Ambion)

value: Wistar

value: male

value: 1 day


title: LQ-144


title: maternal low p. diet 1 day pup rep 3

description: replicate 3


title: Lung C57BL/6 mock infected, rep2

description:
Sample 2
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: Lung C57BL/6 mock infected, rep1

description:
Sample 1
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: maternal lowp.+fol. diet 1 day pup rep 1

description: replicate 1


title: LQ-121


title: LQ-76


title: Lung 129 mock infected, rep1

description:
Sample 5
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: Lung 129 mock infected, rep2

description:
Sample 6
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: maternal lowp.+fol. diet 1 day pup rep 2

description: replicate 2


title: maternal lowp.+fol. diet 1 day pup rep 3

description: replicate 3


title: Lung C57BL/6 mock infected, rep3

description:
Sample 3
Gene expression data from lung cells.
Illumina.SingleColor.MouseWG-6_V2_0_R0_11278593_A


title: LQ-73


title: LQ-71


title: LQ-132


title: LQ-120


title: maternal control diet 1 day pup rep 4

description: replicate 4


title: maternal control diet 1 day pup rep 3

description: replicate 3


title: maternal low p. diet 1 day pup rep 4

description: replicate 4


title: maternal control diet 1 day pup rep 2

description: replicate 2


title: LQ-65


title: LQ-69


title: maternal low p. diet 1 day pup rep 2

description: replicate 2


title: LQ-70


title: maternal low p. diet 1 day pup rep 1

description: replicate 1


title: LQ-94


title: LQ-85


title: LQ-113


title: HOTAIRM1 shRNA2, ATRA_96hr

city: Worcester

first: Peter

last: Newburger

state: United States

address: 364 Plantation Street

institute: University of Massachusetts Medical School

description:
Gene expression data from HOTAIRM1 knockdown NB4 cells after ATRA induction
Sample name: KD3+ATRA

hyb_protocol: Hybridization, washing and staining of ST array using Hybridization, Wash and Stain kit (Affymetrix) were performed by UMass Medical School Genomics Core Facility, equipped with the GeneChip Hybridization Oven 320 and GeneChip Fluidic Station 450 (Affymetrix)

scan_protocol: The arrays were scanned by UMass Medical School Genomics Core Facility equipped with the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: R/Bioconductor (RMA, limma)

source_name: HOTAIRM1 knockdown, ATRA treated

label_protocol: The Ambion WT Expression Kit and Affymetrix GeneChip WT Terminal Labeling Kit were used to prepare cDNA target for ST arrays, according to vendor's protocols

extract_protocol: RNAzol RT extraction of total RNA, performed according to the manufacturer's instructions

treatment_protocol: 0.5 uM all-trans retinoic acid, 96 hours, starting density of cells = 5X104, divide after 48 hours

value: acute promyelocytic leukemia cells

value: HOTAIRM1 shRNA2

tag: cell line

value: ATRA


title: LQ-64


title: LQ-61

value: Female


title: HOTAIRM1 shRNA1, ATRA_96hr, biological rep2

description:
Gene expression data from HOTAIRM1 knockdown NB4 cells after ATRA induction
Sample name: KD2+ATRA

value: HOTAIRM1 shRNA1


title: maternal control diet 1 day pup rep 1

description: replicate 1


title: LQ-56


title: scrambled shRNA, ATRA_96hr, biological rep2

description:
Gene expression data from scrambled shRNA expressing NB4 cells after ATRA induction
Sample name: SCR2+ATRA

source_name: scrambled control, ATRA treated

value: scrambled shRNA


title: scrambled shRNA, ATRA_96hr, biological rep1

description:
Gene expression data from scrambled shRNA expressing NB4 cells after ATRA induction
Sample name: SCR1+ATRA


title: LQ-61


title: LQ-60


title: LQ-65


title: wild type control, ATRA_96hr

description:
Gene expression data from wild type NB4 cells after ATRA induction
Sample name: NB4+ATRA

source_name: wild type, ATRA treated

value: wild type control


title: scrambled shRNA, untreated, biological rep2

description:
Gene expression data from scrambled shRNA expressing NB4 cells before ATRA induction
Sample name: SCR2

source_name: scrambled control, untreated


title: HOTAIRM1 shRNA1, untreated, biological rep2

description:
Gene expression data from HOTAIRM1 knockdown NB4 cells before ATRA induction
Sample name: KD2

source_name: HOTAIRM1 knockdown, untreated


title: LQ-54


title: LQ-53


title: HOTAIRM1 shRNA1, ATRA_96hr, biological rep1

description:
Gene expression data from HOTAIRM1 knockdown NB4 cells after ATRA induction
Sample name: KD1+ATRA


title: LQ-47


title: HOTAIRM1 shRNA1, untreated, biological rep1

description:
Gene expression data from HOTAIRM1 knockdown NB4 cells before ATRA induction
Sample name: KD1


title: HOTAIRM1 shRNA2, untreated

description:
Gene expression data from HOTAIRM1 knockdown NB4 cells before ATRA induction
Sample name: KD3


title: LQ-104


title: scrambled shRNA, untreated, biological rep1

description:
Gene expression data from scrambled shRNA expressing NB4 cells before ATRA induction
Sample name: SCR1


title: LQ-39


title: Sample 6_B586

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: Affymetrix protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: CD14+ monocytes_control

