title: SEG1 vehicle pretreated acid pulsed (24 hr)

city: Columbus

first: Laura

middle: A

last: Kresty

state: OH

address: CCC Building, Rm 302B

department: Internal Medicine

institute: The Ohio State University

description: Gene expression data from acid-pulsed cells pretreated with vehicle, 24 hr

hyb_protocol: Following fragmentation, labeled cRNA was hybridized to the human genoma gene chip U133 2.0 Plus. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and were used to determine differential gene expression by pair-wise comparisons. The genes that were altered by two-fold either ways were sorted and used for further interpretation of the microarray data.

source_name: Derived from human esophageal adenocarcinoma

label_protocol: The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.

growth_protocol: SEG-1 esophageal adenocarcinoma cells were plated at 5 x 10^6 cells/T75 flask.

extract_protocol: Trizol extraction of total RNA was performed per the manufacterer's instructions.

treatment_protocol: Cells were pretreated with vehicle or OSU-HDAC42 (1.6 uM) in DMEM phenol red-free medium containing 5% FBS for 24 hours.  Cells were then rinsed and pulsed with serum-free acidified medium (pH 3.5) or vehicle for 20 mins in a humidified chamber (37C).  Cells were rinsed again and replenished with serum-free media or OSU-HDAC42 (1.6 uM) in serum-free media.  Cells were harvested 6 hours post vehicle or acid exposure.

tag: Human esophageal cancer cell line SEG-1


title: SEG1 OSU-HDAC42 pretreated acid pulsed (6 hr)

status: Public on Mar 20 2008

type: RNA

country: USA

description: Gene expression data from acid-pulsed cells pretreated with OSU-HDAC42, 6 hr

label: biotin

molecule: total RNA

organism: Homo sapiens


title: SEG1 OSU-HDAC42 pretreated acid pulsed (24 hr)

description: Gene expression data from acid-pulsed cells pretreated with OSU-HDAC42, 24 hr


title: SEG1 OSU-HDAC42 pretreated acid pulsed (3 hr)

description: Gene expression data from acid-pulsed cells pretreated with OSU-HDAC42, 3 hr


title: Estrogen-deprived MCF-7:5C cells, biological rep 3

status: Public on Mar 19 2008

city: Philadelphia

first: Dr Joan

last: Lewis-Wambi

state: PA

address: 333 Cottman Ave

department: Medical Sciences

institute: Fox Chase Cancer Center

description: Gene expression data for estrogen deprived MCF-7:5C cells grown in estrogen-free medium

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: Epithelial breast cancer cells

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

growth_protocol: wild-type MCF-7 cells and estrogen-deprived MCF-7:5C, and MCF-7:2A cells were grown in estrogen-free media until they were 70-80% confluent and then RNA was extracted, labeled, and hybridized.

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

treatment_protocol: Cells were not treated with any drugs.

tag: Estrogen-receptor positive, estrogen deprived, hormone-independent


title: SEG1 vehicle pretreated acid pulsed (6 hr)

description: Gene expression data from acid-pulsed cells pretreated with vehicle, 6 hr


title: Estrogen-deprived MCF-7:2A cells, biological rep 3

description: Gene expression data for estrogen deprived MCF-7:2A cells grown in estrogen-free medium


title: Wild-type MCF-7 cells, biological rep 3

description: Gene expression data for wild-type MCF-7 cells grown in estrogen-free medium

tag: Estrogen-receptor positive, estrogen dependent and antihormone responsive


title: Anti-Trem1 2 hrs Donor 3

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

description:
Sample_Treatment_[C] = Anti-Trem1
Sample_Treatment_amount_[C] = 5 ug/ml
Sample_Treatment_2_[C] = (Not applicable)
Sample_Treatment_2_amount_[C] = (Not applicable)
Sample_Treatment_Source = R&D Systems Cat MAB1278
Sample_Treatment_2_Source = (Not applicable)
Sample_Treatment_protocol = For TREM-1 activation, tissue culture treated plates were pre-incubated with an appropriate volume of 5 mg/ml a-TREM-1 antibody (R&D Systems, MAB1278) in PBS overnight in a tissue culture incubator. Wells were washed twice with PBS immediately prior to cell addition. As a control, wells received the same treatment with an isotype-matched murine IgG1 antibody (a-E.tenella; Wyeth). For LPS treatment, gel filtration chromatography purified LPS from Salmonella enterica (SIGMA, L2262) was added to a final concentration of 1 ng/ml. In the wortmannin studies, cells in RPMI/10% FBS were pre-incubated with wortmannin (SIGMA, W1628) at a final concentration of 100 nM for 30 minutes in polypropylene tubes prior to seeding into tissue culture wells. The final DMSO concentration in control and wortmannin treated cultures was 0.1%.

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

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

data_processing: GeneChips were scanned using the Affymetrix 3000 Scanner

label_protocol: Microarray on Affymetrix Human Genome U133_plus 2.0 arrays was performed according to established protocols

growth_protocol: Human monocytes were purified from anonymous healthy donor Buffycoats obtained from Massachusetts General Hospital. Buffycoats were stored at 4°C overnight for cell isolation the following day. Monocytes were isolated by negative selection using RosetteSep (Stem Cell Technologies, 15068) according to the manufacturer’s protocol by density centrifugation over Histopaque (SIGMA, H8889).  Monocytes were maintained in RPMI 1640 (Mediatech, Inc., 15-040-CV) supplemented with 10% fetal bovine serum (SIGMA, F-9423) that had been heat-inactivated. All incubations were at 37°C in a tissue culture incubator maintained at 5% CO2.

extract_protocol: Total RNA was isolated after 2 hour treatment using QIAshredders and RNeasy miniprep kits according to the manufacturer’s protocol (QIAGEN, 79654 and 74104, respectively). Total RNA yields ranged from 1-6 mg. Residual genomic DNA was removed by DNase treatment and phenol/chloroform extraction followed by ethanol precipitation using standard techniques.

tag: Anonymous Donor


title: Wild-type MCF-7 cells, biological rep 2


title: Wild-type MCF-7 cells, biological rep 1


title: Estrogen-deprived MCF-7:2A cells, biological rep 2


title: Estrogen-deprived MCF-7:5C cells, biological rep 1


title: Wild-type MCF-7 cells, biological rep 4


title: SEG1 vehicle pretreated acid pulsed (3 hr)

description: Gene expression data from acid-pulsed cells pretreated with vehicle, 3 hr


title: Estrogen-deprived MCF-7:5C cells, biological rep 2


title: Estrogen-deprived MCF-7:2A cells, biological rep 1


title: Pseudopodia,FN,rep2

status: Public on Mar 18 2008

city: Charlottesville

first: Stavroula

last: Mili

state: VA

address: 1400 Jefferson Park Avenue

department: Microbiology

institute: University of Virginia

hyb_protocol: Standard affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

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

data_processing: Data were analyzed using dChip software version 1.2. PM/MM model was used with either median value of 10th percentile of the intensity of Absent genes or 20, whichever larger.

organism: Mus musculus

source_name: Pseudopodia from fibronectin-stimulated cells

label_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

growth_protocol: NIH/3T3 cells grown in DMEM supplemented with 10% calf serum, sodium pyruvate, penicillin and streptomycin

extract_protocol: Total RNA was isolated using Trizol LS reagent (Invitrogen) according to the manufacturer's instructions

treatment_protocol: NIH/3T3 cells (~1x106 ) were placed in serum-free media in the upper compartment of a Transwell insert equipped with a 3mm porous polycarbonate membrane whose underside only was coated with 5mg/ml fibronectin. Cells were allowed to extend pseudopodial protrusions towards the fibronectin-coated surface for 1 hr, they were briefly rinsed with PBS and fixed with 0.3 % methanol-free formaldehyde (Polysciences, Inc) in PBS for 10 min at room temperature. Glycine was added to 250 mM for 5 min at room temperature and the cells were washed twice with PBS. To isolate pseudopodia, cell bodies on the upper membrane surface were manually removed with cotton swab and laboratory paper and pseudopodia on the underside of the membrane were scraped into crosslink reversal buffer (100mM Tris pH 6.8, 5mM EDTA, 10mM DTT and 1% SDS). Cell bodies were similarly isolated except that pseudopodia on the underside of the membrane were manually removed and cell bodies were scraped into crosslink reversal buffer. Extracts were incubated at 70oC for 45 min to reverse the formaldehyde-induced crosslinks.

tag: NIH/3T3 fibroblasts


title: CellBody,FN,rep1

source_name: Cell body from fibronectin-stimulated cells


title: Estrogen-deprived MCF-7:2A cells, biological rep 4


title: Pseudopodia,FN,rep1


title: CellBody,FN,rep2


title: CellBody,LPA,rep2

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

source_name: Cell body from LPA-stimulated cells

treatment_protocol: NIH/3T3 cells were serum-starved overnight and 1.5x106 cells were placed in the upper compartment of a Transwell insert (24mm diameter, Costar) equipped with a 3mm porous polycarbonate membrane coated on both sides with 5mg/ml fibronectin. Cells were allowed to spread on the upper surface of the membrane for 2 hrs. LPA (150ng/ml) was then added in the bottom chamber to induce the cells to extend pseudopodial protrusions. After 1 hr the cells were briefly rinsed with PBS and fixed with 0.3 % methanol-free formaldehyde (Polysciences, Inc) in PBS for 10 min at room temperature. Glycine was added to 250 mM for 5 min at room temperature and the cells were washed twice with PBS. To isolate pseudopodia, cell bodies on the upper membrane surface were manually removed with cotton swab and laboratory paper and pseudopodia on the underside of the membrane were scraped into crosslink reversal buffer (100mM Tris pH 6.8, 5mM EDTA, 10mM DTT and 1% SDS). Cell bodies were similarly isolated except that pseudopodia on the underside of the membrane were manually removed and cell bodies were scraped into crosslink reversal buffer. Extracts were incubated at 70oC for 45 min to reverse the formaldehyde-induced crosslinks.


title: CellBody,LPA,rep1


title: LPS Low 2 hrs Donor 5

description:
Sample_Treatment_[C] = Lipopolysaccharide
Sample_Treatment_amount_[C] = 1 ng/ml
Sample_Treatment_2_[C] = (Not applicable)
Sample_Treatment_2_amount_[C] = (Not applicable)
Sample_Treatment_Source = Sigma Cat L2262
Sample_Treatment_2_Source = (Not applicable)
Sample_Treatment_protocol = For TREM-1 activation, tissue culture treated plates were pre-incubated with an appropriate volume of 5 mg/ml a-TREM-1 antibody (R&D Systems, MAB1278) in PBS overnight in a tissue culture incubator. Wells were washed twice with PBS immediately prior to cell addition. As a control, wells received the same treatment with an isotype-matched murine IgG1 antibody (a-E.tenella; Wyeth). For LPS treatment, gel filtration chromatography purified LPS from Salmonella enterica (SIGMA, L2262) was added to a final concentration of 1 ng/ml. In the wortmannin studies, cells in RPMI/10% FBS were pre-incubated with wortmannin (SIGMA, W1628) at a final concentration of 100 nM for 30 minutes in polypropylene tubes prior to seeding into tissue culture wells. The final DMSO concentration in control and wortmannin treated cultures was 0.1%.


title: Pseudopodia,LPA,rep2

source_name: Pseudopodia from LPA-stimulated cells


title: Hemocyte_EGFR(1564) (gain of function mutant)

city: Seoul

first: Young-Joon

last: Kim

address: Yonsei Univ 134 Sinchon-dong Seodaemun-gu

country: South Korea

institute: Yonsei University

hyb_protocol: 15 microgram of cRNA was hybridized to the Affymetrix GeneChip Drosophila Genome 2.0 chip according to the protocols provided by the manufacturer.

