title: MSC #5, technical rep-amplification- rep2


title: MSC #5, technical rep-amplification- rep1

status: Public on Jun 06 2008

type: RNA

city: Kawasaki

first: Shihori

last: Tanabe

state: Kanagawa

address: 3-25-26, Tonomachi, Kawasaki-ku

department: Division of Risk Assessment

country: Japan

institute: National Institute of Health Sciences

description: Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), passage number 5

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

scan_protocol: GeneChip array was scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed using GCOS Affymetrix standard analysis settings and mask-file (Affymetrix, hgu133_plus_2norm) scaling as normalization methods. The trimmed mean target intensity of each array was arbitrarily set to 10000.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: mesenchymal stem cells, 5th passage

label_protocol: Biotinylated cRNA were prepared according to Two-cycle or One-cycle Affymetrix protocol from 100 ng (Two-cycle) or 1ug (One-cycle) total RNA (Expression Analysis Technical Manual, 701024 Rev.3, Affymetrix).

growth_protocol: Mesenchymal stem cells were cultured according to manufacturer's protocol (Lonza).

extract_protocol: Total RNA extraction was performed using silica-gel-based membrane according to manufacturer's protocol (QIAGEN, RNeasy)

treatment_protocol: Cells were lysed in 600 ul of buffer RLT (QIAGEN).

tag: two-cycle

tag: bone marrow mesenchymal stem cells


title: MSC #9, technical rep-label-rep5

description: Gene expression data from mesenchymal stem cells cultured in MSCGM (mesenchymal stem cell growth medium), passage number 9

source_name: mesenchymal stem cells, 9th passage

tag: started from 2nd cycle (step6) in two-cycle protocol


title: gene expression of wild type oocyte, replicate 1

status: Public on Jun 05 2008

city: Philadelphia

first: Hua

last: Pan

state: PA

address: 415 S University Avenue

department: Department of Biology

country: USA

institute: University of Pennsylvania

description: Gene expression data from CTCF depleted GV oocyte

hyb_protocol: cRNA was fragmented following the Affymetrix protocol,  and hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 arrays

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

organism: Mus musculus

source_name: wild type oocyte

label_protocol: total RNA was processed to produce biotinylated cRNA targets using Affy Small Sample Target Labeling Assay Version II.

extract_protocol: Total RNA was extracted and purified using an Picopure kit (Arcturus).

tag: Wild type fully-grown GV oocyte from transgenic mice


title: gene expression of wild type oocyte, replicate 2


title: gene expression of CTCF-depleted oocyte, replicate 5

source_name: CTCF-depleted oocyte

tag: CTCF-depleted fully-grown GV oocyte from transgenic mice


title: gene expression of wild type oocyte, replicate 5


title: Memory Tx B cell (EK)_2nd generation screen

city: New Haven

first: Mary

middle: M.

last: Tomayko

state: CT

department: Dermatology

institute: Yale University

description: Memory NP-specific splenic B cells generated in an adoptive transfer system

hyb_protocol: Standard Affymetrix protocol (www.affymetrix.com); chips were stained with streptavidin-PE.

scan_protocol: Standard Affymetrix protocol (www.affymetrix.com).

data_processing: Data were analyzed with GeneSpring GX software (Agilent Technologies). GCRMA normalization was performed.

source_name: Donor mVh186.2 Tg splenocytes adoptively transferred into AM14/Vk8R transgenic recipients

label_protocol: Biotinylated cRNA was prepared with the MessageAmp aRNA kit (Ambion) according to the manufacturer's instructions from 1-2 ug total RNA .

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit with on-column DNase digestion (Qiagen Inc., Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Single cell suspensions of RBC-depleted splenocytes were stained for flow cytometric analysis and sorted on a FACSAria (BD Immunocytometry Systems). Live/dead discrimination was accomplished based on forward/side scatter properties and ethidium monoazide or propidium iodide exclusion. Cells were kept at 4oC in buffer containing 0.05% NaAzide throughout the isolation procedure to minimize alterations in gene expression.

tag: 12-weeks post I.p immunization with NP-CGG in alum

tag: NIP-binding B220pos B lymphocyte

tag: female Balb/c splenic B cell


title: MEF.WT.I

city: Paris

first: Yu

last: Wei

address: 28, rue Dr Roux

department: Virologie

country: France

institute: Institut Pasteur

description: This sample is part of three biological replicates of WT genotype

hyb_protocol: GeneChip® Fluidics Stations, EukGE-WS2v5

scan_protocol: GCOS software (Affymetrix)

data_processing: Raw data were processed using the RMA method.  Values are in Log base 2.

source_name: mouse embryonic fibroblasts derived from WT mice, I

label_protocol: GeneChip Expression 3'Amplification One-Cycle Target Labeling (Affymetrix)

extract_protocol: RNAeasy kit (Qiagen)

tag: embryons of mice at 14.5 days.


title: Memory Tx B cell (I)_2nd generation screen


title: gene expression of CTCF-depleted oocyte, replicate 4


title: gene expression of CTCF-depleted oocyte, replicate 2


title: gene expression of CTCF-depleted oocyte, replicate 1


title: MEF.FHL2mutJ

description: This sample is part of three biological replicates of FHL-/- genotype

source_name: mouse embryonic fibroblasts derived from FHL2-/- mice, FHL2mutJ


title: gene expression of wild type oocyte, replicate 4


title: Memory B cell (E)_1st generation screen

description: Memory NP-specific splenic B cells

data_processing: Data were analyzed with GeneSpring GX software (Agilent Technologies). MAS 4.0 normalization was performed. A scaling factor of 1500 was used.

source_name: mVh186.2 transgenic splenic B lymphocyte

label_protocol: Biotinylated cRNA was prepared with the Affymetrix protocol  (www.affymetrix.com) with EnzoBio reagents (www.enzo.com) starting with 1-4 ug total RNA .

treatment_protocol: Single cell suspensions of RBC-depleted splenocytes were stained for flow cytometric analysis and sorted on a FACSVantage SE (BD Immunocytometry Systems). Live/dead discrimination was accomplished based on forward/side scatter properties and ethidium monoazide or propidium iodide exclusion. Cells were kept at 4oC in buffer containing 0.05% NaAzide throughout the isolation procedure to minimize alterations in gene expression.

