title: FDiPS102_2

description: Illumina HumanHT-12 V3.0


title: CE - 28-cell - Replicate C

status: Public on Aug 31 2009

type: RNA

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

description: C. elegans (N2 strain) and C. briggsae (AF16 strain) embryos were isolated and staged as described previously (Baugh et al. 2003). The five embryonic stages assayed – the 4-, 28-, 55-, 95-, and 190-cell – were determined for each organism by DAPI staining and DIC microscopy. For C. elegans and C. briggsae the minutes following the 4-cell stage for the four later stages are 80’, 115’, 155’ and 200’ and 55’, 80’, 120’, 160’, respectively.

hyb_protocol: Agilent one-color hybridization protocol

scan_protocol: The arrays were scanned at 10% laser power to avoid signal saturation.

data_processing: Feature Extraction software was used to extract the data which was then mean-normalized.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: CE - 28-cell - Replicate C

label_protocol: 10 ug of aRNA was labeled with Cy3 using the Ambion MessageAmpII kit and 1.65µg labeled aRNA was used to hybridize onto each microarray.

extract_protocol: 50 embryos were isolated for each sample and the total RNA was extracted as described previously (Baugh et al. 2003). To obtain sufficient RNA for microarray analysis, RNA was amplified by two rounds of in vitro transcription (IVT) using the MessageAmpII kit (Ambion) with the following modifications designed to increase the average lengths of the aRNA populations (Baugh et al. 2001). First-round cDNA construction from total RNA was carried out at 1/5 of the recommended quantities and total volume, while IVT was carried out at 1/2 of the recommended volume. 100ng aRNA from the first round was used as input for the second round of amplification following the manufacturers protocol for amino-allyl modified nucleotides. Each embryonic stage was produced in biological triplicates, with the exception of C. elegans 55-cell and C. briggsae 4-cell and 95-cell, which were hybridized in duplicates due to poor amplification of one of the triplicates. The same procedure was also used to identify the C. elegans Hawaiian (CB4856) 4-cell stage transcriptome in triplicates.

tag: developmental stage

value: 28-cell stage


title: CE - 4-cell - Hawaiian - Replicate B

source_name: CE - Hawaiian - 4-cell - Replicate B

value: 4-cell stage

tag: strain

value: Hawaiian


title: Mock IP (2)

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82467.gif
Antibody used in IP: not tagged strain

hyb_protocol: cDNAs were fluorescently labeled and hybridized on yeast oligo microarrays over night at 42 degrees in formamide-based hybridization buffer.

scan_protocol: GenePix 4200A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Saccharomyces cerevisiae

source_name: total RNA extract mock (2)

label_protocol: not provided

extract_protocol: not provided

tag: organism

value: Saccharomyces cerevisiae

source_name: total RNA mock IP (2)

label_protocol: RNAs were reverse transcribed using a mixture of oligo-dT and random nonamer oligos in the presence of amino-allyl dUTP/dNTP mixture.

extract_protocol: Cells were grown to mid-log phase in rich media and harvested by centrifugation. TAP-tagged Shg1 was affinity-purified from cell-free extracts with IgG sepharose and eluted with TEV protease. RNA was isolated from extract (=input) and from the purified protein sample with the RNAeasy Kit (Qiagen).


title: wild strain, no inhibitor, biological replicate 2

city: Tianjin

first: Bing-Zhi

last: Li

address: Weijin Road 92#

country: China

institute: Tianjin University

description: Gene expression at exponential phase.

hyb_protocol: The biotin-labeled cRNA was hybridized to the GeneChip® Yeast Genome 2.0 Array from Affymetrix (California, US) after dilution and fragmentation according to Affymetrix’s protocol.

scan_protocol: Microarrays were scanned with the Genechip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operation System (GCOS) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: industrial yeast, without inhibitor addition

label_protocol: Total RNA labeling was conducted according to the Affymetrix GeneChip Expression analysis technical manual (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Strains were incubated in 400 ml high-sugar YPD medium (10 g/L yeast extract, 20 g/L peptone, 100 g/L glucose) in a 2-liter conical flask with an initial OD600 of 0.35.

extract_protocol: Total RNA was isolated according to the hot phenol method.

treatment_protocol: Cultures for microarray analysis were collected 20 minutes after the addition of the inhibitor (furfural, phenol, or acedic acid) or medium, which was added at mid-exponential phase.

value: angel yeast

tag: inhibitor


title: FDiPS22_2

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: Illumina HumanHT-12 V3.0

hyb_protocol: 750ng of labeled cRNA were hybridized on the Illumina HumanHT-12 V3.0 arrays according to Illumina's instructions.

scan_protocol: according to manufacturer

data_processing: Normalization and model-based expression measurements were performed with the Illumina analysis package (LUMI) available through the open-source Bioconductor project (http://www.bioconductor.org) within the statistical programming language R (http://cran.r-project.org/). A pair-wise comparison of neural crest cell from (H9 and C14-iPSC) versus FD-iPSC was performed using the Linear Models for Microarray Data package ( LIMMA) available through Bioconductor. Genes found to have an adjusted P-value < 0.05 and a fold change greater than two were considered significant.

organism: Homo sapiens

source_name: FD#22-iPSC (undifferentiated)

label_protocol: 200ng of total RNA were labeled using the Illumina Total Prep RNA Amplification Kit (Ambion, cat#AMIL1791) according the manufacturer's instructions

extract_protocol: total RNA was extracted from cell pellet using Trizol (invitrogen)

tag: cell type

value: FD#22-iPSC (undifferentiated)


title: FDiPS22_1

description: Illumina HumanHT-12 V3.0


title: wild strain, no inhibitor, biological replicate 1

description: Gene expression at exponential phase.


title: 4589_2

description: Illumina HumanHT-12 V3.0


title: CE - 95-cell - Replicate B

source_name: CE - 95-cell - Replicate B

value: 95-cell stage


title: 4589_1

description: Illumina HumanHT-12 V3.0


title: CE - 28-cell - Replicate B

source_name: CE - 28-cell - Replicate B


title: Yeast_freeze_1day_rep3

city: Tsukuba

first: Jun

last: Shima

state: Ibaraki

address: 2-1-12 Kannondai

country: Japan

institute: National Food Research Institute

description: Statistical analysis after data acquisition and normalization of expression data were performed using GeneSpring ver.7.3.1 (Agilent Technologies, Palo Alto, CA, USA) based on the gene expression data from two independent experiments. After data transformation to GeneSpring, per-chip normalization to the 50th percentile was performed, and per-gene normalization to the control samples (non freeze sample: 0h) was applied to the per-chip normalized data.

hyb_protocol: At 45degree for 16h

scan_protocol: GeneChip scanner

data_processing: GeneChip operating system (GCOS)

label: The biotinyated RNA

molecule: polyA RNA

source_name: Yeast, freeze, 1day

label_protocol: cDNA synthesis, cRNA synthesis, and labeling were performed according to the Affymetrix user's manual (Affymetrix, Santa Clara, USA).

extract_protocol: RNA was extracted from the yeast cells using the hot phenol method. Poly(A)+ RNA was enriched from total RNA by using an Oligotex dt30 (Super) mRNA purification kit (Takara Bio, Ohtsu, Japan).

treatment_protocol: The strain was grown at 30 oC until log growth phase (OD600=1) in YPD medium. Cells were harvested by centrifugation, washed in distilled water, and suspended in equal volume of distilled water. Then an aliquot of 5 ml was taken from the cell cultures and used as the control without freezing (0 h). The remaining cell cultures were divided into 5 ml and frozen at –30 °C for 24 h or 48 h. The frozen cell cultures were then thawed at 30 °C in water bath for 10 min.

tag: genotype


title: Yeast_freeze_2day_rep3

source_name: Yeast, freeze, 2day


title: CE - 55-cell - Replicate B

source_name: CE - 55-cell - Replicate B

value: 55-cell stage


title: CE - 190-cell - Replicate B

source_name: CE - 190-cell - Replicate B

value: 190-cell stage


title: 4959_2

description: Illumina HumanHT-12 V3.0


title: 4959_1

description: Illumina HumanHT-12 V3.0


title: CE - 4-cell - Hawaiian - Replicate A

source_name: CE - 4-cell - Hawaiian - Replicate A


title: Tomato fruit -- DefH9-RolB -- biol replicate 1

city: Davis

first: Abhaya

middle: M

last: Dandekar

state: CA

address: One Shields Ave

department: Plant Sciences

institute: University of California, Davis

description: sample from a pool of eight fruits from transgenic line DefH9-rolB

hyb_protocol: Standard Affymetrix protocols were followed.

scan_protocol: Used Affymetrix 3000 GeneChip Scanner, and standard Affymetrix protocols were followed.

data_processing: Standard Affymetrix protocol was followed for image processing. For statistical analyses, R statistical software was used. We used the RMA method (Irizarry et al., 2003) for background subtraction and normalization to preprocess raw probe data and produce the gene expression matrix. To determine which genes were differentially expressed among different groups, one-way ANOVA was used to obtain a p-value for each gene. Then all p-values were BH adjusted (Benjamini and Hochberg, 2000) for multiple hypotheses. Genes with adjusted p-values < 0.05 were considered differentially expressed in different groups. We used R package LMGene (Rocke and Durbin, 2003; Rocke, 2004) to perform one-way ANOVA and R package mulltest (Pollard and van der Laan, 2004) to adjust multiple hypotheses.

organism: Solanum lycopersicum

source_name: Tomato fruit, DefH9-RolB

label_protocol: RNA labeling was performed according to instructions in the GeneChip One Cycle Target Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: A modified hot borate method (Wan and Wilkins, 1994) was used to extract RNA from the pooled samples. Tissue was ground in liquid nitrogen and PVP-40 (200 mg) and put into a pre-chilled collection tube with 6-8 mg proteinase K and 10 ml 80ºC XT buffer (ratio 5 ml/g).  Each sample was mixed, incubated on ice for 1 hr, and centrifuged at 10,000-13,000 rpm for 20 min at 4ºC. The supernatant was filtered through sterile miracloth into a clean collection tube and 10 M LiCl was added (volume ratio 1:4). Samples were mixed and incubated on ice overnight. Samples were centrifuged at 13,000 rpm for 20 min at 4ºC, then washed three times with cold 2 M LiCl. The pellet was resuspended in 2 ml 10 mM Tris HCl, pH 7.5, by gentle vortexing and then centrifuged at 13,000 rpm for 10 min at 4ºC. The supernatant was decanted, 200 μl (1/10 vol) K-acetate (pH 5.5) was added, and the sample was incubated on ice for 15 minutes. Samples were centrifuged at 13,000 rpm for 10 min at 4ºC, the supernatant collected, and 5 ml 95% EtOH was added.  Tubes were mixed and incubated at -20ºC overnight, then centrifuged at 13,000 rpm for 30 min at 4ºC. The pellet was washed with 4 ml 70 % EtOH, centrifuged at 13,000 rpm for 5 min at 4ºC, dried at room temperature, and resuspended in suitable volume of DEPC-dH2O. Quantitative and qualitative determination of RNA was performed with gel electrophoresis.

