title: EKVX_Passage 4 xenograft_R5

department: DTP

description:
EKVX P04 T5
Gene expression data from EKVX Passage 4 xenograft.

source_name: EKVX, passage 4 xenograft


title: EKVX_Passage 4 xenograft_R3

status: Public on Jul 01 2013

type: RNA

city: Frederick

first: Luke

middle: Hunter

last: Stockwin

state: MD

address: Ft. Detrick

country: USA

institute: NCI Frederick

description:
EKVX P04 T3
Gene expression data from EKVX Passage 4 xenograft.

hyb_protocol: Samples were hybridized according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

scan_protocol: Microarray images were captured using a GeneChip® 3000 Scanner.

data_processing: Affymetrix Expression Console v1.3.

label: Biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: The RNA samples were submitted to Expression Analysis, Inc. (Durham, NC) for microarray analysis using the GeneChip® Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Samples were labeled according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

growth_protocol: All cell lines were obtained from the Division of Cancer Treatment and Diagnosis Tumor Repository (DTP, FNLCR, Frederick, MD) or American Type Culture Collection (ATCC) (Manassas, Va). In addition, the identities of all cell lines used in this study were confirmed using Identifiler® STR genotyping (Applied Biosystems). All mice used in the study were obtained from the Animal Production Program (FNLCR, Frederick, MD). Tumor cells for inoculation were derived from the 4th in vitro passage from cryopreserved cell stocks. Cells (1 x 10^7 cells/0.1 ml/inoculation) were inoculated subcutaneously into mice (n=10 or more mice depending on the tumor cell line). For comparative purposes, 2-3 samples of in vitro cultivated cells at passage 4 post-cryopreservation were also prepared for microarray analysis (P0). When tumors at P1, P4 and P10 reached approximately 500 mg (10x10 mm), 5 tumors were harvested, cut into small pieces and flash frozen in liquid nitrogen using pre-chilled tubes. Samples were transferred to a -70°C freezer for holding prior to processing. Serial tumor passage was achieved by harvesting donor tumor material (n=2 to 5 donors) at each passage, mincing the tumors (2x2 mm fragments), pooling the samples and inoculating the next recipients subcutaneously using tumor implant trocars. Athymic nude mice (nu/nu NCr) served as the primary host for most xenograft studies. In several instances (particularly with human leukemias and lymphomas) it was difficult to establish and passage tumors in nu/nu NCr mice. In these instances, SCID.NCr or NOD.SCID/NCr mice were assessed for suitability. In general, female mice were used as they are less aggressive, easily group-housed and routinely used in xenograft experiments. Male mice were used for prostate tumors (PC-3, PC-3/M). Finally, in those instances where hormone effects on tumor growth are important (e.g., estradiol-dependent breast), mice were supplemented with estradiol.

extract_protocol: Total RNA was isolated using RNeasy (Qiagen).

tag: originating cell line

value: EKVX

tag: tumor type

value: adenocarcinoma lung

tag: in vivo passage


title: HCC-LM3-shNon-3

city: Shanghai

first: fang

middle: fang

last: bu

address: Yin Road, New Building 10-11th Floor

department: 1International Joint Cancer Institute

country: China

institute: Second Military Medical University

description: This sample is of HCC-LM3 cells infected with control shRNA. It is the third of three control shRNA infected biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Labeled cDNA was hybridized in NimbleGen Hybridization System following their standard operating protocol.

scan_protocol: Slides were scanned with the Axon GenePix 4000B microarray scanner following their standard operating protocol.

data_processing: Raw data were extracted as pair files by NimbleScan software (version 2.5). NimbleScan software’s implementation of RMA offers quantile normalization and background correction. The 6 gene summary files were imported into Agilent GeneSpring Software (version11.0) for further analysis.

label_protocol: cDNA was labeled using a NimbleGen One-Color DNA Labeling Kit following their standard operating protocol.

growth_protocol: HCC-LM3 cell lines were cultured with DMEM containing 10% FBS at 37°C, 5% CO2.

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step. RNA was measured on the Nanodrop ND-1000.

treatment_protocol: HCC-LM3 cells were infected with Lv-shNon or Lv-shASPP2 for one week.

tag: cell line

value: HCC-LM3 cells

tag: cell type

value: Hepatocarcinoma cell line

tag: treatment group

value: Infected with control shRNA

tag: genotype/variation

value: control


title: HCC-LM3-shNon-2

description: This sample is of HCC-LM3 cells infected with control shRNA. It is the second of three contol shRNA infected biological replicates used in this experiment, each from separate cultures.


title: HCC-LM3-shNon-1

description: This sample is of HCC-LM3 cells infected with control shRNA. It is the first of three control shRNA infected biological replicates used in this experiment, each from separate cultures.


title: EKVX_Passage 4 xenograft_R2

description:
EKVX P04 T2
Gene expression data from EKVX Passage 4 xenograft.


title: EKVX_Passage 4 xenograft_R4

description:
EKVX P04 T4
Gene expression data from EKVX Passage 4 xenograft.


title: 2 hours broadband THz irradiation, biological rep2

city: Los Alamos

first: Boian

middle: S

last: Alexandrov

state: NM

address: Bikini Atoll Road

department: Theoretical Division

institute: LANL

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The raw microarray .CEL files were analyzed using R and Bioconductor. More specifically, the robust multi-array (RMA) method included in the affy package was used for preprocessing, background correction, and normalization of the raw data. Probes without Entrez identifiers or gene symbols as well as probes with small standard deviation across samples were filtered out from the analysis. Further, features mapping to the same Entrez identifier were consolidated by leaving the one with largest value and, finally, probes with standard deviation less than 0.5 across samples were filtered out from the analysis. Differentially expressed genes were identified using the Bioconductor limma package and ranked by calculating the B statistics for each gene. Gene annotation was performed using the Bioconductor mouse4302.db package, while the hypergeometric test of the Bioconductor’s GOstats package was used for identifying overrepresentation of differentially expressed genes in gene ontology terms.

label: biotin

organism: Mus musculus

source_name: Mouse mesenchymal stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA using an oligo dT-primer containing the T7 RNApolymerase promoter site and the One-Cycle Target Labeling Kit (Affymetrix). Biotin-labeled cRNA was purified and the absorbance measured at 260 nm to determine yield (NanoDrop).

growth_protocol: Mouse mesenchymal stem cells (MSCs) (ScienCell Research Laboratories, CA 92011, Catalog Number M7500) were cultured on tissue culture treated plastic T-75 flasks (Corning). Once the cells reached 80-90% confluence, the cells were sub-cultured in supplemented medium (95% α-MEM, 5% FBS, and antibiotics) for THz irradiation treatment. Roziglitazone (1 µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100 µM), and dexamethasone (1 µM), were added to the medium again 48 hours prior to irradiation.

extract_protocol: Cellular RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: Cells are irradiated for 2 hours with high-energy (~1 µJ, pulsewidth 35 fs  i.e. high peak power per pulse ~30 MW), average density power 1mW/cm2, broadband THz radiation  (~10 THz) at a high repetition rate (1 kHz).

value: mesenchymal stem cells

tag: thz irradiation conditions

value: 2 hours broadband THz irradiation


title: Bone marrow Mostra 5 C.4.1 MO

type: genomic

city: Badalona

first: Mar

last: Mallo

address: Ctra de Can Ruti, s/n, camí de les escoles. Edifici IMPPC

country: Spain

institute: Josep Carreras Leukaemia Research Institute

description: Hybridized to 6.0 Array

hyb_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned according to the manufacturer's instructions.

scan_protocol: CEL files, generated by AGCC Viewer. CNCHP and LOHCHP, generated by Genotyping Console (all provided by Affymetrix)

data_processing:
CNCHP (from 6.0 arrays) provide data for copy number and LOH analysis.
Genotyping Console; algorithm-name = CN5

molecule: genomic DNA

source_name: Bone marrow

label_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

extract_protocol: Genomic DNA was extracted from whole bone marrow, whole peripheral blood or CD3 lymphocytes isolated from peripheral blood prior to treatment with lenalidomide, at the individual centers participating in the study. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: Bone marrow


title: EKVX_Passage 1 xenograft_R5

description:
EKVX P01 T5
Gene expression data from EKVX Passage 1 xenograft.

source_name: EKVX, passage 1 xenograft


title: 2 hours broadband THz irradiation, biological rep1


title: Control for 2 hours broadband THz irradiation, biological rep1


title: EKVX_Passage 1 xenograft_R4

description:
EKVX P01 T4
Gene expression data from EKVX Passage 1 xenograft.


title: EKVX_Passage 4 xenograft_R1

description:
EKVX P04 T1
Gene expression data from EKVX Passage 4 xenograft.


title: DBS_WGA_SwedenInfantRepository_born1982

city: Houston

first: Tara

middle: Leah

last: Klassen

state: TX

address: One Baylor Plaza

department: Neurology

institute: Baylor College of Medicine

description:
Sample name: 1982
10ng gDNA extracted from DBS was whole genome amplified with the Repli-G ultrafast whole genome amplfication kit (GE)

hyb_protocol: DNA was hybridized for 40 hours at 65oC under constant rotation in a light impermeable hybridization oven (Agilent). Arrays were then washed and stabilized prior to scanning.

scan_protocol: Acquisition on the SureScan “D” Scanner (Agilent Technologies)

data_processing: Feature Extraction using Agilent Feature Extraction Software v10.7.3.1.