tag: >12-weeks post secondary i.p immunization with NP-CGG in alum

tag: male and female Balb/c splenic B cell


title: MEF.FHL2mutE

source_name: mouse embryonic fibroblasts derived from FHL2-/- mice, FHL2mutE


title: MEF.FHL2mutH

source_name: mouse embryonic fibroblasts derived from FHL2-/- mice, FHL2mutH


title: Memory B cell (D)_1st generation screen

description: Memory NP-specific splenic B cells

tag: male Balb/c splenic B cell


title: Memory B cell (G)_1st generation screen

description: Memory NP-specific splenic B cells


title: Naive AA4.1- B cell (B)_2nd generation screen

description: Naïve NP-specific  AA4.1neg splenic B cells

source_name: mVh186.2 transgenic Jk KO splenic B lymphocyte

tag: Unimmunized

tag: NIP-binding B220pos AA4.1neg B lymphocyte


title: Naive AA4.1- B cell (D)_2nd generation screen


title: Memory Tx B cell (FG)_2nd generation screen


title: MEF.WT.E

source_name: mouse embryonic fibroblasts derived from WT mice, E


title: gene expression of CTCF-depleted oocyte, replicate 3


title: MEF.WT.F

source_name: mouse embryonic fibroblasts derived from WT mice, F


title: Memory B cell (F)_1st generation screen

description: Memory NP-specific splenic B cells


title: Naive AA4.1- B cell (A)_2nd generation screen


title: Naive AA4.1- B cell (C)_2nd generation screen


title: Memory Tx B cell (HJ)_2nd generation screen


title: Naive  B cell (B)_1st generation screen

description: Naïve NP-specific   splenic B cells

tag: NIP-binding B220pos  B lymphocyte


title: Naive  B cell (C)_1st generation screen

description: Naïve NP-specific   splenic B cells


title: gene expression of wild type oocyte, replicate 3


title: Naive  B cell (A)_1st generation screen

description: Naïve NP-specific   splenic B cells


title: Gastric biopsy HP+ ER-, sample8

status: Public on Jun 04 2008

city: Budapest

first: Norbert

last: Solymosi

state: Budapest

address: István u. 2.

country: Hungary

institute: ATE

description: Gene expression data from Helicobacter positive human non-erosive gastric biopsy sample

data_processing: The data were preprocessed by the function mas5 from the Bioconductor affy package. (mas5(sample, normalize = TRUE))

source_name: human gastric biopsy

tag: Age

tag: Gender

value: male

tag: Tissue

value: HP+ erosive gastritis, non-erosive site


title: Gastric biopsy HP+ ER-, sample3

value: female


title: Gastric biopsy HP- ER-, sample1

description: Gene expression data from Helicobacter negative human non-erosive gastric biopsy sample

value: HP- erosive gastritis, non-erosive site


title: Gastric biopsy HP- ER-, sample5


title: Gastric biopsy HP+ ER-, sample2


title: Gastric biopsy HP+ ER+, sample5

description: Gene expression data from Helicobacter positive human erosive gastric biopsy sample

value: HP+ erosive gastritis, site of erosion


title: Gastric biopsy HP+ ER-, sample4


title: Gastric biopsy HP+ ER-, sample6


title: Gastric biopsy HP+ ER-, sample1


title: Gastric biopsy HP+ ER+, sample7


title: Gastric biopsy HP- ER-, sample6


title: Gastric biopsy HP+ ER-, sample7


title: Gastric biopsy HP- ER-, sample3


title: Gastric biopsy HP- ER+, sample7

description: Gene expression data from Helicobacter negative human erosive gastric biopsy sample

value: HP- erosive gastritis, site of erosion


title: Gastric biopsy HP- ER-, sample4


title: Gastric biopsy HP+ ER-, sample5


title: Gastric biopsy HP+ ER+, sample3


title: Gastric biopsy HP+ ER+, sample6


title: Gastric biopsy HP+ ER+, sample2


title: Gastric biopsy HP+ ER+, sample4


title: Gastric biopsy HP- ER+, sample5


title: Gastric biopsy HP- ER+, sample4


title: Gastric biopsy HP+ ER+, sample8


title: Gastric biopsy HP- ER+, sample6


title: Gastric biopsy HP+ ER+, sample1


title: Gastric biopsy HP- ER+, sample8


title: Arabidopsis plant (Col-0), 4h_response to OPDA_rep2

status: Public on Jun 02 2008

city: Wuerzburg

first: Susanne

last: Berger

address: Julius-von-Sachs-Platz 2

department: Pharmaceutical Biology

country: Germany

institute: Julius-von-Sachs-Institute

description: Three independent replicates were done for each treatment.

hyb_protocol: 15 µg of labeled and fragmented cRNA was hybridized to Arabidopsis ATH1 Gene Chip® arrays (Affymetrix). After hybridization the arrays were washed and stained in a Fluidics Station 450 (Affymetrix) with the recommended washing procedure. Biotinylated cRNA bound to target molecules was detected with streptavidin-coupled phycoerithrin, biotinylated anti-streptavidin IgG antibodies and again streptavidin-coupled phycoerithrin according to the protocol.

scan_protocol: Arrays were scanned using the GCS3000 Gene Chip scanner (Affymetrix) and GCOS 1.3 software. Scanned images were subjected to visual inspection to control for hybridization artifacts and proper grid alignment and analyzed with Microarray Suite 5.0 (Affymetrix) to generate report files for quality control.

data_processing: For statistical data analysis the CEL-files were imported into Genespring 7.1 (Agilent Technologies, Santa Clara, CA) using Genesprings implementation of GC-RMA for normalization and probe summarization (Wu et al., 2003). Additionally, genes were median centered by dividing all signal values for a gene by the median of all signals for that gene. Transcripts with a high variance in replicate measurements were removed. From the remaining set genes that show an at least two-fold increase or decrease in average expression were analyzed in a Welsh’s t-test for significant differences and corrected for multiple testing according to Benjamini and Hochberg (1995). Functions of differentially expressed transcripts were annotated using the NetAFFX analysis center.

organism: Arabidopsis thaliana

source_name: plant material (Col-0), 4h treatment with 75 µM OPDA, second replicate

label_protocol: 1 µg of total RNA was linearly amplified and biotinylated using the One-Cycle Target Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions. Labelling and hybridization were conducted by the microarray facility of the Universitaetsklinikum Tuebingen, Germany.

extract_protocol: For microarray analysis total RNA was extracted using the RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol.

tag: 10 days old Arabidopsis plants (ecotype Col-0) were grown in Murashige and Skoog liquid medium; 4h treatment with 75 µM OPDA, second replicate


title: Control male mouse liver

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universidad de Oviedo

description: Control liver sample from 3-month-old male mouse

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix MAS 5.0

source_name: Liver sample from control male mouse

label_protocol: Double-stranded cDNA was synthesized using the SuperScriptTM cDNA synthesis kit (Invitrogen). In vitro transcription was carried out with the Bioarray high yield RNA transcript labelling kit (Enzo Diagnostics).