tag: Solanum lycopersicum cv. Micro-Tom


title: Tomato fruit -- DefH9-RolB -- biol replicate 2


title: Yeast_freeze_0day_rep3

source_name: Yeast, freeze, 0day


title: Tomato fruit -- INO-RolB -- biol replicate 3

description: sample from a pool of eight fruits from transgenic line INO-rolB

source_name: Tomato fruit, INO-RolB


title: SB432542-treated ES cells #2

city: Kansas City

first: Jay

last: Vivian

state: KS

address: 3901 Rainbow Blvd.

department: Pathology

institute: University of Kansas Medical Center

description: SB 9

hyb_protocol: Per standard Affymetrix protocol.

scan_protocol: Automated process conducted using the Agilent GeneArray Scanner.

data_processing: Bioconductor package in R; RMA normalization.

organism: Mus musculus

source_name: ES cells in defined media + SB431542 5uM, 24 hrs

label_protocol: Oligo-dT first-strand synthesis, biotin labelled via in vitro transcription.

growth_protocol: Defined ES cell media (N2B27) supplemented with BMP4 (20ng/ml) and LIF (10^3U/ml).

extract_protocol: Qiagen Rneasy RNA purification.

treatment_protocol: Untreated, 10ng/ml activin for 2 hrs, or 5uM SB431542 for 24 hrs.

tag: cell line

value: mouse embryonic stem cells

tag: condition


title: CE - 4-cell - Replicate B

source_name: CE - 4-cell - Replicate B


title: CE - 190-cell - Replicate A

source_name: CE - 190-cell - Replicate A


title: SB431542-treated ES cells #1

description: SB 8


title: activin-treated ES cells #1

description: activin 4

source_name: ES cells in defined media + activin 10ng/ml, 2 hrs

value: activin


title: activin-treated ES cells #2

description: activin 6


title: CE - 28-cell - Replicate A

source_name: CE - 28-cell - Replicate A


title: CE - 4-cell - Replicate A

source_name: CE - 4-cell - Replicate A


title: Tomato fruit -- INO-RolB -- biol replicate 2


title: CE - 55-cell - Replicate A

source_name: CE - 55-cell - Replicate A


title: Ctrol vs Pasha-Drosha

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

description: This is a comparision between the signal obtained with labeled cDNA from Tim-Drosha and Tim-Pasha fly heads against a control sample.

hyb_protocol: Labeled cDNA was hybridized for 18 hrs at 45C on GeneChip Drosophila Tiling 1.0R  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneArray Scanner 3000 7G

data_processing:
The data were processed with MAT. MAT score is reported in the BAR file.
timctrl_dropas_300.tag is the input file for MAT program. timctrl_dropas_300.Dm35b_MR_v02-3_BDGPv4h.NR.bpmap_matscore.bar is the resulting MAT score. Comparison is TIMCtrl vs TIMPasha and TIMDrosha.

organism: Drosophila melanogaster

source_name: Total RNA from Tim-Drosha and Tim-Pasha fly heads

label_protocol: RNA was utilized to prepare cDNA that was labeled using the double strand cDNA labeling Kit (Affymetrix)

growth_protocol: Flies were grown under standard conditions in 12hs light and 12hs dark cycles

extract_protocol: Heads were collected and RNA extracted using TRIZOL

tag: tissue

value: fly head

source_name: Total RNA from Tim-gal4 fly heads


title: control ES cells #2

description: control 3

source_name: ES cells in defined media

value: untreated


title: Tomato fruit -- control with seeds -- biol replicate 3

description: sample from a pool of eight wild-type fruits

source_name: Tomato fruit, control with seeds


title: Tomato fruit -- DefH9-IaaM -- biol replicate 3

description: sample from a pool of eight fruits from transgenic line DefH9-iaaM

source_name: Tomato fruit, DefH9-IaaM


title: Tomato fruit -- DefH9-IaaM -- biol replicate 1


title: Tomato fruit -- INO-IaaM -- biol replicate 1

description: sample from a pool of eight fruits from transgenic line INO-iaaM

source_name: Tomato fruit, INO-IaaM


title: Tomato fruit -- INO-RolB -- biol replicate 1


title: Tomato fruit -- INO-IaaM -- biol replicate 3


title: control ES cells #1

description: control 2


title: Tomato fruit -- INO-IaaM -- biol replicate 2


title: CE - 95-cell - Replicate A

source_name: CE - 95-cell - Replicate A


title: Tomato fruit -- control with seeds -- biol replicate 2


title: Tomato fruit -- control with seeds -- biol replicate 1


title: Tomato fruit -- DefH9-IaaM -- biol replicate 2


title: CB - 28-cell - Replicate C

organism: Caenorhabditis briggsae

source_name: CB - 28-cell - Replicate C


title: CB - 190-cell - Replicate C

source_name: CB - 190-cell - Replicate C


title: CB - 95-cell - Replicate B

source_name: CB - 95-cell - Replicate B


title: CB - 55-cell - Replicate B

source_name: CB - 55-cell - Replicate B


title: CB - 95-cell - Replicate A

source_name: CB - 95-cell - Replicate A


title: Tomato fruit -- control no seeds -- biol replicate 3

description: sample from a pool of eight wild-type fruits, seeds were manually removed

source_name: Tomato fruit, control no seeds


title: CB - 190-cell - Replicate A

source_name: CB - 190-cell - Replicate A


title: CB - 190-cell - Replicate B

source_name: CB - 190-cell - Replicate B


title: CB - 55-cell - Replicate A

source_name: CB - 55-cell - Replicate A


title: CB - 55-cell - Replicate C

source_name: CB - 55-cell - Replicate C


title: CB - 28-cell - Replicate A

source_name: CB - 28-cell - Replicate A


title: Tomato fruit -- control no seeds -- biol replicate 2


title: 13697307 - bou homozygote 5 days cotyledons  set2 vs Col 0 5 days cotyledons  set2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Autotrophic growth acquisition is abolished in the bou mutant in Arabidopsis thaliana. BOU encodes a putative mitochondrial acyl carnitine carrier. bou mutant is blocked at the cotyledon stage. Autotrophic growth of the bou mutant can be achieved with addition of sugar in the medium or in darkness. Moreover, BOU gene expression is activated by light and depends on plant developmental stage. We wish to determine what are the consequences of bou gene mutation at the transcriptome level. We wish to understand whether bou growth arrest is due to the modification of specific genes expression or to a general effect on metabolism at the transition from heterotrophic to autotrophic growth.

hyb_protocol: Col 0 5 days cotyledons  set2 Cy5 / bou homozygote 5 days cotyledons  set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: Col 0 5 days cotyledons  set2

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - Media=MS 1/2	 hygrometry=100%	 Temperature=21°C	 Light=continuous

extract_protocol: Col 0 5 days cotyledons  set2:20ug.

treatment_protocol: no treatment

tag: arabidopsis thaliana (col-0)  - dev.stage (boyes et al. plant cell 2001)

source_name: bou homozygote 5 days cotyledons  set2

extract_protocol: bou homozygote 5 days cotyledons  set2:20ug.

tag: arabidopsis thaliana (col-0)  mutant (at5g46800 = bou (a bout de souffle) ) - dev.stage (boyes et al. plant cell 2001)


title: CB - 4-cell - Replicate B

source_name: CB - 4-cell - Replicate B


title: 13697305 - Col 0 5 days cotyledons  set2 vs bou homozygote 5 days cotyledons  set2

hyb_protocol: bou homozygote 5 days cotyledons  set2 Cy5 / Col 0 5 days cotyledons  set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CB - 4-cell - Replicate A

source_name: C. briggsae - 4-cell - Replicate A


title: CB - 28-cell - Replicate B

source_name: CB - 28-cell - Replicate B


title: C14_HNK1_2

description: Illumina human ref-6V2.0

hyb_protocol: 750ng of labeled cRNA were hybridized on the Illumina Human Ref-6 V2.0 arrays according to Illumina's instructions.

source_name: C14_derived neural crest precursors

value: control-hiPSC derived neural crest precursors


title: FAN +/+, TNF treated

city: Toulouse

first: bruno

last: Ségui

address: Av Jean Poulhes

institute: INSERM U858

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Standard Affymetrix procedures. Processed by AROS applied biotechnology (Sweden)

data_processing: Affymetrix Microarray Suite version 5.0. Processed by AROS applied biotechnology (Sweden)

source_name: FAN +/+, TNF treated

growth_protocol: MEFs were prepared from C57BL/6 embryos with either FAN +/+ or FAN -/- genotypes and grown in DMEM 0% FCS.

extract_protocol: RNA was extracted using RNeasy MidiKit following manufacturer's instructions

treatment_protocol: Untreated cells were incubated in DMEM 0% FCS for 24h and treated cells were incubated in DMEM 0% FCS for 8h followed by a 16h TNF (50ng/ml) treatment.

tag: Genotype

value: FAN -/- C57BL/6 MEFs

tag: Treatment

value: 16h TNF treatement (50ng/ml)


title: FD22_HNK1_2

description: Illumina human ref-6V2.0

source_name: FD#22-hiPSC derived neural crest precursrors


title: FD22_HNK1_3

description: Illumina human ref-6V2.0

value: FD#22-hiPSC derived neural crest precursrors


title: C14_HNK1_3

description: Illumina human ref-6V2.0


title: H9_HNK1_3

description: Illumina human ref-6V2.0

source_name: H9_derived neural crest precursors

value: hESC-derived neural crest precursors


title: Tomato fruit -- control no seeds -- biol replicate 1


title: FAN +/+, untreated

scan_protocol: Standard Affymetrix procedures. Processed by AROS applied biotechnology (Sweden)

source_name: FAN +/+, untreated

value: wild type C57BL/6 MEFs


title: FAN -/-, untreated

description: Gene expression data from embryos in slow phase of cellularisation.

source_name: FAN -/-, untreated

label_protocol: Standard Affymetrix procedures. Processed by AROS applied biotechnology (Sweden)


title: FAN -/-, TNF treated

source_name: FAN -/-, TNF treated


title: H9_HNK1_2

description: Illumina human ref-6V2.0


title: S10_ swine

status: Public on Aug 29 2009

type: genomic

city: Ames

first: Zuo-Wei

last: Wu

state: IA

address: 1113 Veterinary Medicine Bldg

institute: Iowa state university

description: S10_ swine

hyb_protocol: Labeled genomic DNA was hybridized to arrays in the NimbleGen Hybridization Buffer for 16 hours at 42oC using a MAUI hybridization system (BioMicro Systems, Inc. Salt Lake City, Utah). Labeled genomic DNA (5ug) from the reference strain Streptococcus suis 05ZYH33 and from each test SS2 strain were co-hybridized to each array. Arrays were washed with NimbleGen wash buffer, and then were spun dry in a microarray high-speed centrifuge (TeleChem International, Inc., Sunnyvale, CA) and stored until scanned.(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 CGS data extraction.