source_name: whole genome amplified gDNA from DBS born 1982

label_protocol: All aCGH experiments were performed using the manufacturer’s recommended protocol and the Agilent Genome Enzymatic Label Kit. Briefly, 1.125 mg of each post-WGA sample and 1.125 mg of control female reference genomic DNA were digested with RsaI and AluI restriction enzymes for 2 hrs at 37oC followed by heat inactivation at 65oC for 20 min. The complete digestion was confirmed visually by running 2ml of each sample on a 1% agarose/Ethidium Bromide TAE gel. The remaining digested DNA was subsequently purified and labeled with either Cy-3-dUTP (reference DNA) or Cy-5-dUTP (post-WGA DNA)

extract_protocol: A single 3 mm DBS from each sample was transferred to a fresh 1.5 ml microfuge tube. Using the QiaAmp Mini Spin Kit (Qiagen) genomic DNA was extracted according to the manufacturer’s protocol for DBS.  In brief, the DBS was incubated for 10 minutes at 85 oC in buffer ATL and then proteinase K solution was added. The sample was vortexed and incubated for one hour at 56 oC to facilitate enzymatic digestion of the sample. Buffer AL was then added and the sample was incubated at 70oC for 10 minutes, absolute ethanol was then added and the sample was vortexed thoroughly to mix. The supernatant solution was applied to the QIAamp mini spin column and was bound to the column via a 1 minute centrifugation at 6000xg. Filtrate was discarded and the sample was washed on the column by the application of buffer AW1, followed by a 1 minute 6000xg spin where the filtrate was discarded. Buffer AW2 was then applied and the sample was spun at 20000xg for 3 minutes, the filtrate was discarded and the spin column was centrifuged again for 1 minute at 20000xg to remove all trace ethanol. The DNA containing column was then moved to a clean 1.5ml microcentrifuge tube and 50ml DNAase/RNAase free water (Qiagen) pre-warmed to 55oC was applied to the column. The columns were incubated with water for 2 minutes and collected by centrifugation. The 50ul elutant was immediately reapplied to the column and recollected by centrifugation to maximally recover and concentrate the genomic DNA in a small end volume.

tag: gender

value: male

tag: developmental stage

value: neonate

tag: tissue

value: dried blood spots (DBS)

tag: birth year

tag: sample type

value: post-WGA DNA

source_name: Female Reference Control

value: female

value: control female reference genomic DNA


title: EKVX_Passage 1 xenograft_R1

description:
EKVX P01 T1
Gene expression data from EKVX Passage 1 xenograft.


title: Meg01-chIP2

city: Detroit

first: Yubin

last: Ge

state: MI

address: 110 East Warren Ave.

institute: Karmanos Cancer Institute

hyb_protocol: Hybridization mixture contained 5ug each cyanine 5- and 3-labeled DNA sample  in 158µl, 50µl of Human Cot-1 DNA, 50ul of Agilent 10X Blocking Agent and 250 ul of Agilent 2x HI-RPM Hybridization Buffer. After incubation at 95° C for 3 minutes, hyb mixtures were placed in a water bath for the incubation at 37° C for 30 minutes.  Samples were immediately loaded to an array in an Agilent SureHyb hybridization chamber and co-hybridize on the array for 40 hours at 65° C and 20rpm.  Washing was done using Agilent Oligo aCGH/ ChIP-on-chip Wash buffer 1 and 2 according to the Agilent protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner with extended dynamic range (XDR) at 5 micron resolution.

data_processing: Tiff images were analyzed with Agilent's feature extraction software (v9.5.3.1) using protocol ChIP-v1_95_May07.

source_name: IgG control

label_protocol: Sample fluorescent labeling started with heating 2 µg amplified control or IP DNA with Random primer at 95°C, followed by cooling on ice and mixing with Exo(-) Klenow fragment master mix. During the incubation of 2 hour at 37°C, control amplified DNA was labeled with Cyanine 3-dUTP, and IP amplified DNA was labeled with Cyanine 5-dUTP. The clean-up of labeled samples was performed using Microcon Ultra YM-30 filters (Millipore, Chicago, IL).

growth_protocol: The parental Meg01 cells and the shRNA stable clones were cultured in RPMI 1640 with 10% fetal bovine serum (Hyclone, Logan, UT) and 2 mM L-glutamine plus 100 U/ml penicillin and 100 µg/ml streptomycin, in a 37 °C humidified atmosphere containing 5% CO2/95% air and maintained at a density between 1x105 and 8x105 cells/mL.

extract_protocol: Cells were fixed with formaldehyde, swelled in a hypotonic buffer containing protease inhibitors, and nuclei were isolated.  Isolated nuclei were sonicated and an average DNA fragment size of 500-1000bp was verified on an agarose gel.  The chromatin solution was precleared by the addtition of protein G beads.  The precleared chromatin was incubate with protein G beads and 10 ug of GATA1 (C-20) or normal goat IgG.  Immune complexes were eluted, cross-links reversed, and samples were extracted with phenol/chloroform then precipitated.  Blunt ends were created and linker DNA was ligated to the blunt ends, then the samples were amplified, labeled and hybridized to the microarray.

treatment_protocol: The cells used for the chip-on-chip were non-treated Meg-01 cells.

tag: chip antibody

value: IgG

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #

tag: chip antibody lot #

source_name: Meg01 GATA1 IP


title: DBS_WGA_SwedenInfantRepository_born1975

description:
Sample name: 1975
10ng gDNA extracted from DBS was whole genome amplified with the Repli-G ultrafast whole genome amplfication kit (GE)

source_name: whole genome amplified gDNA from DBS born 1975


title: EKVX_Passage 1 xenograft_R2

description:
EKVX P01 T2
Gene expression data from EKVX Passage 1 xenograft.

tag: originating cell line

value: EKVX


title: EKVX_Passage 1 xenograft_R3

description:
EKVX P01 T3
Gene expression data from EKVX Passage 1 xenograft.

tag: tumor type

value: adenocarcinoma lung


title: CD3 lymphocytes from Mostra 5 C.4.1 MO

description: Hybridized to 6.0 Array

source_name: CD3 lymphocytes isolated from peripheral blood


title: EKVX_originating cell line_R2

description:
EKVX P0 T2
Gene expression data from EKVX originating cell line.

source_name: EKVX, originating cell line

tag: in vivo passage


title: DBS_WGA_SwedenInfantRepository_born1986

description:
Sample name: 1986
10ng gDNA extracted from DBS was whole genome amplified with the Repli-G ultrafast whole genome amplfication kit (GE)

source_name: whole genome amplified gDNA from DBS born 1986


title: DBS_WGA_SwedenInfantRepository_born1980

description:
Sample name: 1980
10ng gDNA extracted from DBS was whole genome amplified with the Repli-G ultrafast whole genome amplfication kit (GE)

source_name: whole genome amplified gDNA from DBS born 1980


title: EKVX_originating cell line_R1

description:
EKVX P0 T1
Gene expression data from EKVX originating cell line.


title: DBS_WGA_SwedenInfantRepository_born1984

description:
Sample name: 1984
10ng gDNA extracted from DBS was whole genome amplified with the Repli-G ultrafast whole genome amplfication kit (GE)

source_name: whole genome amplified gDNA from DBS born 1984


title: Meg01-chIP1

tag: cell line


title: DBS_WGA_SwedenInfantRepository_born1977

description:
Sample name: 1977
10ng gDNA extracted from DBS was whole genome amplified with the Repli-G ultrafast whole genome amplfication kit (GE)

source_name: whole genome amplified gDNA from DBS born 1977


title: CP70_Passage 10 xenograft_R5

description:
CP70 P10 T5
Gene expression data from CP70 Passage 10 xenograft.

source_name: CP70, passage 10 xenograft

value: carcinoma ovarian


title: Exponential 2M NaCl, biological rep 1

city: Rochester

first: Paul

last: Dunman

state: NY

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

description: Gene expression data from late exponential phase wildtype USA300-lac cells grown in 2M NaCl

hyb_protocol: 1.5 ug of cDNA were hybrized for 16 hr at 45C on a S. aureus Affymetrix GeneChip.  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

organism: Staphylococcus aureus subsp. aureus USA300

source_name: Staphylococcus aureus late exponential

label_protocol: cDNA was synthesized, fragmented and biotinylated according to the manufacturer's protocol for prokaryotic antisense labeling (Affymetrix)

growth_protocol: Cells were grown to late exponential phase in LB0 broth supplemented with 0 or 2 M NaCl at 37C with aeration (225 rpm in a rotary shaker)

extract_protocol: Total bacterial RNA was isolated using Rneasy kits according to the manufacturer's recommendations (Qiagen)

treatment_protocol: Once reaching late exponential phase (Optical Density 600nm of 0.7) 1:1 acetone-ethanol was added to inhibit cellular ribonucleases

tag: genotype

value: Wildtype

tag: protocol

tag: growth phase

value: Late exponential


title: CP70_Passage 10 xenograft_R3

description:
CP70 P10 T3
Gene expression data from CP70 Passage 10 xenograft.


title: Exponential 2M NaCl, biological rep 2


title: DBS_WGA_SwedenInfantRepository_born1976

description:
Sample name: 1976
10ng gDNA extracted from DBS was whole genome amplified with the Repli-G ultrafast whole genome amplfication kit (GE)

source_name: whole genome amplified gDNA from DBS born 1976


title: CP70_Passage 10 xenograft_R4

description:
CP70 P10 T4
Gene expression data from CP70 Passage 10 xenograft.