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

data_processing: The data were condensed by RMA using the GeneChip Operating Software (GCOS) 1.4 (Affymetrix, Inc).

organism: Drosophila melanogaster

source_name: Hemocytes from 200-300 third instar larvae

label_protocol: Biotinylated cRNA were prepared from 1 microgram total RNA using the GeneChip IVT labeling kit (Affymetrix, Inc).

extract_protocol: total RNA (1.0-1.3 microgram) was isolated with TRIzol (Invitrogen, Carsbad, CA) from the dissected hemocytes (from 200-300 third instar larvae). The antisense RNA was generated by in vitro amplification with the RiboAmp RNA amplification kit (ARCTURUS KIT0201).

tag: Strain

value: BL1564 (Bloomington stock center, Indiana Univ, Bloomington, USA).

tag: Tissue

value: Hemocyte

tag: Stage

value: Third instar larvae


title: hIgG1-treated MDMs_2 days_rep2

city: Taipei

first: Yung-Chi

last: Chang

address: 155, Sec. 2, Li-Nong St.

department: Microbiology and Immunology

country: Taiwan

institute: National Yang-Ming University

description: biotinylated cRNA were prepared according to the standard Affymetrix protocol

hyb_protocol: Fragmentation, hybridizatio, washing and staining were performed according Affymetrix's instructions

data_processing: Background correlation, normalization and log2 transformation were carried out using RMA method with their default settings within the Bioconductor suite for R software package

source_name: control hlgG1

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

growth_protocol: Monocytes were cultured with RPMI 1640 with 10% FCS

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

treatment_protocol: Freshly isolated monocytes were treated for 2 days in the presence of 10 ng/ml M-CSF

tag: MDMs at day 2, biological rep2


title: flu_2h

city: Zurich

first: Christophe

last: Laloi

address: Universitaetstrasse 2

department: Institute of Plant Science

country: Switzerland

institute: ETH Zurich

description: Gene expression data from rosette leaves of 3-week-old flu mutant plants (Ler) grown under continuous light, 2 h after a 8hdark/light shift

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400, protocol EukGE-WS2v4.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner

organism: Arabidopsis thaliana

source_name: Rosette leaves of the flu mutant (Ler) grown under continuous light, transferrd to the dark for 8h and shifted to light for 2h.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20 ug total RNA (Eukaryotic Target Preparation, 2002, Affymetrix).

growth_protocol: Plants were grown on soil for 3 weeks under continuous light at 90 mmol. m-2 . s-1

extract_protocol: total RNA extraction was performed according to the guanidine-hydrochloride method as described in Melzer, S., Majewski, D. M. & Apel, K. (1990) Plant Cell 2, 953-961.

treatment_protocol: Plants were transferred to the dark for 8 h and rosette leaves were harvested at 30 min, 60 min, and 2 h after reillumination.

tag: ecotype

value: Landsberg erecta (Ler)

tag: Genotype

tag: Plant material

value: rosette leaves of 3 week-old plants grown under continuous light 90 mmol. m-2 . s-1, before bolting


title: Hemocyte_E(spl) (loss of function mutant)

value: E(spl)rvl, BL199 (Bloomington stock center, Indiana Univ, Bloomington, USA)


title: flu_30min

description: Gene expression data from rosette leaves of 3-week-old flu mutant plants (Ler) grown under continuous light, 30min after a 8hdark/light shift

source_name: Rosette leaves of the flu mutant (Ler) grown under continuous light, transferrd to the dark for 8h and shifted to light for 30 min.


title: Pseudopodia,LPA,rep1


title: H522-BRG1-v-Tb

city: New York

first: Qiaoran

last: Xi

state: NY

address: 1275, York ave.

department: Cancer biology and genetics

institute: MSKCC

description: H522 cells with expression of BRG1  were treated with TGFbeta for 2 h.

hyb_protocol: 10 ug cRNA were hybridized to the affymetrix HG-U133 plus chips

scan_protocol: genechips were scanned using the Hewiett-Packard genearray scanner

data_processing: median-normalized across chips

source_name: H522 lung cancer cell

label_protocol: biotinylated cRNA were prepared from 10 ug of total RNA using the standard labeling techniques for affymetrix chips

extract_protocol: USB total RNA extraction kit

tag: BRG1 was put back to H522 cells. The cells were treated with TGFbeta for 2h.


title: DcR3-treated MDMs_2 days_rep2

source_name: DcR3 treatment


title: flu_60min

description: Gene expression data from rosette leaves of 3-week-old flu mutant plants (Ler) grown under continuous light, 60min after a 8hdark/light shift

source_name: Rosette leaves of the flu mutant (Ler) grown under continuous light, transferrd to the dark for 8h and shifted to light for 60 min.


title: Hemocyte_Spen (loss of function mutant)

description: Hemocyte_Spen (loss of function mutant)

source_name: Hemocyte frome 200-300 third instar larvae

value: spen(GE10359), containing a P-element at the UTR of the spen gene (GenExel, Daejon, Korea).


title: Ler_30min

description: Gene expression data from rosette leaves of 3-week-old wild type plants (Ler) grown under continuous light, 30min after a 8hdark/light shift

source_name: Rosette leaves of wild type plants (Ler) grown under continuous light, transferrd to the dark for 8h and shifted to light for 30 min.

value: Ler


title: Ler_2h

description: Gene expression data from rosette leaves of 3-week-old wild type plants (Ler) grown under continuous light, 2 h after a 8hdark/light shift

source_name: Rosette leaves of wild type plants (Ler) grown under continuous light, transferrd to the dark for 8h and shifted to light for 2h.


title: H522-TbRII

description: H522 cells with expression of TGFbRII were untreated.

tag: TGFbRII was put back to H522 cells. Cells were untreated.


title: Hemocyte_Su(H) (loss of function mutant)

value: Su(H)l(417), BL417 (Bloomington stock center, Indiana Univ, Bloomington, USA).


title: DcR3-treated MDMs_2 days_rep1

tag: MDMs at day 2, biological rep1


title: H522-BRG1-TbRII

description: H522 cells with expression of BRG1 and TGFbRII were untreated.

tag: BRG1 and TbRII were put back to H522 cells.


title: hIgG1-treated MDMs_2 days_rep1


title: Hemocyte_Control

value: W1118 (Control Strain)

value: hemocyte

value: third instar larvae


title: H522-TbRII-Tb

description: H522 cells with expression of TGFbRII were treated with TGFbeta for 2h.

tag: TGFbRII was put back to H522 cells. Cells were treated with TGFbeta for 2h.


title: Human induced pluripotent stem cell clone 2-4 cultured in ESM on MEF

status: Public on Mar 16 2008

city: Chuo-ku

first: Tetsuya

last: Ishikawa

state: Tokyo

address: 1-1, Tsukiji 5-chome

department: Research Institute

country: Japan

institute: Japanease National Cancer Center

description: Gene expression data from human induced pluripiotent stem cells culture in mTeSR on Matrigel

hyb_protocol: Fifteen micrograms of cRNA was fragmented and hybridized to Affymetrix U133 plus 2 GeneChip arrays at 45C for 16 h and then washed and stained using Affimetrix Fluidics.

scan_protocol: The arrays were scanned using an Affimetrix GCS3000 scanner.

data_processing: The images obtained were processed to data using the GCOS software. Data were analysed with the GeneSpring 7.3.1. software

source_name: human induced pluripotent stem cells from fibroblast (5F0416) cultured in ESM on MEF

label_protocol: Biotin-labelled cRNA was reverse transcribed from 1 µg of total RNA according to Affymetrix technical protocols.

growth_protocol: cultured in ESM on MEF

extract_protocol: RNeasy

treatment_protocol: preparation at passage 8 (102 days after 4 factor retroviral gene transfer)

tag: human embryonic stem cells like pluripotent stem cells (46XY)


title: Human neonatal dermal fibroblast (5F0416)

source_name: human neonatal dermal fibroblast (5F0416) at passage 2

growth_protocol: cultured in FBM (Lonza)

tag: the parental fibroblast of human induced pluripotent stem cells (clone 2-4)


title: Human induced pluripotent stem cell clone 3-2 cultured in mTeSR1 on Matrigel

description:
Gene expression data from human induced pluripiotent stem cells culture in mTeSR on Matrigel
The same RNA sample was also employed for Agilent array analysis.

source_name: human induced pluripotent stem cells from fibroblast (5F0438) cultured in mTeSR1 on Matrigel

growth_protocol: cultured in mTeSR on Matrigel

treatment_protocol: preparation at passage 7(80 days after 4 factor retroviral gene transfer)


title: Human induced pluripotent stem cell clone 1-8 cultured in mTeSR1 on Matrigel after freeze-thaw treatment

description:
Gene expression data from human induced pluripiotent stem cell culture in mTeSR on Matrigel
The same RNA sample was also employed for Agilent array analysis.

growth_protocol: cultured in mTeSR1 on Matrigel

treatment_protocol:
preparation at total passage 29 (183 day culture after 4 factor retroviral gene transfer),
at passage 8 via the second freezing & thawing treatment after 5 passages via the first freezing & thawing treatment after 16 passages following gene transfer


title: Human induced pluripotent stem cell clone 1-8 cultured in MEF-conditioned medium on Matrigel

description: Gene expression data from human induced pluripiotent stem cells cultured in MEF-conditioned medium on Matrigel

scan_protocol: The arrays were scanned using an Affimetrix GCS3000 scanner Data.

data_processing: The images obtained were processed to data using the GCOS software. Data were analysed with the GeneSpring 7.3.1. software.

source_name: human induced pluripotent stem cells from fibroblast (5F0438) cultured in MEF-conditioned medium on Matrigel

treatment_protocol: preparation at passage 14 (94 days after 4 factor retroviral gene transfer)


title: H522-BRG1

description: H522 cells overexpressed with BRG1

tag: BRG1 was put back to H522 cells


title: Human neonatal dermal fibroblast (5F0438)

description: Gene expression data from fibroblast (5F0438)

source_name: human neonatal dermal fibroblast (5F0438) at passage 2

tag: the parental fibroblasts of human induced pluripotent stem cells (clones 1-8 and 3-2)


title: ALL_BCell_Leu_41_R

status: Public on Mar 15 2008

city: Monterrey

first: Angel

last: Lugo-Trampe

state: Nuevo León

address: Av. Madero y Dr. Eduardo Aguirre Pequeño

department: Bioquímica

country: Mexico

institute: Universidad Autónoma de Nuevo León

hyb_protocol: The labeled cRNAs were then fragmented and hybridized onto the Affymetrix GeneChip arrays (Affymetrix HG U133 plus 2.0), according to manufacturer’s instructions. Briefly, appropriate amounts of fragmented cRNA and control oligonucleotide B12 were added to the hybridization buffer along with control cRNA (BioB, BioC, BioD), herring sperm DNA, and bovine serum albumin (BSA). The hybridization mixture was heated at 99ºC for 5 min followed by incubation at 45ºC for 5 min before injecting the sample into the GeneChip. Then the hybridization was done at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. After hybridization, the solution was removed and arrays were washed and stained with streptavidin-phycoerythrin provided by Affymetrix. The quality of the fragmented biotin-labeled cRNA in each experiment was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies).

scan_protocol: Probe arrays were scanned in the Affymetrix GeneChip system confocal scanner by using Affymetrix GeneChip Operating System v1.3 software. Chips were scaled to a value of 500 to allow array-to-array comparisons.

data_processing: The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Algorithm. Finally the gene expression differences were calculated.