label_protocol: Affymetrix single amplification protocol

extract_protocol: QIAGEN Rneasy Kit

tag: subject

value: healthy volunteer

value: blood (buffy coat)

value: CD14+ monocytes

tag: treated with

value: none (control)


title: LQ-47

value: oral lichenoid disease

value: buccal cells


title: LQ-30

value: Oral Lichenoid disease


title: LQ-03

value: Male


title: Sample 5_B586

source_name: CD14+ monocytes_IL-17A

value: IL-17A (200ng/ml) for 24hrs in culture


title: Sample 3_B585


title: LQ-43

value: female


title: LQ-34


title: LQ-29


title: wild type control, untreated

description:
Gene expression data from wild type NB4 cells before ATRA induction
Sample name: NB4

source_name: wild type, untreated

value: acute promyelocytic leukemia cells


title: LQ-26


title: 0.1% DMSO at 72hr, vehicle control, rep3 (rat)

description: Gene expression data from rat primary hepatocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with the Affymetrix Console using RMA summarization

source_name: Primary hepatocytes

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

growth_protocol: Hepatocytes were plated in 60-mm dishes at a density of 3.5 X 106 cell/dish or in 6-well BD BioCoat plated (BD Biosciences, San Jose, CA) at a density of 1.5 X 106 cells/well in attachment medium and cultured under a CO2/air (5%/95%) humidified atmostpher at 37oC.

treatment_protocol: After a 24h attachment period, the medium was discarded and replaced by incubation medium, consisting of Dulbecco’s modified Eagle’s medium, supplemented with 50 mg/l gentamicin, 4 mg/l insulin, and 10-5 M hydrocortisone and containing 0 [vehicle control, 0.1% (v/v) dimethyl sulfoxide], 30, or 100 µM EMD

value: liver

tag: strain

value: Wistar

value: 0.1% DMSO at 72hr


title: Sample 4_B585


title: 30µM EMD at 72hr, biological rep3 (rat)

value: 30µM EMD at 72hr


title: LQ-152


title: LQ-156


title: Sample 1_B584


title: Sample 2_B584


title: 100µM EMD at 72hr, biological rep3 (rat)

value: 100µM EMD at 72hr


title: 100µM EMD at 72hr, biological rep2 (rat)


title: 100µM EMD at 24hr, biological rep3 (rat)

value: 100µM EMD at 24hr


title: 30µM EMD at 24hr, biological rep3 (rat)

value: 30µM EMD at 24hr


title: 100µM EMD at 24hr, biological rep2 (rat)


title: LQ-150


title: 0.1% DMSO at 24hr, vehicle control, rep3 (rat)

value: 0.1% DMSO at 24hr


title: 0.1% DMSO at 72hr, vehicle control, rep2 (rat)

value: 0.1% DMSO at 72h


title: 30µM EMD at 72hr, biological rep2 (rat)


title: LQ-149


title: 30µM EMD at 24hr, biological rep2 (rat)


title: LQ-146

value: male


title: 0.1% DMSO at 24hr, vehicle control, rep2 (rat)


title: LQ-145

value: oral lichenoid disease


title: Kasumi-1_Control_rep2

city: Shanghai

first: Junyan

last: Lu

state: Shanghai

address: 555 Zuchongzhi Road, Zhangjiang High Tech Park

department: Drug Discovery and Design Center

country: China

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

description: This sample is of Kasumi-1 cells untreated with FTY720, used as control group. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

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

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

data_processing: The raw data (.pair file) was 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 as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: Kasumi-1 cells, untreated

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

growth_protocol: Kasumi-1 cells were incubated in RPMI 1640 media supplemented with 10% FBS and 1% antibiotic/antimycotic

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: Kasumi-1 cells were treated with DMSO or 5μM FTY720 for 6 hours


title: Kasumi-1_Control_rep1

description: This sample is of Kasumi-1 cells untreated with FTY720, used as control group. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: 100µM EMD at 72hr, biological rep1 (rat)


title: LQ-144

value: buccal cells


title: Kasumi-1_FTY720_6hours_rep3

description: This sample is of Kasumi-1 cells treated with 5 μM FTY720 for 6 . It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Kasumi-1 cells treated with FTY720 for 6 hours

value: 5 μM FTY720


title: Kasumi-1_Control_rep3

description: This sample is of Kasumi-1 cells untreated with FTY720, used as control group. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: 30µM EMD at 72hr, biological rep1 (rat)


title: LQ-143


title: LQ-136


title: LQ-134


title: LQ-133


title: LQ-132


title: Kasumi-1_FTY720_6hours_rep1

description: This sample is of Kasumi-1 cells treated with 5 μM FTY720 for 6 . It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: MCF-7/AZ.Pcad cells untreated with azurin, biological replicate_3