title: DBS_WGA_SwedenInfantRepository_born1978

description:
Sample name: 1978
10ng gDNA extracted from DBS was whole genome amplified with the Repli-G ultrafast whole genome amplfication kit (GE)

source_name: whole genome amplified gDNA from DBS born 1978


title: Control for 2 hours broadband THz irradiation, biological rep2

source_name: Mouse mesenchymal stem cells

tag: cell type

tag: thz irradiation conditions


title: Exponential No NaCl, biological rep 1

description: Gene expression data from late exponential phase wildtype USA300-lac cells grown in absence of NaCl


title: Exponential No NaCl, biological rep 2


title: CP70_Passage 10 xenograft_R1

description:
CP70 P10 T1
Gene expression data from CP70 Passage 10 xenograft.


title: cJun_2_diff

city: Chapel Hill

first: Julian

last: Rozenberg

state: NC

address: Brinkhous-Bullitt Bldg., CB#7525

department: Pathology and Lab Medicine

institute: University Of North Carolina

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: cJun ChIP from differentiated keratinocytes replicate 2

label_protocol: ChIP and INPUT DNA was labeled by Cy3 and Cy3 labelled primers during PCR amplification  according to round A/B/C random amplification protocol.

growth_protocol: Primary keratinocytes cultured for 1 day and Ca differentiated for 2 days

extract_protocol: Cells were chemically cross-linked by 0.6 % formaldehyde for 10 minutes.  The cross-linking reaction was stopped by adding 125 mM glycine. Cells were washed twice with ice-cold PBS and harvested in ice-cold PBS.  Cells where incubates in Cell lysis (5 mM PIPES pH 8.0 85 mM KCL 0.5% NP40 1 mM NF 1 mM NaVa Roche protease inhibitors cocktail) resuspended in SDS nuclear lysis buffer (50 mM Tris-Cl pH 8.1 10 mM EDTA, 1% SDS proteases and phosphates inhibitors as above) and sonicated to average size of DNA 500bp. After centrifugation supernatant was diluted 3 times by Chip dilution buffer (0.01% SDS, 1.1% Trition × 100, 1.2 mM EDTA, 16.7 mM Tris-Cl pH 8.1, 167 mM NaCl). 300 ul of sonicated chromatin preparation with protein concentration 1-2 µg/µl  was incubated overnight with antibodies. A fraction of lysate was left untreated to serve as input control. Immunocomplexes were captured using protein G agarose beads (Invitrogen) blocked with 1g/l yeast tRNA and BSA (Sigma) and washed twice with the buffer containing 2 mM EDTA, 100 mM Tris-Cl pH 8.0 and 0.18 % Sarkosyl, and four times with the Chip wash buffer (100 mM Tris-Cl pH 8.5, 500 mM LiCl, 1% NP40, 1% deoxycholic acid) and two times with TE. After incubating with RNaseA and Proteinase K, DNA was purified using QIAquick PCR Purification Kit.

treatment_protocol: cultured in 0.05mM Ca with serum for one day and in 0.4 mM Ca for two days

value: cJun

value: differentiated keratinocyte

tag: strain

value: FVB

source_name: Inpt DNA from primary keratinocytes cultured for 1 day and Ca differentiated for 2 days


title: CP70_Passage 10 xenograft_R2

description:
CP70 P10 T2
Gene expression data from CP70 Passage 10 xenograft.


title: CEBPb_2_diff

source_name: CEBP ChIP from differentiated keratinocytes replicate 2

value: CEBP


title: CP70_Passage 4 xenograft_R3

description:
CP70 P04 T3
Gene expression data from CP70 Passage 4 xenograft.

source_name: CP70, passage 4 xenograft


title: pho2_ko_shoot_+P_rep3

city: Bundoora

first: Reena

last: Narsai

address: 5 Ring road

country: Australia

institute: La trobe University

description: Gene expression data from rice shoots of pho2 plants

hyb_protocol: Following fragmentation, cRNA was hybridized, washed and stained as per manufacterers' instructions.

scan_protocol: GeneChips were scanned using the approved Affymetrix scanner.

data_processing: The data were analyzed with Affymetrix Gene Expression colsole using the Microarray Suite version 5.0 (MAS 5.0) under Affymetrix default analysis settings.

organism: Oryza sativa Japonica Group

source_name: Rice shoots from 21-day old pho2 plants

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

growth_protocol: Rice seeds were germinated in tap water for 2 days before being transferred for 19 days into a hydroponic solution containing Pi sufficient media (modified from Yoshida et al., 1976). Plants were grown with a day/night temperature of 30/22℃ and a 12h photoperiod (200 µmol photons m-2 s-1)

extract_protocol: Total RNA extracted using the Qiagen Rneasy kit as per manufacturer's instructions.

treatment_protocol: Not applicable

tag: tissue

value: shoots

value: OsPHO2 KO

tag: genetic background

value: Nipponbare

tag: age

value: 21-day old plants


title: pho2_ko_shoot_+P_rep2


title: CP70_Passage 4 xenograft_R5

description:
CP70 P04 T5
Gene expression data from CP70 Passage 4 xenograft.


title: CP70_Passage 4 xenograft_R4

description:
CP70 P04 T4
Gene expression data from CP70 Passage 4 xenograft.


title: CP70_Passage 4 xenograft_R2

description:
CP70 P04 T2
Gene expression data from CP70 Passage 4 xenograft.


title: pho2_ko_shoot_+P_rep1


title: 2 hours broadband THz irradiation, biological rep3

value: mesenchymal stem cells

value: 2 hours broadband THz irradiation


title: gi_ko_shoot_+P_rep3

description: Gene expression data from rice shoots of gi plants

source_name: Rice shoots from 21-day old gi plants

value: OsGIGANTEA KO


title: CP70_Passage 4 xenograft_R1

description:
CP70 P04 T1
Gene expression data from CP70 Passage 4 xenograft.


title: gi_ko_shoot_+P_rep2


title: CP70_Passage 1 xenograft_R5

description:
CP70 P01 T5
Gene expression data from CP70 Passage 1 xenograft.

source_name: CP70, passage 1 xenograft


title: PTE1_120_M3 with array type poplar from Affymetrix

type: other

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description:
Genes regulated by PtaZFP2 in absence of mechanical stress - genes regulated by PtaZFP2 after one bending.Species: Populus tremula x Populus alba.
populus tremula x populus alba  mutant (ptazfp2 overexpressor (line a39)) - age: 3month

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

molecule: other

organism: Populus tremula x Populus alba

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: stem - - growth media: NaCl 85µM; MgSO4 550µM; (NH4)2SO4 275µM; Ca(NO3)2 730µM; KNO3 1mM; K2HPO4 550µM; KH2PO4 550µM; (NH4)2MoO4 0.102nM; MnSO4 0.722nM; ZnSO4 0.612nM; H3BO3 1.812nM; CuSO4 0.246nM; 1/10000 masquolate ® FeA 2% - 16h/8h (day/night) - 22°C/18°C (day/night)

treatment_protocol: Name:PMDC7-ptaZFP2 - environmental treatment - abiotic stress,stem bending:time 2hour . Factor value : 5.0-5.3

tag: genotype/variation

value: PtaZFP2-overexpressing line

tag: agent

value: estradiol

tag: treatment protocol

value: stem bending


title: CREB_1_diff

source_name: CREB ChIP from differentiated keratinocytes replicate 1

tag: chip antibody

value: CREB


title: CP70_Passage 1 xenograft_R4

description:
CP70 P01 T4
Gene expression data from CP70 Passage 1 xenograft.

tag: originating cell line

value: carcinoma ovarian


title: cJun_1_diff

source_name: cJun ChIP from differentiated keratinocytes replicate 1


title: CREB_2_diff

source_name: CREB ChIP from differentiated keratinocytes replicate 2


title: CP70_Passage 1 xenograft_R3

description:
CP70 P01 T3
Gene expression data from CP70 Passage 1 xenograft.

tag: tumor type


title: PTE1_120_M2 with array type poplar from Affymetrix


title: gi_ko_shoot_+P_rep1


title: Melanoma sample 0412799

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

description: genomic DNA extracted from FFPE primary cutaneous melanoma sample vs commercial genomic DNA, Promega

hyb_protocol: Samples showing a degree of labeling lower than 0.6 where excluded from the aCGH analysis. DNA concentration was then recorded by measuring the intensities at 260 nm and 280 nm and equal amounts (250 ng) of test and reference ULS-labeled-DNA were combined as gender matched and hybridized on the Agilent 8x60k human CGH oligo microarray chip (Agilent-021924 SurePrint G3 Human CGH 8x60K Microarray, cat. G4450A). Test DNA was combined only with reference DNA having comparable degree of labeling. Hybridization was performed at 65°C for 40 h, 20 rpm.  Slides were then washed in Agilent Oligo aCGH Wash Buffer 1 at room temperature for 5 min followed by a 1 min wash with Agilent Oligo aCGH Wash Buffer 2 at 37°C. After washing steps, hybridized microarray slides were dried by using the stabilization and drying solution, and promptly protected with the Agilent Ozone-Barrier Slide Cover.

scan_protocol: Microarray slides were scanned with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies, Santa Clara, CA) at 3 μm resolution with the manufacturer’s software (Agilent ScanControl 8.1.3).

data_processing: The scanned microarray TIFF images were analyzed numerically using the Agilent Feature Extraction Software version 10.7.7.1 according to the Agilent standard protocol CGH_107_Sep09. Data quality and probe-to-probe noise of each array was estimated on the basis of the Derivative Log Ratio Spread (DLRS), according to Agilent’s indication, and Log2 ratio signal distributions.  Log2 ratio signal distributions were normalized adjusting the median value to 0.