extract_protocol: Qiagen RNeasy kit

tag: Strain

tag: Sex

value: Male

value: 3 months

value: liver


title: Arabidopsis plant (tga2-5-6), 4h_response to OPDA_rep3

source_name: plant material (tga2-5-6), 4h treatment with 75 µM OPDA, third replictate

tag: 10 days old Arabidopsis plants (tga2-5-6) were grown in Murashige and Skoog liquid medium; 4h treatment with 75 µM OPDA, third replicate


title: Arabidopsis plant (tga2-5-6), 4h_response to OPDA_rep2

source_name: plant material (tga2-5-6), 4h treatment with 75 µM OPDA, second replictate

tag: 10 days old Arabidopsis plants (tga2-5-6) were grown in Murashige and Skoog liquid medium; 4h treatment with 75 µM OPDA, second replicate


title: Arabidopsis plant (tga2-5-6), 4h_control_rep3

source_name: plant material (tga2-5-6), 4h treatment with 0.5% methanol in water, third replicate

tag: 10 days old Arabidopsis plants (tga2-5-6) were grown in Murashige and Skoog liquid medium; 4h treatment with 0.5% methanol in water (Control), third replicate


title: Arabidopsis plant (tga2-5-6), 4h_response to phytoprostane A1_rep1

source_name: plant material (tga2-5-6), 4h treatment with 75 µM phytoprostane A1, first replictate

tag: 10 days old Arabidopsis plants (tga2-5-6) were grown in Murashige and Skoog liquid medium; 4h treatment with 75 µM phytoprostane A1, first replicate


title: Arabidopsis plant (tga2-5-6), 4h_response to phytoprostane A1_rep2

source_name: plant material (tga2-5-6), 4h treatment with 75 µM phytoprostane A1, second replictate

tag: 10 days old Arabidopsis plants (tga2-5-6) were grown in Murashige and Skoog liquid medium; 4h treatment with 75 µM phytoprostane A1, second replicate


title: Gastric biopsy HP- ER+, sample1


title: MMH-D3 cell line rep2

status: Public on Jun 03 2008

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: Synthesis of biotinylated cRNA targets, arrays hybridization (Mouse430_2 GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 5μg of total RNA.

hyb_protocol: The fragmented cRNA was then hybridized to an identical lot of Affymetrix Mouse430_2 GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v5 protocol, using antibody-mediated signal amplification.

scan_protocol: GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.

data_processing: Scaling to TGT value=200. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.

label: biotin-labeled

source_name: MMH-D3 line

label_protocol: One-cycle target labeling assays were performed, using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

growth_protocol: Primary cultures were performed in accord to previously described protocol (Amicone L, Spagnoli FM, Spath G, Giordano S, Tommasini C, Bernardini S, De Luca V, et al. Transgenic expression in the liver of truncated Met blocks apoptosis and permits immortalization of hepatocytes. Embo J 1997;16:495-503). Briefly, livers from 14 dpc foetuses and 6 days newborn mice were dissected, mechanically dissociated and plated at high density on collagen-I (Transduction Laboratories, Lexington, UK) coated dishes (Falcon-BD, Franklin Lakes, NJ) in RPMI-1640 (Gibco, Carlsbad, CA), supplemented with 10% Foetal Bovin Serum (FBS) (Gibco), 50ng/ml Epidermal-Growth-Factor, 30ng/ml Insulin-like-Growth-Factor-II (PeproTech Inc, Rocky Hill, NJ), 10µg/ml insulin (Roche, Mannheim, Germany), 2mmol/L L-glutamine, 100u/mL penicillin and 100µg/mL streptomycin (Gibco). The cultures were washed and maintained without transfer for several weeks.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer.

tag: Hepatocytic differentiated cell line MMH-D3 characterised by L. Amicone et al. (Amicone L, Spagnoli FM, Spath G, Giordano S, Tommasini C, Bernardini S, De Luca V, et al. Transgenic expression in the liver of truncated Met blocks apoptosis and permits immortalization of hepatocytes. Embo J 1997;16:495-503).


title: Arabidopsis plant (tga2-5-6), 4h_control_rep1

source_name: plant material (tga2-5-6), 4h treatment with 0.5% methanol in water, first replicate

tag: 10 days old Arabidopsis plants (tga2-5-6) were grown in Murashige and Skoog liquid medium; 4h treatment with 0.5% methanol in water (Control), first replicate


title: Gastric biopsy HP- ER+, sample3


title: Arabidopsis plant (Col-0), 4h_control_rep3

source_name: plant material (Col-0), 4h treatment with 0.5% methanol in water, third replicate

tag: 10 days old Arabidopsis plants (ecotype Col-0) were grown in Murashige and Skoog liquid medium; 4h treatment with 0.5% methanol in water (Control); third replicate


title: Arabidopsis plant (Col-0), 4h_control_rep1

description: Three independent replictates were done for each treatment

source_name: plant material (Col-0), 4h treatment with 0.5% methanol in water, first replicate

tag: 10 days old Arabidopsis plants (ecotype Col-0) were grown in Murashige an Skoog liquid medium; 4h treatment with 0.5% methanol in water (Control); first replicate


title: MMH-D3 cell line rep1


title: WTE14/1 RLSC cell line

source_name: WT E14/3 resident liver stem cells (RLSCs)

growth_protocol:
Primary cultures were performed in accord to previously described protocol (Amicone L, Spagnoli FM, Spath G, Giordano S, Tommasini C, Bernardini S, De Luca V, et al. Transgenic expression in the liver of truncated Met blocks apoptosis and permits immortalization of hepatocytes. Embo J 1997;16:495-503). Briefly, livers from 14 dpc foetuses and 6 days newborn mice were dissected, mechanically dissociated and plated at high density on collagen-I (Transduction Laboratories, Lexington, UK) coated dishes (Falcon-BD, Franklin Lakes, NJ) in RPMI-1640 (Gibco, Carlsbad, CA), supplemented with 10% Foetal Bovin Serum (FBS) (Gibco), 50ng/ml Epidermal-Growth-Factor, 30ng/ml Insulin-like-Growth-Factor-II (PeproTech Inc, Rocky Hill, NJ), 10µg/ml insulin (Roche, Mannheim, Germany), 2mmol/L L-glutamine, 100u/mL penicillin and 100µg/mL streptomycin (Gibco). The cultures were washed and maintained without transfer for several weeks.
Cell colonies with palmate morphology were expanded slowly in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) containing 10%FBS (basal medium) on collagen-I coated dishes of increasing size, and frozen after ~50 cell generations. Passages are calculated from initial thawing.

tag: to isolate rlscs we used the same culture conditions previously described for the establishment of mmh lines (amicone l, spagnoli fm, spath g, giordano s, tommasini c, bernardini s, de luca v, et al. transgenic expression in the liver of truncated met blocks apoptosis and permits immortalization of hepatocytes. embo j 1997;16

value: 495-503), selecting for “palmate” morphology. Primary cultures were prepared from livers of embryo 14 dpc (WT E14).