city: Lisboa

first: Nuno

last: Bernardes

state: Lisboa

address: Avenida Rovisco Pais, 1

department: Departamento de Bioengenharia

country: Portugal

institute: Instituto Superior Técnico

description: Gene expression data from untreated cells

hyb_protocol: PREHYBRIDIZATION: 1. Make 100 ml prehybridization buffer (for a maximum of 4 slides) containing 5xSSC, 25% formamide (Merck Cat# 1.09684.10), 0.1% SDS and 1% bovine serum albumin (BSA; Sigma Cat# A-9418): 25 ml 20x SSC, 25 ml pure formamide, 49 ml ddH2O, 1 ml 10% SDS and 1 g BSA. After BSA has dissolved the solution becomes clear in about 5 minutes. 2. Filter prehybridization buffer through a 0.22 micron syringe filter. 3. Heat the prehybridization solution to 42 ÂºC in a 100 ml Coplin Jar. 4. Place slides to be analyzed into the pre-heated pre-hybridization buffer. Incubate for 45 minutes at 42 ÂºC. 5. Wash the slides by dipping 5 times in room temperature ddH2O (staining dish). 6. Dip the slides 5 times in room temperature isopropanol (staining dish). 7. Air dry in fume hood (15 ml tube rack upside down). Slides should be used immediately following prehybridization. HYBRIDIZATION: Note: The first steps of the hybridization protocol can be completed during the prehybridization step. The hybridization volume for a whole slide (25x60mm) is 500 ul if using Agilent SureHyb technology or 80 ul if using LifterSlips (Erie Scientific). Maximum volume of Cy3 and Cy5 combined target is half the total hybridization volume. 1. Prepare 2x hybridization buffer containing 50% formamide, 10xSSC and 0.2% SDS: 2.5 ml formamide, 2.5 ml 20xSSC and 0.1 ml 10% SDS. 2. Immediately filter the hybridization buffer through a 0.22 micron filter (before SDS precipitates out of solution). 3. Take 250 ul of the 2x hybridization buffer and add 5 ul Herring sperm DNA (stock 10 ug/ul, sheared). Final concentration in 2x hybridization buffer is 200 ug/ml. 4. Pre-heat to 42 ÂºC to overcome SDS precipitation. Combine target with hybridization buffer (preheated to 42 ÂºC) in a 1:1 proportion. Heat at 95 ÂºC for 5 minutes. Spin at 12000 rpm for 4 minutes. DO NOT place on ice after the 4 minute spin. Using Agilent gasket slides (G2534-60003), Agilent SureHyb hybridization chambers (G2534A) and hybridization oven (G2545A), see Agilent User Manual for instructions: 1. For each array, put a gasket slide onto a SureHyb chamber and add a total of 500 ul target as 1 dot in the center of the chamber. 2. Put a microarray slide on the gasket slide by holding it in place with your fingertips, towards the top edge of the gasket chamber. 3. Gently (!) allow the microarray slide to drop onto the gasket chamber by lowering it with the aid of your other hand. Do not move the microarray slide after it is in place. 4. Place the SureHyb chamber into the hybridization oven at 42 ÂºC for 16-20 hours. Using LifterSlips (Erie Scientific): 1. Place clean LifterSlip, teflon side down, over the array area. 2. Place the pipette tip along an open edge of the LifterSlip and slowly pipette 80 ul target out of the tip. Capillary action will draw the probe mix under the slip. 3. Place the slide in a Corning Hybridization Chamber (Corning Cat# 2551). 4. Add 20 ul of water to each well in the chamber and clamp the hybridization chamber closed. 5. Gently place the hybridization chamber into a 42 ÂºC water bath for 16-20 hours. WASHING OF THE HYBRIDIZED ARRAYS: 1. Remove the slide from the hybridization chamber, taking care not to disturb the coverslip. 2. Separate the slide form the cover while submersed in Low-stringency wash buffer (see below), inside a staining dish (250 ml buffer may be used to disassemble up to 6 hybridizations). Gently remove the coverslip while the slide is in solution. LifterSlips and Agilent gasket slides may be reused up to 4 times and should be washed in 70 % Ethanol prior to use. 3. Perform the following washes: (i) Low-stringency wash: Place the slides in a Wheaton staining Dish (118mm x 88 mm x 70 mm, Wheaton ref. 900303) containing 500 ml 1xSSC and 0.2% SDS (= 500 ml 1xSSC and 10 ml of 10% SDS). Incubate for 4 minutes at room temperature, with gentle magnetic stirring. (ii) High-stringency wash: Place the slides in a Wheaton staining Dish (118mm x 88 mm x 70 mm, Wheaton ref. 900303) containing 500 ml 0.1xSSC and 0.2% SDS (= 50 ml 1xSSC, 450 ml water and 10 ml of 10% SDS). Incubate for 4 minutes at room temperature, with gentle magnetic stirring. (iii) Wash the slide finally in 500 ml 0.1xSSC to remove particles of SDS. Incubate for 4 minutes at room temperature, with gentle magnetic stirring. 4. Allow the slides to dry by centrifuging 3 minute 800 rpm (do this immediately after the third wash).

scan_protocol: Scanning of slides using the Agilent G2565AA DNA microarray scanner: Resolution: 10 um Red laser PMT= 30%, Green laser PMT= 30% Feature extraction was performed with QuantArray v3.0 software, using the Histogram method for measuring the Mean signal intensity and Mean background intensity.For background calculations were considered the 5-20 percentile of least intense pixels and for signal calculations the 80-95 percentile of most intense pixels. The feature extraction grid was adjusted manually and visually bad spots were flagged using the software flag tool.

data_processing: The Agilent Feature Extraction processed signal was annotated and filtered using BRB Array Tools 3.8.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html). Features with signal intensity below 10 were excluded before averaging of the probe replicates. Probes absent in at least 33% of the microarrays were discarded from the dataset and a total of 29426 probes were considered for further analysis.