molecule: genomic DNA

organism: Streptococcus suis

label_protocol: Genomic DNA was labeled with a Random prime reaction. DNA (1 ug) was mixed with 1 O.D. of 5’-fluorescence dye labeled random nonamer (Cy3 for Suis test strains and Cy5 for reference strain 05ZYH33) (TriLink Biotechnologies) in 62.5 mM Tris-HCl, 6.25 mM MgCl2 and 0.0875% ß-mercaptoethanol, denatured at 98°C for 5 min, chilled on ice, and incubated with 100 units Klenow fragment (NEB) and dNTP mix (6 mM each in TE) for 2 h at 37°C. Reactions were terminated with 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water. A fifty-fold amplification was typically achieved,(http://www.nimblegen.com/products/lit/lit.html)

growth_protocol: Cells were cultured in Todd-Hewitt broth (THB)(Difco Laboratories, Detroit, MI) medium.

extract_protocol: Genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit (Qiagen)

tag: origin

value: The Netherlands

tag: pathogenicity

value: Virulent

source_name: Reference DNA from 05ZYH33


title: 8011_swine_1996


title: 2f_Healthy swine_2006

description: 2f_Healthy swine_2006

value: Jiangsu, China

value: Avirulent


title: T15_Healthy Swine

description: T15_Healthy Swine


title: 1941_Diseased swine_1980s

description: 1941_Diseased swine_1980s

value: China


title: S735_Diseased swine_1963

description: S735_Diseased swine_1963


title: 05HAS68_Healthy swine_2005

description: 05HAS68_Healthy swine_2005


title: SS2-N_Diseased swine_1996

description: SS2-N_Diseased swine_1996

value: German


title: 1940_Diseased swine_1980s

description: 1940_Diseased swine_1980s


title: 606_Diseased swine_1980s

description: 606_Diseased swine_1980s


title: 98T003_STSS patient_1998

description: 98T003_STSS patient_1998


title: ZYH354-1_Diseased swine_2005

description: ZYH354-1_Diseased swine_2005

value: Sichuan, China


title: 607_Diseased swine_1980s

description: 607_Diseased swine_1980s

value: Japan


title: JZD-1_Diseased swine_2005

description: JZD-1_Diseased swine_2005

value: Jiangxi, China


title: Habb_STSS patient_1998

description: Habb_STSS patient_1998

source_name: Habb

value: Habb


title: Control, biological replicate 4, technical replicate 1

city: Omaha

first: Howard

last: Fox

state: NE

address: 985800 Nebraska Medical Center - DRC 3008

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical Center

description: Gene expression from control monkey hippocampus

hyb_protocol: Standard Affymetrix 49 Format Hybridization with 15 ug of fragmented cRNA

scan_protocol: Affymetrix EukGE-WS2v4

data_processing: CEL files were analyzed with the Bioconductor implementation of the RMA (Robust Multichip Average) algorithm).

organism: Macaca mulatta

source_name: Rhesus hippocampus

label_protocol: Ambion MessageAmp Biotin II Enhance

extract_protocol: Total RNA was extracted using Trizol Reagent per manufacturer's instructions.

tag: Gender

value: Male

tag: Age (yrs)

tag: Anti-CD8 Treatment

value: No


title: JR_STSS patient_2005

description: JR_STSS patient_2005

source_name: JR

tag: strain

value: JR


title: Control, biological replicate 3, technical replicate 2


title: Control, biological replicate 2, technical replicate 2


title: Control, biological replicate 4, technical replicate 2


title: Control, biological replicate 3, technical replicate 1


title: SIVE, biological replicate 4, technical replicate 1

description: Gene expression from SIVE monkey hippocampus

value: Yes


title: SIVE, biological replicate 3, technical replicate 2


title: SIVE, biological replicate 4, technical replicate 2


title: ZYH214_STSS patient_2005

description: ZYH214_STSS patient_2005


title: SIVE, biological replicate 2, technical replicate 1


title: Control, biological replicate 1, technical replicate 2


title: Control, biological replicate 1, technical replicate 1


title: ZYH215_STSS patient_2005

description: ZYH215_STSS patient_2005


title: CD34+ and CD34- human umbilical cord blood cells (SET4)

city: Seoul

first: Il-Hoan

last: Oh

address: Banpo-Dong, Socho-Gu

department: Institute of Cell and Gene Therapy

country: South Korea

institute: The Catholic University of Korea, Medical College

description: Experiments were repeated for four times by independent sample preparation.

hyb_protocol: Labeled DNA was hybridized onto Agilent human CpG island microarrays using conditions specified by the manufacturer (Agilent, Santa Clara, CA).

scan_protocol: After washing, the slides were scanned using an Agilent scanner and images were quantified using the Feature Extraction Software v. 9.3 (Agilent).

data_processing: The hybridization intensity was normalized by global LOWESS method and the intensity ratio of CD34(+) and CD34(-) was log transformed.

label_protocol: Purified genomic DNA was amplified using a whole genome amplification kit as recommended by Agilent. Amplified DNA products from CD34+ cells were labeled with Cy3-dUTP.

extract_protocol: Genomic DNA was fragmented by either sonication or digestion with MseI. Recombinant methyl-binding domain (Genomictree, Daejeon, Korea) was incubated with sonicated genomic DNA in a binding reaction mixture. The methyl-enriched DNA fraction was washed 3 times and purified using Qiaquick PCR purification kits (Qiagen, Hilden, Germany).

treatment_protocol: Cells were purified by immunomagnetic selection (Dynal Biotech, Oslo, Norway) followed by flow cytometric sorting in the FACS VantageTM (BD Bioscience, San Jose, CA)

tag: health status

value: Full-term normal deliveries

label_protocol: Purified genomic DNA was amplified using a whole genome amplification kit as recommended by Agilent. Amplified DNA products from CD34- cells were labeled with Cy5-dUTP.


title: Control, biological replicate 2, technical replicate 1


title: SIVE, biological replicate 1, technical replicate 2


title: CD34+ and CD34- human umbilical cord blood cells (SET2)

tag: cell type


title: SIVE, biological replicate 1, technical replicate 1


title: SIVE, biological replicate 3, technical replicate 1


title: CD34+ and CD34- human umbilical cord blood cells (SET3)


title: SIVE, biological replicate 2, technical replicate 2


title: SIVE, biological replicate 9, technical replicate 2


title: SIVE, biological replicate 9, technical replicate 1


title: SIVE, biological replicate 8, technical replicate 2


title: SIVE, biological replicate 7, technical replicate 1


title: SIVE, biological replicate 7, technical replicate 2


title: SIVE, biological replicate 8, technical replicate 1


title: 8W-ERKObeta-MB1

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: Standard Affymetrix protocol for Mouse 430 plus 2.0 arrays

data_processing: Raw CEL files were processed using Affymetrix Gene Chip Operating Software using MAS5

source_name: ERbetaKO, male

label_protocol: 1ug of total RNA was labeled according to Standard Affymetrix  Eukaryotic protocol for Mouse  430 plus 2.0 arrays

extract_protocol: total RNA was extracted from brain tissue using Trizol protocol followed by RNEasy cleanup protocol

treatment_protocol: whole brains were extracted and flash frozen in liquid nitrogen followed by storage at -80oC

tag: genotype

value: ERbetaKO

value: whole brain

tag: gender

value: male

tag: age

value: 8 weeks


title: 8W-ERKObeta-MB3

scan_protocol: Standard Affymetrix protocol for Mouse 430 plus 2.0 arrays


title: S10_ swine

description: S10_ swine

value: The Netherlands

value: Virulent


title: 8W-ERKObeta-FB2

source_name: ERbetaKO, female

value: female


title: SIVE, biological replicate 6, technical replicate 2


title: 05HAS68_Healthy swine_2005

description: 05HAS68_Healthy swine_2005

value: Jiangsu, China

value: Avirulent


title: Control, biological replicate 9, technical replicate 2


title: S735_Diseased swine_1963

description: S735_Diseased swine_1963


title: 8W-ERKObeta-FB1


title: CD34+ and CD34- human umbilical cord blood cells (SET1)


title: 8011_swine_1996


title: 8W-ERKObeta-FB3


title: SIVE, biological replicate 6, technical replicate 1


title: T15_Healthy Swine

description: T15_Healthy Swine


title: 8W-ERKObeta-MB2


title: SS2-N_Diseased swine_1996

description: SS2-N_Diseased swine_1996

value: German


title: 8W-ERKOalpha-MB3

source_name: ERalphaKO, male

value: ERalphaKO


title: Control, biological replicate 8, technical replicate 1


title: Control, biological replicate 8, technical replicate 2


title: 1941_Diseased swine_1980s

description: 1941_Diseased swine_1980s

value: China


title: Control, biological replicate 9, technical replicate 1

value: Male


title: 8W-ERKOalpha-MB2


title: 8W-ERKOalpha-FB1

source_name: ERalphaKO, female


title: SIVE, biological replicate 5, technical replicate 2

value: No


title: 8W-ERKOalpha-FB2


title: 1940_Diseased swine_1980s

description: 1940_Diseased swine_1980s


title: Control, biological replicate 7, technical replicate 1


title: 8W-B6-MB2

source_name: wild type, male

value: wild type


title: 8W-B6-MB3


title: 8W-ERKOalpha-MB1


title: 8W-ERKOalpha-FB3


title: 607_Diseased swine_1980s

description: 607_Diseased swine_1980s

value: Japan


title: ZYH354-1_Diseased swine_2005

description: ZYH354-1_Diseased swine_2005

value: Sichuan, China


title: 98T003_STSS patient_1998

description: 98T003_STSS patient_1998


title: SIVE, biological replicate 5, technical replicate 1


title: JZD-1_Diseased swine_2005

description: JZD-1_Diseased swine_2005

value: Jiangxi, China


title: 606_Diseased swine_1980s

description: 606_Diseased swine_1980s


title: Control, biological replicate 7, technical replicate 2


title: Habb_STSS patient_1998

description: Habb_STSS patient_1998

value: Habb


title: 8W-B6-MB1

value: whole brain

value: male


title: 8W-B6-FB2

source_name: wild type, female

value: 8 weeks


title: Control, biological replicate 5, technical replicate 2


title: Control, biological replicate 5, technical replicate 1


title: Control, biological replicate 6, technical replicate 1


title: JR_STSS patient_2005

description: JR_STSS patient_2005

value: JR

value: Virulent


title: ZYH215_STSS patient_2005

description: ZYH215_STSS patient_2005


title: 8W-B6-FB1

value: female


title: Control, biological replicate 6, technical replicate 2


title: Microacinar (1705-1)

status: Public on Aug 28 2009

city: East Lansing

first: Eran

last: Andrechek

state: MI

address: 2120 BPS Building

department: Physiology

institute: Michigan State University

description: Gene expression data from mouse mammary tumor tissue.