title: Arabidopsis plant (Col-0), 4h_response to OPDA_rep3

source_name: plant material (Col-0), 4h treatment with 75 µM OPDA, third replicate

tag: 10 days old Arabidopsis plants (ecotype Col-0) were grown in Murashige and Skoog liquid medium; 4h treatment with 75 µM OPDA, third replicate


title: Arabidopsis plant (Col-0), 4h_response to phytoprostane A1_rep1

source_name: plant material (Col-0), 4h treatment with 75 µM phytoprostane A1, first replicate

tag: 10 days old Arabidopsis plants (ecotype Col-0) were grown in Murashige and Skoog liquid medium; 4h treatment with 75 µM phytoprostane A1, first replicate


title: Arabidopsis plant (Col-0), 4h_response to OPDA_rep1

source_name: plant material (Col-0), 4h treatment with 75 µM OPDA, first replicate

tag: 10 days old Arabidopsis plants (ecotype Col-0) were grown in Murashige and Skoog liquid medium; 4h treatment with 75 µM OPDA, first replicate


title: Arabidopsis plant (Col-0), 4h_response to phytoprostane A1_rep3

source_name: plant material (Col-0), 4h treatment with 75 µM phytoprostane A1, third replicate

tag: 10 days old Arabidopsis plants (ecotype Col-0) were grown in Murashige and Skoog liquid medium; 4h treatment with 75 µM phytoprostane A1, third replicate


title: Arabidopsis plant (Col-0), 4h_response to phytoprostane A1_rep2

source_name: plant material (Col-0), 4h treatment with 75 µM phytoprostane A1, second replicate

tag: 10 days old Arabidopsis plants (ecotype Col-0) were grown in Murashige and Skoog liquid medium; 4h treatment with 75 µM phytoprostane A1, second replicate


title: MetE14/3 RLSC cell line

source_name: resident liver stem cells (RLSCs)

value: 495-503), selecting for “palmate” morphology. Primary cultures were prepared from livers of cyto-Met transgenic embryo 14 dpc (MetE14). This cell line originated from clone B2.


title: Arabidopsis plant (tga2-5-6), 4h_response to OPDA_rep1

source_name: plant material (tga2-5-6), 4h treatment with 75 µM OPDA, first replictate

tag: 10 days old Arabidopsis plants (tga2-5-6) were grown in Murashige and Skoog liquid medium; 4h treatment with 75 µM OPDA, first replicate


title: Arabidopsis plant (Col-0), 4h_control_rep2

source_name: plant material (Col-0), 4h treatment with 0.5% methanol in water, second replicate

tag: 10 days old Arabidopsis plants (ecotype Col-0) was grown in Murashige and Skoog liquid medium; 4h treatment with 0.5% methanol in water (Control); second replicate


title: Arabidopsis plant (tga2-5-6), 4h_response to phytoprostane A1_rep3

source_name: plant material (tga2-5-6), 4h treatment with 75 µM phytoprostane A1, third replictate

tag: 10 days old Arabidopsis plants (tga2-5-6) were grown in Murashige and Skoog liquid medium; 4h treatment with 75 µM phytoprostane A1, third replicate


title: Arabidopsis plant (tga2-5-6), 4h_control_rep2

source_name: plant material (tga2-5-6), 4h treatment with 0.5% methanol in water, second replicate

tag: 10 days old Arabidopsis plants (tga2-5-6) were grown in Murashige and Skoog liquid medium; 4h treatment with 0.5% methanol in water (Control), second replicate


title: Tmprss6 ko male mouse liver

description: Liver sample from a Tmprss6-deficient 3-month-old male mouse

source_name: Liver sample from Tmprss6-deficient male mouse

tag: Strain

tag: Sex

tag: Age

tag: Tissue

tag: Genotype


title: Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2

source_name: cell culture, 4 h treatment with 75µM phytoprostane A1, second replicate

tag: mixotrophic cell culture, 4 h treatment with 75 µM phytoprostane A1


title: Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3

source_name: cell culture, 4 h treatment with 75µM phytoprostane A1, thtird replicate


title: R26Pax3/Pax3 E14.5 palatal shelves 7

status: Public on Jun 01 2008

first: Jonathan

middle: A.

last: Epstein

address: 421 Curie Blvd

department: Cell and Developmental Biology

description: Gene expression data during developmental stage of palatal shelves at E14.5

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.

label: Biotin

source_name: Mouse palatal shelf tissue at E14.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

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

value: C57BL/6 X SV129, Age:Embryonic Day 14.5, Tissue:Palatal Shelves


title: Arabidopsis cell culture, 4 h_control_rep3

source_name: cell culture, 4 h treatment with 0.5% methanol in water (control), third replicate

tag: mixotrophic cell culture, 4 h treatment with 0.5% methanol in water, control


title: R26Pax3/Pax3 E14.5 palatal shelves 3


title: wild-type normoxic pooled male whole lung with mixed strain

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

description: Whole lung homogenate from a pool of three male mice with mixed strain, wild-type for 5HTT, 8 weeks old when sacrificed.

hyb_protocol: following Affymetrix GeneChip Expression Analysis Manual

data_processing: Affymetrix chp and cel files

source_name: Whole lung homogenate

extract_protocol: heparin was injected into the jugular 5 minutes before sacrifice; right lung was flushed with PBS immediately after sacrifice,removed, and immediately converted to RNA using Qiagen rnEasy columns


title: Arabidopsis cell culture, 4 h_control_rep1

source_name: cell culture, 4 h treatment with 0.5% methanol in water (control), first replicate

tag: mixotrophic cell culture, 4 h treatment with 0.5 % methanol in water, control


title: 5HTT(+/-) normoxic pooled female whole lung with mixed strain

description: Whole lung homogenate from a pool of three female mice with mixed strain, 5HTT(+/-), 8 weeks old when sacrificed.

scan_protocol: following Affymetrix GeneChip Expression Analysis Manual


title: 5HTT(-/-) normoxic pooled female whole lung with mixed strain

description: Whole lung homogenate from a pool of three female mice with mixed strain, 5HTT(-/-), 8 weeks old when sacrificed.

label_protocol: following Affymetrix GeneChip Expression Analysis Manual


title: Pax3 WT E14.5 palatal shelves 2

source_name: Mouse wt palatal shelf tissue at E14.5


title: wild-type normoxic pooled female whole lung with mixed strain

description: Whole lung homogenate from a pool of three female mice with mixed strain, wild-type for 5HTT, 8 weeks old when sacrificed.