source_name: MCF-7/AZ.Pcad untreated cells

label_protocol: RT REACTION (ratio 7 aa-dUTP : 3 dTTP): 1. Prepare the following RNA/primer mix on ice: 3 ul of mRNA (1ug/ul), 6 ul of oligo dT12-18 primer (0.25 ug/ul, Invitrogen Cat. No. 18418-012), and 4 ul H2O. 2. Incubate at 70 ºC for 10 minutes. 3. After a short spindown chill on ice for 5 minutes. 4. During the 70 ºC incubation of the RNA/primer mix prepare the following labeling mix. (If multiple cDNA synthesis reactions are going to be performed a single labeling mix can be prepared by scaling up the volumes proportionally). On ice add, in the following order: 3 ul of dGAC-mix (1 mM each), 0.9 ul of 1 mM dTTP, 2.1 ul of 1 mM aa-dUTP (Sigma, A-0410), 6 ul of 5X first strand buffer and 3 ul of 0.1 M DTT (total volume = 15 ul). 5. Add the labeling mix to the RNA/primer mix. 6. Incubate at room temperature for 2 minutes. 7. Add 2 ul SuperScript(TM) II Reverse Transcriptase (200 u/ul, Invitrogen Cat. No. 18064-014). Incubate at 42 ºC for 60 minutes. NOTES: 1. 3 ug yeast mRNA gives 300-400 ng target. Other sources of mRNA give different results, e.g. 1 ug of mammalian cell culture mRNA yields 200-300 ng target. In some cases 250 ng of mRNA still resulted in 160 ng cDNA and optimal hybridizations. 2. Prepare the labeling mix just prior to use. 3. Preparation of the RNA/primer and labeling mixes may be scaled up for synthesis of multiple probes. However, the volume of each individual cDNA synthesis reaction should not exceed 30 ul. 4. When a fresh tube of SuperScript(TM) II is opened, change the DTT and 5X first strand buffer as well. 5. Results with total RNA have varied (background on arrays), depending on the source of total RNA, how it was cleaned up, etc. Generally speaking mRNA will give better results and is easier for determining amounts of cDNA and specific yield. 20 ug is a good starting point for total RNA but each source of total RNA needs prior testing on arrays first. Protocol also works well with 5 ug total RNA from biopsy. 6. Unless otherwise specified all water (including water for RNA dilution, measurements, etc) is fresh Milli-Q from Milli-Q Synthesis A10 Model. REMOVAL OF THE RNA TEMPLATE BY HYDROLYSIS: 1. Incubate at 95 ºC for 2 minutes. Chill on ice immediately. 2. Mix together: 10 ul of 1 M NaOH, 10 ul of 0.5 M EDTA, add to the cDNA reaction and incubate at 65 ºC for 15 minutes. 3. After a short spindown, add 25 ul HEPES buffer (1 M, pH 7.5), mixing well. CLEANUP WITH MICROCON-30 CONCENTRATORS: Note: to continue with the amino-allyl dye coupling procedure all Tris must be removed from the reaction to prevent the monofunctional NHS-ester Cy-dyes coupling to free amine groups in solution. 1. Fill one Microcon-30 concentrator (Amicon Microcon YM-30, 42410) with 450 ul H2O. 2. Add neutralized reaction. 3. Spin at 10000 g for 10 minutes. 4. Dump flow-through. 5. Repeat process two times, refilling orginal filter with 450 ul H2O. 6. Elute. Place filter upside down in new tube and spin at 1000 g (3000 rpm) for 3 minutes. Goal is a 30-40 ul eluate. If this is obviously more then spin an extra minute. Adjust protocol next time accordingly. We usually get 40-80 ul eluates. Optional: take 1 ul eluate for spectrophotometry in NanoDrop (190 to 400 nm range) to determine the amount of cDNA produced. Samples in bicarbonate (next step) may be stored at -20 ºC for at least two weeks prior to coupling. COUPLING MONOFUNCTIONAL NHS-ESTER CY-DYES: Note: Cy dyes are not easy to work with. They are sensitive to light, water, perhaps also temperature, pH and freeze-thaw cycles. Avoid ALL possible light. Use dark (amber) Eppendorf tubes. Use aluminium foil. Switch lighting off. 1. Concentrate samples to 16 ul by using a SpeedVac. Try to keep this step less than 30 min by using a good speedvac. Avoid complete drying of sample. 2. If samples were below 16 ul then add water as required. Add 2 ul of 0.5 M Sodium Bicarbonate buffer, pH 9. Mix well. Proceed with next step only when all samples are ready. Keep on ice when delayed. 3. Resuspend monofunctional NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): Quickly resuspend entire tube in 10 ul DMSO (Merck 8.02912.10). Add 1.25 ul per sample. Mix immediately and quickly. Incubate in the dark at room temperature for 60 minutes. At the moment we aim for 8 reactions at a time so that the whole tube (10 ul) is used. Storage of aliquots is possible by making 1.25 ul aliquots, SpeedVaccing them dry, storing them and using them by adding the 18 ul sample to the aliquot. QUENCHING: Before combining Cy3 and Cy5 samples for hybridizations the reactions much be quenched to prevent cross coupling. 1. Add 9 ul of 4 M hydroxylamine (Sigma Aldrich 46,780-4). 2. Incubate in the dark at room temperature for 15 minutes. Before proceeding to clean-up, add 8 ul of H2O to raise the sample volume to 35 ul. CLEAN-UP USING CLONTECH CHROMASPIN-30 COLUMNS (DEPC version: K1331-2): Note: avoid light contact as much as possible by performing all steps quickly. 1. Upon removing a CHROMA SPIN column from the protective plastic bag, invert it several times to resuspend the gel matrix completely. Before removing the top make sure that all the matrix is at the bottom by vigorously flicking the cloumn downwards to remove matrix that is stuck to the top cap. 2. Holding the CHROMA SPIN column upright, grasp the break-away end between your thumb and index finger and snap off. Place the end of the spin column into one of the 2-ml microcentrifuge (collection) tubes provided, and lift off the top cap. Save the top cap and the white-end cap. 3. Centrifuge at 700 g for 5 min. After centrifugation, the column matrix will appear semi-dry. This step purges the equilibration solution from the column and reestablishes the matrix bed. Make sure that the matrix bed is flat. 4. Remove the spin column and collection tube from the centrifuge rotor, and discard the collection tube and column equilibration buffer. 5. Place the spin column into the second 2-ml microcentrifuge tube. Carefully and slowly apply the sample to the center of the gel bed's flat surface. Drop by drop! Do not allow any sample to flow along the inner wall of the column - this will completely mess up the sample. 6. Centrifuge at 700 g for 5 min. 7. Remove the spin column and collection tube from the rotor and detach them from each other. The purified sample is at the bottom of the collection tube. Immediately store on ice and dark. Purified sample is about 20-35 ul. Take 1 ul eluate aside for spectrophotometry in NanoDrop (190 to 750 nm range) to determine the amount of cDNA produced and the frequency of dye incorporation. Samples may be stored at -20 ºC for at least two weeks prior to use. CONTROL OF TARGETS: The amount of cDNA generated can be checked at two stages: prior to coupling (optional) and after coupling. All targets should have their (specific) activities and yields determined at least prior to use. Because of variations in the amount of background at OD260, 550 and 649 nm it is absolutely essential that proper negative controls are included in the reactions to correct the determinations for this background. Once it has been determined that a particular source of RNA and/or labeling protocol ALWAYS has negligible background values, then these control reactions can be left out. An ideal control is minus RT enzyme (2x, one for each dye). For comparison of experiments all identical types of measurements should be carried out with the same cuvette/spectophotometer/dilution water combinations. The cDNA measurements are all done in a NanoDrop spectrophotometer. Use an identical batch of elution water for blank (or use the negative control itself). Amount of cDNA: OD 260nm x 37 x total volume of probe (ul) = ng of probe. pmol of dye incorporated: Cy3 OD 550nm x (total volume of probe)/0.15 = pmol of Cy3 dye incorporated Cy5 OD 649nm x (total volume of probe)/0.25 = pmol of Cy5 dye incorporated. (If pathlength of the spectrophotometer is diferent from 1 cm, then divide the result by pathenght). Frequency of incorporation: # dye labeled nucleotides per 1000 nucleotides=(pmol of dye incorporated x 324.5)/(ng of probe). For full slides (i.e. 3/4 surface coverslip) use at least 200 ng of each probe. 100 ng also works, but more is better, up to 300 ng as far as we know. Use at least 15 pmol incorporated dye. 10 pmol also works but is weaker. For smaller coverslips (1/4 total slide surface), use 100 ng target and at least 5 pmol incorporated dye. Frequency of incorporation is usualy between 30 and 70. Match the amounts of cDNA for Cy3 and Cy5 on a single slide rather than the activity.