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage B, 41_R

label_protocol: 3 ug of the isolated total RNA was converted to cDNA and amplified according to the manufacturer’s instructions for the Affymetrix GeneChip System (Santa Clara, CA) at the National Institute of Genomic Medicine (INMEGEN, México, DF). Double stranded cDNA was then clean-up by affinity resin columns provided by the Affymetrix Labelling Kit. Purified cDNA was used as a template for an in vitro transcription reaction for the synthesis of biotinylated cRNA using RNA transcript labeling reagent (affymetrix, Inc., Santa Clara, CA).

extract_protocol: Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water.  The B-Cells from this sample were purified with DynaBeads CD19 Pan B (INVITROGEN).  Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN).  The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: Gender

value: Male

tag: Age

value: 12 Years

tag: Acute Lymphoblastic Leukemia Lineage

value: B

tag: Sample

value: Lymphocytes B from Periferical Blood

tag: Prognosis

value: Poor


title: Ler_60min

description: Gene expression data from rosette leaves of 3-week-old wild type plants (Ler) grown under continuous light, 60min after a 8hdark/light shift

source_name: Rosette leaves of wild type plants (Ler) grown under continuous light, transferrd to the dark for 8h and shifted to light for 60 min.

tag: ecotype


title: Human induced pluripotent stem cell clone 1-8 cultured in ESM on MEF

source_name: human induced pluripotent stem cells from fibroblast (5F0438) cultured in ESM on MEF

treatment_protocol: preparation at passage 31 (184 days after 4 factor retroviral gene transfer)


title: ALL_BCell_Leu_41

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage B, 41


title: ALL_TCell_Leu_30

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage T, 30

extract_protocol: Periferical blood was centrifuged by gradient with Histopaque 1077 (SIGMA-ALDRICH) at 4ºC, and the buffy was washed twice with PBS + 0.1% BSA + 2 mM EDTA, in DEPC-Water.  The T-Cells from this sample were purified with DynaBeads CD2 Pan T (INVITROGEN). Total RNA was isolated from fresh lymphocytes using RNeasy Mini Kit (QIAGEN).  The quality of RNA was checked using the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: 21 Years

value: T

value: Lymphocytes T from Periferical Blood

value: Favorable


title: Human induced pluripotent stem cell clone 1-8 cultured in mTeSR1 on Matrigel (1)


title: 165 E3_WT_Normal_repl 3

status: Public on Mar 17 2008

city: Omaha

first: Janee

last: Gelineau-van Waes

state: NE

address: 985455 Nebraska Medical Center

department: Genetics, Cell Biology & Anatomy

institute: University of Nebraska Medical Center

description: Gene expression data of RFC KO, Folic Acid trt, E9.5, WT, normal neural tube and chorioallantoic membrane

hyb_protocol: cRNA probes were hybridized to the Affymetrix Mouse Genome 430_2.0 chip, which profiles the expression of 45,101 unique transcripts. Hybridization, washing and staining procedures were all performed according to manufacturers instructions and reagents used were all purchased from Affymetrix and recommended vendors.

scan_protocol: Chips were scanned using a GeneChip Scanner 3000 6G in the UNMC Microarray Core Facility. Images were analyzed using GCOS imaging software. Quality metric parameters including noise level, background, and the efficiency of reverse transcription were ascertained for all hybridizations. Data Sets passing the stringent quality recommendations were then exported for RMA normalization and subsequent statistical analysis.

data_processing: Analyses were conducted with BRB ArrayTools developed by Dr. Richard Simon and Amy Peng. Low-level analysis which converts probe level data to a gene level expression data was done using robust multiarray average (RMA), implemented using the rma function of the Affymetrix package of the Bioconductor project in the R programming language. The RMA background correction method corrects the perfect match (PM) probe intensities by using a model based on the assumption that the observed intensities are the sum of signal and noise. Quantile normalization was used to normalize the PM probes and the calculation of summary expression measures was done using the median polish method, which fits a multichip linear model to the data, and gives the expression on the log2 scale. Prior to statistical analysis a filter was applied to reduce the number of genes examined. A gene was excluded unless at least 1 out of the 6 arrays had expression data with a 1.5-fold change or greater in either direction from the gene's median value. This filter reduced the number of transcripts examined to 2982. For differential expression calculations the mice were paired as littermates (one wildtype and one nullizygous embryo from each litter) and for each gene, a random-variance paired t-test was conducted to determine if there was a significant difference in expression between the mutant and wildtype groups for that gene. P-value adjustment for multiple comparisons was done with the false discovery rate (FDR) method of Benjamini-Hochberg. A significance level of 0.001 for the adjusted univariate test was used to select differentially expressed genes. This reduced the number probe sets examined to 288.

source_name: E9.5 embryo with normal neural tube and normal chorioallantois

label_protocol: 100 ng total RNA was reverse-transcribed and cRNA generated per Affymetrix (Santa Clara, CA) instructions using the Affymetrix 2-cycle Target Labeling Kit.

growth_protocol: RFC1 knockout mice were generated by targeted inactivation of the RFC1 (SLC19a1) allele. Following identification of germline chimeras, the mutation was transferred from the hybrid stock genetic background (C57BL/6J) onto an inbred SWV genetic background. RFC/SWV heterozygous mice were housed in microisolator cages, maintained on a 12-hour light/dark cycle, and allowed access to normal Harlan-Teklad (Madison, WI) rodent chow [#8604] and autoclaved water. Virgin females 50-70 days of age were mated to males between the hours of 5-10 PM each evening. Females exhibiting vaginal plugs at the end of this period were weighed and housed up to 5 females per cage, and subsequently placed in treatment groups. The time of conception was considered to be 10 PM on the evening of the mating.

extract_protocol: Total RNA from each whole E9.5 embryo was isolated using the Arcturus (Mountain View, CA) PicoPure kit with an on-column DNase treatment following a 30 second homogenization using a Kontes Pellet Pestle. Total RNA was quantitated and checked on a NanoChip using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) to determine sample integrity prior to microarray analysis. All RNAs were stored at -80oC until downstream analysis was performed.

treatment_protocol: Folate Supplementation: Folic acid was purchased from Sigma Chemical (St. Louis, MO) and dissolved in Nanopure water to make a solution of the desired concentration. Pregnant dams received folic acid (25 mg/kg) by subcutaneous injection on E 0.5 and continuing daily throughout gestation until the time of sacrifice.

tag: RFC (reduced folate carrier) KO mouse

tag: Folic acid trt, 25 mg/kg

tag: Genotype

value: WT

tag: embryo with normal neural tube and chorioallantois


title: H522-BRG1-TbRII-Tb

description: BRG1 and TGFbRII were put back to H522 cells. the cells were treated with TGFbeta for 2h.

hyb_protocol: 10 ug cRNA were hybridized to the affymetrix HG-133 plus chips

data_processing: median -normalized across chips

source_name: H522 lung cancer cell

tag: H522 cell's TGFbeta response was restored by putting back BRG1 and TGFbRII


title: Human induced pluripotent stem cell clone 2-4 cultured in mTeSR1 on Matrigel

source_name: human induced pluripotent stem cells from fibroblast (5F0416) cultured in mTeSR1 on Matrigel

treatment_protocol: preparation at passage 5 (102 days after 4 factor retroviral gene transfer)


title: 165 E11_Null_Affected_repl 3

description: Gene expression data of RFC KO, Folic Acid trt, E9.5, Nullizygote, abnormal neural tube (craniorachiscisis) and chorioallantoic membrane with lack of fusion

source_name: E9.5 embryo with craniorachiscisis and lack of chorioallantoic fusion

value: Nullizygote

tag: embryo with craniorachiscisis and lack of fusion of chorioallantois


title: 164 E8_WT_Normal_repl 2


title: 164 E11_Null_Affected_repl 2


title: ALL_TCell_Leu_29_R

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage T, 29_R

value: 18 Years

tag: Note

value: Technical Replicate of ALL_TCell_Leu_29


title: ALL_TCell_Leu_29

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage T, 29


title: ALL_BCell_Leu_33

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage B, 33

value: Female

value: 9 Months


title: ALL_TCell_Leu_30_R

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage T, 30_R

value: Technical Replicate of ALL_TCell_Leu_30


title: ALL_TCell_Leu_28

data_processing: The batch CEL files generated by GeneChip Operating Software (GCOS) were analyzed into R software with the affy module from the Bioconductor consortium. Samples with technical replicates were normalized applying the Quantile Normalization method. Then all the data were globally normalized applying the Loess Normalization Altorithm. Finally the gene expression differences were calculated.

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage T, 28

value: 16 Years


title: ALL_BCell_Leu_33_R

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage B, 33_R

value: Technical Replicate of ALL_BCell_Leu_33


title: ALL_TCell_Leu_14

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage T, 14

value: 14 Years


title: ALL_BCell_Leu_24_R

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage B, 24_R

value: Male

value: 43 Years

value: B

value: Technical Replicate of ALL_BCell_Leu_24


title: ALL_BCell_Leu_24

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage B, 24

value: Lymphocytes B from Periferical Blood

value: Poor


title: 150 E2_WT_Normal_repl 1


title: Human induced pluripotent stem cell clone 1-8 cultured in mTeSR1 on Matrigel (2)

source_name: human induced pluripotent stem cells from fibroblast (5F0438) cultured in mTeSR1 on Matrigel

tag: human embryonic stem cells like pluripotent stem cells (46XY)


title: 150 E9_Null_Affected_repl 1


title: ALL_BCell_Leu_22

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage B, 22

value: 37 years

value: Favorable


title: ALL_BCell_Leu_07

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage B, 07

value: 12 years


title: ALL_BCell_Leu_12_R

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage B, 12_R

value: 8 months

value: Technical Replicate of ALL_BCell_Leu_12


title: ALL_BCell_Leu_12

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage B, 12


title: ALL_TCell_Leu_19

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage T, 19

value: 3 Years

value: T

value: Lymphocytes T from Periferical Blood


title: ALL_TCell_Leu_28_R

source_name: Periferical blood, Acute Lymphoblastic Leukemia lineage T, 28_R

value: 16 Years

value: Technical Replicate of ALL_TCell_Leu_28


title: C. parvum infected (3Cp24 1838_7643)

status: Public on Mar 14 2008

city: Houston

first: Alejandro

last: Castellanos

state: TX

address: One Baylor Plaza

department: Medicine-Infectious Diseases

institute: Baylor College of Medicine

description: Human ileal explant cultures infected with cryptosporidium

hyb_protocol: Affymetrix One Cycle Target and Labeling Protocol Hybridization and Staining, as described in Expression Analysis Technical Manual with following exception(s):  Hybridization volume increased to 250.0µL.  Fluidics Script: EukGE ws2v5; Array: HGU133 Plus 2.0; Date Scanned: 07/28/05.