title: Gastric biopsy HP- ER-, sample2

source_name: human gastric biopsy

tag: Gender


title: Gastric biopsy HP- ER-, sample7


title: Arabidopsis cell culture, 4 h_control_rep2

source_name: cell culture, 4 h treatment with 0.5 % methanol in water (control), second replicate


title: Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep1

source_name: cell culture, 4 h treatment with 75µM phytoprostane A1, first replicate


title: Pax3 WT E14.5 palatal shelves 8


title: R26Pax3/Pax3 E14.5 palatal shelves 4


title: Pax3 WT E14.5 palatal shelves 6


title: 5HTT(-/-) normoxic pooled male whole lung with mixed strain

description: Whole lung homogenate from a pool of three male mice with mixed strain, 5HTT(-/-), 8 weeks old when sacrificed.


title: Gastric biopsy HP- ER+, sample2


title: 5HTT(+/-) normoxic pooled male whole lung with mixed strain

description: Whole lung homogenate from a pool of three male mice with mixed strain, 5HTT(+/-), 8 weeks old when sacrificed.


title: R26Pax3/Pax3 E14.5 palatal shelves 1


title: Liver 2

city: Chicago

first: John

last: Marioni

state: IL

address: 920 East 58th Street

department: Human Genetics

institute: University of Chicago

description: Gene expression data from liver mRNA sample

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: RMA

label: Affymetrix protocol

source_name: Liver mRNA

label_protocol: Affymetrix protocol

extract_protocol: trizol

tag: human male


title: Liver 1


title: Liver 3


title: SM22-BMPR2-R899X with 9 weeks doxycycline and normal RVSP - 4445

description: Whole lung homogenate from female FVB/N mouse heterozygous for both SM22-rtTA  and TetO7-BMPR2-R899X transgenes, fed doxycycline from age 4 weeks for 9 weeks, sacrificed at age 13 weeks. Mouse had near normal right ventricular systolic pressure (RVSP) at time of sacrifice.

data_processing: Array: Affymetrix Mouse 430 2.0 Array, Algorithm:  Mas 5.0


title: SM22-BMPR2-R899X with 9 weeks doxycycline and high RVSP - 4444

description: Whole lung homogenate from female FVB/N mouse heterozygous for both SM22-rtTA and TetO7-BMPR2-R899X transgenes, fed doxycycline from age 4 weeks for 9 weeks, sacrificed at age 13 weeks. Mouse had substantially elevated right ventricular systolic pressure (RVSP) at time of sacrifice


title: Gastric biopsy HP- ER-, sample8

description: Gene expression data from Helicobacter negative human non-erosive gastric biopsy sample


title: Pax3 WT E14.5 palatal shelves 11


title: SM22-BMPR2-R899X with 9 weeks doxycycline and high RVSP - 4453

tag: Whole lung homogenate from female FVB/N mouse heterozygous for both SM22-rtTA and TetO7-BMPR2-R899X transgenes, fed doxycycline from age 4 weeks for 9 weeks, sacrificed at age 13 weeks. Mouse had substantially elevated right ventricular systolic pressure (RVSP) at time of sacrifice


title: Kidney 3

description: Gene expression data from kidney mRNA sample

source_name: Kidney mRNA


title: Kidney 2


title: Kidney 1


title: Control SM22-rtTA +9 weeks dox - mouse 4443

description: Whole lung homogenate from FVB/N mice with SM22-rtTA transgene (control) fed doxycycline from age 4 weeks for 9 weeks, sacrificed at age 13 weeks.


title: high grade serous carcinoma_patient 11

status: Public on May 31 2008

city: Toronto

first: Patricia

middle: A

last: Shaw

state: Ontario

address: 200 Elizabeth St

department: Department of Pathology

country: Canada

institute: University Health Network

description: Gene expression profile of high grade serous carcinoma of ovary

hyb_protocol: Biotin-labeled cDNA was hybridized to Affymetrix GeneChip U133A Plus 2.0 arrays according to manufacturer's instructions.

scan_protocol: Slides were scanned using the Affymetrix 7G scanner, and CEL files generated using the GeneChip Operating System (GCOS)

data_processing: All CEL files were imported into ArrayAssist and the Robust Multi-Array Averge (RMA) algorithm was applied.

source_name: Laser-capture microdissected high grade serous carcinoma

label_protocol: Reverse-transcription, linear amplification and biotin labeling was performed using the NuGEN Biotin Ovation kit (from 10ng of input total RNA).

extract_protocol: Laser capture microdissection was used to isolate epithelial cells from snap-frozen surgical specimens. Total RNA was then isolated using the Stratagene Absolutely RNA MicroPrep kit.

tag: Cycle

tag: BRCA1/2 mutation

tag: Family History

value: Yes


title: high grade serous carcinoma_patient 6

description: Gene expression profile of high grade serous carcinoma of fallopian tube


title: SM22-BMPR2-R899X with 9 weeks doxycycline and normal RVSP - 4518

tag: Whole lung homogenate from female FVB/N mouse heterozygous for both SM22-rtTA  and TetO7-BMPR2-R899X transgenes, fed doxycycline from age 4 weeks for 9 weeks, sacrificed at age 13 weeks. Mouse had near normal right ventricular systolic pressure (RVSP) at time of sacrifice.


title: high grade serous carcinoma_patient 3_sample 1

value: Unknown

value: No


title: high grade serous carcinoma_patient 9

value: BRCA1 917delTT


title: high grade serous carcinoma_patient 3_sample 2


title: non-malignant FTEb_patient 6

description: Gene expression profile of non-malignant FTE from BRCA1/2-mutation carrier during the luteal phase

source_name: Laser-capture microdissected non-malignant FTE from BRCA1/2-mutation carrier

value: Luteal

value: BRCA2 C5910G


title: non-malignant FTEb_patient 12

description: Gene expression profile of non-malignant FTE from BRCA1/2-mutation carrier during the follicular phase

value: Follicular

value: BRCA1 185delAG


title: high grade serous carcinoma_patient 7


title: high grade serous carcinoma_patient 10

value: BRCA1 3875delGTCT


title: non-malignant FTEb_patient 8


title: non-malignant FTEb_patient 5


title: high grade serous carcinoma_patient 8


title: high grade serous carcinoma_patient 2_sample 2


title: non-malignant FTEb_patient 10

value: BRCA1 1293del40


title: high grade serous carcinoma_patient 5


title: high grade serous carcinoma_patient 2_sample 1


title: Control SM22-rtTA +9 weeks dox - mouse 4446

description: Whole lung homogenate from female FVB/N mouse with SM22-rtTA transgene (control) fed doxycycline from age 4 weeks for 9 weeks, sacrificed at age 13 weeks.