source_name: Melanoma sample 0412799

label_protocol: Array CGH was performed using the Agilent Sureprint G3 8x60k kit (Agilent Technologies, Santa Clara, CA), following the manufacturer’s protocol but with some modifications. Briefly, DNA was labeled with the Universal Linkage System (ULS) using cyanine-3 (Cy3) dye for the tumor test DNA and cyanine-5 (Cy5) dye for the reference DNA. Instead of the recommended 250 ng, 420 ng of each test sample were used for the labeling with 0.7 μl of ULS-Cy3 whereas 300 ng of commercial reference DNA (Promega Corporation, Madison, WI, cat. G1417 and G1521) were labeled with 0.5 μl of ULS-Cy5. Before labeling, reference DNA was heat fragmented to achieve equal fragmented sized DNA in both test and reference samples. Labeled samples were then purified using the Agilent KREApure columns. Labeling efficiency was determined using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) by measuring the absorbance at A260 nm (DNA), A550 nm (Cy3), and A649 nm (Cy5) and calculating the degree of labeling (DoL), according to Agilent’s instructions.

extract_protocol: Genomic DNA (gDNA) was isolated from all FFPE archival samples using an optimized DNA isolation protocol based on Qiagen extraction kit (QIAamp DNA micro kit, cat. 51306, Qiagen, Hilden, Germany). Two 1.5 mm diameter tissue-cylinders were punched and mounted into a recipient paraffin block. Samples were then heated at 37°C for 15 min to allow punches to coalesce into the encircling paraffin. Twenty to thirty 25 μm thick sections were collected into a 2 ml eppendorf tube and deparaffinized twice for 15 min at 62°C in 1 ml xylene by vigorously mixing  (800 rpm), followed by two steps of 100% ethanol incubation, 15 min each. Samples were then pelleted and air-dry, suspended in 360 μl of Qiagen ATL buffer supplemented with 40 μl of Qiagen proteinase-K (600 mAU stock) and vigorously vortexed. Additional 40 μl of proteinase-K were added after 24 and 48 h during a total 72-h incubation time at 56°C, with 500 rpm shacking. Proteinase-k was then inactivated at 90°C for 15 minutes and samples were subsequently processed according to Qiagen instruction (QIAamp DNA micro kit, cat. 51306, Qiagen, Hilden, Germany) except that 80% ethanol was used in place of Qiagen AW2 buffer, to avoid excessive salts contamination. Finally, gDNA samples were eluted in 30 μl of 37°C preheated DNase-free water and gDNA concentrations were measured using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE).

tag: sample type

value: Melanoma FFPE clinical sample

tag: gender

value: M

value: Nodular

source_name: Human Genomic DNA: Male (Promega)

extract_protocol: reference commercial DNA purchased from Promega

value: reference commercial DNA


title: PTE1_120_M1 with array type poplar from Affymetrix

description:
Genes regulated by PtaZFP2 in absence of mechanical stress - genes regulated by PtaZFP2 after one bending.Species: Populus tremula x Populus alba.
populus tremula x populus alba  mutant (ptazfp2 overexpressor (line a39)) - age: 3monthdev.stage (Boyes et al. Plant Cell 2001):(from beginning of acclimation)tree n°5 serie1


title: RNAP_2_diff

source_name: RNAP ChIP from differentiated keratinocytes replicate 2

value: RNAP

value: differentiated keratinocyte

value: FVB


title: WT_shoot_+P_rep3

description: Gene expression data from rice shoots of WT plants

source_name: Rice shoots from 21-day old WT plants

value: shoots

tag: genotype

value: WT, Nipponbare

value: Nipponbare


title: Melanoma sample 0410159

source_name: Melanoma sample 0410159


title: WT_shoot_+P_rep2

value: 21-day old plants


title: PTE_M3 with array type poplar from Affymetrix

description:
Genes regulated by PtaZFP2 in absence of mechanical stress - genes regulated by PtaZFP2 after one bending.Species: Populus tremula x Populus alba.
populus tremula x populus alba  - age: 3month

extract_protocol: Pool of extract, PTEA_M3:125ug, PTEB_M3:125ug.

treatment_protocol: no treatment

value: no treatment


title: WT_shoot_+P_rep1


title: Melanoma sample 0313807

source_name: Melanoma sample 0313807

value: Superficial spreading


title: Melanoma sample 018258

source_name: Melanoma sample 018258

value: F

value: Acral lentiginous

source_name: Human Genomic DNA: Female (Promega)


title: PTE_M2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, PTEA_M2:125ug, PTEB_M2:125ug.

value: PtaZFP2-overexpressing line

value: estradiol


title: pho2_ko_root_+P_rep2

description: Gene expression data from rice roots of pho2 plants

source_name: Rice roots from 21-day old pho2 plants

value: roots

value: OsPHO2 KO


title: CREB_1_undiff

source_name: CREB ChIP from undifferentiated keratinocytes replicate 1

growth_protocol: Primary keratinocytes cultured for 3 days

treatment_protocol: cultured in 0.05mM Ca with serum

value: CREB

value: undifferentiated keratinocyte

source_name: Inpt DNA from primary keratinocytes cultured for 3 days


title: cJun_2_undiff

source_name: cJun ChIP from undifferentiated keratinocytes replicate 2

value: cJun


title: pho2_ko_root_+P_rep3


title: CP70_Passage 1 xenograft_R1

description:
CP70 P01 T1
Gene expression data from CP70 Passage 1 xenograft.

value: carcinoma ovarian

tag: in vivo passage


title: RNAP_1_diff

source_name: RNAP ChIP from differentiated keratinocytes replicate 1

value: RNAP

value: differentiated keratinocyte

value: FVB

source_name: Inpt DNA from primary keratinocytes cultured for 1 day and Ca differentiated for 2 days


title: CP70_originating cell line_R1

description:
CP70 P0 T1
Gene expression data from CP70 originating cell line.

source_name: CP70, originating cell line


title: CP70_originating cell line_R2

description:
CP70 P0 T2
Gene expression data from CP70 originating cell line.


title: CREB_2_undiff

source_name: CREB ChIP from undifferentiated keratinocytes replicate 2


title: cJun_1_undiff

source_name: cJun ChIP from undifferentiated keratinocytes replicate 1


title: CP70_Passage 1 xenograft_R2

description:
CP70 P01 T2
Gene expression data from CP70 Passage 1 xenograft.

source_name: CP70, passage 1 xenograft


title: RNAP_2_undiff

source_name: RNAP ChIP from undifferentiated keratinocytes replicate 2


title: PCE_M3 with array type poplar from Affymetrix

extract_protocol: Pool of extract, PCE1_M3:125ug, PCE2_M3:125ug.

value: WT


title: PTE_M1 with array type poplar from Affymetrix

description:
Genes regulated by PtaZFP2 in absence of mechanical stress - genes regulated by PtaZFP2 after one bending.Species: Populus tremula x Populus alba.
populus tremula x populus alba  mutant (ptazfp2 overexpressor (line a39)) - age: 3monthdev.stage (Boyes et al. Plant Cell 2001):(from beginning of acclimation)tree n°11 serie1

extract_protocol: Pool of extract, PTEA_M1:125ug, PTEB_M1:125ug.


title: RNAP_1_undiff

source_name: RNAP ChIP from undifferentiated keratinocytes replicate 1


title: CEBPb_1_undiff

source_name: CEBP ChIP from undifferentiated keratinocytes replicate 1

value: CEBP


title: Melanoma sample 0822761

source_name: Melanoma sample 0822761

value: Melanoma FFPE clinical sample

value: Nodular

value: reference commercial DNA


title: Melanoma sample 005450

source_name: Melanoma sample 005450

value: M

source_name: Human Genomic DNA: Male (Promega)


title: COLO 829_Passage 10 xenograft_R4

description:
COLO 829 P10 T4
Gene expression data from COLO 829 Passage 10 xenograft.

source_name: COLO 829, passage 10 xenograft

value: COLO 829

value: malignant melanoma


title: COLO 829_Passage 10 xenograft_R5

description:
COLO 829 P10 T5
Gene expression data from COLO 829 Passage 10 xenograft.


title: Melanoma sample 0816497

source_name: Melanoma sample 0816497

value: F

source_name: Human Genomic DNA: Female (Promega)


title: gi_ko_root_+P_rep3

description: Gene expression data from rice roots of gi plants

source_name: Rice roots from 21-day old gi plants

value: roots

value: OsGIGANTEA KO

value: Nipponbare

value: 21-day old plants


title: CEBPb_2_undiff

source_name: CEBP ChIP from undifferentiated keratinocytes replicate 2

value: undifferentiated keratinocyte

source_name: Inpt DNA from primary keratinocytes cultured for 3 days


title: PCE_M2 with array type poplar from Affymetrix

description:
Genes regulated by PtaZFP2 in absence of mechanical stress - genes regulated by PtaZFP2 after one bending.Species: Populus tremula x Populus alba.
populus tremula x populus alba  - age: 3monthdev.stage (Boyes et al. Plant Cell 2001):3 months (from beginning of acclimation)  tree n°2 serie2

extract_protocol: Pool of extract, PCE2_M2:125ug, PCE1_M2:125ug.

value: estradiol

value: no treatment


title: PCE_M1 with array type poplar from Affymetrix

description:
Genes regulated by PtaZFP2 in absence of mechanical stress - genes regulated by PtaZFP2 after one bending.Species: Populus tremula x Populus alba.
populus tremula x populus alba  - age: 3monthdev.stage (Boyes et al. Plant Cell 2001):(from beginning of acclimation)tree n°3 serie1,harvested plant number : tree n°2 serie2

extract_protocol: Pool of extract, PCE1_M1:125ug, PCE2_M1:125ug.