scan_protocol: Affymetrix standard protocol

data_processing: GeneChip® Scanner 3000, GCOS version 1.2

source_name: Subject #3: a 5 cm terminal ileum was obtained from ileostomy takedown. The mucosal layers were dissected from the underlying muscular layersThe tissue was sectioned into 3 mm2 segments

label_protocol: Affymetrix One Cycle Target and Labeling Protocol, exactly as described in Affymetrix Expression Analysis Technical Manual

growth_protocol: Ileal tissue was obtained from 3 individuals undergoing surgical procedures for unrelated non-infectious conditions. Laboratory personnel collected ileal tissue in the operating room at time of surgery. The tissue was immediately transported to the laboratory in CMRL Medium-1066. The mucosal layers were removed mechanically and the mucosa from each patient was divided into four 3 mm2 pieces. Each piece was placed luminal side up, onto polycarbonate coated insert cups. The inserts were then placed into culture wells containing CMRL Medium-1066 supplemented with 5 g/L D-glucose, 0.3 mM Glutamax, 0.3 g/L L-methionine, 0.3 g/L tricine, 5% heat inactivated FBS, 100,000 units/L penicillin, 100,000 mcg/L streptomycin, and 250 mcg/L Amphotericin B. A small amount of culture medium was also added to the apical surface of each insert cup to keep the explants hydrated. The explants were incubated for at least 3 hours in a chamber containing 95% O2 and 5% CO2 prior to ex vivo infection.

extract_protocol:
Total RNA was extracted with the RNAeasy Mini Kit (Qiagen) per manufacturer’s protocol.
Total RNA was extracted with the RNAeasy Mini Kit (Qiagen) per manufacturer’s protocol.

treatment_protocol: 1 x 106 oocysts per sample of C. parvum, C. hominis or sterile excystation solution were inoculated onto the apical surface of the explants. The explant tissues were kept in vitro for 24 hours at 37°C in a chamber containing 95% O2 and 5% CO2 and then collected in RNA later (RNase inhibitor solution) and stored frozen. Control tissue from prior to infection was placed immediately in RNA later. Explant samples were disrupted and homogenized mechanically by sonication and total RNA was extracted with the RNAeasy Mini Kit (Qiagen) per manufacturer’s protocol. To extract the RNA from cultured cells we disrupt cells using QIAsheredder colums and the RNAeasy plus extraction kit (Qiagen). The quality of the RNA obtained was confirmed by capillary electrophoresis on an Agilent 2100 Bioanalyzer. Subsequently, gene expression profiles were probed by microarray analysis using the Affymetrix Human Genome U133 Plus 2.0 Array (33,000 human genes). Data were background adjusted, normalized and summarized by the RMA method. The Bioconductor package was used for this analysis. The result was a data set of expression value, with each probe set having a single expression value per chip, and the data was in log 2 scale. This data was then filtered by the present (“P”) or absent (“A”) calls which were calculated by Affymetrix’ software GCOS 2.0 (Affymetrix, Santa Clara, CA). Probe sets that had “A” calls on all chips were excluded in further analysis. The data were then imported into SAS 9.0 (SAS Institute Inc., Cary, NC). The Type III test p-values were adjusted by the Benjamini-Hochberg method  to control FDR, resulting in 2370 probe sets.

tag: Ileal tissue


title: WT Col, biological rep2

status: Public on Mar 13 2008

description: Gene expression data from rosette leaves of 3-week-old wild type plants (Ler) grown under continuous light, 2h after a 8hdark/light shift

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450, protocol EukGE-WS2v4.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: wild type plants (Col) grown under continuous light, transferrd to the dark for 8h and shifted to light for 2h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Eukaryotic Target Preparation, 2002, Affymetrix).

treatment_protocol: Plants were transferred to the dark for 8 h and rosette leaves were harvested 2 h after reillumination.

value: Col

tag: Plant material

value: rosette leaves of 3 week-old plants grown under continuous light 90 mmol. m-2 . s-1, before bolting


title: brain, PbK-infected, day 6

city: Sydney

first: Jenny

last: Miu

state: NSW

address: 92-94 Parramatta Rd

department: Department of Pathology

country: Australia

institute: University of Sydney

hyb_protocol: Labelled cRNA was then hybridised to Affymetrix GeneChip Mouse Genome 430 2.0 arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station 400.

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

data_processing: Single array analyses were carried out using the GeneChip Operating Software, according to the Affymetrix GeneChip Expression Analysis: Data Analysis Fundamentals Manual.

source_name: brain, PbK-infected, day 6

label_protocol: cRNA was labelled with biotin using the one-cycle target labelling protocol, according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Manual).

extract_protocol: Total RNA was extracted using the TRIzol method, according to the manufacturer's instructions.

tag: Strain

value: C57BL/6, Gender:Female, Age:6-8 weeks, Tissue:brain, Disease:P. berghei K173, day 6


title: Uninfected (3U24 1838_7642_refrag)


title: flu, biological rep1

source_name: the flu mutant (SAIL_136_E05) grown under continuous light, transferrd to the dark for 8h and shifted to light for 2h


title: Baseline (2BO 1838_7636)

source_name: Subject #2: a 5 cm terminal ileum was obtained from ileostomy takedown. The mucosal layers were dissected from the underlying muscular layers. The tissue was sectioned into 3 mm2 segments


title: brain, PbA-infected, day 6

source_name: brain, PbA-infected, day 6

value: C57BL/6, Gender:Female, Age:6-8 weeks, Tissue:brain, Disease:P. berghei ANKA, day 6


title: brain, PbK-infected, day 14

source_name: brain, PbK-infected, day 14

value: C57BL/6, Gender:Female, Age:6-8 weeks, Tissue:brain, Disease:P. berghei K173, day 14


title: Uninfected (2U24 1838_7638)


title: C. parvum infected (1Cp24 1838_7635)

source_name: Subject #1: a 7cm terminal ileum was obtained from right hemi-colectomy specimen. The mucosal layers were dissected from the underlying muscular layers. The tissue was sectioned into 3 mm2 segments.


title: flu over-tAPX 14-2, biological rep1

description: Gene expression data from rosette leaves of 3-week-old flu mutant plants (Ler) grown under continuous light, 60min after a 8hdark/light shift

source_name: the flu mutant (SAIL_136_E05) overexpressing thylakoidal ascorbate peroxidase (line 14/2, PMID: 15165186 ) grown under continuous light, transferrd to the dark for 8h and shifted to light for 2h

value: flu (SAIL_136_E05 ) over-tAPX (line 14-2)


title: Baseline (1BO 1838_7632)


title: flu over-tAPX 14-2, biological rep2

description: Gene expression data from rosette leaves of 3-week-old flu mutant plants (Ler) grown under continuous light, 2 h after a 8hdark/light shift


title: Uninfected (1U24 1838_7634)


title: C. parvum infected (2Cp24 1838_7639)


title: C. hominis infected (3Ch24 1838_7641_refrag)


title: over-tAPX 14-2, biological rep2

source_name: thylakoidal ascorbate peroxidase overexpressor plants (line 14/2, PMID: 15165186 ) grown under continuous light, transferrd to the dark for 8h and shifted to light for 2h

value: Col over-tAPX (line 14-2, PMID:15165186)


title: C. hominis infected (1Ch24 1838_7633)


title: Baseline (3BO 1838_7640)


title: flu, biological rep2

description: Gene expression data from rosette leaves of 3-week-old wild type plants (Ler) grown under continuous light, 2 h after a 8hdark/light shift


title: over-tAPX 14-2, biological rep1

description: Gene expression data from rosette leaves of 3-week-old flu mutant plants (Ler) grown under continuous light, 30min after a 8hdark/light shift


title: brain, uninfected

source_name: brain, uninfected

value: C57BL/6, Gender:Female, Age:6-8 weeks, Tissue:brain, Disease:Uninfected


title: WT Col, biological rep1

source_name: wild type plants (Col) grown under continuous light, transferred to the dark for 8h and shifted to light for 2h


title: AML 5284

status: Public on Mar 12 2008

first: Roel

last: Verhaak

address: 1400 Pressler St

department: Bioinformatics and Comp Bio

institute: MD Anderson Cancer Center

description: Blasts and mononuclear cells were purified from bone marrow or peripheral blood aspirates of AML patients. Samples contained 80-100 percent blast cells.

hyb_protocol: Affymetrix protocol.

scan_protocol: Affymetrix protocol.

data_processing: MAS5 with global scaling to target value 100, followed by setting all values lower than 30 at 30, and then log2 transformation.

source_name: Blasts and mononuclear cells, AML patient

label_protocol: Affymetrix protocol.

extract_protocol: Total RNA was extracted by lysis with guanidium isothiocyanate followed by cesium chloride gradient purification.

tag: disease state

value: Acute myeloid leukemia

tag: cell type

value: blasts and mononuclear cells

value: neg

tag: gender

value: male

tag: age

value: 41 years

tag: score

value: FAB M2

tag: risk

value: cytogenetic intermediate

tag: cebpa

value: wild type

tag: karyotype

value: NN

value: Neg

tag: flt3 itd mutation

value: Pos

tag: flt3 tkd mutation

tag: n-ras mutation

tag: k-ras mutation

tag: evi1 expression

tag: cebpa mutation


title: AML 7061

value: female

value: 31 years

value: FAB M1

value: nd


title: NHE3-/- replicate 1

status: Public on Mar 06 2008

city: Tucson

first: Pawel

middle: R.

last: Kiela

state: AZ

address: 1501 N. Campbell Ave.

department: Pediatrics

institute: University of Arizona

description:
Gene expression data from the colon of NHE3-deficient mice
whole colonic tissue was dissected from mice 6-8 weeks of age

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC to GeneChip® Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were initially analyzed with Afymetrix GCOS software using Affymetrix default analysis settings and global scaling as normalization method. Subsequently, data were imported to GeneSpring v.7.3.1 (Agilent).