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix Mouse 430A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

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

data_processing: The data were analyzed using Stratagene's ArrayAssist Enterprise using Affymetrix default analysis settings.

source_name: mouse mammary tumor

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

extract_protocol: Total RNA from mouse mammary tumors was extracted using the Qiagen RNeasy Midi kit.

tag: tumor type

value: MMTV-Myc

tag: histological subtype

value: Microacinar


title: Mix (1809-5)

value: Mix


title: EMT (1938-1)

value: EMT


title: Mix (1855-1)


title: ZYH214_STSS patient_2005

description: ZYH214_STSS patient_2005


title: Squamous (1569-1)

value: Squamous


title: Mix (1807-2)


title: Solid (1806-1)

value: Solid


title: Squamous (1575-2)


title: Adenocarcinoma (1572-1)

value: Adenocarcinoma


title: Microacinar (1576-1)


title: EMT (1663-1)


title: Solid (1807-1)


title: Papillary (1567-2)

value: Papillary


title: Mix (1567-1)


title: Microacinar (1568-1)


title: Mix (1513-1)


title: Squamous (1445-1)


title: Papillary (1445-2)


title: Mix (1565-1)


title: Microacinar (1444-1)


title: Mix (1351-1)


title: EMT (1356-2)


title: Squamous (1359-1)


title: Mix (1350-1)


title: EMT (1398-1)


title: Adenocarcinoma (1359-2)


title: Papillary (1352-1)


title: Microacinar (1572-2)


title: EMT (1139-1)


title: Solid (1269-2)


title: Squamous (1346-1)


title: Solid (1088-1)


title: Adenocarcinoma (1345-5)


title: Solid (1347-1)


title: Adenocarcinoma (1345-6)


title: Papillary (1086-1)


title: Squamous (1066-2)


title: Microacinar (1062-1)


title: Squamous (1066-1)


title: Microacinar (1052-1)


title: Microacinar (1087-1)


title: Microacinar (863-2)


title: Microacinar (1052-3)


title: Mix (1086-3)


title: Mix (862-1)


title: Mix (1085-1)


title: Day 0 ganglia D0_R1301_V2

city: Philadelphia

first: Jayanti

last: Jagannathan

state: PA

address: 34th & Civic center blvd

department: Oncology

institute: Childrens Hospital of Philadelphia

hyb_protocol: Samples hybridized using  Applied Biosystems Mouse Genome Survey Microarray version 1.0 standard protocol

scan_protocol: ABI Mouse Genome Survery Microarray version 1.0 standard scanning protocol

data_processing: ABI Mouse Genome Survery Microarray version 1.0 standard data processing protocol. Raw probe-level measurements were processed by quantile normalization for sample quality control.

label: Digoxigenin

source_name: Day 0, ganglia

label_protocol: standard ABI protocol

growth_protocol: TH-MYCN transgenic mice were bred to homozygosity and sympathetic ganglia containing foci of neuroblast hyperplasia were harvested at Day 0, Day 7 and Day 14 of life. Two tumors were  harvested after weaning at Day 28 when tumor dimensions were in the Small tumor predetermined size range

extract_protocol: RNA was extracted from 10µm frozen sections using Qiagen RNeasy Micro Kit (Qiagen, Valencia, CA). Tumor total RNA (76ng-1.6µg) was used to generate cDNA targets.

tag: time point

value: day 0

tag: tissue

value: ganglia


title: Day 14 ganglia D14_R0305_V2

source_name: Day 14, ganglia

value: day 14


title: Day 14 ganglia D14_R0611_V2


title: Mix (862-2)


title: Microacinar (864-1)


title: Small tumor 3287S_2R_V2

source_name: Size: Small, tumor

tag: tumor weight

tag: life span

value: 28 days

value: neuroblastoma tumor


title: Day 7 ganglia D7_R0370_V2

source_name: Day 7, ganglia

value: day 7


title: Small tumor 3772S_2R_V2

value: 42 days


title: Microacinar (854-2)


title: Papillary (1053-1)


title: Day 7 ganglia D7_R0361_V2


title: EMT (1061-1)


title: Mix (854-1)


title: Day 0 ganglia D0_R1297_V2


title: 8W-B6-FB3

value: wild type

value: whole brain

value: 8 weeks


title: Microacinar (840-2)

value: MMTV-Myc

value: Microacinar


title: Day 0 ganglia D0_R0583_V2


title: Mix (750-1)

value: Mix


title: Microacinar (840-1)


title: Day 0 ganglia D0_R1298_V2


title: Squamous (598-1)

value: Squamous


title: Very large tumor 3036U

source_name: Size: very large, tumor

growth_protocol: TH-MYCN transgenic mice were bred to homozygosity and examined with high frequency ultrasonography (Vevo770 Visual Sonics Inc) three times per week was initiated immediately upon weaning at day 28 to detect asymptomatic tumors and track tumor growth. Mice were sacrificed when tumor dimensions were within one of four predetermined size ranges.Six replicates harvested within four size cohorts.

tag: size

value: very large

value: 35 days


title: Papillary (599-1)

value: Papillary


title: Very large tumor 734U

value: 38 days


title: Very large tumor 3512U


title: EMT (642-1)

value: EMT


title: EMT (812-1)


title: Microacinar (599-2)


title: Day 0 ganglia D0_R0581_V2

value: day 0

value: ganglia


title: Squamous (525-1)


title: Very large tumor 3557U

value: neuroblastoma tumor

value: 45 days


title: Microacinar (842-1)


title: Very large tumor 3964U

value: 37 days


title: Very large tumor 556U

value: 44 days


title: Large tumor 962L

source_name: Size: Large, tumor

value: Large


title: Papillary (523-3)


title: Large tumor 487L

value: 46 days


title: Papillary (523-1)

value: MMTV-Myc


title: Large tumor 3556L


title: Microacinar (520-5)

value: Microacinar


title: Medium tumor 558M

source_name: Size: Medium, tumor

value: Medium

value: 39 days


title: Microacinar (518-2)


title: Squamous (521-1)

value: Squamous


title: Microacinar (520-1)


title: Microacinar (520-2)


title: Large tumor 3086L

value: 42 days


title: Microacinar (520-3)


title: Large tumor 733L

value: 36 days


title: Medium tumor 3742M


title: Mix (421-3)

value: Mix


title: Medium tumor 3981M


title: Medium tumor 3754M

value: 35 days


title: Medium tumor 3055M


title: Microacinar (503-1)


title: Mix (518-1)


title: Mix (521-2)


title: Medium tumor 3757M


title: Large tumor 3104L


title: Small tumor 3772S

source_name: size:small, tumor

value: small


title: Mix (339-2)


title: Small tumor 3753S

value: 28 days


title: Small tumor 3235S

value: neuroblastoma tumor

value: 31 days


title: Papillary (338-1)

value: Papillary


title: Small tumor 3230S


title: PSG-F-Cy3-4

city: BeiBei

first: Qingyou

last: Xia

state: Chongqing

address: No.2 Tiansheng Road

institute: Southwest University

hyb_protocol: Labeled cDNAs were dissolved in 80 l hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide, then denatured at 95℃ for 3 min before hybridization. The mixed hybridization buffer was loaded onto a microarray slide then covered with a LifterSlipTM coverslip (Erie Company, Portsmouth, NH). The hybridization was performed in a hybridization chamber and the chamber was laid on a three-phase-tiling agitator BioMixerTM (CapitalBio) to provide continuous mixing of the hybridization buffer, with more uniform hybridization across the entire slide surface and to prevent edge effects. After hybridization, the slide was washed with washing solution one (0.2% SDS, 2× SSC) and washing solution two (2× SSC) at 42℃ for 5 min respectively.   We used dual-dye experiment to analyze expression patterns; one of the dyes (Cy3) is used to label a female sample of a tissue type (for example fat body), the other to label a male sample of the same tissue type. Each experiment was performed a dye-swap. Additionally, biological replicate experiment was also applied in expression profiling of the important tissue type.   Additionally, to obtained enough tissue RNA sample and minimize stochastic variations such as circadian rhythms or individual dissection, we adopted sample pooling strategy, each pooling sample containing 30 individual RNA sample. In our pilot experiments, we performed several self-to-self hybridizations to evaluate system noises. In addition, in order to minimize the microarray data variation, each hybridization test was performed with dye-reversal method, and at least two independent pooling RNA samples for each tissue were analyzed. Also, we adopted DNA-DNA hybridization replacing RNA-DNA hybridization in the present study concerning that the former may reduce microarray cross-hybridization.

scan_protocol: Arrays were scanned with a confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio).

data_processing: For individual channel data extract, faint spots were removed for which fewer than 80% of the signal pixels exceeded the local background value for either or both channels (Cy3 and Cy5) by at least 2 standard deviations of the local background.

organism: Bombyx mori

source_name: posterior silk gland Female

label_protocol: Five microgram of total RNA was used to prepare fluorescent dye-labeled cDNA through Eberwine’s linear RNA amplification method followed with subsequent reverse transcription and Klenow enzyme reaction according to the previously described methods.

growth_protocol: Chinese silkworm strains Dazao were reared at stable 25℃. Most larvae began wandering on day 7 of the fifth instar under these conditions.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) according to manufacturer’s instructions. The total RNA was quantified by Spectrophotometer and subjected to 1% Formaldehyde denatured agarose gel electrophoresis. The average yield of RNA was ~0.5 µg/mg.

treatment_protocol: We have prepared a total of 30 samples across 10 representative tissue types, including silk gland (anterior/median silk gland (A/MSG) and posterior silk gland (PSG)), testis, ovary, fat body, midgut, head, epidermis, hemocyte and malpighian tubule.All tissues were separated from silkworm individuals on day 3 of the fifth instar, and exception for testis and ovary, remaining 8 tissues were collected from male and female individuals respectively. The dissected tissues were snap-frozen in liquid nitrogen and kept continuously liquid nitrogen until RNA extraction.

value: posterior silk gland

value: female

value: Dazao


title: Small tumor 3291S


title: Papillary (B1503-3)

value: MMTV-Myc T58A


title: Microacinar (281-1)

value: MMTV-Myc

value: Microacinar


title: Papillary (339-1)


title: Small tumor 3287S


title: Adenocarcinoma (281-2)

value: Adenocarcinoma


title: PSG-M-Cy5-4

source_name: posterior silk gland Male

value: male


title: EMT (222-1)

value: EMT


title: PSG-F-Cy3-2


title: Papillary (B1503-2)


title: PSG-F-Cy5-3


title: PSG-M-Cy5-2


title: Papillary (1313-2)


title: PSG-M-Cy3-3


title: Papillary (1796-1)


title: Papillary (1313-1)


title: PSG-F-Cy5-1


title: Papillary (1505-1)


title: PSG-M-Cy3-1


title: A/MSG-F-Cy3-6

source_name: anterior/median silk gland Female

value: anterior/median silk gland


title: Papillary (1165-3)


title: Papillary (1165-1)


title: Papillary (1139-4)


title: A/MSG-F-Cy3-2


title: A/MSG-M-Cy5-4

source_name: anterior/median silk gland Male


title: A/MSG-F-Cy5-3


title: A/MSG-M-Cy3-3


title: Papillary (736-1)


title: Papillary (1140-1)


title: Papillary (745-1)


title: Papillary (745-2)


title: A/MSG-M-Cy5-2


title: A/MSG-F-Cy3-4


title: Papillary (641-1)


title: A/MSG-M-Cy3-5


title: Papillary (957-1)


title: A/MSG-F-Cy5-5


title: Papillary (1101-2)


title: Papillary (589-1)


title: Papillary (746-1)


title: A/MSG-M-Cy3-1


title: Papillary (534-2)


title: Malpighian tubule-F-Cy3-4

description: Malpighian tubule-F-Cy3-4

source_name: Malpighian_tubule Female


title: Malpighian tubule-M-Cy5-4

description: Malpighian tubule-M-Cy5-4

source_name: Malpighian_tubule Male


title: Papillary (494-1)


title: embryo 005x301:005x005 rep4

city: Hamburg

first: Stefan

last: Scholten

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

country: Germany

institute: University of Hamburg

description: Analysis of isolated embryos or endosperm samples 6 days after pollination of reciprocal maize hybrids and the corresponding inbred lines.