title: COLO 829_Passage 10 xenograft_R2

description:
COLO 829 P10 T2
Gene expression data from COLO 829 Passage 10 xenograft.

extract_protocol: Total RNA was isolated using RNeasy (Qiagen).


title: Melanoma sample 0819499

source_name: Melanoma sample 0819499

value: Superficial spreading


title: 2242-T

city: Dallas

first: Luc

last: Girard

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

source_name: Lung cancer specimen

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

extract_protocol: After homogenization, total RNA was extracted using TRI Reagent (Life Technologies, Grand Island, NY) according to manufacturer’s protocol. The nanodrop spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE) was used to estimate the concentration of RNA and the quality of the RNA (RIN number) was assessed on Nano Series II RNA LAB-chips using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA)

tag: histology

value: Adenosquamous

tag: race

value: Caucasian

tag: tobacco history

value: Y

tag: final patient stage

value: IIB

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 2189-T

value: Adenocarcinoma

value: M

value: N

value: IV


title: Melanoma sample 0816624

source_name: Melanoma sample 0816624

value: Melanoma FFPE clinical sample

value: F

value: Lentigo maligna

value: reference commercial DNA


title: gi_ko_root_+P_rep2

tag: tissue

value: roots

value: OsGIGANTEA KO

tag: genetic background

value: Nipponbare

tag: age

value: 21-day old plants


title: COLO 829_Passage 10 xenograft_R3

description:
COLO 829 P10 T3
Gene expression data from COLO 829 Passage 10 xenograft.

tag: originating cell line

value: COLO 829

tag: tumor type

value: malignant melanoma


title: Melanoma sample 0816065

description: genomic DNA extracted from FFPE primary cutaneous melanoma sample vs commercial genomic DNA, Promega

source_name: Melanoma sample 0816065

tag: sample type

tag: gender

value: Nodular


title: 2214-T

tag: histology

value: Caucasian

value: IIIA

value: A

value: Y


title: COLO 829_Passage 10 xenograft_R1

description:
COLO 829 P10 T1
Gene expression data from COLO 829 Passage 10 xenograft.

tag: in vivo passage


title: pho2_ko_root_+P_rep1

source_name: Rice roots from 21-day old pho2 plants

tag: genotype

value: OsPHO2 KO


title: gi_ko_root_+P_rep1


title: WT_root_+P_rep3

description: Gene expression data from rice roots of WT plants

source_name: Rice roots from 21-day old WT plants

value: WT, Nipponbare


title: COLO 829_Passage 4 xenograft_R5

description:
COLO 829 P04 T5
Gene expression data from COLO 829 Passage 4 xenograft.

source_name: COLO 829, passage 4 xenograft


title: WT_root_+P_rep2


title: CEBPb_1_diff

source_name: CEBP ChIP from differentiated keratinocytes replicate 1

tag: chip antibody

value: CEBP

tag: cell type

value: differentiated keratinocyte

tag: strain

value: FVB

source_name: Inpt DNA from primary keratinocytes cultured for 1 day and Ca differentiated for 2 days


title: Melanoma sample 0013734

source_name: Melanoma sample 0013734

value: Melanoma FFPE clinical sample

value: M

value: reference commercial DNA


title: 2442-T

value: Adenocarcinoma

value: F

tag: race

tag: tobacco history

value: N

tag: final patient stage

value: IIB

tag: date of birth

tag: date of surgery

tag: vital statistics


title: Melanoma sample 0722965

source_name: Melanoma sample 0722965

value: Nodular

source_name: Human Genomic DNA: Male (Promega)


title: Melanoma sample 0810123

source_name: Melanoma sample 0810123

value: Malignant, NOS


title: COLO 829_Passage 4 xenograft_R4

description:
COLO 829 P04 T4
Gene expression data from COLO 829 Passage 4 xenograft.

value: COLO 829

value: malignant melanoma


title: 2382-T

value: Caucasian

value: IIIA

value: D

tag: last follow-up survival

tag: recurrence

value: Y

tag: last follow-up recurrence


title: 2235-T

value: Sarcomatoid

value: IIA


title: Melanoma sample 0722395

source_name: Melanoma sample 0722395

tag: sample type

value: Melanoma FFPE clinical sample

tag: tumor type

value: Superficial spreading

source_name: Human Genomic DNA: Female (Promega)


title: COLO 829_Passage 4 xenograft_R3

description:
COLO 829 P04 T3
Gene expression data from COLO 829 Passage 4 xenograft.

tag: originating cell line


title: Melanoma sample 0720461

source_name: Melanoma sample 0720461

tag: gender

value: M

value: reference commercial DNA


title: 2181-T

tag: histology

value: SCLC & NSCLC

value: F

value: African American

value: IIIB


title: Melanoma sample 0707564

source_name: Melanoma sample 0707564

value: Nodular


title: E0_R1 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa  - harvest date: 14-02-11

organism: Oryza sativa

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: embryonic axis - - 450ml sterile distilled water - Constant atmospheric air bubbling (10ml per minute) - 30°C - Darkness

tag: tissue

value: embryo

tag: protocol

value: sterile distilled water imbibition

tag: time (hr)

tag: harvest date


title: COLO 829_Passage 1 xenograft_R5

description:
COLO 829 P01 T5
Gene expression data from COLO 829 Passage 1 xenograft.

source_name: COLO 829, passage 1 xenograft

value: COLO 829

value: malignant melanoma

tag: in vivo passage


title: COLO 829_Passage 1 xenograft_R4

description:
COLO 829 P01 T4
Gene expression data from COLO 829 Passage 1 xenograft.


title: A4_R3 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 16-02-11

growth_protocol: endosperm - - 450ml sterile distilled water - Constant atmospheric air bubbling (10ml per minute) - 30°C - Darkness

treatment_protocol: Name:imbibition_4 - environmental treatment - water,h2o:time 4hour .

value: endosperm


title: COLO 829_Passage 4 xenograft_R1

description:
COLO 829 P04 T1
Gene expression data from COLO 829 Passage 4 xenograft.


title: Melanoma sample 0716077

source_name: Melanoma sample 0716077


title: 2193-T

source_name: Lung cancer specimen

value: Adenocarcinoma

tag: race

tag: tobacco history

value: Y

tag: final patient stage

value: IIB

value: A

value: N


title: 2203-T

value: Sarcomatoid-squamous

value: Caucasian

tag: date of birth

tag: date of surgery

tag: vital statistics

value: D


title: Melanoma sample 0705014

source_name: Melanoma sample 0705014

value: Melanoma FFPE clinical sample

value: F

value: reference commercial DNA


title: 2287-T

value: M

value: IB

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: COLO 829_Passage 4 xenograft_R2

description:
COLO 829 P04 T2
Gene expression data from COLO 829 Passage 4 xenograft.

tag: originating cell line

tag: tumor type


title: Melanoma sample 06739

source_name: Melanoma sample 06739

tag: sample type

tag: gender

value: Superficial spreading


title: A4_R1 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 14-02-11

tag: tissue

tag: protocol

value: sterile distilled water imbibition


title: E4_R1 with array type rice from Affymetrix

value: embryo

tag: time (hr)

tag: harvest date


title: 2337-T

tag: histology

value: Squamous

tag: race


title: A24_R3 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 17-02-11

treatment_protocol: Name:Iimbibition_24 - environmental treatment - water,h2o:time 24hour .

value: endosperm


title: WT_root_+P_rep1

source_name: Rice roots from 21-day old WT plants

value: roots

tag: genotype

value: WT, Nipponbare

tag: genetic background

value: Nipponbare

tag: age

value: 21-day old plants


title: E0_R5 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 21-02-11


title: 2157-T

value: Adenocarcinoma

tag: tobacco history

value: Y

tag: final patient stage

value: IA

tag: date of birth

tag: date of surgery

tag: vital statistics


title: A16_R1 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 15-02-11

treatment_protocol: Name:imbibition_16 - environmental treatment - water,h2o:time 16hour .


title: COLO 829_Passage 1 xenograft_R1

description:
COLO 829 P01 T1
Gene expression data from COLO 829 Passage 1 xenograft.

tag: originating cell line

value: COLO 829

tag: tumor type

value: malignant melanoma

tag: in vivo passage


title: 2156-T

tag: gender

value: Caucasian

value: A

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: COLO 829_Passage 1 xenograft_R3

description:
COLO 829 P01 T3
Gene expression data from COLO 829 Passage 1 xenograft.


title: COLO 829_Passage 1 xenograft_R2

description:
COLO 829 P01 T2
Gene expression data from COLO 829 Passage 1 xenograft.


title: 2145-T

tag: histology

value: LCC-NE

value: M

value: IIB

value: D


title: A0_R1 with array type rice from Affymetrix

tag: tissue

tag: protocol

value: sterile distilled water imbibition

tag: time (hr)

tag: harvest date


title: Melanoma sample 065167

description: genomic DNA extracted from FFPE primary cutaneous melanoma sample vs commercial genomic DNA, Promega

source_name: Melanoma sample 065167

tag: sample type

value: Melanoma FFPE clinical sample

value: Nodular

value: reference commercial DNA


title: Melanoma sample 06104147

source_name: Melanoma sample 06104147


title: E24_R5 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 23-02-11

value: embryo


title: E16_R5 with array type rice from Affymetrix


title: 2138-T

tag: race

tag: tobacco history

tag: final patient stage


title: COLO 829_originating cell line_R2

description:
COLO 829 P0 T2
Gene expression data from COLO 829 originating cell line.