source_name: colon

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

tag: Genotype

tag: Age

value: 6-8 weeks


title: NHE3-/- replicate 3


title: NHE3+/+ replicate 3

description:
Gene expression data from the colon of wild-type mice
whole colonic tissue was dissected from mice 6-8 weeks of age

value: wild-type


title: AML 2305

value: Acute myeloid leukemia

value: 27 years

value: FAB M5


title: AML 2212

value: blasts and mononuclear cells

value: neg

value: 60 years

value: cytogenetic poor


title: AML 2276

value: 56 years

value: FAB M0

value: wild type

value: Other


title: AML 6241

value: male

value: 48 years

value: FAB M4

value: cytogenetic intermediate

value: NN

value: Pos

value: Neg


title: NHE3-/- replicate 2

value: 6-8 weeks


title: AML 2283

value: Acute myeloid leukemia

value: 57 years


title: NHE3+/+ replicate 2

value: wild-type


title: AML 2173

value: blasts and mononuclear cells

value: neg

value: female

value: 55 years

value: FAB M1


title: AML 2191

value: pos

value: 45 years

value: FAB Mx

value: wild type


title: AML 3319

value: male

value: 49 years

value: FAB M5

value: cytogenetic intermediate


title: AML 2686

value: 31 years

value: NN

value: Neg


title: AML 6465

value: Acute myeloid leukemia

value: 54 years

value: Other

value: Pos


title: NHE3+/+ replicate 1

value: wild-type

value: 6-8 weeks


title: ATF6-MER TG mouse_vehicle3

city: San Diego

first: Peter

middle: J

last: Belmont

state: CA

address: 10724 Science Center Drive

description: See Affymetrix Gene Expression Protocol

hyb_protocol: See Affymetrix Gene Expression Protocol

scan_protocol: See Affymetrix Gene Expression Protocol

data_processing: See Affymetrix Gene Expression Protocol

source_name: TG mouse heart left ventricle

label_protocol: See Affymetrix Gene Expression Protocol

extract_protocol: Tel-Test Inc RNAzol

tag: Transgenic ATF6-MER mouse

tag: Strain

tag: Gender

tag: Tissue

value: heart LV

tag: Treatment

value: tamoxifen


title: NTG mouse_tamoxifen1

description: See Affymetrix Gene Expression Protocol

source_name: NTG mouse heart left ventricle

tag: Nontransgenic littermate mouse


title: NTG mouse_vehicle3

description: See Affymetrix Gene Expression Protocol

value: vehicle


title: ATF6-MER TG mouse_vehicle1

description: See Affymetrix Gene Expression protocol

hyb_protocol: See Affymetrix Gene Expression protocol

scan_protocol: See Affymetrix Gene Expression protocol

data_processing: See Affymetrix Gene Expression protocol

label: See Affymetrix Gene Expression protocol

label_protocol: See Affymetrix Gene Expression protocol

extract_protocol: Tel-Test Inc. RNAzol


title: NTG mouse_vehicle1

description: See Affymetrix Gene Expression Protocol


title: NTG mouse_tamoxifen3

description: See Affymetrix Gene Expression Protocol

source_name: NTG mouse heart left ventricl


title: ATF6-MER TG mouse_vehicle2

description: See Affymetrix Gene Expression Protocol

tag: TG ATF6-MER mouse


title: ATF6-MER TG mouse_tamoxifen2

description: See Affymetrix genechip expression analysis protocol

source_name: TG mouse left ventricle treated with tamoxifen

extract_protocol: Tel-Test Inc RNAzol protocol

value: ~30 weeks


title: NTG mouse vehicle2

description: See Affymetrix Gene Expression Protocol

value: Male


title: NTG mouse_tamoxifen2

description: See Affymetrix Gene Expression Protocol

value: male


title: ATF6-MER TG mouse_tamoxifen3

description: See Affymetrix Gene Expression protocol

source_name: TG mouse left ventricle

tag: treatment


title: Smoke 24h repC

status: Public on Mar 05 2008

first: Ellen

last: Jorgensen

address: 712 Fifth Avenue

institute: Vector Research Ltd.

description: Smoke 24h repC

hyb_protocol: Fragmented biotin-labeled cRNA at a concentration of 50 ng/ul was hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip® expression arrays according to the manufacturer’s recommendations for a minimum of sixteen hours.  Post-hybridization washing and staining was performed on the GeneChip® Fluidics Station 450

scan_protocol: Arrays were scanned with the GeneChip® Scanner 3000 7G, under the control of the Affymetrix GeneChip® Operating Software (GCOS).

data_processing: MAS5 algorithm

source_name: smoke exposed NHBE cells

label_protocol: Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix

growth_protocol: NHBE cells from nonsmoking, nondiabetic donors were purchased from Cambrex Corporation (Walkersville, MD).  Cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).

extract_protocol: NHBE cell lysates were homogenized using a QIAshredder spin column and RNA extracted using Qiagen RNeasy spin columns according to the manufacturer’s protocol

treatment_protocol: Cells were seeded into 35mm Petri dishes at a density of 10^5 cells/dish and were typically at 70% confluency at the time of exposure to CS.  Three replicate dishes were treated for each condition, and each replicate was analyzed using a separate microarray (i.e., the RNA from the dishes was not pooled).  The cell culture medium was replaced with 37°C Dulbecco’s PBS (D-PBS) containing calcium and magnesium (Gibco/Invitrogen) for the smoke exposure.  The covers were removed from the Petri dishes and they were placed in a smoke exposure chamber designed to deliver a consistent dose of diluted smoke.  Smoke was generated under Federal Trade Commission smoking conditions (35 ± 0.3cc puff, one puff every 60 seconds, 2-second puff duration with none of the ventilation holes blocked) using a KC 5 Port Smoker (KC Automation, Richmond, VA)

tag: NHBE cells


title: ATF6-MER TG mouse_tamoxifen1

hyb_protocol: See Affymetrix genechip expression analysis protocol

source_name: TG mouse_left ventricle_tamoxifen treated_1

tag: Transgenic ATF6-MER

value: 40 weeks

value: left ventricle


title: Smoke 2h repA

description: Smoke 2h repA


title: Smoke 1h repA

description: Smoke 1h repA


title: Smoke 24h repA

description: Smoke 24h repA


title: Smoke 1h repC

description: Smoke 1h repC


title: Smoke 4h repC

description: Smoke 4h repC


title: Smoke 4h repB

description: Smoke 4h repB


title: Smoke 24h repB

description: Smoke 24h repB


title: Smoke 2h repC

description: Smoke 2h repC


title: Smoke 2h repB

description: Smoke 2h repB


title: Smoke 4h repA

description: Smoke 4h repA


title: Mock 24h repC

description: Mock 24h repC

source_name: mock exposed NHBE cells


title: Smoke 1h repB

description: Smoke 1h repB


title: Mock 4h repA

description: Mock 4h repA


title: Mock 4h repC

description: Mock 4h repC


title: Mock 4h repB

description: Mock 4h repB


title: Mock 24h repB

description: Mock 24h repB


title: Mock 2h repA

description: Mock 2h repA


title: Mock 1h repC

description: Mock 1h repC


title: Mock 2h repC

description: Mock 2h repC


title: Mock 2h repB

description: Mock 2h repB


title: Mock 1h repB

description: Mock 1h repB


title: Mock 24h repA

description: Mock 24h repA


title: Mock 1h repA

description: Mock 1h repA


title: Alymphoplasia Dendritic Cells_LPS+anti-CD40_replicate2

city: Portland

first: Evan

middle: F.

last: Lind

state: OR

address: Mail Code L220, 3181 SW Sam Jackson Park Road

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

description: DCs were CD11c+ bead selected from spleen then flow-sorted to high purity

hyb_protocol: 15 μg of biotinylated  cRNA targets were fragmented and hybridized to GeneChip® array during the overnight incubation at 45oC in rotating hybridization oven.

scan_protocol: After staining the arrays were scanned using Affymetrix GeneChip® Scanner with the laser filter set at 570 nm, pixel size 2.5 μm. The array image data were acquired, and the fluorescent signal intensities were quantified using Affymetrix® MAS 5.0 software with following settings of quantitation parameters: Alpha1=0.05, Alpha2=0.065, Tau=0.015, Gamma1H=0.0045, Gamma1L=0.0045, Gamma2H=0.006, Gamma2L=0.006,

data_processing: Raw signal.

label: phycoerythrin

source_name: Alymphoplasia splenic DC ex-vivo from LPS and agonistic anti-CD40 treated

label_protocol: Double-stranded cDNA is then amplified and labeled using a biotinylated nucleotide analog/ribonucleotide mix in the second IVT reaction.

extract_protocol: Qiagen RNeasy

treatment_protocol: Mice were treated I.P. with 25 micrograms LPS and 100 micrograms agonistic anti-CD40 antibody clone FGK4.5.  6 hours later splenic DCs were isolated and RNA was isolated.

tag: Alymphoplasia mouse


title: Alymphoplasia Dendritic Cells_LPS+anti-CD40_replicate3


title: WT Dendritic Cells_LPS+anti-CD40_replicate3

source_name: WT splenic DC ex-vivo from Mice treated with LPS and anti-CD40 agonist

tag: Alymphoplasia mouse Heterozygous littermate


title: WT Dendritic Cells_untreated_replicate3

description: DCs were CD11c+ bead selected from spleen then flow-sorted to high purity.

scan_protocol: After staining the arrays were scanned using Affymetrix GeneChip® Scanner with the laser filter set at 570 nm, pixel size 2.5 μm. The array image data were acquired, and the fluorescent signal intensities were quantified using Affymetrix® MAS 5.0 software with following settings of quantitation parameters: Alpha1=0.05, Alpha2=0.065, Tau=0.015, Gamma1H=0.0045, Gamma1L=0.0045, Gamma2H=0.006, Gamma2L=0.006, Perturbation=1.1, Target Intensity=150.

data_processing: Raw scores.

label: Phycoerythrin

source_name: WT splenic DC ex-vivo from untreated

tag: Alymphoplasia mouse Heterozygous littermate.


title: A431_wt, biological rep3

city: Nashville

first: Shizhen Emily

last: Wang

state: TN

address: 2220 Pierce AVE, PRB-771

department: Cancer Biology

institute: Vanderbilt University

description: Gene expression data from wild-type A431

hyb_protocol: The biotinylated cRNA (15 µg) was fragmented and hybridized to an Affymetrix GeneChip Mouse Genome 430 2.0 Array  containing 45,000 sets of 11 to 25-mer oligomers, representing 39,000 mouse transcripts (34,000 are annotated as well-defined genes). Hybridized cRNA was detected using streptavidin coupled to phycoerythrin.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G Plus 2 and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files.

data_processing: CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis). The "Value" column shows this normalized signal intensity value.

source_name: A431_wt cells

label_protocol: Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA).  Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter.  In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.

growth_protocol: Cells were grown in Improved MEM (IMEM) Zn2+ Option (Invitrogen, Carlsbad, CA) supplemented with 10% FBS in a humidified 5% CO2 incubator at 37°C.

extract_protocol: Total RNA was isolated from parental and GR A431 cells using TRIzol reagent (Invitrogen, Carlsbad, CA), followed by RNeasy Mini Kit column purification (Qiagen, Valencia, CA) including an in column DNAse clean-up using RNAse-free DNAse Set (Qiagen). Agilent’s Bioanalyzer microfluidic assay (Agilent Technologies, Palo Alto CA) was used to assay RNA integrity. Spectrophotometric and fluorometric methods were combined to quantitate protein and nucleic acids present in the sample, and to ensure quality control of each sample.

treatment_protocol: Cells grown in complete medium were rinsed with PBS and placed on ice in the TRIzol reagent.

tag: Organ

value: skin; Tissue:epidermis; Disease:epidermoid carcinoma; Age:85 years; Gender:female


title: A431_GR, biological rep1

description: Gene expression data from gefitinib-resistant A431

source_name: A431_GR cells

value: skin; Tissue:epidermis; Disease:epidermoid carcinoma; Age:85 years; Gender:female; these cells were selected and maintained in gefitinib (3uM)


title: A431_GR, biological rep3


title: Alymphoplasia splenic DC ex-vivo from untreated replicate 1


title: Vervet Limbus

city: Los Angeles

first: Sophie

last: deng

address: 100 Stein plaza

institute: Jules Stein Eye Institute-UCLA

description: All microarrays were scanned using an Affymetrix 3000 one-color, microarray scanner. Raw images were examined for surface defects and for proper grid placement. Background intensity, housekeeping gene expression, and a 3’/5’ ratio of probe sets from genes of varying lengths were also used to assess the quality. Probe intensity values were generated using the Affymetrix Gene Chip Operating System (GCOS).