title: non-malignant FTEb_patient 7

value: BRCA1 5382insC


title: non-malignant FTEb_patient 3

value: BRCA1 A1959T


title: non-malignant FTEb_patient 11


title: high grade serous carcinoma_patient 1

value: Negative


title: non-malignant FTEb_patient 4


title: high grade serous carcinoma_patient 4


title: non-malignant FTEb_patient 2


title: non-malignant FTEb_patient 9

value: BRCA2 6174delT


title: non-malignant FTEb_patient 1


title: non-malignant FTEn_patient 10

description: Gene expression profile of non-malignant FTE from control patient during the follicular phase

source_name: Laser-capture microdissected non-malignant FTE from normal control patient


title: non-malignant FTEn_patient 7


title: non-malignant FTEn_patient 4

description: Gene expression profile of non-malignant FTE from control patient during the luteal phase


title: non-malignant FTEn_patient 9


title: non-malignant FTEn_patient 3


title: non-malignant FTEn_patient 6


title: non-malignant FTEn_patient 1


title: non-malignant FTEn_patient 8


title: non-malignant FTEn_patient 5


title: non-malignant FTEn_patient 11


title: non-malignant FTEn_patient 2


title: Human_Lung_Unclassified22

city: Rochester

first: Soumyaroop

last: Bhattacharya

state: NY

address: 601 Elmwood Avenue Box 850

department: Pediatrics

institute: University of Rochester Medical Center

description: FEV1: 2.56; Ratio: 61; Diagnosis: NSC Adeno; ArrayID: 840S

hyb_protocol: Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays.  Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station.  Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred to a mirrored storage disk and to  a raid 5 server operating on the Partners Healthcare network and backed up nightly via the Partners Healthcare Systems IT backup utility.  All systems are CFR21-11 and HIPPA compliant

source_name: Whole Lung

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

extract_protocol: For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed.   Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431).  Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).

value: 70; Race:Caucasian; Gender:Male; Ht:69 in.


title: Human_Control15

description: FEV1: 2.42; Ratio: 80; Diagnosis: Lymphoma; ArrayID: 840C

value: 71; Race:Caucasuian; Gender:Female; Ht:66in.


title: Human_Lung_Unclassified21

description: FEV1: 1.7; Ratio: 72; Diagnosis: NSC Adeno; ArrayID: 840Q

value: 71; Race:Caucasian; Gender:Female; Ht:71in.


title: non-malignant FTEn_patient 12


title: Human_Lung_Unclassified23

description: FEV1: 2.25; Ratio: 72; Diagnosis: NSC Squamous; ArrayID: 840W

value: 77; Race:Caucasian; Gender:Male; Ht:66in.


title: Human_Control17

description: FEV1: 2.68; Ratio: 71; Diagnosis: NSC Squamous; ArrayID: 840V

value: 59; Race:Caucasian; Gender:Female; Ht:69 in.


title: Human_Lung_Unclassified17

description: FEV1: 2.26; Ratio: 83; Diagnosis: NSC Adeno; ArrayID: 840M

source_name: Whole lung

value: 64; Race:Caucasian; Gender:Male; Ht:66in.


title: Human_COPD_Case13

description: FEV1: 0.99; Ratio: 63; Diagnosis: Giant Cell Tumor; ArrayID: 840B

value: 72; Race:Caucasian; Gender:Female; Ht:60in.


title: Human_COPD_Case12

description: FEV1: 0.55; Ratio: 44; Diagnosis: NSC Squamous; ArrayID: 744R

value: 59; Race:Caucasian; Gender:Female; Ht:58in.


title: Human_Lung_Unclassified15

description: FEV1: 2.73; Ratio: 80; Diagnosis: NSC Adeno; ArrayID: 744S

value: 39; Race:caucasian; Gender:Male; Ht:73in.


title: Human_Lung_Unclassified16

description: FEV1: 2.32; Ratio: 76; Diagnosis: Carcinoid; ArrayID: 840A

value: 71; Race:caucasian; Gender:Male; Ht:69 in.


title: Human_COPD_Case14

description: FEV1: 0.67; Ratio: 42; Diagnosis: NSC Adeno; ArrayID: 840R

value: 75; Race:Caucasian; Gender:Male; Ht:63in.


title: Human_Control14

description: FEV1: 1.37; Ratio: 82; Diagnosis: NSC Squamous; ArrayID: 744Q

value: 77; Race:Caucasian; Gender:Female; Ht:58in.


title: Human_Control16

description: FEV1: 3.11; Ratio: 73; Diagnosis: NSC Squamous; ArrayID: 840U

value: 67; Race:Caucasian; Gender:Male; Ht:71 in.


title: Human_Lung_Unclassified19

description: FEV1: 2.12; Ratio: 73; Diagnosis: NSC Adeno; ArrayID: 840O

value: 79; Race:Caucasian; Gender:Male:Ht:69 in.


title: Human_COPD_CaseX

description:
FEV1: 0.88; Ratio: 52; Diagnosis: NSC; ArrayID: 744P
Not used in final analysis.

tag: Age:52; Race

value: caucasian; Gender:Female; Ht:66in

tag: Not used in final analysis.


title: Human_Lung_Unclassified20

description: FEV1: 2.34; Ratio: 81; Diagnosis: NSC Adeno; ArrayID: 840P

value: 82; Race:Caucasian; Gender:Male; Ht:68in.


title: Human_Lung_Unclassified18

description: FEV1: 2.43; Ratio: 69; Diagnosis: NSC Adeno; ArrayID: 840N

value: 73; Race:Caucasian; Gender:Male; Ht:68in.


title: Human_Lung_Unclassified14

description: FEV1: 1.28; Ratio: 89; Diagnosis: NSC-Adeno; ArrayID: 744O

value: 61; Race:Caucasian; Gender:Female; Ht:65in.


title: Human_COPD_Case11

description: FEV1: 1.29; Ratio: 53; Diagnosis: NSC-Squamous; ArrayID: 744K

value: 77; Race:Caucasian; Gender:Female; Ht:67in


title: Human_Control13

description: FEV1: 2.83; Ratio: 75; Diagnosis: NSC-Squamous; ArrayID: 744N

tag: Age:54; Race

value: Caucasian; Gender:Female; Ht:75in


title: Human_Control12

description: FEV1: 1.94; Ratio: 86; Diagnosis: NSC-Squamous; ArrayID: 744M

tag: Age:62; Race

value: Caucasian; Gender:Female; Ht:62in


title: Human_Control11

description: FEV1: 3.66; Ratio: 78; Diagnosis: NSC-Mixed; ArrayID: 744J

tag: Age

value: 78; Race:Caucasian; Gender:Male; Ht:70in


title: Human_COPD_Case9

description: FEV1:1.64, Ratio 41: Diagnosis:NSC Adeno, ArrayID: 689L.

scan_protocol: Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred to a mirrored storage disk and to  a raid 5 server operating on the Partners Healthcare network and backed up nightly via the Partners Healthcare Systems IT backup utility.  All systems are CFR21-11 and HIPPA compliant Please take note: this material is available only for use in support of grant applications or publications by PHS investigators intending to use or using  the HPCGG services.  Any other use of this material without express authorization is prohibited. HPCGG Operations, 2006.