source_name: COLO 829, originating cell line


title: Melanoma sample 057585

source_name: Melanoma sample 057585

value: Superficial spreading


title: Melanoma sample 0612349

source_name: Melanoma sample 0612349

value: F


title: COLO 205_Passage 10 xenograft_R5

description:
COLO 205 P10 T5
Gene expression data from COLO 205 Passage 10 xenograft.

source_name: COLO 205, passage 10 xenograft

value: COLO 205

value: adenocarcinoma colon


title: E24_R4 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 22-02-11


title: COLO 205_Passage 10 xenograft_R3

description:
COLO 205 P10 T3
Gene expression data from COLO 205 Passage 10 xenograft.


title: 2019-T

value: Pleomorphic carcinoma

value: Y

value: IIIA

tag: date of birth

tag: date of surgery

tag: vital statistics


title: COLO 829_originating cell line_R1

description:
COLO 829 P0 T1
Gene expression data from COLO 829 originating cell line.

tag: originating cell line

value: COLO 829

tag: tumor type

value: malignant melanoma

tag: in vivo passage


title: Melanoma sample 0514600

source_name: Melanoma sample 0514600

tag: gender

value: Lentigo maligna


title: Melanoma sample 0519058

source_name: Melanoma sample 0519058

value: M

source_name: Human Genomic DNA: Male (Promega)


title: Melanoma sample 0515392

source_name: Melanoma sample 0515392

value: Malignant, NOS


title: COLO 205_Passage 10 xenograft_R4

description:
COLO 205 P10 T4
Gene expression data from COLO 205 Passage 10 xenograft.


title: E16_R4 with array type rice from Affymetrix

value: sterile distilled water imbibition


title: 1973-T

value: Squamous

value: African American

value: D

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 2045-T

tag: histology

value: Adenocarcinoma

value: Caucasian

value: A

value: N


title: 1981-T

value: LCC-NE

value: F


title: 1890-T

value: Y


title: COLO 205_Passage 10 xenograft_R2

description:
COLO 205 P10 T2
Gene expression data from COLO 205 Passage 10 xenograft.

value: COLO 205

value: adenocarcinoma colon


title: E12_R4 with array type rice from Affymetrix

treatment_protocol: Name:imbibition_12 - environmental treatment - water,h2o:time 12hour .

tag: tissue

value: embryo

tag: protocol

tag: time (hr)


title: E0_R4 with array type rice from Affymetrix

tag: harvest date


title: 1806-T

tag: race

tag: tobacco history

value: IV


title: A0_R3 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 16-02-11

value: endosperm


title: A12_R2 with array type rice from Affymetrix


title: Melanoma sample 0514214

source_name: Melanoma sample 0514214

tag: sample type

value: Melanoma FFPE clinical sample

value: Malignant, NOS

source_name: Human Genomic DNA: Female (Promega)

value: reference commercial DNA


title: Melanoma sample 0512622

source_name: Melanoma sample 0512622

value: Nodular


title: COLO 205_Passage 4 xenograft_R4

description:
COLO 205 P04 T4
Gene expression data from COLO 205 Passage 4 xenograft.

source_name: COLO 205, passage 4 xenograft


title: COLO 205_Passage 10 xenograft_R1

description:
COLO 205 P10 T1
Gene expression data from COLO 205 Passage 10 xenograft.


title: 1280-T

source_name: Lung cancer specimen

value: Sarcomatoid

tag: final patient stage

value: IIB

tag: date of birth

tag: date of surgery


title: COLO 205_Passage 4 xenograft_R5

description:
COLO 205 P04 T5
Gene expression data from COLO 205 Passage 4 xenograft.

tag: originating cell line

tag: tumor type


title: E12_R5 with array type rice from Affymetrix

value: sterile distilled water imbibition


title: A24_R1 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 15-02-11


title: Melanoma sample 0513156

source_name: Melanoma sample 0513156

tag: gender

value: M


title: Melanoma sample 048963

source_name: Melanoma sample 048963


title: 1255-T

value: NSCLC

value: Caucasian

value: IA

tag: vital statistics

value: D

tag: last follow-up survival

value: N


title: COLO 205_Passage 4 xenograft_R3

description:
COLO 205 P04 T3
Gene expression data from COLO 205 Passage 4 xenograft.

value: COLO 205

value: adenocarcinoma colon

tag: in vivo passage


title: COLO 205_Passage 4 xenograft_R2

description:
COLO 205 P04 T2
Gene expression data from COLO 205 Passage 4 xenograft.


title: A0_R2 with array type rice from Affymetrix

hyb_protocol: labelled extract quantity: 15mg


title: Melanoma sample 0803974

source_name: Melanoma sample 0803974

value: F

value: malignant, NOS


title: E8_R5 with array type rice from Affymetrix

treatment_protocol: Name:imbibition_8 - environmental treatment - water,h2o:time 8hour .

value: embryo


title: 796-T

tag: histology

value: Sarcomatoid-Adenocarcinoma

value: Y

value: IIIA

value: A

tag: recurrence

tag: last follow-up recurrence


title: COLO 205_Passage 4 xenograft_R1

description:
COLO 205 P04 T1
Gene expression data from COLO 205 Passage 4 xenograft.


title: A12_R3 with array type rice from Affymetrix

tag: tissue

value: endosperm

tag: protocol

tag: time (hr)


title: Melanoma sample 0422476

description: genomic DNA extracted from FFPE primary cutaneous melanoma sample vs commercial genomic DNA, Promega

source_name: Melanoma sample 0422476

value: Melanoma FFPE clinical sample

value: Malignant, NOS

value: reference commercial DNA


title: COLO 205_Passage 1 xenograft_R5

description:
COLO 205 P01 T5
Gene expression data from COLO 205 Passage 1 xenograft.

source_name: COLO 205, passage 1 xenograft


title: COLO 205_Passage 1 xenograft_R3

description:
COLO 205 P01 T3
Gene expression data from COLO 205 Passage 1 xenograft.


title: Melanoma sample 0421527

source_name: Melanoma sample 0421527

value: M

value: Superficial spreading


title: A16_R3 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 17-02-11

value: sterile distilled water imbibition

tag: harvest date


title: COLO 205_Passage 1 xenograft_R2

description:
COLO 205 P01 T2
Gene expression data from COLO 205 Passage 1 xenograft.


title: AG amiRNA knockdown 3

city: Dublin

first: Pat

last: Ryan

address: College Green

country: Ireland

institute: TCD

description: Biological Replicate 3: several plants (approx 20-25) pooled per replicate and genotype

hyb_protocol: Fragmentation buffer and Hybridization Buffer HI-RPM (Agilent Gene Expression Hybridization Kit) were added and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized for 16 hrs at 65°C. After hybridization, slides were washed sequentially according to the manufacturer's instruction.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (v 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization

organism: Arabidopsis thaliana

source_name: LhG4 GR set3

label_protocol: 500ng of total RNA were primed with 0.6µl of T7 DNA primer at 65°C for 10 min, then reverse transcribed at 40°C  for 2 hrs in the presence of 300 U MMLV Reverse Transcriptase and 10mM dNTP mix, with Cy3-label and Cy5- label.

growth_protocol: Plants were grown on a soil:vermiculite:perlite (3:1:1) mixture at 20 degrees under constant illumination with cool white fluorescent light

extract_protocol: Total RNA was isolated from tissue samples using the Plant Total RNA kit (Sigma-Aldrich), according to the manufacturer's instructions

treatment_protocol: For all experiments,  ~4 week-old plants were used. For experiments using the FIS (35S:AP1-GR ap1-1 cal-1 plants), flower development was induced using a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol and 0.015% (v/v) Silwet L-77 (De Sangosse) – as described in  Wellmer F, et al. (2006) Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development. PLoS Genetics 2(7):e117.

tag: time

value: 0 d

tag: treatment

value: No Dexamethasone

value: Whole infloresence

tag: sample type

value: Whole infloresence, no Dexamethasone treatment

tag: genotype

value: LhG4-GR_N6XpOp-AmiRNA-AG (ler)

tag: genetic background

value: ler

value: Whole infloresence, Dexamethasone treatment

value: Dexamethasone


title: 1960-T

value: Adenocarcinoma

value: F

tag: race

value: Caucasian

tag: tobacco history

value: Y

tag: final patient stage

value: IIIB

tag: date of birth

tag: date of surgery

value: D

value: N


title: 2311-T

tag: histology

tag: gender

value: IB

tag: vital statistics

value: A

tag: last follow-up survival


title: AG amiRNA knockdown 4

description: Biological Replicate 4: several plants (approx 20-25) pooled per replicate and genotype

source_name: LhG4 GR set4

value: 1 d

tag: tissue


title: E4_R5 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 22-02-11

value: embryo

tag: protocol

value: sterile distilled water imbibition

tag: time (hr)


title: E4_R4 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa  - harvest date: 21-02-11

tag: harvest date


title: 2319-T

tag: recurrence

tag: last follow-up recurrence


title: 2313-T

value: IA


title: COLO 205_Passage 1 xenograft_R4

description:
COLO 205 P01 T4
Gene expression data from COLO 205 Passage 1 xenograft.

tag: originating cell line

value: COLO 205

tag: tumor type

value: adenocarcinoma colon

tag: in vivo passage


title: Melanoma sample 048311

source_name: Melanoma sample 048311

tag: sample type

value: Melanoma FFPE clinical sample

value: M

value: Superficial spreading

value: reference commercial DNA


title: AG amiRNA knockdown 2

description: Biological Replicate 2: several plants (approx 20-25) pooled per replicate and genotype

source_name: LhG4 GR set2

tag: time

tag: treatment

value: Dexamethasone

value: Whole infloresence

value: Whole infloresence, Dexamethasone treatment

tag: genotype

value: LhG4-GR_N6XpOp-AmiRNA-AG (ler)

tag: genetic background

value: ler

value: Whole infloresence, no Dexamethasone treatment

value: No Dexamethasone


title: COLO 205_Passage 1 xenograft_R1

description:
COLO 205 P01 T1
Gene expression data from COLO 205 Passage 1 xenograft.