hyb_protocol: Standard Affymetrix GeneChip Hybridization Protocol for Eukaryotic Organisms

scan_protocol: Scans were done using an Affymetrix GeneChip 3000 Scanner

data_processing: For the analysis of gene expression measures, we used the RMA (Robust Multiarray Average) normalized data, which had been described in detail elsewhere by Irizarry, et al.{Irizarry, 2003 #108} All Affymetrix data were normalized using the justRMA algorithm from the Bioconductor group.{Gentleman, 2004 #109} Each array was further individually normalized using a pool of 50 fixed reference arrays in UCLA Microarray Core Facility.

organism: Chlorocebus sabaeus

source_name: Limbus

label_protocol: Standard Affymetrix Gene Expression Protocol for Two-Rounds of Amplification and Biotin Labeling

extract_protocol: To ensure complete homogenization, a serrated Omni homogenizer (Omni International, Marietta, GA) was used. Each sample was bathed in a lysis buffer provided in Qiagen’s RNA easy mini kits (Qiagen, Valencia, CA). β-mercaptoethanol (Invitrogen, Carlsbad, CA) was added to the lysis buffer in a 1:100 ratio. In between homogenizations, the blade was rinsed subsequently twice in filtered ddI water (Millipore, Billerica, MA), 70% ethanol, and twice again in fresh Millipore ddI water. All samples are kept on dry ice before homogenization. Total RNA was isolated using the Qiagen’s RNA easy mini columns Qiagen, Valencia, CA). The extracted total RNA was assessed for purity and integrity using both the Nanodrop 1000 spectrophotometer (Nanodrop, Wilmington, DE) and the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Because of the sample’s low concentration all integrity checks were run on Agilent’s RNA Pico Chips. Only those samples with a 28s/18s ratio of 1.0 to 2.0 with minimal degradation were used.

tag: Male Vervet.


title: A431_GR, biological rep2


title: Alymphoplasia Dendritic Cells_LPS+anti-CD40_replicate1


title: Vervet Cornea

source_name: Cornea


title: WT Dendritic Cells_LPS+anti-CD40_replicate1

source_name: WT splenic DC ex-vivo from mice treated with LPS and anti-CD40 agonist


title: WT Dendritic Cells_untreated_replicate2


title: A431_wt, biological rep1


title: A431_wt, biological rep2


title: Vervet Conjunctiva

source_name: Conjunctiva

tag: Male vervet.


title: WT Dendritic Cells_LPS+anti-CD40_replicate2


title: Alymphoplasia splenic DC ex-vivo from untreated replicate 2


title: Alymphoplasia splenic DC ex-vivo from untreated replicate 3


title: Incubator Control rep4

status: Public on Mar 04 2008

description: Incubator Control rep4

source_name: incubator controls

label_protocol: Two micrograms of total RNA was reverse transcribed into double stranded cDNA using a oligo(dT)/T7 promotor chimeric primer, and in vitro transcribed using reagents provided by Affymetrix (Santa Clara, CA).

growth_protocol: NHBE cells were cultured in complete Bronchial Epithelial Cell Growth Medium, prepared by supplementing Bronchial Epithelial Basal Medium with retinoic acid, epidermal growth factor, epinephrine, transferrin, T3, insulin, hydrocortisone, antimicrobial agents and bovine pituitary extract by addition of SingleQuots,TM (Cambrex Corporation).

extract_protocol: total RNA was extracted using Qiagen Rneasy kits according to manufacturer's instructions

treatment_protocol: In a custom-built smoke exposure chamber, NHBE cells were exposed to 15min FTC smoking with each 35mL puff diluted into 500cc air. Following exposure the medium was replaced with fresh and the cells placed in a 37C incubator for the times indicated.

tag: normal human bronchial epithelial cells


title: Incubator Control rep3

description: Incubator Control rep3


title: Incubator Control rep1

description: Incubator Control rep1


title: WT Dendritic Cells_untreated_replicate1

label_protocol: Double-stranded cDNA is amplified and labeled using a biotinylated nucleotide analog/ribonucleotide mix in the second IVT reaction.


title: Lights 24h rep4

description: Lights 24h rep4

source_name: smoke-exposed NHBE cells, 24h


title: Incubator Control rep2

description: Incubator Control rep2


title: Lights 24h rep3

description: Lights 24h rep3


title: Lights 24h rep2

description: Lights 24h rep2


title: Lights 8h rep4

description: Lights 8h rep4

source_name: smoke-exposed NHBE cells, 8h


title: Lights 24h rep1

description: Lights 24h rep1


title: 2R4F 8h rep2

description: 2R4F 8h rep2


title: Lights 2h rep1

description: Lights 2h rep1

source_name: smoke-exposed NHBE cells, 2h


title: Lights 8h rep3

description: Lights 8h rep3


title: 2R4F 4h rep2

description: 2R4F 4h rep2

source_name: smoke-exposed NHBE cells, 4h


title: Lights 2h rep4

description: Lights 2h rep4


title: 2R4F 8h rep3

description: 2R4F 8h rep3


title: Lights 8h rep1

description: Lights 8h rep1


title: Lights 8h rep2

description: Lights 8h rep2


title: 2R4F 8h rep4

description: 2R4F 8h rep4


title: Lights 4h rep3

description: Lights 4h rep3


title: 2R4F 4h rep4

description: 2R4F 4h rep4


title: Lights 2h rep3

description: Lights 2h rep3


title: Lights 4h rep2

description: Lights 4h rep2


title: 2R4F 24h rep1

description: 2R4F 24h rep1


title: 2R4F 8h rep1

description: 2R4F 8h rep1


title: Lights 4h rep1

description: Lights 4h rep1


title: 2R4F 24h rep2

description: 2R4F 24h rep2


title: Lights 4h rep4

description: Lights 4h rep4


title: 2R4F 24h rep3

description: 2R4F 24h rep3


title: 2R4F 4h rep3

description: 2R4F 4h rep3


title: Lights 2h rep2

description: Lights 2h rep2


title: 2R4F 2h rep3

description: 2R4F 2h rep3


title: 2R4F 24h rep4

description: 2R4F 24h rep4


title: 2R4F 4h rep1

description: 2R4F 4h rep1


title: 2R4F 2h rep4

description: 2R4F 2h rep4


title: 2R4F 2h rep1

description: 2R4F 2h rep1


title: Mock 24h rep3

description: Mock 24h rep3

source_name: mock-exposed NHBE cells, 24h


title: Mock 24h rep2

description: Mock 24h rep2


title: 2R4F 2h rep2

description: 2R4F 2h rep2


title: Mock 4h rep4

description: Mock 4h rep4

source_name: mock-exposed NHBE cells, 4h


title: Mock 24h rep4

description: Mock 24h rep4


title: Mock 8h rep3

description: Mock 8h rep3

source_name: mock-exposed NHBE cells, 8h


title: Mock 8h rep4

description: Mock 8h rep4


title: Mock 2h rep1

description: Mock 2h rep1

source_name: mock-exposed NHBE cells, 2h


title: Mock 8h rep2

description: Mock 8h rep2


title: Mock 24h rep1

description: Mock 24h rep1


title: Mock 4h rep2

description: Mock 4h rep2


title: Mock 8h rep1

description: Mock 8h rep1


title: Mock 2h rep2

description: Mock 2h rep2


title: Mock 2h rep4

description: Mock 2h rep4


title: Mock 2h rep3

description: Mock 2h rep3


title: MO-pre-donor1

status: Public on Mar 01 2008

city: Seattle

first: Lynn

last: Graf

state: WA

address: 1100 Fairview Ave. N. D1-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: standard Affymetrix protocol and reagents

scan_protocol: standard Affymetrix protocol and instruments

data_processing: Affymetrix CEL files were imported into GeneSpring 7.3.1 and samples were preprocessed with GC-RMA to obtain the normalized natural hybridization values. The Per gene normalization feature of Genespring, in which each measurement is divided by the median of its measurements in all simples, was also applied.

source_name: CD14+ donor 1, fresh

label_protocol: cRNA was prepared from 2-5 ug total RNA according to Affymetrix protocols using the SuperScriptChoice kit (Invitrogen) and the High Yield RNA transcription labeling kit (Enzo Diagnostics).

growth_protocol: Cells were cultured for 2 days in RPMI1640 medium supplemented with 10% FBS/2mM glutamine at 37ºC in 5% CO2. Conditioned medium from the stromal cell lines was collected from 3 million stromal cells grown for 5 days. It was clarified by centrifugation and diluted 1:1 with fresh supplemented RPMI1640 medium as described above just prior to use.

extract_protocol: Total RNA was isolated with Qiagen RNeasy kits according to manufacturer's protocols.

treatment_protocol: Monocytes (CD14+ cells) were isolated with Tuek4 Ab (Dako M0825) and IgG2a+b magnetic beads (Miltenyi) by AutoMacs. They were cultured with CM from each of the 2 stromal cell lines

value: M, age 28


title: MO-pre-donor2

source_name: CD14+ donor 2, fresh

value: F, age 43


title: Gene Expression of a Parathyroid Tumour

city: St Leonards

first: Roderick

last: Clifton-Bligh

address: Pacific Hwy

institute: Kolling Institute of Medical Research

description: RNA labeling, hybridization to the Affymetrix GeneChip Human Genome U133 plus 2.0 Arrays and scanning was performed by the Clive and Vera Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Sydney, Australia).

hyb_protocol: Hybridization was conducted according to the manuals provided by Affymetrix. Mix the following for each target, scaling up volumes for hybridization to multiple probe arrays. 2. Equilibrate probe array to room temperature immediately before use. 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block. If using the GeneChip IVT Labeling Kit to prepare the target, a final concentration of 10% DMSO needs to be added in the hybridization cocktail for optimal results. Table 2.2.1 Hybridization Cocktail for Single Probe Array* Component 49 Format (Standard) / 64 Format Array 100 Format (Midi) Array 169 Format (Mini) Array / 400 Format (Micro) Array Final Concentration Fragmented cRNA ** 15 µg 10 µg 5 µg 0.05 µg/µL Control Oligonucleotide B2 (3 nM) 5 µL 3.3 µL 1.7 µL 50 pM 20X Eukaryotic Hybridization Controls (bioB, bioC, bioD, cre) 15 µL 10 µL 5 µL 1.5, 5, 25, and 100 pM respectively Herring Sperm DNA (10 mg/mL) 3 µL 2 µL 1 µL 0.1 mg/mL BSA (50 mg/mL) 3 µL 2 µL 1 µL 0.5 mg/mL 2X Hybridization Buffer 150 µL 100 µL 50 µL 1X DMSO*** 30 µL 20 µL 10 µL 10% H2O to final volume of 300 µL to final volume of 200 µL to final volume of 100 µL Final volume 300 µL 200 µL 100 µL *Please refer to specific probe array package insert for information on array format. **Please see Section 2, Chapter 1, for amount of adjusted fragmented cRNA to use when starting from total RNA. *** Note that the addition of DMSO is different from previous recommendations. Follow this protocol for best results on arrays when using the GeneChip IVT Labeling Kit. It is imperative that frozen stocks of 20X GeneChip Eukaryotic Hybridization Controls are heated to 65°C for 5 minutes to completely resuspend the cRNA before aliquotting. It is important to allow the arrays to equilibrate to room temperature completely. Specifically, if the rubber septa are not equilibrated to room temperature, they may be prone to cracking, which can lead to leaks. Meanwhile, wet the array by filling it through one of the septa (see Figure 2.2.1 for location of the probe array septa) with appropriate volume of 1X Hybridization Buffer using a micropipettor and appropriate tips (Table 2.2.2). 5. Incubate the probe array filled with 1X Hybridization Buffer at 45°C for 10 minutes with rotation. 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes. 7. Spin hybridization cocktail(s) at maximum speed in a microcentrifuge for 5 minutes to remove any insoluble material from the hybridization mixture. 8. Remove the buffer solution from the probe array cartridge and fill with appropriate volume (Table 2.2.2) of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube. 9. Place probe array into the Hybridization Oven, set to 45°C. Avoid stress to the motor; load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm. 10. Hybridize for 16 hours. During the latter part of the 16-hour hybridization, proceed to Section 2, Chapter 3 to prepare reagents required immediately after completion of hybridization.