hyb_protocol: For each hybridization 20 pmoles dye of two samples were combined, dried under vacuum and resuspended in 45 µl hybridization solution (25 % formamide, 5 x SSC, 0,1 % SDS, 100 µg/ml sonicated salmon sperm DNA, 400 µg/ml polyA DNA). After denaturation the targets were hybridized with arrays, prehybridized for 1 hour in 5 x SSC, 0.1 % SDS, 1 % BSA, for 16 hours. Stringent washing conditions were: 5 min., 42°C (2 x SSC, 0.1 % SDS); 10 min., RT (0.1 x SSC, 0.1 % SDS); 3 x 1 min., RT, 0.1 x SSC.

scan_protocol: An ArrayWorx microarray reader (AppliedPrecision) was used with scan times of 2 sec for Cy3 and 7 sec for Cy5.

data_processing: Analysis of the images was conducted with GenePix 4.0 software (Axon). Flagged spots were removed and the local background subtracted. LOWESS within-chip-normalization of log2-ratios and computing mean of replicated spots was performed for each array.

organism: Zea mays

source_name: 6 dap embryo of hybrid 005x301

label_protocol: Beads with mRNA were resuspended in 3µl ddH2O and used for first strand cDNA synthesis, applying the template switch mechanism at the 5’ end (SMART) and long distance PCR (LDPCR, Clontech) following the manufacturer’s instructions. For each sample the optimal LDPCR cycle number was empirically determined with an aliquot of the reaction to ensure that the cDNA remain in the exponential phase of amplification. For indirect random prime labelling the cDNA was purified with GFX PCR DNA and Gel band purification columns (Amersham). 2 µg cDNA was labeled in 50 µl reactions. Each reaction contained 6 µM of 5’-amino modified random hexamer oligonucleotide; 50 mM Tris-HCl, pH 8.0; 5 mM MgCl2; 1 mM DTT; 500 µM each dATP, dCTP, dGTP; 200 µM dTTP; 300 µM aminoallyl-dUTP (Sigma); 10 units Klenow Fragment (MBI Fermentas) and was incubated at 37°C for 12 to 16 hours. Labeled cDNAs were washed in Microcon-30 concentrators (Millipore), dried under vacuum, resuspended in 0,05 M sodium bicarbonate, pH 9.0, added to Cy3 or Cy 5 mono-reactive dye (Amersham) and incubated for 1 hour at room temperature (RT). After addition of 4.5 µl 4 M hydroxylamine and incubation for further 15 min, the reaction was purified with GFX PCR DNA and Gel band purification columns (Amersham).

growth_protocol: The maize inbred lines were grown in the glasshouse with a 16 h illumination period (25 klux) at 25/20°C (day/night).

extract_protocol: After six days nucellus pieces containing the embryo sac were dissected from the ovules under a dissecting microscope. Endosperm tissues with therein embedded embryos were isolated with tweezers and collected in 650 mosmol mannitol solution. Embryos were manually isolated with glass needles under an inverted microscope. After homogenization of the frozen tissue in liquid nitrogen mRNA isolation was carried out with oligo dT(25) magnetic beads (Dynal).

treatment_protocol: Ears were bagged before silk emergence. Each set of inbred and reciprocal hybrid genotypes under comparison were generated the same day by self- and crosspollination to provide identical growth conditions for all genotypes compared.

value: embryo

source_name: 6 dap embryo of inbred 005


title: embryo 301x005:005x005 rep4

source_name: 6 dap embryo of hybrid 301x005


title: Malpighian tubule-F-Cy5-3

description: Malpighian tubule-F-Cy5-3


title: embryo 301x005:301x301 rep4

source_name: 6 dap embryo of inbred 301


title: endosperm 005x301:301x301 rep4

source_name: 6 dap endosperm of hybrid 005x301

value: endosperm

source_name: 6 dap endosperm of inbred 301


title: A/MSG-F-Cy5-1


title: embryo 005x301:301x301 rep4


title: Malpighian tubule-M-Cy5-2

description: Malpighian tubule-M-Cy5-2


title: Papillary (384-1)

source_name: mouse mammary tumor


title: Malpighian tubule-M-Cy3-3

description: Malpighian tubule-M-Cy3-3


title: Papillary (381-4)


title: Papillary (382-1)


title: Papillary (381-2)


title: Neu (9168)

value: MMTV-Neu


title: Papillary (381-3)


title: Malpighian tubule-F-Cy3-2

description: Malpighian tubule-F-Cy3-2


title: Malpighian tubule-F-Cy5-1

description: Malpighian tubule-F-Cy5-1


title: A/MSG-M-Cy5-6


title: endosperm 301x005:005x005 rep4

source_name: 6 dap endosperm of hybrid 301x005

source_name: 6 dap endosperm of inbred 005


title: embryo 005x005:005x301 rep3


title: endosperm 301x005:301x301 rep4


title: Neu (9117)


title: Malpighian tubule-M-Cy3-1

description: Malpighian tubule-M-Cy3-1


title: embryo 005x005:301x005 rep3


title: endosperm 005x301:005x005 rep4


title: embryo 301x301:301x005 rep3


title: embryo 005x301:005x005 rep2


title: endosperm 301x301:005x301 rep3


title: endosperm 005x005:005x301 rep3


title: endosperm 301x301:301x005 rep3


title: endosperm 005x005:301x005 rep3


title: embryo 301x301:005x301 rep3


title: Hemocyte-F-Cy3-2

source_name: Hemocyte Female

value: Hemocyte


title: Hemocyte-F-Cy5-1


title: embryo 301x005:005x005 rep2


title: Hemocyte-M-Cy3-1

source_name: Hemocyte Male


title: Hemocyte-M-Cy5-2


title: Midgut-F-Cy3-2

source_name: Midgut Female

value: Midgut


title: Neu (9115)


title: Neu (7311)


title: Neu (7313)


title: Neu (7582)


title: Midgut-M-Cy5-2

source_name: Midgut Male


title: Neu (7006)


title: embryo 005x301:301x301 rep2


title: embryo 301x005:301x301 rep2


title: Neu (5849)


title: embryo 005x005:301x005 rep1


title: endosperm 005x301:005x005 rep2


title: embryo 301x301:301x005 rep1


title: embryo 301x301:005x301 rep1


title: Midgut-F-Cy5-1


title: Neu (5847)


title: endosperm 301x005:301x301 rep2


title: endosperm 301x005:005x005 rep2


title: endosperm 005x301:301x301 rep2


title: embryo 005x005:005x301 rep1


title: Fat body-F-Cy3-2

description: Fat body-F-Cy3-2

source_name: Fat_body Female


title: Fat body-M-Cy5-2

description: Fat body-M-Cy5-2

source_name: Fat_body Male


title: Fat body-F-Cy5-1

description: Fat body-F-Cy5-1


title: Neu (5819)


title: Fat body-M-Cy3-1

description: Fat body-M-Cy3-1


title: Neu (5846)


title: Midgut-M-Cy3-1


title: cow 4, week 3

city: Guelph

first: Michael

middle: Alexander

last: Steele

state: Ontario

address: 50 Stone Road East, Building #70

department: Animal and Poultry Science

country: Canada

institute: University of Guelph

description: rumen papillae from third week of grain challenge

hyb_protocol: 10 μg of labeled cRNA was hybridized to Affymetrix Bovine Genome arrays for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400.  GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: Gene level data was generated using the GC Robust Multichip Analysis (GCRMA) preprocessor in GeneSpring GX 10 (Agilent Technologies)

organism: Bos taurus

source_name: cow 4, rumen papillae, third week of grain challenge

label_protocol: Biotinylated complimentary RNA (cRNA) was prepared from 10 ug of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA). Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers.  Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP.

extract_protocol: Qiagen RNeasy Midi Kit

value: rumen papillae (ventral sac)

tag: protocol

value: grain challenge

tag: time

value: week 3


title: cow 4, week 1

description: rumen papillae from first week of grain challenge

source_name: cow 4, rumen papillae, first week of grain challenge

value: week 1


title: Neu (5816-2)


title: Neu (5816)


title: Neu (5818)


title: cow 4, week 0

description: rumen papillae from high forage diet

source_name: cow 4,rumen papillae, high forage baseline

value: high forage diet (control)

value: week 0


title: endosperm 005x005:005x301 rep1


title: endosperm 301x301:005x301 rep1


title: Integument-F-Cy3-2

source_name: Integument Female

value: Integument

value: female

value: Dazao


title: Neu (5815)


title: cow 3, week 3

source_name: cow 3, rumen papillae, third week of grain challenge


title: Integument-M-Cy3-1

source_name: Integument Male

value: male


title: embryo 250x301:301x301 rep2

source_name: 6 dap embryo of hybrid 250x301

source_name: 6 dap embryo of inbred 301


title: endosperm 301x301:301x005 rep1

source_name: 6 dap endosperm of inbred 301


title: embryo 250x301:250x250 rep2

source_name: 6 dap embryo of inbred 250


title: Neu (5814)

source_name: mouse mammary tumor


title: Integument-M-Cy5-2


title: cow 3, week 0

description: rumen papillae from high forage diet

source_name: cow 3,rumen papillae, high forage baseline


title: Integument-F-Cy5-1


title: cow 3, week 1

source_name: cow 3,rumen papillae, first week of grain challenge


title: Neu (380)


title: Neu (772)


title: cow 2, week 3

source_name: cow 2, rumen papillae, third week of grain challenge


title: Head-M-Cy5-2

source_name: Head Male

value: Head


title: cow 2, week 1

source_name: cow 2, rumen papillae, first week of grain challenge


title: Neu (540)


title: Neu (770)


title: cow 2, week 0

description: rumen papillae from high forage diet

source_name: cow 2, rumen papillae, high forage baseline


title: endosperm 005x005:301x005 rep1

source_name: 6 dap endosperm of inbred 005

source_name: 6 dap endosperm of hybrid 301x005


title: embryo 301x250:250x250 rep2

source_name: 6 dap embryo of hybrid 301x250


title: Neu (315)


title: Head-F-Cy3-2

source_name: Head Female


title: embryo 301x250:301x301 rep2


title: cow 1, week 3

source_name: cow 1, rumen papillae, third week of grain challenge


title: Cse4-3HA ChIP-chip 1

first: Raymond

last: Camahort

state: MO

institute: Stowers Institute

description: yeast expressing Cse4-3HA

hyb_protocol: Hybridizations were performed at 63 °C overnight under standard conditions, and slides were washed successively with 0.6X SSC/0.03% SDS and then 0.06X SSC prior to scanning.