title: 2309-T

tag: histology

value: Adenocarcinoma

tag: gender

tag: race

value: Caucasian

tag: tobacco history

value: Y

tag: final patient stage

value: IB

tag: date of birth

tag: date of surgery

value: A

value: N


title: 830-T

value: Adenosquamous

value: F

value: IIIB

tag: vital statistics

value: D

tag: last follow-up survival

tag: recurrence


title: E8_R4 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 21-02-11

tag: tissue

value: embryo

tag: protocol

value: sterile distilled water imbibition

tag: time (hr)

tag: harvest date


title: 2307-T

value: Squamous

value: IIB

tag: last follow-up recurrence


title: AG null mutant perturbation 12

source_name: Day5 AG set4

tag: time

value: 5 d

tag: treatment

value: Dexamethasone

value: stage 5-6 flowers

tag: sample type

value: 5 days after Dexamethasone treatment (early-intermediate floral stage ~ stage 5-6 flowers)

tag: genotype

value: FIS (ap1 cal AP1-GR); ag-1 heterozygous

value: ler

value: FIS (ap1 cal AP1-GR); ag-1 homozygous


title: COLO 205_originating cell line_R3

description:
COLO 205 P0 T3
Gene expression data from COLO 205 originating cell line.

source_name: COLO 205, originating cell line

tag: originating cell line

value: COLO 205

tag: tumor type

value: adenocarcinoma colon

tag: in vivo passage


title: A12_R1 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 14-02-11

value: endosperm


title: AG null mutant perturbation 10

source_name: Day0 AG set4

value: 0 d

value: No Dexamethasone

value: undifferentiated meristematic tissue

value: no Dexamethasone treatment (undifferentiated meristematic tissue)

tag: genetic background


title: 2308-T

tag: histology

value: Adenocarcinoma

tag: gender

value: M

tag: race

value: Caucasian

tag: tobacco history

value: Y

tag: final patient stage

tag: date of birth

tag: date of surgery

value: A

value: N


title: AG amiRNA knockdown 1

description: Biological Replicate 1: several plants (approx 20-25) pooled per replicate and genotype

source_name: LhG4 GR set1

tag: tissue

value: Whole infloresence

value: Whole infloresence, no Dexamethasone treatment (indicate time after treatments - 24h - also it's not no treatment, it's a mock treatment)

value: LhG4-GR_N6XpOp-AmiRNA-AG (ler)

value: Whole infloresence, Dexamethasone treatment

value: Dexamethasone


title: COLO 205_originating cell line_R2

description:
COLO 205 P0 T2
Gene expression data from COLO 205 originating cell line.

value: COLO 205

value: adenocarcinoma colon


title: CCRF-CEM_Passage 10 xenograft_R5

description:
CCRF-CEM P10 T5
Gene expression data from CCRF-CEM Passage 10 xenograft.

source_name: CCRF-CEM, passage 10 xenograft

value: CCRF-CEM

value: acute lymphoblastic (T-ALL) leukemia


title: 2302-T

value: F

value: IA

tag: vital statistics

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: 2303-T

value: Squamous


title: 2305-T

value: Adenocarcinoma

value: M

value: IIIA


title: AG null mutant perturbation 9

source_name: Day5 AG set3

tag: time

value: 5 d

tag: treatment

value: stage 5-6 flowers

tag: sample type

value: 5 days after Dexamethasone treatment (early-intermediate floral stage ~ stage 5-6 flowers)

tag: genotype

value: FIS (ap1 cal AP1-GR); ag-1 homozygous

value: ler

value: FIS (ap1 cal AP1-GR); ag-1 heterozygous


title: 2299-T

source_name: Lung cancer specimen

value: Caucasian

value: Y

value: A

value: N


title: A16_R2 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 18-02-11

value: endosperm

tag: protocol

value: sterile distilled water imbibition

tag: time (hr)

tag: harvest date


title: AG null mutant perturbation 11

source_name: Day2.5 AG set4

value: Dexamethasone

value: stage 3-4 flowers

value: 2.5 days after Dexamethasone treatment (early floral stages ~ stage 3-4 flowers)

tag: genetic background


title: E16_R1 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa  - harvest date: 15-02-11

value: embryo


title: A8_R1 with array type rice from Affymetrix


title: CCRF-CEM_Passage 10 xenograft_R4

description:
CCRF-CEM P10 T4
Gene expression data from CCRF-CEM Passage 10 xenograft.

tag: originating cell line

value: CCRF-CEM

tag: tumor type

value: acute lymphoblastic (T-ALL) leukemia

tag: in vivo passage


title: E12_R1 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa  - harvest date: 14-02-11


title: CCRF-CEM_Passage 10 xenograft_R2

description:
CCRF-CEM P10 T2
Gene expression data from CCRF-CEM Passage 10 xenograft.


title: COLO 205_originating cell line_R1

description:
COLO 205 P0 T1
Gene expression data from COLO 205 originating cell line.

value: COLO 205

value: adenocarcinoma colon


title: AG null mutant perturbation 7

description: Biological Replicate 3: several plants (approx 20-25) pooled per replicate and genotype

source_name: Day0 AG set3

value: 0 d

value: No Dexamethasone

value: undifferentiated meristematic tissue

value: no Dexamethasone treatment (undifferentiated meristematic tissue)

value: FIS (ap1 cal AP1-GR); ag-1 homozygous


title: AG null mutant perturbation 6

source_name: Day2.5 AG set2

value: FIS (ap1 cal AP1-GR); ag-1 heterozygous

value: ler


title: AG null mutant perturbation 8

source_name: Day2.5 AG set3


title: A24_R2 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 16-02-11

value: endosperm


title: CCRF-CEM_Passage 10 xenograft_R1

description:
CCRF-CEM P10 T1
Gene expression data from CCRF-CEM Passage 10 xenograft.


title: 2280-T

tag: histology

value: Squamous

tag: gender

value: F

tag: race

value: Caucasian

tag: tobacco history

value: Y

tag: final patient stage

value: IIIB

tag: date of birth

tag: date of surgery

value: D


title: CCRF-CEM_Passage 10 xenograft_R3

description:
CCRF-CEM P10 T3
Gene expression data from CCRF-CEM Passage 10 xenograft.

value: CCRF-CEM

value: acute lymphoblastic (T-ALL) leukemia


title: 2296-T

value: Adenocarcinoma

value: IA

tag: vital statistics

value: A

tag: last follow-up survival

tag: recurrence

value: N

tag: last follow-up recurrence


title: A8_R3 with array type rice from Affymetrix

description:
During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination.
oryza sativa (nipponbare)  - harvest date: 15-02-11

tag: tissue

tag: protocol

value: sterile distilled water imbibition

tag: time (hr)


title: 2293-T

value: M


title: A8_R2 with array type rice from Affymetrix

tag: harvest date


title: E8_R1 with array type rice from Affymetrix

value: embryo


title: 2284-T


title: 2281-T


title: 2279-T


title: AG null mutant perturbation 3

source_name: Day0 AG set1

tag: time

value: 0 d

tag: treatment

value: No Dexamethasone

value: undifferentiated meristematic tissue

tag: sample type

value: no Dexamethasone treatment (undifferentiated meristematic tissue)

tag: genotype

value: FIS (ap1 cal AP1-GR); ag-1 homozygous

tag: genetic background

value: ler

value: FIS (ap1 cal AP1-GR); ag-1 heterozygous


title: AG null mutant perturbation 1

source_name: Day5 AG set1

value: 5 d

value: Dexamethasone

value: stage 5-6 flowers

value: 5 days after Dexamethasone treatment (early-intermediate floral stage ~ stage 5-6 flowers)


title: AG null mutant perturbation 5

description: Biological Replicate 2: several plants (approx 20-25) pooled per replicate and genotype

source_name: Day0 AG set2


title: AG null mutant perturbation 2

source_name: Day5 AG set2


title: A4_R2 with array type rice from Affymetrix

value: endosperm


title: E24_R1 with array type rice from Affymetrix


title: CCRF-CEM_Passage 4 xenograft_R2

description:
CCRF-CEM P04 T2
Gene expression data from CCRF-CEM Passage 4 xenograft.

source_name: CCRF-CEM, passage 4 xenograft

tag: originating cell line

value: CCRF-CEM

tag: tumor type

value: acute lymphoblastic (T-ALL) leukemia

tag: in vivo passage


title: Ubi::OsYHB/Nip line #9, Rc50, biol rep 2

city: Davis

first: Wei

last: Hu

state: CA

address: One Shields Ave.

department: Department of Molecular and Cellular Biology

institute: Univ of California at Davis

hyb_protocol: Fifteen micrograms (15 µg) of aRNA were fragmented, and used for hybridization for 16 hr at 45 degree on Affymetrix Rice Genome Array in the Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the 3000 GeneChip Scanner with Autoloader.

data_processing: The data were analyzed in R/Bioconductor. Data were normalized with the 'RMA' function, ABS calls were obtained by Affymetrix GCOS algorithm, and statistical analysis were performed by LIMMA.

source_name: Rice 5-day-old seedling

label_protocol: Biotinylated aRNA were prepared using the GeneChip 3' IVT Express Kit (Affymetrix) from 500ng total RNA according to the manufacturer's instructions.