growth_protocol: MCF7/AZ [kindly provided by Prof. Marc Mareel (Ghent University, Belgium  Both cell lines were routinely maintained at 37°C, 5% CO2, in the following media (Invitrogen Ltd, Paisley, UK): DMEM, supplemented with 10% heat-inactivated fetal bovine serum (Lonza, Basel, Switzerland), 100 IU/ml penicillin and 100 mg/ml streptomycin (Invitrogen). MCF-7/AZ cell line was retrovirally stable transduced to encode human P-cadherin cDNA together with EGFP (MCF-7/AZ.Pcad cell line).

extract_protocol: Cells were detached from culture plates with trypsine, and were pelleted at 1200 rpm, for 5 minutes. The pellet was washed twice with PBS and conserved at -80ºC. Tota RNA extraction was performed using the RNeasy kit from Qiagen, following the manufacturer's instructions. Briefly, lysis buffer (Buffer RLT) was added to the pellet and 1 volume of 70% ethanol was added to the homogenized lysate, mixing well by pipetting. The total volume of the sample (up to 700 μl), including any precipitate that may have formed, was transfered to an RNeasy spin column placed in a 2 ml collection tube (supplied) and centrifuged for 15 s at 8000 x g (10,000 rpm). After discarding the flow-through, the spin column membrane was washed with 700 μl Buffer RW1 by centrifugation for 15 s at 8000 x g (10,000 rpm). The flow-through was discarded the RNeasy spin column was washed twice with 500 μl Buffer RPE, by centrifugation at 8000 x g (10,000 rpm) for 15 s. The flow-through was discarded. Total RNA was eluted after placing the column in a new 1.5 ml collection tube (supplied), adding 30–50 μl RNase-free water directly to the spin column membrane and centrifuging for 1 min at 8000 x g (10,000 rpm). A typical extraction yielded around 20-30ug of total RNA.