scan_protocol: The arrays were scanned using an Axon Instruments (Union City, California, United States) 4000B scanner and quantitated using GenePix 4.0. Results were stored in the AMAD database

data_processing: Data were normalized and filtered by requiring intensity to be 200 or more, and spots to have a correlation coefficient of 0.5 or more. For analysis purposes, any feature with less than two measurements was excluded.

source_name: yeast expressing Cse4-3HA

label_protocol: DNA from the immunoprecipitation was labeled with Cy5 and competitively hybridized with total genomic DNA labeled with Cy3.

growth_protocol: 37 degrees YPD Media

extract_protocol: Resuspend yeast pellet in 2ml lysis buffer (~1ml buffer/.4g cells) - Add approx. 1-1.5ml to a 2ml screwcap microfuge tube. Add ~ .4g acid washed glass beads (fill until liquid is close to top of tube, but not completely full) - Beat in beadbeater for 1min., 5X. Put on ice ~2-3min. between each round of beadbeating - Poke hole in bottom of tube with 26 gauge needle. Use a 5ml syringe to plunge yeast lysate through hole into a fresh 2ml microfuge tube. Wash beads with additional 500ul lysis buffer. - Sonicate yeast lysate to obtain DNA fragments of ~ 300bp-1000bp size range. Every sonicator is different. I generally sonicate at 30-40% power 6-8 times. Be careful not to sonicate on too high a power levels as samples will “explode” out of tube. Run 15ul of your lysate on a .8% agarose gel to check sonication - Spin down lysates at 4°, full speed for 10min. and collect supe. Dilute to 10ml with IP dilution buffer. This is now your total chromatin (TC). IP’s - Use ~ 1.5-2ml of TC for each IP. Also set aside 300ul of TC for your TC input control for comparing IP’s to TC sample by qPCR or microarray. - Add 4ul of anti-myc (Santa Cruz 9E10) or 5ul of anti-HA (Roche 12CA5) to sample. Incubate 4hr, ON at 4°. - While IP’s are incubating with antibody, block proteinG sepharose (Amersham) beads (40ul/IP) in TE/0.1%BSA. Add 40ul of blocked beads to IP’s and incubate @ 4° for 2hrs. -Wash beads for 3-5 minutes in each of the following buffers, with rotation, (4k spin, 2min between washes) -TSE-100 (2X) -LiCl Detergent wash -TE (2X) On 2nd TE wash change to a new tube - After final wash remove as much TE as possible and add 250ul of SDS Lysis Buffer. Incubate for 10min @ 42° with shaking. Spin down 8k 2min and collect supe. Repeat elution with additional 250ul of SDS lysis buffer. - add 20ul of 5M NaCl to IPs and 3ul 5M NaCl to TC input control. Vortex and incubate ON (8hrs.) @ 65° to reverse X-links - Remove from 65° and add 1.5ul of RNase (10mg/ml). Vortex to mix. Add 2.5ul proteinase K (Roche, 14-22mg/ml in 10mM Tris), incubate @42° for 2hrs. - Add 300ul PCI to each sample, mix well and spin at RT for 5min full speed. Carefully remove supe (the TC input will be extra gunky, try to avoid that white interphase layer) - Add 1ul linear acrylamide, NaOac to 300mM (1/10 3M solution), and 2X volume 100% EtOH to each sample, mix well. Precipitate ON @ -20°. Spin down @ 4° for 20min., wash with 70% EtOH, spin again. Remove most of the EtoH (be careful not to disturb pellet, it may be pretty small for IPs) and dry in a speed vac. Resuspend DNA in 50ul TE (ph 8.0) for IP and 200ul for input. Solutions Lysis Buffer 50mM Hepes (7.5 ph) 10mM MgCl2 150mM KCl 10% glycerol 0.1mM EDTA 0.1% NP-40 or Triton X-100 Add fresh each time- 1mM DTT, protease inhibitors For 250ml IP Dilution buffer .01% SDS .25ml 10% SDS 1% Triton X-100 13.8ml 20% Triton X-100 1.2mM EDTA 0.6ml 0.5M EDTA 16.7mM Tris 8.0 ph 4.2ml 1M Tris 8.0 167mM NaCl 8.35ml %M NaCl TSE-100 0.1% SDS 2.5ml 10%SDS 1% Triton X-100 12.5ml 20% Triton X-100 2mM EDTA 1ml 0.5M EDTA 20mM Tris 8.0 ph 5ml 1M Tris 8.0 150mM NaCl 7.5ml 5M NaCl LiCl Detergent Wash .25M LiCl 2.65g LiCl 1% NP-40 25ml 10% NP-40 1% DOC 50ml 5% DOC 1mM EDTA 0.5ml 0.5M EDTA 10mM Tris 8.1 ph 2.5ml 1M Tris 8.0

treatment_protocol: Grow 220ml of cells to mid-log phase (~ O.D. 0.5-0.8), arrest at this point with nocodozole if desired (increases signal due to kinetochore formed on all DNA) -Add 37% formaldehyde to 1% final (~6.1ml/220ml culture), incubate with gentle shaking, crosslinking times vary, I generally use 10min for Cse4 and 30 minutes for other KT proteins - (optional) Quench X-linking rxn by addition of 10ml 2.5M glycine -Spin cells down and wash twice w/ ice cold PBS. After 2nd wash cells can either be frozen in liquid N2 and stored at -80° for long term or stored at 4° in PBS for a few days

tag: test

value: ChIP, yeast expressing Cse4-3HA

tag: reference

value: Input, yeast expressing Cse4-3HA


title: Cse4-3HA ChIP-chip 2

description: Yeast expressing Cse4-3HA

source_name: Yeast expressing Cse4-3HA


title: embryo 250x250:250x301 rep1

value: embryo

source_name: 6 dap embryo of hybrid 250x301


title: pGAL Cse4-12Myc ChIP-chip 2

description: Yeast expressing 12-Myc Cse4 from the galactose promoter

growth_protocol: 37 degrees YP-Gal Media

value: ChIP, yeast expressing Cse4-12-Myc under the control of the Galactose promoter, GAL1-10

value: Input, yeast expressing Cse4-12-Myc under the control of the Galactose promoter, GAL1-10


title: pGAL Cse4-12Myc ChIP-chip 1

description: Yeast expressing Cse4-12Myc under the control of the Galactose promoter

value: ChIP, yeast expressing Cse4-12Myc under the control of the Galactose promoter, GAL1-10

value: Input, yeast expressing Cse4-12Myc under the control of the Galactose promoter, GAL1-10


title: embryo 301x301:250x301 rep1

source_name: 6 dap embryo of inbred 301


title: embryo 250x250:301x250 rep1

source_name: 6 dap embryo of inbred 250


title: Head-M-Cy3-1

tag: strain


title: Head-F-Cy5-1


title: Testis-Cy3-6

source_name: Testis

value: Testis


title: cow 1, week 1

source_name: cow 1, rumen papillae, first week of grain challenge

value: rumen papillae (ventral sac)

value: grain challenge


title: Cse412MycNZ ChIP-chip 2

description: Yeast expressing 12-Myc Cse4

source_name: Yeast expressing 12-Myc Cse4

value: ChIP, yeast expressing 12-Myc Cse4

value: Input, yeast expressing 12-Myc Cse4


title: embryo 301x301:301x250 rep1


title: cow 1, week 0

description: rumen papillae from high forage diet

source_name: cow 1, rumen papillae, high forage baseline

value: high forage diet (control)

value: week 0


title: endosperm 250x301:250x250 rep2

source_name: 6 dap endosperm of hybrid 250x301

value: endosperm

source_name: 6 dap endosperm of inbred 250


title: Ovary-Cy5-6

source_name: Ovary

value: Ovary

value: Dazao


title: Foxp3 sufficient Treg CD4+ T cells from healthy B6 mice_3

city: Augusta

first: Piotr

last: Kraj

state: GA

address: 1120 15th Street

department: Centr. for Biotech. and Gen. Medicine

institute: Medical College of Georgia

description:
Molecular profiles of Foxp3 sufficient Treg CD4+ T cells from healthy B6 mice
B6_Tr.3

hyb_protocol: Hybridization according to Affymetrix protocol, 45 degrees celcius, 16 hours, 50 rpm

scan_protocol: Scanned on Affymetrix scanner 3000 with 7G upgrade

data_processing: The data were condensed with RMA transformation algorithm using the R (Bioconductor) - an open source and open development software project for the analysis and comprehension of genomic data.

label: Biotin

label_protocol: Total RNA was labeled according to Eberwine protocol using Target Amp kit, Epicentre

extract_protocol: Total RNA was isolated from the cells of different samples using RNeasy Mini Kit spin columns (Qiagen)

tag: Strain

tag: healthy mouse

tag: Gender

value: Male

tag: Age

value: 3-4 weeks

tag: Tissue

value: lymph node cells


title: Ovary-Cy3-5


title: Foxp3 sufficient Treg CD4+ T cells from healthy B6 mice_1

description:
Molecular profiles of Foxp3 sufficient Treg CD4+ T cells from healthy B6 mice
B6_Tr.1


title: Foxp3 sufficient Treg CD4+ T cells from healthy B6 mice_2

description:
Molecular profiles of Foxp3 sufficient Treg CD4+ T cells from healthy B6 mice
B6_Tr.2


title: Testis-Cy5-5


title: endosperm 301x250:250x250 rep2

source_name: 6 dap endosperm of hybrid 301x250


title: Effector CD4+ T cells from healthy B6 mice_3

description:
Molecular profiles of effector CD4+ T cells from healthy B6 mice
Teff_B6.3


title: Ovary-Cy5-4


title: endosperm 250x301:301x301 rep2

source_name: 6 dap endosperm of inbred 301


title: Testis-Cy3-4


title: endosperm 301x250:301x301 rep2


title: Ovary-Cy3-3


title: Cse412MycNZ ChIP-chip 1

description: Yeast expressing 12-Myc Cse4

scan_protocol: The arrays were scanned using an Axon Instruments (Union City, California, United States) 4000B scanner and quantitated using GenePix 4.0. Results were stored in the AMAD database.

growth_protocol: 37 degress YPD Media


title: Effector CD4+ T cells from healthy B6 mice_2

description:
Molecular profiles of effector CD4+ T cells from healthy B6 mice
Teff_B6.2


title: Effector CD4+ T cells from healthy B6 mice_1

description:
Molecular profiles of effector CD4+ T cells from healthy B6 mice
Teff_B6.1


title: Treg Foxp3-deficient CD4+ T cells from scurfy mice_3

description:
Molecular profiles of Treg Foxp3-deficient CD4+ T cells from scurfy mice
Sf-Tr.3

source_name: SfGFP+

tag: scurfy mutant


title: Testis-Cy5-3


title: endosperm 250x250:250x301 rep1


title: endosperm 250x250:301x250 rep1


title: Ovary-Cy3-2


title: Testis-Cy5-2


title: Treg Foxp3-deficient CD4+ T cells from scurfy mice_1

description:
Molecular profiles of Treg Foxp3-deficient CD4+ T cells from scurfy mice
Sf-Tr.1


title: endosperm 301x301:250x301 rep1


title: endosperm 301x301:301x250 rep1


title: Treg Foxp3-deficient CD4+ T cells from scurfy mice_2

description:
Molecular profiles of Treg Foxp3-deficient CD4+ T cells from scurfy mice
Sf-Tr.2


title: Effector CD4+ T cells from scurfy mice_1

description:
Molecular profiles of effector CD4+ T cells from scurfy mice
Teff_Sf.1

source_name: SfGFP-

tag: gender

tag: age


title: Ultrasonic + 3.3% microbubbles only (slide 2)

status: Public on Aug 27 2009

city: Toronto

first: Azza

last: Al-Mahrouki

address: 2075 Bayview Avenue

department: Radiation Oncology & Imaging Research

institute: Radiation Oncology, Sunnybrook Health Sciences Centre

description: Hybridized to 70-mer oligo of the whole human 28k genome. The individual oligo-probe was printed on in-house epoxy coated slides under 50% humidity by Perkin Elmer SpotArray 72 in 4 x 12 pin configuration and 18 x 17 spot configuration of each subarray.  The spot diameter was 150 µm and distance from center to center was 235µm.  Each array was printed on two slides.