tag: Race:Caucasian, Age:75, Gender

value: Male, Height:71in


title: Mice_c-myc trans, biological rep4

city: Hannover

first: Jürgen

last: Borlak

address: Nikolai-Fuchs-Strasse 1

institute: Fraunhofer Institut

description: Mice_c-myc trans, biological rep4

hyb_protocol: 10 µg of biotinylated fragmented cRNA were hybridized onto the GeneChip® Mouse Genome 430 2.0 array according to the manufacturer's recommendation. The hybridization was performed for 16 hours at 60 rpm and 45 °C in the GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays was done on the GeneChip® Fluidics Station 400 (Affymetrix) according to the manufacturer's recommendation. The antibody signal amplification, washing, and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE; Invitrogen, USA). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000. Scanned image files were visually inspected for artifacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data, and to analyze hybridization intensity data. Default parameters provided in the Affymetrix data analysis software package were applied for analysis.

data_processing: For the comparison analysis, it was ensured that the scale factors for the compared chips did not differ by a factor larger than 3. In this study, with four replicates per group, 16 comparison analyses (4 transgenic versus 4 non-transgenic) were conducted. Comparison ranking analysis was additionally done to study concordance between increase calls (I) or decrease calls (D) for replicates (this is counting the number of I-calls and D-calls out of 16). The unpaired one-sided t-test converting the p-value to a two-sided p-value was used to determine the direction and significance of change in a transcript's expression level (Data Mining Tool, version 3.1). Signal values of each group were used as basis for calculation, with the original p-value cutoff determined to be 0.05. To select up-regulated genes in the c-Myc experiments, the following criteria were applied for the comparison conducted: the average signal value of the treatment had to be higher than 100; 4 P-calls had to be in the 4 treatment arrays; the fold change had to be 2.0 or higher (ratio of average signal values); the result of the t-test had to be an Up-change call (p-value < 0.05) (based on single signal values of 4 replicates); there had to be more than 13 (out of 16) induced calls in the comparison ranking.

source_name: Lung Adenocarcinomas of c-Myc-Transgenic Female Mice

label_protocol: 8 µg of total RNA were used as starting material to prepare cDNA. Synthesis of double-stranded cDNA was done with the GeneChip® one-cycle cDNA Kit (Affymetrix). The cleanup of double-stranded cDNA was done using the GeneChip® Sample Cleanup module (Affymetrix). 12 µl of cDNA solution were used for in vitro transcription. The in vitro transcription was conducted with the GeneChip® IVT Labeling Kit (Affymetrix). The total amount of the reaction product was purified with the GeneChip® Sample Cleanup module (Affymetrix). Purified cRNA was quantified and checked for quality using the NanoDrop ND-1000 and the Agilent 2100 Bioanalyzer. Purified cRNA was cleaved into fragments of 35-200 bases by metal-induced hydrolysis. The degree of fragmentation and the length distribution of the fragmented biotinylated cRNA were checked by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

extract_protocol: Transcriptome analysis was done according to the manufacturer's recommendation (Affymetrix GeneChip® Expression Analysis Technical Manual (Santa Clara, CA)), using the GeneChip® Test Arrays and GeneChip® Mouse Genome 430 2.0. The frozen lung tissues (10-15 mg) were disrupted and homogenized using a rotor-stator homogenizer, and total RNA was isolated from the tissues using the RNeasy total RNA isolation kit (QIAGEN). RNA of individual samples was pooled as described above, and a second cleanup of isolated RNA was done using the RNeasy Mini Kit (QIAGEN). RNA was checked for quantity, purity, and integrity of the 18S and 28S ribosomal bands by capillary electrophoresis using the NanoDrop ND-1000 and the Agilent 2100 Bioanalyzer.

tag: Genotype

value: c-Myc transgenic

tag: c-Myc transgenic female mice displayed morphological alterations with varying degree of nuclear atypia, such as bronchiolo-adenomas and bronchiolo-adenocarcinomas. Thus, different stages of malignant transformation of alveolar epithelium were observed.


title: Human_Lung_Unclassified8

description: FEV1:1.69, Ratio:76 Diagnosis: Carcinoid, ArrayID: 689G.

tag: Race:Caucasian, Age:64, Gender

value: Female, Height:63in


title: Mice_non trans, biological rep2

description: Mice_non trans, biological rep2

source_name: Lung Tissue of Non-Transgenic Female Mice

value: non-transgenic

tag: In the non-transgenic control animals no abnormalities in lung tissue was detected with the exception of a single animal which showed a slight focal interstitial mononuclear cell infiltration.


title: Human_Lung_Unclassified9

description: FEV1:1.44, Ratio 86 : Diagnosis: NSC Adeno, ArrayID: 689M.

tag: Race:Caucasian, Age:61, Gender

value: Female, Height:60


title: Human_COPD_Case8

description: FEV1:1.7, Ratio:59 Diagnosis: NSC Squamous, ArrayID: 689H.

tag: Race

value: Caucasian, Age:61, Gender:Male, Height:66in.


title: Mice_non trans, biological rep3

description: Mice_non trans, biological rep3


title: Mice_non trans, biological rep4

description: Mice_non trans, biological rep4


title: Human_COPD_Case6

description: FEV1:0.9, Ratio:55.9, Diagnosis: NSC Squamous, ArrayID: 689E

value: Caucasian, Age:70, Gender:Male, Height:71in.


title: Human_Control7

description: FEV1:3.66, Ratio 72: Diagnosis:NSC Adeno , ArrayID: 689K.

tag: Race:Caucasian, Age:71, Gender

value: Male, Height:71in.


title: Human_Lung_Unclassified12

description: Fev1:1.6, Ratio:77, Diagnosis:No Malignancy Seen, ArrayID: 744F

tag: Race:Caucasian, Age:81, Gender:Female, Height:66in


title: Mice_c-myc trans, biological rep3

description: Mice_c-myc trans, biological rep3


title: Human_Control8

description: Fev1:4.04, Ratio:79, Diagnosis:Inflammation, ArrayID: 744C


title: Mice_c-myc trans, biological rep2

description: Mice_c-myc trans, biological rep2


title: Human_COPD_Case10

description: Fev1:2.06, Ratio:54, Diagnosis:NSC Squamous, ArrayID: 744H

tag: Race:Caucasian, Gender:Male, Age:64, Height:65in.


title: Mice_non trans, biological rep1

description: Mice_non trans, biological rep1


title: Human_Lung_Unclassified13

description: Fev1:1.3, Ratio:78, Diagnosis:NSC Squamous, ArrayID: 744I

tag: Race:Caucasia, Age:79, Gender:Female, Height:63in.


title: Human_Lung_Unclassified7

description: FEV1: 1.53, Ratio:74, Diagnosis: NSC Adeno, ArrayID: 689A.