scan_protocol: Scanning and washing was conducted according to the manuals provided by Affymetrix. The Fluidics Station 450 was used to wash and stain the probe arrays. It is operated using GCOS/Microarray Suite. The following steps were taken to set up the Fluidics Station 1. Turn on the Fluidics Station using the toggle switch on the lower left side of the machine. 2. Select Run → Fluidics from the menu bar. ⇒ The Fluidics Station dialog box appears with a drop-down list for selecting the experiment name for each of the fluidics station modules. A second drop-down list is accessed for choosing the Protocol for each of the fluidics station modules. Priming ensures that the lines of the fluidics station are filled with the appropriate buffers and the fluidics station is ready for running fluidics station protocols. Priming should be done: ■ when the fluidics station is first started. ■ when wash solutions are changed. ■ before washing, if a shutdown has been performed. ■ if the LCD window instructs the user to prime. 1. To prime the fluidics station, select Protocol in the Fluidics Station dialog box. 2. Choose Prime_450 for the respective modules in the Protocol drop-down list. 3. Change the intake buffer reservoir A to Non-Stringent Wash Buffer, and intake buffer reservoir B to Stringent Wash Buffer. 4. For MAS, click Run for each module to begin priming. In GCOS, select the All Modules check box, then click Run. After 16 hours of hybridization, remove the hybridization cocktail from the probe array and fill the probe array completely with the appropriate volume of Non-Stringent Wash Buffer (Wash Buffer A), Washing and Staining the Probe Array 1. In the Fluidics Station dialog box on the workstation, select the correct experiment name from the drop-down Experiment list. ⇒ The Probe Array Type appears automatically. 2. In the Protocol drop-down list, select the appropriate antibody amplification protocol to control the washing and staining of the probe array format being used 3. Choose Run in the Fluidics Station dialog box to begin the washing and staining.The instructions in the LCD window on the fluidics station were followed. 4. Insert the appropriate probe array into the designated module of the fluidics station while the cartridge lever is in the down, or eject, position. When finished, verify that the cartridge lever is returned to the up, or engaged, position. 5. Remove any microcentrifuge vial remaining in the sample holder of the fluidics station module(s) being used. 6. If prompted to “Load Vials 1-2-3,” place the three experiment sample vials (the microcentrifuge vials) into the sample holders 1, 2, and 3 on the fluidics station. ■ Place one vial containing 600 µL of streptavidin phycoerythrin (SAPE) solution in sample holder 1. ■ Place one vial containing 600 µL of anti-streptavidin biotinylated antibody solution in sample holder 2. ■ Place one vial containing 600 µL of streptavidin phycoerythrin (SAPE) solution in sample holder 3. ■ Press down on the needle lever to snap needles into position and to start the run. The run begins. The Fluidics Station dialog box at the workstation terminal and the LCD window display the status of the washing and staining as they progress. 7. At the end of the run, or at the appropriate prompt, remove the microcentrifuge vials and replace with three empty microcentrifuge vials. 8. Remove the probe arrays from the fluidics station modules by first pressing down the cartridge lever to the eject position. 9. Check the probe array window for large bubbles or air pockets. ■ If bubbles are present, proceed to Table 2.3.6. ■ If the probe array has no large bubbles, it is ready to scan on the GeneArray® Scanner or the GeneChip® Scanner 3000. Pull up on the cartridge lever to engage washblock and proceed to Probe Array Scan on page 2.3.15. If you do not scan the arrays right away, keep the probe arrays at 4°C and in the dark until ready for scanning. The scanner is also controlled by Affymetrix® Microarray Suite or GCOS. The probe array is scanned after the wash protocols are complete. Make sure the laser is warmed up prior to scanning by turning it on at least 15 minutes before use if you are using the Agilent GeneArray® Scanner, or 10 minutes if you are using the Affymetrix® GeneChip® Scanner 3000. If probe array was stored at 4°C, warm to room temperature before scanning. Refer to the Microarray Suite or GCOS online help and the appropriate scanner user’s manual for more information on scanning.

data_processing: Pre-processing of the data was carried out using the R statistical software (Version 2.0.1) libraries contained within the Bioconductor open software (http://www.bioconductor.org/). Robust Multichip Average (RMA) was used to normalize the data. The AffylmGUI analysis suite (Bioconductor) which uses a moderated t statistic was applied to the normalized data-set using the Benjamini-Hochberg correction and differentially expressed genes were identified using an M-value of < -1 or >1. These boundary values are equivalent to a 0.5 decrease and a 2-fold increase respectively.

source_name: Parathyroid Tumour

label_protocol:
fragmented, and hybridized to GeneChip expression arrays.
reaction. The labeled cRNA is then cleaned up, fragmented, and hybridized to GeneChip

extract_protocol: Parathyroid tumour tissue RNA was isolated by TRIReagent (Sigma-Aldrich, MI) then further purified by lithium chloride as per manufacturer’s instructions.

tag: This sample is a parathyroid tumour that is adjacent to the normal tissue (directly compared)


title: Gene Expression of Normal Parathyroid Tissue

scan_protocol: Scanning and washing was conducted according to the manuals provided by Affymetrix. The Fluidics Station 450 was used to wash and stain the probe arrays. It is operated using GCOS/Microarray Suite. The following steps were taken to set up the Fluidics Station 1. Turn on the Fluidics Station using the toggle switch on the lower left side of the machine. 2. Select Run → Fluidics from the menu bar. ⇒ The Fluidics Station dialog box appears with a drop-down list for selecting the experiment name for each of the fluidics station modules. A second drop-down list is accessed for choosing the Protocol for each of the fluidics station modules. Priming ensures that the lines of the fluidics station are filled with the appropriate buffers and the fluidics station is ready for running fluidics station protocols. Priming should be done: ■ when the fluidics station is first started. ■ when wash solutions are changed. ■ before washing, if a shutdown has been performed. ■ if the LCD window instructs the user to prime. 1. To prime the fluidics station, select Protocol in the Fluidics Station dialog box. 2. Choose Prime_450 for the respective modules in the Protocol drop-down list. 3. Change the intake buffer reservoir A to Non-Stringent Wash Buffer, and intake buffer reservoir B to Stringent Wash Buffer. 4. For MAS, click Run for each module to begin priming. In GCOS, select the All Modules check box, then click Run. After 16 hours of hybridization, remove the hybridization cocktail from the probe array and fill the probe array completely with the appropriate volume of Non-Stringent Wash Buffer (Wash Buffer A), Washing and Staining the Probe Array 1. In the Fluidics Station dialog box on the workstation, select the correct experiment name from the drop-down Experiment list. ⇒ The Probe Array Type appears automatically. 2. In the Protocol drop-down list, select the appropriate antibody amplification protocol to control the washing and staining of the probe array format being used 3. Choose Run in the Fluidics Station dialog box to begin the washing and staining.The instructions in the LCD window on the fluidics station were followed. 4. Insert the appropriate probe array into the designated module of the fluidics station while the cartridge lever is in the down, or eject, position. When finished, verify that the cartridge lever is returned to the up, or engaged, position. 5. Remove any microcentrifuge vial remaining in the sample holder of the fluidics station module(s) being used. 6. If prompted to “Load Vials 1-2-3,” place the three experiment sample vials (the microcentrifuge vials) into the sample holders 1, 2, and 3 on the fluidics station. ■ Place one vial containing 600 µL of streptavidin phycoerythrin (SAPE) solution in sample holder 1. ■ Place one vial containing 600 µL of anti-streptavidin biotinylated antibody solution in sample holder 2. ■ Place one vial containing 600 µL of streptavidin phycoerythrin (SAPE) solution insample holder 3. ■ Press down on the needle lever to snap needles into position and to start the run. The run begins. The Fluidics Station dialog box at the workstation terminal and the LCD window display the status of the washing and staining as they progress. 7. At the end of the run, or at the appropriate prompt, remove the microcentrifuge vials and replace with three empty microcentrifuge vials. 8. Remove the probe arrays from the fluidics station modules by first pressing down the cartridge lever to the eject position. 9. Check the probe array window for large bubbles or air pockets. ■ If bubbles are present, proceed to Table 2.3.6. ■ If the probe array has no large bubbles, it is ready to scan on the GeneArray® Scanner or the GeneChip® Scanner 3000. Pull up on the cartridge lever to engage washblock and proceed to Probe Array Scan on page 2.3.15. If you do not scan the arrays right away, keep the probe arrays at 4°C and in the dark until ready for scanning. The scanner is also controlled by Affymetrix® Microarray Suite or GCOS. The probe array is scanned after the wash protocols are complete. Make sure the laser is warmed up prior to scanning by turning it on at least 15 minutes before use if you are using the Agilent GeneArray® Scanner, or 10 minutes if you are using the Affymetrix® GeneChip® Scanner 3000. If probe array was stored at 4°C, warm to room temperature before scanning. Refer to the Microarray Suite or GCOS online help and the appropriate scanner user’s manual for more information on scanning.

source_name: Normal Parathyroid Tissue

extract_protocol: Parathyroid tissue RNA was isolated by TRIReagent (Sigma-Aldrich, MI) then further purified by lithium chloride as per manufacturer’s instructions.

tag: Normal tissue adjacent to the parathyroid tumour


title: Mock 4h rep3

description: Mock 4h rep3


title: control_32hr_rep2

city: Cincinnati

first: Xiang

last: Zhang

address: Kettering labs PO box 670056, 3223 Eden Ave

department: Environmental Health

institute: University of Cincinnati

description: Immortalized normal prostate epithelial cell line (NPrEC), which showed basal epithelial cell phenotype, was established in our lab (Mobley et al., 2003).

hyb_protocol: Hybridized to arrays at 45°C for 16 hr.

scan_protocol: Arrays were scanned with an Affymetrix scanner.

data_processing: All steps of data preprocessing including background correction, normalization and expression set summaries were performed using the RMA algorithm. Chip quality was assessed with the affyQCReport package of Bioconductor and one chip (Cd_04hr) was removed from analysis due to poor quality.