treatment_protocol: Cells were plated at a density of 5x10^5 in 6-well plates and left to adhere. In the next day, media was exchanged to contain azurin (100 uM) – treated cells - or PBS – control cells. After 48h, cells were collected.

value: untreated

tag: p-cadherin overexpression

value: P-cadherin-overexpressing cells (stable transfection)


title: MCF-7/AZ.Pcad cells untreated with azurin, biological replicate_2


title: LQ-128


title: 30µM EMD at 24hr, biological rep1 (rat)

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

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


title: MCF-7/AZ.Pcad cells untreated with azurin, biological replicate_1


title: Kasumi-1_FTY720_6hours_rep2

description: This sample is of Kasumi-1 cells treated with 5 μM FTY720 for 6 . It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: G4G6_M3

city: Milwaukee

first: Michele

last: Battle

state: WI

address: 8701 Watertown Plank Rd

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

hyb_protocol: Affymetrix Whole Transcript Sense Protocol

data_processing: dChip 2010

source_name: E18.5 Gata4Gata6 cKO

label_protocol: Affymetrix Whole Transcript Sense Labeling

growth_protocol: Embryonic small intestine was harvested at E18.5.

treatment_protocol: Small intestinal tissue was harvested, epithelial cells were isolated, and RNA was prepared.

value: small intestine epithelium


title: G4G6_M2

scan_protocol: Affymetrix Whole Transcript Sense Protocol


title: MCF-7/AZ.Pcad cells treated with azurin 100µM, 48h, biological replicate_3

description: Gene expression data from cells treated with azurin 100µM

value: azurin 100µM


title: 0.1% DMSO at 72hr, vehicle control, rep1 (rat)

first: John

last: Okyere

address: BioCity Nottingham

institute: CrossGen Limited

value: liver


title: 100µM EMD at 24hr, biological rep1 (rat)

value: Wistar


title: 0.1% DMSO at 24hr, vehicle control, rep1 (rat)


title: MCF-7/AZ.Pcad cells treated with azurin 100µM, 48h, biological replicate_2


title: LQ-126

source_name: Oral rinse, oral lichenoid disease


title: LQ-125

value: female


title: SCCNC7 primary tumor

description: Tumor vs normal DNA of same patient

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Images were acquired using a Microarray scanner G2505B (Agilent Technologies, Palo Alto CA, USA). Analysis and data extraction were quantified using feature extraction software (version 9.1, Agilent Technologies, Palo Alto CA, USA).

data_processing: Log2ratios of signal intensities between tumor and reference for every probe were median-normalized and after segmentation mode normalization was performed (van de Wiel et al., Brief Bioinform 2011). aCGH quality was assessed by means of the MAD of the log2ratios.

source_name: SCCNC7 squamous carcinoma tissue

label_protocol: 500 ng genomic DNA was combined with a mixture of primers and reaction buffer to a final volume of 39 ul. The DNA was denatured at 99ºC for 10 min, and placed on ice. While on ice, 10 ul cyanine 3-dUTP and cyanine 5-dUTP nucleotide mixture was added to the test and reference DNA, respectively, and finally 1 ul Klenow DNA polymerase was added to each sample to extend the primers. After 4 hr incubation at 37ºC, 5 ul stop buffer was added to stop the reaction. Label was purified using the QIAquick PCR Purification Kit.

value: SCCNC7 primary tumor

tag: Stage

tag: grade

value: poorly differentiated

tag: tobacco smoker

value: yes

source_name: SCCNC7 normal blood lymphocytes

tag: reference

value: SCCNC7 normal blood lymphocytes


title: MCF-7/AZ.Mock cells untreated with azurin, biological replicate_3

source_name: MCF-7/AZ untreated cells

tag: treatment

value: basal level


title: SCCNC7 cell line

description: Cell line vs normal DNA of same patient

source_name: SCCNC7 squamous carcinoma cells

value: SCCNC7 cell line

tag: age

tag: gender


title: SCCNC6 cell line

description: Cell line vs normal DNA of same patient

source_name: SCCNC6 squamous carcinoma cells

value: SCCNC6 cell line

value: male

value: well differentiated

source_name: SCCNC6 normal blood lymphocytes

value: SCCNC6 normal blood lymphocytes


title: MCF-7/AZ.Pcad cells treated with azurin 100µM, 48h, biological replicate_1


title: MCF-7/AZ.Mock cells untreated with azurin, biological replicate_2

value: untreated


title: LQ-124

tag: disease state

value: oral lichenoid disease

value: buccal cells


title: G4G6_M1

tag: tissue

value: small intestine epithelium


title: SCCNC6 primary tumor

description: Tumor vs normal DNA of same patient

source_name: SCCNC6 squamous carcinoma tissue

value: SCCNC6 primary tumor


title: LQ-123

tag: Sex

tag: tobacco


title: LQ-121

tag: cell type

tag: alcohol


title: G4G6_C2

source_name: E18.5 control


title: SCCNC4 cell line

description: Cell line vs normal DNA of same patient

source_name: SCCNC4 squamous carcinoma cells

tag: cell line

value: SCCNC4 cell line

value: no

source_name: SCCNC4 normal blood lymphocytes

value: SCCNC4 normal blood lymphocytes


title: LQ-118


title: SCCNC5 primary tumor

description: Tumor vs normal DNA of same patient

source_name: SCCNC5 squamous carcinoma tissue

value: SCCNC5 primary tumor

source_name: SCCNC5 normal blood lymphocytes

value: SCCNC5 normal blood lymphocytes


title: LQ-116

value: female


title: SCCNC5 cell line

description: Cell line vs normal DNA of same patient

source_name: SCCNC5 squamous carcinoma cells

value: SCCNC5 cell line


title: LQ-108


title: MCF-7/AZ.Mock cells treated with azurin 100µM, 48h, biological replicate_1