hyb_protocol: 200ng of each labeled aRNA was mixed with hybridization buffer containing 5X SSC and 0.1% SDS and was denatured at 95C for 5 min. Adjusted the final volume to 50ul containing 1%BSA. The hybridization mix was incubated with the microarray slides at RT for 26 hours; the slides were dried after several washing with 3SSC/0.1%SDS and 1XSSC/0.1%SDS.

scan_protocol: Processed chips were scanned by using a Perkin Elmer ScanArray Express Scanner. The software version 3.0.1 with the laser set to 555 nm, set power fixed at 90 and PMT flexible, and a scan resolution of 10 microns. Images were quantified by PerkinElmer QuantArray® Software 3.0.1 Quantitation method where Adaptive circle and quantification output were median intensities. Confidence calculation was weighted average.

data_processing: Signal intensities for each spot were calculated by subtracting local background (based on the median intensity of the area surrounding each spot) from total intensities. Raw data were normalized and analyzed using GeneSpring software (Version 7.3.1). After data transformation (to convert any negative to 0.01), normalization was performed by using a per-chip 50th percentile method that normalizes each chip on its median, allowing comparison among chips. To highlight genes that characterize each tissue, a per-gene on median normalization was performed, which normalizes the expression of every gene on its median among samples.

source_name: HUVEC

label_protocol: 1 ug of total RNA was used to synthesize cDNA, which was purified. 26ul were then used to Synthesize amino ally-modified aRNA. aRNA was then purified and 2ug were coupled to Alexa555 dye.

growth_protocol: HUVEC cells were cultured using Endothelial Cell Basal medium-2 kit from Lonza (Walkersville, MD). Cells were grown to confluence and were split and treated after three passages.

extract_protocol: About One million cells were used to isolate total RNA using  Qiagen RNeasy Mini Kit.

treatment_protocol: A concentration of 2 million cells/ mL was used in each of the treatments that included subjecting the cells to radiation at  8 Gy alone, or adding 3.3% (6X10^8 microbubbles) definity micro-bubbles (Lipid-Encapsulated Perfluoropropane micro-bubbles, from Bristol-Myers Squibb Medical imaging, Massachusetts, US), and exposing cells to ultrasound with 570kPa peak negative pressure and a low mechanical-index of  0.8, or by using a combination of radiation, micro-bubbles and ultrasound. After treatment, cells were incubated at 37°C water bath for one hour.

tag: cell line

value: HUVEC


title: Untreated - replicate (slide 2)


title: Ultrasonic + 3.3% microbubbles + 8 Gy - replicate (slide 2)


title: Untreated (slide 2)


title: 8 Gy only - replicate (slide 2)


title: 8 Gy only (slide 2)


title: Testis-Cy3-1

tag: tissue


title: Ultrasonic + 3.3% microbubbles + 8 Gy (slide 2)


title: Ovary-Cy5-1


title: Effector CD4+ T cells from scurfy mice_2

description:
Molecular profiles of effector CD4+ T cells from scurfy mice
Teff_Sf.2


title: Ultrasonic + 3.3% microbubbles only - replicate (slide 2)


title: 7 hr control (for 50 uM NE suspension cells)

city: College Station

first: Manjunath

last: Hegde

state: TX

address: 524 Jack E. Brown Building TAMU

department: Chemical Engineering

institute: Texas A&M University

description: RNA extracted from suspension cells of Pseudomonas aeruginosa PA14 WT untreated (control 50 uM NE expt) for 7 hours in serum-RPMI medium at 37ºC

hyb_protocol: Prepared hybridization cocktail for Single Probe Array (100 midi Format) with total 130 ul volume including 1X hybrization buffer, 3 nM B2 Control Oligo, 10 mg/mL Herring Sperm DNA, 50 mg/mL BSA, 100 % DMSO and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix P.aeruginosa Genome Array, the hybridization was performed at 50ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Pseudomonas aeruginosa UCBPP-PA14

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: A single colony from a fresh plate (<24 hr) plate was inoculated in 25 mL of LB medium and grown overnight at 37 degC at 250 rpm. Two flasks containing 100 mL serum-RPMI medium was inoculated with overnight culture of PA14 WT with a starting OD600 of 0.05. NE (50 uM) was added in one of the flask with equal volume of water in the other. The culture was grown for 7 hours and cell pellets were made subsequently. After breaking the cells with a bead beater, the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).


title: 7 hr 50 uM NE suspension cells

description: RNA extracted from suspension cells of Pseudomonas aeruginosa PA14 WT treated with 50 uM norepinephrine for 7 hour in serum-RPMI medium at 37ºC


title: Effector CD4+ T cells from scurfy mice_3

description:
Molecular profiles of effector CD4+ T cells from scurfy mice
Teff_Sf.3


title: 7 hr control (for 500 uM NE suspension cells)

description: RNA extracted from suspension cells of Pseudomonas aeruginosa PA14 WT untreated (control for 500uM NE expt) for 7 hours in serum-RPMI medium at 37ºC

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS)

extract_protocol: A single colony from a fresh plate (<24 hr) plate was inoculated in 25 mL of LB medium and grown overnight at 37 degC at 250 rpm. Two flasks containing 100 mL serum-RPMI medium was inoculated with overnight culture of PA14 WT with a starting OD600 of 0.05. NE (500 uM) was added in one of the flask with equal volume of water in the other. The culture was grown for 7 hours and cell pellets were made subsequently. After breaking the cells with a bead beater, the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).


title: 7 hr 500 uM NE suspension cells

description: RNA extracted from suspension cells of Pseudomonas aeruginosa PA14 WT treated with 500 uM norepinephrine for 7 hours in serum-RPMI medium at 37ºC


title: colon_INT_T78_snp

city: Milano

first: James

middle: F

last: Reid

address: Via Adamello, 16

department: Molecular Genetics of Cancer

country: Italy

institute: Fondazione Istituto FIRC di Oncologia Molecolare

description: Copy number data of sporadic colon cancer patient (INTcartella:9900192, INTistologico:282949I)

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures using Gene ChIP Scanner 3000.

data_processing: Copy number estimates (log-ratios and state) were calculated using Affymetrix v. 1.5.6 CNAT copy-number pipeline. A set of 48 Hapmap samples were used as anun-paired reference set <http://www.affymetrix.com/support/technical/sample_data/500k_data.affx>.  All additional analysis was performed in R/Bioconductor and is available as a reproducible Sweave document from <http://pierotti.group.ifom-ieo-campus.it/suppl/crc.html>.

source_name: Colon, DNA

label_protocol: Standard Affymetrix procedures.

extract_protocol: DNA was extracted using the QIAamp Tissue Extraction kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

value: F

tag: dimension

tag: stage

value: III

tag: status

tag: survival

tag: apc

tag: kras


title: colon_INT_T186_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:2005246, INTistologico:297449I)

value: II


title: colon_INT_T200_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:2009495, INTistologico:298745I)


title: colon_INT_T164_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9932567, INTistologico:294641I)


title: colon_INT_T144_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9922436, INTistologico:290605I)

value: M


title: colon_INT_T71_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9829987, INTistologico:282397I)

value: IV


title: colon_INT_T210_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:2014274, INTistologico:299140I)


title: colon_INT_T106_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9914153, INTistologico:287517I)


title: colon_INT_T150_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9700586, INTistologico:292001I)


title: colon_INT_T42_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9810570, INTistologico:273244I)


title: colon_INT_T24_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9804607, INTistologico:271543I)


title: colon_INT_A16_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9801968, INTistologico:270642I)


title: colon_INT_T11_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9802485, INTistologico:270464I)


title: colon_INT_T212_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:2013268, INTistologico:299340I)


title: colon_INT_T112_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9913000, INTistologico:287677I)


title: colon_INT_T7_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9803554, INTistologico:270132I)


title: colon_INT_A29_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9807359, INTistologico:272258I)


title: colon_INT_T82_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9901435, INTistologico:283622I)


title: colon_INT_T136_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:8205701, INTistologico:289768I)


title: colon_INT_T1_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9800950, INTistologico:269527I)


title: colon_INT_T59_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9826128, INTistologico:279556I)


title: colon_INT_T55_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9818244, INTistologico:276358I)


title: colon_INT_T214_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9504693, INTistologico:299641I)


title: colon_INT_T138_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9919915, INTistologico:289796I)


title: colon_INT_T78_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9900192, INTistologico:282949I)

data_processing: RMA implementation of Affymetrix Power Tools version 1.8.6 was used to analyze the 'core' subset of probes (HuEx-1_0-st-v2.r2.dt1.hg18.core.mps). All additional analysis was performed in R/Bioconductor and is available as a reproducible Sweave document from <http://pierotti.group.ifom-ieo-campus.it/suppl/crc.html>.

source_name: Colon, RNA

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


title: colon_INT_T210_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:2014274, INTistologico:299140I)


title: colon_INT_A206_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:2012976, INTistologico:298894I)


title: colon_INT_T136_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:8205701, INTistologico:289768I)


title: colon_INT_T200_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:2009495, INTistologico:298745I)


title: colon_INT_T196_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:NA, INTistologico:298516I)


title: colon_INT_T202_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:2013277, INTistologico:298768I)


title: colon_INT_A206_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:2012976, INTistologico:298894I)


title: colon_INT_T146_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9922877, INTistologico:290612I)


title: colon_INT_T112_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9913000, INTistologico:287677I)


title: colon_INT_T106_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9914153, INTistologico:287517I)


title: colon_INT_T71_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9829987, INTistologico:282397I)


title: colon_INT_R124_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9631971, INTistologico:288577I)


title: colon_INT_T146_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9922877, INTistologico:290612I)


title: colon_INT_T132_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9919318, INTistologico:289386I)


title: colon_INT_T160_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9931971, INTistologico:293777I)


title: colon_INT_T110_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9913569, INTistologico:287573I)


title: colon_INT_R124_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9631971, INTistologico:288577I)


title: colon_INT_T170_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:2001393, INTistologico:295811I)


title: colon_INT_T196_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:NA, INTistologico:298516I)


title: colon_INT_T100_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9713125, INTistologico:287046I)

value: I


title: colon_INT_T92_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9214707, INTistologico:285150I)


title: colon_INT_T96_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9910919, INTistologico:286573I)


title: colon_INT_T160_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9931971, INTistologico:293777I)


title: colon_INT_T202_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:2013277, INTistologico:298768I)


title: Ultrasonic + 3.3% microbubbles only (slide 1)

description: Hybridized to 70-mer oligo of the whole human 28k genome. The individual oligo-probe was printed on in-house epoxy coated slides under 50% humidity by Perkin Elmer SpotArray 72 in 4 x 12 pin configuration and 18 x 17 spot configuration of each subarray.  The spot diameter was 150 µm and distance from center to center was 235µm.  Each array was printed on two slides.