label: Biotin.

label_protocol: According to Affymetrix protocols.

growth_protocol:
The cells were grown in Defined Keratinocyte-SFM medium (Invitrogen, Carlsbad, CA) with growth promoting supplement. Cell cultures were maintained at 37°C in a humidified incubator with a 5% CO2 atmosphere.
Before cadmium treatment, the cells were synchronized via starvation by maintaining the cells in medium without supplement for 72 hr.

extract_protocol: Total RNA was extracted from NPrEC cells by using TRIzol reagent (Invitrogen) according to the manufacture’s instruction. The quality of RNA was assessed by the absorbance ratio at 260/280 nm and gel electrophoresis before further analysis.

treatment_protocol: After 72 hrs of starvation, the cells were maintained in complete medium without CdCl2 for 32 hrs.

tag: Gender

value: Male; Tissue:Prostate.


title: Mock 4h rep1

description: Mock 4h rep1


title: control_16hr_rep2

treatment_protocol: After 72 hrs of starvation, the cells were maintained in complete medium without CdCl2 for 16 hrs.


title: control_00hr_rep1

treatment_protocol: After 72 hrs of starvation, the cells were briefly exposed to complete medium without CdCl2.


title: control_08hr_rep2

treatment_protocol: After 72 hrs of starvation, the cells were maintained in complete medium without CdCl2 for 8 hrs.


title: control_16hr_rep1


title: control_00hr_rep2


title: control_04hr_rep1

treatment_protocol: After 72 hrs of starvation, the cells were maintained in complete medium without CdCl2 for 4 hrs.


title: control_04hr_rep2


title: cadmium_16hr_rep1

treatment_protocol: Cells were treated with 2.5 uM CdCl2 in the complete medium for 16 hours.


title: X20025

city: Melbourne

first: Prof David

last: Bowtell PhD.

state: VIC

address: Locked Bag 1 A' Beckett St

department: Research Division

institute: PeterMacCallum Cancer Centre

description: Gene expression data from human ovarian carcinoma

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

scan_protocol: GeneChips were scanned using Affymetrix GS300-7G scanner

data_processing: The data were analyzed with Gene Chip Operating Software Version 1.4 using Affymetrix default analysis settings. The CEL files generated was later normalized using the RMA method

source_name: Carcinoma of ovary, fallopian tube or peritonem

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

extract_protocol: Trizol extraction and column chromotogrpahy

treatment_protocol: Frozen tissue stored at -80oC taken after surgery

value: Peritoneum

tag: Type

value: Malignant

tag: Subtype

value: Ser/PapSer

tag: StageCode

value: IIIC


title: control_32hr_rep1


title: control_08hr_rep1


title: cadmium_16hr_rep2


title: cadmium_08hr_rep1

treatment_protocol: Cells were treated with 2.5 uM CdCl2 in the complete medium for 8 hours.


title: X152

value: Ovary


title: X146

value: III


title: Cadmium_00hr_rep2

treatment_protocol: Briefly exposred the cells to 2.5 uM CdCl2.


title: X129


title: X20019

value: IIC


title: Cadmium_00hr_rep1

treatment_protocol: Briefly exposed the cells to 2.5 uM CdCl2.

value: Male; Tissue:prostate.


title: cadmium_04hr_rep1

treatment_protocol: Cells were treated with 2.5 uM CdCl2 in the complete medium for 4 hours.


title: X20027


title: X20031

value: Endo


title: cadmium_08hr_rep2


title: cadmium_32hr_rep1

treatment_protocol: Cells were treated with 2.5 uM CdCl2 in the complete medium for 32 hours.


title: cadmium_32hr_rep2


title: X20032

value: IV


title: X20041


title: X20074

value: Fallopian

value: IIIB


title: X22031


title: X20046

value: IIIA


title: X22029


title: X23053


title: X23043


title: X22047


title: X22046


title: X22013


title: X22012


title: X22020


title: X22058


title: X2219


title: X22037


title: X22057


title: X22048


title: X22023


title: X23026


title: X23070


title: X23074

value: IC


title: X23098


title: X2227


title: X23055


title: X23030


title: X23102


title: X23077


title: X23084


title: X23106


title: X23116


title: X23143


title: X23167


title: X23165


title: X23172


title: X23128


title: X23202


title: X23197


title: X23139


title: X23187


title: X23182


title: X23170


title: X23162


title: X23204

value: IA


title: X261


title: X32013


title: X23210

value: Adeno


title: X23178


title: X23221


title: X23213


title: X32022


title: X32034


title: X23212


title: X26047


title: X32049


title: X27098


title: X27006


title: X32032


title: X32054


title: X32048


title: X32089


title: X32098


title: X34086


title: X32103


title: X34066


title: X32055


title: X34085


title: X34102


title: X34019


title: X34113


title: X34168


title: X34103


title: X3498


title: X34117


title: X34202


title: X34049


title: X34080


title: X34165


title: X34801


title: X34186


title: X34090

value: IB


title: X34125


title: X34207


title: X34172


title: X34111


title: X374


title: X386


title: X379


title: X41264


title: X387


title: X41079


title: X41285

value: Peritoneum


title: X41203

value: Malignant


title: X351

value: Ser/PapSer


title: X41165

value: IIIC


title: X41010

value: Ovary


title: X381


title: X41300


title: X41324


title: X424


title: X41064


title: X41192


title: X44080


title: X41358


title: X41266


title: X44078


title: X427


title: X41170


title: X41310


title: X428


title: X41023


title: X41307


title: X41325


title: X434


title: X440


title: X44087


title: X44186


title: X44285


title: X44189


title: X44163


title: X44110


title: TG_pool

first: Simon

last: Hogan

address: 3333 burnet avenue

department: Allergy and Immunology

institute: Cincinnati Children's Hospital

description: small intestine of a pool of three Wt mice and a pool of 3 IL-9tg mice in a balb/c backround

hyb_protocol: Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.067 mg/mL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer.  Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 mL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 mL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol EukGE-WS2v5_450. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.

scan_protocol: Images were scanned using a GeneChip scanner 3000 [Affymetrix]

data_processing:
Affymetrix murine MOE 430 2.0  gene chips were used.GeneChip CEL  files were subjected to RMA  normalization using  the  GeneSpring GX 7.1.
Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring GX (Agilent technologies Inc. Palo Alto, California) was used in normalization, Clustering and filtering. Individual clusters were then analyzed for functional relatedness of genes within the cluster using David 2.0 (http://david.abcc.ncifcrf.gov/summary.jsp).

source_name: small intestine from IL-9 transgenic mice

label_protocol: 10ug of total RNA from 1 pool of 3 wild type [WT] mice and 1 pool of 3 Il-9 Transgenic mice were amplified and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase

extract_protocol:
trizol (invitrogen)
Quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].

tag: small intestine, IL-9 transgenic mice


title: X44090


title: X44102


title: Distal and Proximal Large Intestine, 8week old Wild-type mouse 2

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

institute: Queensland Facility for Advanced Bioinformatics

description: C57Bl/6 strain used as the wild-type for comparative analysis.

hyb_protocol: 10ug of fragmented biotin labelled cRNA was hybridised to a Mouse Genome 430 2.0 Array GeneChip, according to manufacturer’s instructions. GeneChip was incubated for 16hrs at 45oC in a rotating hybridisation oven at 60rpm. GeneChip was washed using Affymetrix washing script EukGE-WS2v5_450 on a Affymetrix Fluidics Station 450

scan_protocol: GeneChip was scanned on a Affymetrix GeneSchip Scanner 3000.

data_processing: The data was extracted from the CEL files using Affymetrix GeneChip Operating Software (1.4) using Affymetrix default analysis settings. Tabulated data (CHP) was generated with global scaing trimmed mean target intensity of 500.

source_name: Distal and Proximal Large Intestine, 8week old mouse

label_protocol: cRNA was prepared using the Affymetrix One-Cycle Labelling Kit, using 2ug total RNA as starting material.

extract_protocol: Large Intestine was removed from the mouse, cut longitudinally and rinsed in PBS prior to homogenisation. Tissue was homogenised in 1ml Trizol reagent (Invitrogen) and processed according to manufacturer’s instructions. Precipitated RNA was resuspended in 100ul RNase free water and cleaned using RNeasy Mini columns (Qiagen). RNA was eluted in 40ul elution buffer and the quality confirmed using a Bio-Analyser 2100 (Agilent), only samples with a RNA Integrity score >8 were labelled.

tag: Strain

value: Male

tag: Age

value: 8 weeks

tag: Tissue

value: Large Intestine (Distal and Proximal)


title: Distal and Proximal Large Intestine, 8week old Winnie mouse 2

description: Winnie mouse is a C57BL/6 strain from a N-ethyl-N-nitrosourea (ENU)-treated C57BL/6 founder line. It carries a unique missense mutation (G9492A, Accession AJ511872) resulting in a cysteine to tyrosine substitution in the D3-domain at the N-terminus of Mucin2 (Muc2).

tag: C57BL/6 Winnie G9492A


title: WT_pool

state: OH

source_name: small intestine from WT mice

tag: small intestine, WT mice


title: Distal and Proximal Large Intestine, 8week old Wild-type mouse 1


title: Distal and Proximal Large Intestine, 8week old Winnie mouse 1


title: X44192

value: Endo


title: Distal and Proximal Large Intestine, 8week old Eeyore mouse 2

description: Eeyore mouse is a mixed strain (C57BL/6, NOD-SCID) from a N-ethyl-N-nitrosourea (ENU)-treated C57BL/6 founder line. It carries a unique missense mutation (T2996C, Accession AJ511873) resulting in a serine to proline substitution in the C-terminal D4-domain of Mucin 2 (Muc2).

value: C57BL/6, NOD-SCID

tag: C57BL/6, NOD-SCID Eeyore T2996C


title: X44234


title: X44219


title: Distal and Proximal Large Intestine, 8week old Winnie mouse 3


title: X44242


title: X44196


title: X44288


title: X44286

value: IV


title: Distal and Proximal Large Intestine, 8week old Eeyore mouse 1

scan_protocol: GeneChip was scanned on a Affymetrix GeneSchip Scanner 3000


title: Distal and Proximal Large Intestine, 8week old Wild-type mouse 3


title: X34078


title: Distal and Proximal Large Intestine, 8week old Eeyore mouse 3


title: X44303


title: X44306


title: ken_103_medullo

city: Memphis

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: Not applicable

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

label: Standard Affymetrix

source_name: mouse medulloblastoma

label_protocol: Standard Affymetrix

extract_protocol: Roche Trizol

tag: mixed background C57 and 129


title: hmk_021_medulloblastoma

description: Standard Affymetrix

data_processing: Standard Affymetrix

tag: Patch1 heterozygote C57BL6 Cd1 mixed background


title: X44341


title: X44417


title: hmk_022_medullo

description: not applicable

extract_protocol: Standard Affymetrix

tag: mixed background Patched1 heterozygote


title: X44349


title: X44428


title: X457


title: X44366


title: X445


title: X44377


title: ken_111_medullo

description: Not applicable


title: hmk_109_P5_cerebellum

description: Not applicable

source_name: mouse brain

tag: C57BL6, wild type