source_name: MCF-7/AZ cells treated with azurin 100µM

value: azurin 100µM

value: basal level


title: SCCNC4 primary tumor

description: Tumor vs normal DNA of same patient

source_name: SCCNC4 squamous carcinoma tissue

value: SCCNC4 primary tumor

value: poorly differentiated


title: G4G6_C1


title: P003, Biological rep3 RESTENOSIS (+)

city: Chandigarh

first: Dr. Yashpaul

last: Sharma

state: Chandigarh

department: Dept of Cardiology

institute: PGIMER, Chandigarh

description: CAD (Restenosis plus) group: patient having stent and also developed restenosis

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console and Gene springGX 12.5 using Affymetrix default analysis settings and RMA as normalization method has been used. The probes of intensities less than the 20.0 percentile in the raw data were excluded from the analysis.

source_name: RESTENOSIS (+), with restenosis patient's Blood

growth_protocol: Patient Blood (res + & res -) was collected and stored in PAXgene tubs

extract_protocol: PAXgene Blood RNA Kit used for extraction of total RNA  according to the manufacturer's instructions.

treatment_protocol: Coronary Artery Disease (CAD) pataient diagnosed with restenosis - and restenosis + after  insertion of stent

tag: blood

value: Blood

tag: genotype

value: Male

value: 50 Years


title: LQ-114

source_name: Oral rinse, oral lichenoid disease

value: oral lichenoid disease

value: buccal cells


title: MCF-7/AZ.Mock cells treated with azurin 100µM, 48h, biological replicate_2

tag: p-cadherin overexpression


title: G4G6_C3

value: small intestine epithelium


title: 264_255

city: Columbus

first: Susan

middle: Elizabeth

last: Olivo-Marston

state: OH

address: 1841 Neil Avenue

institute: The Ohio State University

description: Calorie restriction or diet-induced obesity

hyb_protocol: Labeled targets from 5ug of total RNA were used for hybridization on each miRNA microarray chip containing human and mouse miRNA genes. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6x SSPE (0.9 M NaCl / 60 mM NaH2PO4 H20 / 8 mM EDTA, pH 7.4) / 30% formamide at 25C for 18 hr, washed in 0.75x TNT (Tris HCL/NaCl/Tween 20) at 37C for 40 min.

scan_protocol: Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 um.

data_processing: The microarrays used for this analysis were pin-spotted microRNA microarrays (from the Ohio State University Comprehensive Cancer Center, version 4.0). Intensities of each spot were the median intensities of foreground. All spots where foreground intensity was less than background were reassigned as NA (NA marks missing data spots). All spots flagged as deficient by the scanner were also reassigned as NA. All blank (no oligo) spots with high foreground intensity were reassigned as NA. Each microRNA oligo is represented by quadruplicate spots on these arrays as two distant pairs of two adjacent spots. If there were 0 or 1 NA for an oligo quadruple, and the means of the distant oligo pairs differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned as NA. If there were 2 NAs for an oligo quadruple and the two non-NA spot intensities differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned NA. If there were 3 NA spots for a quadruple, the final spot was reassigned as NA. LOESS (Locally Weighted Scatterplot Smoothing) normalization was performed using the R software package and all replicate spots were averaged.

source_name: Colon tissue from mouse_high_fat

label_protocol: Processed by using a method of direct detection of the biotin-containing transcripts by streptavidin-Alexa647 conjugate.

extract_protocol: Tissues were flash frozen immediately after euthanasia. RNA from frozen tissue samples was extracted using standard TRIZOL (Invitrogen) protocol.

tag: disease

value: Colon cancer

tag: diet

value: High fat


title: 265_257

treatment_protocol: Calorie restriction or diet-induced obesity


title: P010, Biological rep5 RESTENOSIS (+)

value: 60 Years


title: LQ-107


title: P002, Biological rep2 RESTENOSIS (+)

value: 58 Years


title: SBC-3 control

city: Sapporo

first: Nozomi

last: Yanagihara

address: South-1, West-16, Chuo-Ku

department: Department of Clinical Laboratory Medicine

institute: Sapporo Medical University School of Medicine

description: SBC-3 control

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60Karray slides (G4851A) 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 (G2565CA) using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1. (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028004_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: lung cancer cells_control vector

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN), according to the protocol provided by the manufacturer.