title: Untreated - replicate (slide 1)


title: Ultrasonic + 3.3% microbubbles + 8 Gy - replicate (slide 1)


title: Ultrasonic + 3.3% microbubbles only - replicate (slide 1)


title: colon_INT_T150_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9700586, INTistologico:292001I)


title: Untreated (slide 1)


title: colon_INT_T92_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9214707, INTistologico:285150I)


title: colon_INT_T74_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9833433, INTistologico:282636I)


title: Ultrasonic + 3.3% microbubbles + 8 Gy (slide 1)


title: colon_INT_T144_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9922436, INTistologico:290605I)


title: Sub1-HA ChIP S1

city: Gif-sur-Yvette cedex

first: Christine

last: Conesa

address: CEA Saclay

department: iBiTeC-S

institute: CEA

description: Immunopurified DNA and DNA from the whole-cell extracts of 3HA-Sub1 cells, fluorescently labelled, were competitively hybridized to DNA microarrays harbouring yeast ORF and intergenic regions.

hyb_protocol: The immunopurified DNA and DNA from the whole-cell extracts, fluorescently labelled, were competitively hybridized to DNA microarrays as described in (Harismendy et al., 2003; Oficjalska-Pham et al., 2006)

scan_protocol: Hybridized arrays were scanned using a GenePix 4000A scanner (Axon Instruments, Inc.) and fluorescence ratio measurements were determined with the GenePix Pro 6.0 software (Axon Instruments, Inc.).

data_processing: Analyses were undertaken using the Limma package  version 2.12.0 (Smyth, 2005) from the R/Bioconductor software version 2.6.1 (R-Development-Core-Team, 2007). spot intensities have been normalized using the weighted median as implemented in the 'normalizeWithinArrays' function of the Limma package. Normalized measures served to compute the log2-ratios for each probe.

source_name: Sub1-HA ChIP

label_protocol: indirect via aa-dUTP

growth_protocol: YPD OD600=1

extract_protocol: Chromatin immunoprecipitations and DNA extraction was done as described by (Harismendy et al., 2003 - PMID: 12970186)

treatment_protocol: No treatment

source_name: Sub1-HA Whole cell extract


title: 8 Gy only (slide 1)


title: colon_INT_T59_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9826128, INTistologico:279556I)


title: colon_INT_T74_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9833433, INTistologico:282636I)


title: Sub1-HA ChIP S3


title: 8 Gy only - replicate (slide 1)


title: colon_INT_T63_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9830939, INTistologico:280935I)


title: HIF2-alpha siRNA Treated A498 Cells_4

city: Jenkintown

first: Amar

last: Majmundar

address: 434 Hillside Avenue

institute: University of Pennsylvania

description: 48 hours post-H2 siRNA treatment, paired with Sample 4

hyb_protocol: Labeled cDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Affymetrix Human Gene 1.0 ST Arrays (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe sets for positive and negative controls were examined in Expression Console, and Facility quality control parameters were confirmed to fall within normal ranges.  Probes for each targeted gene were averaged and inter-array normalization performed using the RMA algorithm in Partek software. CT and H2 groups were compared using Significance Analysis of Microarrays (SAM) software as logged paired data.

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence.  Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: A498 pBabe cells were cultured in DMEM/10%FBS/2mM L-Glutamine/100 U/mL penicillin/10 ug/mL Streptomycin/0.1 mM MEM non-essential amino acids.

extract_protocol: RNA was harvested and extracted as previously described previously (Gordan JD et al. Cancer Cell. 2007).

treatment_protocol: Cells were treated with either control or HIF2-alpha siRNA 48 hours prior to RNA harvesting.

tag: sirna treatment

value: HIF2-alpha (H2)

tag: cell type

value: A498 pBabe cells


title: HIF2-alpha siRNA Treated A498 Cells_3

description: 48 hours post-H2 siRNA treatment, paired with Sample 3


title: colon_INT_T55_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9818244, INTistologico:276358I)


title: Sub1-HA ChIP S2


title: colon_INT_T35_snp

description: Copy number data of sporadic colon cancer patient (INTcartella:9807305, INTistologico:272343I)


title: colon_INT_T42_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9810570, INTistologico:273244I)


title: colon_INT_A16_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9801968, INTistologico:270642I)


title: HIF2-alpha siRNA Treated A498 Cells_1

description: 48 hours post-H2 siRNA treatment, Paired with Sample 1


title: colon_INT_T7_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9803554, INTistologico:270132I)


title: colon_INT_T3_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9736918, INTistologico:269537I)


title: Control siRNA Treated A498 Cells_4

description: 48 hours post-CT siRNA treatment, Paired with Sample 8

value: control (CT)


title: Control siRNA Treated A498 Cells_3

description: 48 hours post-CT siRNA treatment, Paired with Sample 7


title: HIF2-alpha siRNA Treated A498 Cells_2

description: 48 hours post-H2 siRNA treatment, Paired with Sample 2


title: colon_INT_A33_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9806081, INTistologico:272342I)


title: Control siRNA Treated A498 Cells_2

description: 48 hours post-CT siRNA treatment, Paired with Sample 6


title: colon_INT_T100_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9713125, INTistologico:287046I)


title: renal-cortex_wild-type recipent_ABCC2-/- graft_repl.14

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

institute: Universitätsmedizin Greifswald

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Rat Genome RAE 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the protocol EukGe-Ws2v5.

scan_protocol: GeneChips were scanned using the GeneChip System Confocal Scanner 3000.

data_processing: After probe set summarization using MAS5.0 algorithm in GCOS, expression raw data were transferred to GeneSpring GX software (7.3.1) to perform per Chip median normalization for signals which were flagged present or marginal.

organism: Rattus norvegicus

source_name: renal cortex, MRP2 (ABCC2) deficient graft

label_protocol: Probes for Affymetrix microarray analysis were prepared using 4µg total RNA with GeneChip Expression 3´Amplification One Cycle Target labeling and Control Reagents Kits according to the manufacturers instructions (Affymetrix).

extract_protocol: Renal cortical tissue was snap frozen in liquid nitrogen and homogenized in Trizol reagent using a MIKRO Dismembrator S. For gene expression profiling RNA was prepared according to manufacturer´s TRIZOL protocol. RNA integrity was checked using RNA 6000 N

tag: LEWIS rat

value: male

tag: renal graft of congenic LEW.1W MRP2-deficient rats


title: colon_INT_T12_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9804643, INTistologico:270530I)


title: renal-cortex_wild-type recipent_ABCC2-/- graft_repl.11


title: colon_INT_T11_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9802485, INTistologico:270464I)


title: Mouse wild-type skeletal muscle 3

city: San Antonio

first: Koichi

last: Nishijo

address: 7703 Floyd Curl Dr.

department: Greehey Children's Cancer Research Institute I

institute: University of Texas Health Science Center at San Antonio

description: Affymetrix

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

source_name: wild-type skeletal muscle

label_protocol: Standard Affymetrix protocol

extract_protocol: Trizol and RNAeasy

tag: disease state

value: control


title: Mouse alveolar rhabdomyosarcoma 5

description: Affymetrix

source_name: alveolar rhabdomyosarcoma

value: alveolar rhabdomyosarcoma


title: Mouse wild-type skeletal muscle 2

description: Affymetrix


title: renal-cortex_wild-type recipent_ABCC2-/- graft_repl.10


title: renal-cortex_wild-type recipent_ABCC2-/- graft_repl.3


title: Control siRNA Treated A498 Cells_1

description: 48 hours post-CT siRNA treatment, Paired with Sample 5


title: colon_INT_T1_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9800950, INTistologico:269527I)


title: mouse wild-type skeletal muscle 1

description: Affymetrix


title: colon_INT_T24_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9804607, INTistologico:271543I)


title: Mouse alveolar rhabdomyosarcoma 6

description: Affymetrix


title: colon_INT_T214_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9504693, INTistologico:299641I)


title: renal-cortex_wild-type recipent_wildtype graft_repl.8

source_name: renal cortex, wildtype graft

tag: renal graft of wildtype LEWIS rats (controls)


title: colon_INT_T224_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:2023670, INTistologico:302042I)


title: colon_INT_T152_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9930748, INTistologico:293058I)


title: Mouse alveolar rhabdomyosarcoma 3

description: Affymetrix


title: renal-cortex_wild-type recipent_ABCC2-/- graft_repl.9


title: Mouse alveolar rhabdomyosarcoma 4

description: Affymetrix


title: renal-cortex_wild-type recipent_wildtype graft_repl.7


title: Mouse alveolar rhabdomyosarcoma 2

description: Affymetrix


title: renal-cortex_wild-type recipent_ABCC2-/- graft_repl.5


title: colon_INT_T41_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9810617, INTistologico:273045I)


title: colon_INT_T82_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:9901435, INTistologico:283622I)


title: renal-cortex_wild-type recipent_wildtype graft_repl.9


title: colon_INT_T212_exon

description: Gene expression data of sporadic colon cancer patient (INTcartella:2013268, INTistologico:299340I)


title: renal-cortex_wild-type recipent_wildtype graft_repl.4


title: memory P14 T cells #2

city: seattle

first: Ruka

last: Setoguchi

state: WA

address: 1959 NE Pacific Street

institute: University of Washington

description:
FACS sorted CD8 P14 memory cells.
This sample is called memory P14 T cells #2.

hyb_protocol: by the Center for Array Technologies (University of Washington, Seattle, WA)

data_processing:
The array used was GeneChip Mouse Genome 430 2.0 Array. There are 2 groups, memory P14 and memory HD-/-P14 T cells. Each group has 2 biological replicates. The biological replicates are numbered #1 to #2.
MAS5.0.

source_name: Mouse Spleen CD8 T cells

extract_protocol: RNA was isolated with Trizol (Invitrogen) from FACS-sorted memory P14 T cells after enrichment of CD8 T cells using negative selection. RNA was prepared using RNeasy Mini Kit (Qiagen) before amplification.

tag: genotype/variation

value: wildtype ThPOK (control)


title: memory HD-/- P14 T cells #2

description:
FACS sorted CD8 P14 memory cells.
This sample is called memory HD-/- P14 T cells #2.

scan_protocol: by the Center for Array Technologies (University of Washington, Seattle, WA)

value: mutant ThPOK


title: memory HD-/- P14 T cells #1

description:
FACS sorted CD8 P14 memory cells.
This sample is called memory HD-/- P14 T cells #1.

label_protocol: by the Center for Array Technologies (University of Washington, Seattle, WA)