growth_protocol: Rice seeds were dehusked, surface sterilized with 2% sodium hypochlorite for 30 min with shaking, and rinsed 4 times thoroughly with sterile water.  Seeds were then submerged in water at 37ºC for 2 d for germination promotion before transferring onto 1x MS growth medium. Seeds were germinated and grown at 28ºC for 5 days in darkness or in an LED red light growth chamber for continuous red light growth (50 µmol m-2 s-1 irradiance).

extract_protocol: QIAGEN RNeasy Plant Mini kit was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: After 5 days of growth, during the subjective morning time, continuous red light-grown seedlings (Rc50) were directly harvested under red light, dark-grown seedlings (D) were harvested under safe dim green light (approximately 1 µmol m-2 s-1 irradiance).

tag: cultivar

value: Nipponbare

value: above-ground tissues

tag: growth conditions

tag: age

value: 5 d old


title: AG null mutant perturbation 4

source_name: Day2.5 AG set1

value: stage 3-4 flowers

value: 2.5 days after Dexamethasone treatment (early floral stages ~ stage 3-4 flowers)


title: Ubi::OsYHB/Nip line #1, Rc50, biol rep 1


title: CCRF-CEM_Passage 4 xenograft_R5

description:
CCRF-CEM P04 T5
Gene expression data from CCRF-CEM Passage 4 xenograft.


title: CCRF-CEM_Passage 4 xenograft_R4

description:
CCRF-CEM P04 T4
Gene expression data from CCRF-CEM Passage 4 xenograft.


title: CCRF-CEM_Passage 4 xenograft_R3

description:
CCRF-CEM P04 T3
Gene expression data from CCRF-CEM Passage 4 xenograft.


title: CCRF-CEM_Passage 4 xenograft_R1

description:
CCRF-CEM P04 T1
Gene expression data from CCRF-CEM Passage 4 xenograft.


title: 2275-T

tag: histology

value: Adenocarcinoma

tag: gender

value: M

tag: race

value: African American

tag: tobacco history

value: Y

tag: final patient stage

value: IA

tag: date of birth

tag: date of surgery

tag: vital statistics

value: A

tag: last follow-up survival

tag: recurrence


title: CCRF-CEM_Passage 1 xenograft_R5

description:
CCRF-CEM P01 T5
Gene expression data from CCRF-CEM Passage 1 xenograft.

source_name: CCRF-CEM, passage 1 xenograft


title: Ubi::OsYHB/Nip line #9, Dark, biol rep 2

tag: tissue

tag: genotype

value: dark


title: 2278-T

value: Caucasian

value: IV

value: D

tag: last follow-up recurrence


title: CCRF-CEM_Passage 1 xenograft_R4

description:
CCRF-CEM P01 T4
Gene expression data from CCRF-CEM Passage 1 xenograft.

tag: originating cell line

value: CCRF-CEM

tag: tumor type

tag: in vivo passage


title: Ubi::OsYHB/Nip line #1, Dark, biol rep 1

tag: cultivar

tag: growth conditions

tag: age


title: 2274-T

tag: histology

tag: gender

value: F

tag: race

value: N


title: WT (Nipponbare), Dark, biol rep 1

value: Nipponbare

value: above-ground tissues

value: WT (Nip)


title: CCRF-CEM_Passage 1 xenograft_R3

description:
CCRF-CEM P01 T3
Gene expression data from CCRF-CEM Passage 1 xenograft.

value: acute lymphoblastic (T-ALL) leukemia


title: WT (Nipponbare), Rc50, biol rep 1

value: 5 d old


title: head and neck squamous cell carcinoma 262

city: Tokyo

first: Mitsuyoshi

last: Urashima

address: Nishishimbashi 3-25-8, Minato-ku

country: Japan

institute: Jikei University School of Medicine

hyb_protocol: Scanned on an Agilent G4449A scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: tumor sample

label_protocol: following manufacturer's instructions

growth_protocol: Clinical samples

extract_protocol: 0.5 µg of total DNA were extracted using DNeasy and primed following manufacturer's instructions

tag: age at operation (yrs)

value: male

tag: primary tumor site

value: Oral Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

source_name: healthy non-smoking volunteer

tag: sample type

value: non-drinker control

value: peripheral blood


title: head and neck squamous cell carcinoma 260

value: Oropharyngeal

tag: tissue


title: head and neck squamous cell carcinoma 256


title: 2264-T

value: Adenocarcinoma

value: M

tag: tobacco history

value: Y

tag: final patient stage

value: IB

tag: date of birth

tag: date of surgery

tag: vital statistics

value: A

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: WT (Nipponbare), Rc50, biol rep 2

tag: cultivar

tag: genotype

tag: growth conditions

tag: age


title: 2257-T

tag: histology

value: Squamous

tag: gender

tag: race

value: Caucasian

value: IIA


title: WT (Nipponbare), Dark, biol rep 2

value: Nipponbare

value: above-ground tissues

value: dark


title: CCRF-CEM_Passage 1 xenograft_R1

description:
CCRF-CEM P01 T1
Gene expression data from CCRF-CEM Passage 1 xenograft.

tag: originating cell line

value: CCRF-CEM

tag: tumor type

value: acute lymphoblastic (T-ALL) leukemia

tag: in vivo passage


title: 2247-T

tag: tobacco history

tag: final patient stage

value: IIIB

value: D


title: 2249-T

value: F

value: IA

tag: date of birth

tag: date of surgery

value: N


title: CCRF-CEM_originating cell line_R2

description:
CCRF-CEM P0 T2
Gene expression data from CCRF-CEM originating cell line.

source_name: CCRF-CEM, originating cell line


title: head and neck squamous cell carcinoma 261

tag: age at operation (yrs)

value: male

tag: primary tumor site

value: Sinonasal Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status

tag: alcohol drinking

tag: sample type

value: non-drinker control

tag: tissue

value: peripheral blood


title: CCRF-CEM_originating cell line_R1

description:
CCRF-CEM P0 T1
Gene expression data from CCRF-CEM originating cell line.

tag: originating cell line

tag: tumor type

tag: in vivo passage


title: CCRF-CEM_Passage 1 xenograft_R2

description:
CCRF-CEM P01 T2
Gene expression data from CCRF-CEM Passage 1 xenograft.


title: head and neck squamous cell carcinoma 259

tag: gender

value: Oropharyngeal


title: A673_CloneAsp14_Dox_96h_1

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 96 hours, replica 1

hyb_protocol: Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-A2 microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the gcRMA algorithm

source_name: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown construct

label_protocol: Target labelling and hybridization. For Affymetrix GeneChip analysis, 2.0µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).

growth_protocol: DMEM + GlutaMAXTM-I (+ 4,5g/L D-Glucose + Pyruvate) (Gibco/invitrogen 31966)  + Penicillin/Streptomycin (1x) (100x Stock PAA)  +  50 µg/ml Zeocin (for the shRNA expression vector) (powder Cayla)  and 2 µg/ml Blasticidin (for the TR expression vector)(powder Invitrogen)

extract_protocol: RNA was extrated using the Qiagen RNA extrction kit according to the manufacturer's instructions.

treatment_protocol: 96 hours after addition of 1 µg/ml Doxycyline

tag: treatment

value: 1 ug/ml doxycyline

tag: time

tag: cell line

tag: transgene

value: doxycyclin  inducible EWS-FLI1 knockdown


title: A673_CloneAsp14_Dox_96h_2

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 96 hours, replica 2

value: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown construct


title: head and neck squamous cell carcinoma 254

tag: age at operation (yrs)

tag: primary tumor site

value: Hypopharyngeal

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage


title: A673_CloneAsp14_Dox_72h_2

description: Asp14 Clone of Ewing's sarcoma A673 cell line with doxycyclin  inducible EWS-FLI1 knockdown, timepoint 72 hours, replica 2

treatment_protocol: 72 hours after addition of 1 µg/ml Doxycyline


title: head and neck squamous cell carcinoma 255

tag: tumor grade

tag: chemoradiotherapy

tag: relapse

tag: survival status

tag: smoking status


title: 2244-T

source_name: Lung cancer specimen

tag: histology

value: Squamous

value: M

tag: race

value: African American

tag: tobacco history

value: Y

tag: final patient stage

value: IIB

tag: date of birth

tag: date of surgery

tag: vital statistics

value: A

tag: last follow-up survival

tag: recurrence

tag: last follow-up recurrence


title: CCRF-CEM_originating cell line_R3

description:
CCRF-CEM P0 T3
Gene expression data from CCRF-CEM originating cell line.

hyb_protocol: Samples were hybridized according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

label_protocol: The RNA samples were submitted to Expression Analysis, Inc. (Durham, NC) for microarray analysis using the GeneChip® Human U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA). Samples were labeled according to the "Affymetrix Technical Manual" (www.expressionanalysis.com).

tag: originating cell line

value: CCRF-CEM

tag: tumor type

value: acute lymphoblastic (T-ALL) leukemia

tag: in vivo passage


title: CAKI-1_Passage 10 xenograft_R5

description:
CAKI-1 P10 T5
Gene expression data from CAKI-1 Passage 10 xenograft.

source_name: CAKI-1, passage 10 xenograft

value: carcinoma renal cell


title: head and neck squamous cell carcinoma 257

tag: age at operation (yrs)

tag: gender

value: male

tag: primary tumor site

value: Sinonasal Cavity

tag: hpv infection

tag: p16 protein immunohistochemistry

tag: tnm stage

tag: tumor grade

tag: chemoradiotherapy

tag: alcohol drinking

tag: sample type

tag: tissue


title: head and neck squamous cell carcinoma 253

value: non-drinker control

value: peripheral blood