value: lung small cell calcinoma

tag: transduced with

value: control vector (pCMV6-Mock)

tag: time point

value: 24h after transduction


title: A549 SALL4

description: A549 SALL4

source_name: lung cancer cells_SALL4 vector

value: lung adenocarcinoma

value: SALL4 vector (pCMV6-SALL4)


title: LQ-08

value: female


title: SBC-3 SALL4

description: SBC-3 SALL4


title: P001, Biological rep1 RESTENOSIS (+)

value: Female

value: 78 Years


title: P006, Biological rep4 RESTENOSIS (+)

value: Blood

value: Male

value: 56 Years


title: MCF-7/AZ.Mock cells treated with azurin 100µM, 48h, biological replicate_3

tag: treatment

value: azurin 100µM

value: basal level


title: P023, Biological rep6 RESTENOSIS (-)

description: CAD (Restenosis minus) group: patient having stent but did not develop restenosis

source_name: RESTENOSIS (-), without restenosis patient's Blood

tag: age


title: A549 control

description: A549 control


title: LQ-07

value: oral lichenoid disease

value: buccal cells


title: LQ-06


title: 263_253

value: Colon cancer

value: High fat


title: P016, Biological rep4 RESTENOSIS (-)

value: 34 years


title: 262_249


title: 261_245


title: CN-13

source_name: Oral rinse, control

value: control

value: male


title: CN-14


title: 260_239


title: P007, Biological rep1 RESTENOSIS (-)

value: 55 Years


title: 256_223


title: 255_215


title: P018, Biological rep5 RESTENOSIS (-)


title: P015, Biological rep3 RESTENOSIS (-)

value: 75 Years


title: MCF-7/AZ.Mock cells untreated with azurin, biological replicate_1

source_name: MCF-7/AZ untreated cells

value: untreated


title: 259_237


title: CN-20


title: 257_225


title: LQ-03


title: LQ-01


title: LQ-05


title: P013, Biological rep2 RESTENOSIS (-)

value: Female

value: 64 years


title: 258_233


title: del1-1 5dpi, biological rep 2

city: Berkeley

first: Mary

middle: C

last: Wildermuth

address: 221 Koshland Hall MC3102

department: Plant and Microbial Biology

institute: University of California Berkeley

description: Gene expression data from 5d infected leaves of del1 mutant plants

hyb_protocol: Microarray hybridizations to Affymetrix Arabidopsis ATH1 GeneChips were performed according to the protocol given in the Affymetrix GeneChip Expression Analysis Technical Manual 702646 Rev. 8.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip® Scanner 3000 7G at the Univeristy of California, Berkeley, functional genomics lab.

data_processing: Log2 (expression values) were extracted using robust multi-array analysis (RMA) using Partek Genomics Suite software (Partek, Inc).

organism: Arabidopsis thaliana

source_name: del1 5d G. orontii-infected leaves

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: Arabidopsis seeds were stratified in 0.1% agarose for 3-5 days and planted in boxes containing Metromix 200 soil. Seeds of wild type and mutant were equally distributed in each box using a template, with 6 plants each per box.  The flats (6 boxes per flat) were covered with plastic trays for 1 week and then uncovered. Flats were watered from below and fertilized at 3 weeks. Plants were grown in Percival AR66L growth chambers at 22°C, 70% RH, 12 h photoperiod with photosynthetically active radiation=150 µE m-2 s-1. Seeds for del1-1 were obtained from Vlieghe et al. 2005, Current Biology, 15:59–63.

extract_protocol: Total RNA was extracted using the RNeasy plant mini kit from Qiagen according to the manufacturer's instructions.  RNA quality was determined by the A260/A280 ratio and by its profile on an Agilent 2100 Bioanalyzer.

treatment_protocol: At four weeks, a subset of boxes was infected with a moderate innoculum of G.orontii using a settling tower. Moderate innoculum is 2 half G.orontii.-infected leaves with conidia 10-14 dpi.  Infected plants were placed in a separate Percival growth chamber under the same conditions as the pathogen-free Percival. Infections were performed at 1 pm to standardize experiments and minimize circadian effects. Samples were harvested at 5 dpi. Uninfected 5 d samples were also collected.  For each sample, three fully expanded mature leaves were harvested per plant and immediately frozen in liquid nitrogen. Two independent experiments were performed with triplicate samples collected within each experiment.  Two biological replicates were processed.

tag: genotype/variation

value: del1-1 mutant

value: 4 weeks old at time 0 (inoculation)

value: mature, fully expanded leaves

tag: infected

value: Golovinomyces ororntii infected


title: CN-12

tag: disease state

value: female


title: del1-1 5dpi, biological rep 1

tag: tissue


title: del1-1 mutant 5d uninfected, biologcal rep 2

description: Gene expression data from 5d uninfected leaves of del1 mutant plants

source_name: del1 5d uninfected leaves

value: no


title: CN-11

tag: Sex

value: buccal cells

tag: tobacco


title: 253_165

source_name: Colon tissue from mouse_calorie_restricted

value: Colon cancer

value: Calorie restricted


title: 254_167


title: del1-1 mutant 5d uninfected, biologcal rep 1


title: 252_163


title: Col-0 5dpi, biological rep 2

description: Gene expression data from 5d infected leaves of wild type Col-0 plants

source_name: Col-0 5d G. orontii-infected leaves

value: wild type


title: 249_155


title: Col-0 5d uininfected, biological rep 1

description: Gene expression data from 5d uninfected leaves of wild type Col-0 plants

source_name: Col-0 5d uninfected leaves


title: Col-0 5dpi, biological rep 1


title: 248_149