value: Caucasian, Age:73, Gender:Female, Height:66in


title: Human_Lung_Unclassified11

description: Fev1:2.61, Ratio:70, Diagnosis:NSC Squamous, ArrayID:744D

tag: Race:Caucasian, Age:74, Gender:Male, Height:70in


title: Human_Control10

description: Fev1:3.7, Ratio:81.86, Diagnosis:Carcinoisd, ArrayID: 744G

tag: Race:Caucasian, Age:40, Gender:Male, Height:67in.


title: Human_Lung_Unclassified10

description: Fev1:2.13, Ratio:71, Diagnosis:NSC Squamous, ArrayID:744A

value: Caucasian, Gender:Male, Age:69, Height:67in


title: Human_Control9

description: Fev1:1.99, Ratio:85, Diagnosis:Metastatic Renal Cell Carcinoma, ArrayID: 744E

tag: Race:Caucasian , Age:78, Gender:Female, Height:63in.


title: Human_COPD_Case7

description: FEV1:0.4, Ratio:45 Diagnosis: Giant Bullae, ArrayID: 689F

value: Caucasian, Age:61, Gender:Male, Height:73in.


title: Human_Control6

description: FEV1: 2.17, Ratio:76, Diagnosis: NSC Adeno, ArrayID: 689B.

tag: Race:Caucasian, Age:55, Gender


title: Mice_c-myc trans, biological rep1

description: Mice_c-myc trans, biological rep1


title: Human_COPD_Case15

description: Fev1:0.52, Ratio: 58 , Diagnosis: NSC Squamos, ArrayID: 851B

value: Caucasian, Gender:Female, Age:56, Height:60in


title: Human_Control5

description: Fev1:2.31 , Ratio: 75   , Diagnosis: NSC Adeno, ArrayID: 610R

value: Caucasian, Age:50, Gender:Female, Height:65in.


title: Human_Lung_Unclassified6

description: Fev1:1.63, Ratio: 80.78 , Diagnosis: Unknown, ArrayID: 610T

tag: Race:Caucasian, Age:67, Gender

value: Female, Height:66in.


title: Human_Control18

description: Fev1:2.3, Ratio: 74 , Diagnosis: NSC Adeno ArrayID: 851C

tag: Race:Caucasian , Age:, Gender

value: Female:57, Height:65in


title: pif1-2, dark sample, biological rep2

status: Public on May 30 2008

city: Austin

first: Enamul

last: Huq

state: TX

address: BIO21B, 205 W 24th St,

department: Molecular Cell & Developmental Biology

institute: The University of Texas at Austin

description: Gene expression data from 4 days dark grown Arabidopsis seedlings

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

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

data_processing: The data were analyzed with 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.

source_name: 4 days dark grown pif1-2 Arabidopsis whole seedlings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: After 4 days cold treatment, Arabidopsis seeds which plated on MS medium, were given 1 hour light for germination induction then grown at 21ºC for 4 days in the darkness.

extract_protocol: Pine tree method (tepperman et al, 2001) isolate total RNA, purified with Qiagen RNeasy spin column.

treatment_protocol: Dark grown seedlings.

tag: phynotype

value: etiolated Wt seedlings are about 2mm taller than pif1-6

tag: genotype

value: PIF1 mRNA expression level is very low in pif1-6


title: Wt, dark sample, biological rep3

source_name: 4 days dark grown Wt Arabidopsis whole seedlings

value: etiolated Wt seedlings are about 2mm taller than pif1-4

value: PIF1 mRNA expression level is very low in pif1-4


title: Human_Control4a

description: FEV1:2.59, Ratio:74, Diagnosis: NSC Adeno, ArrayID: 610N

value: Caucasian, Age:68, Gender:Female, Height:65in.


title: pif1-2, dark sample, biological rep1

value: etiolated Wt seedlings are about 2mm taller than pif1-5

value: PIF1 mRNA expression level is very low in pif1-5


title: Human_Lung_Unclassified3

description: Fev1: 1.2 , Ratio:72, Diagnosis:Metastatic Adenocarcinoma, ArrayID: 610J

value: Caucasian, Age:65 , Gender:female , Height:63in


title: Human_Lung_Unclassified4

description: FEV1:2.76, Ratio:70.58, Diagnosis: NSC Adeno, ArrayID: 610K

value: 61 Gender:Male, Height:69in


title: Wt, dark sample, biological rep2

value: etiolated Wt seedlings are about 2mm taller than pif1-3

value: PIF1 mRNA expression level is very low in pif1-3


title: Human_Control1

description: FEV1:1.69, Ratio:83.66, Diagnosis: NSC Adeno, ArrayID: 610B

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader

value: AfricanAmerican, Gender:Female, Age:84, Height:60in.


title: Human_COPD_Case4

description: FEV1:1.87, Ratio:56, Diagnosis:NSC Squamous, ArrayID: 610G

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate R

value: Caucasian, Age:56, Gender:Male, Height:72in


title: Human_COPD_Case5

description: FEV1:1.16, Ratio:43, Diagnosis: Emphysema, ArrayID: 610O

scan_protocol: Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred to a mirrored storage disk and to  a raid 5 server operating on the Partners Healthcare network and backed up

value: Caucasian, Age:68, Gender:Male, Height:67in.


title: Human_Lung_Unclassified5

description: Fev1:4.08, ratio: 68.68, Diagnosis: Hamartoma, ArrayID: 610S


title: Wt, dark sample, biological rep1

value: etiolated Wt seedlings are about 2mm taller than pif1-2

value: PIF1 mRNA expression level is very low in pif1-2


title: pif1-2, dark sample, biological rep3

value: etiolated Wt seedlings are about 2mm taller than pif1-7

value: PIF1 mRNA expression level is very low in pif1-7


title: B6 WT_Rep3

city: Madison

first: Sakae

last: Ikeda

state: WI

address: 425-G Henry Mall Room 5350 Genetics/Biotech

department: Department of Medical Genetics

institute: University of Wisconsin-Madison

description: Gene expression data from corneas of 14 day old of C.129S2(B6)-Il8rbtm1Mwm/J (Il8rb-/-)(B6 wild type)

hyb_protocol: 10 µg of purified, fragmented labeled cRNA was hybridized according to the manufactures instructions as described in the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004) in Affymetrix 640 hybridization oven.

scan_protocol: Scanning was performed according to the manufactures instructions as described in the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004) on Affymetrix GC3000 G7 scanner.

data_processing: The data was generated from normalizing the raw data by using GCRMA Version 2.0.0 by using the R statistic 2.4.1.

source_name: Cornea

label_protocol: Labeling was performed by using 5.5 µg of total RNA according to the manufactures instructions as described in the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004) with Affymetrix IVT amplification and labeling kit.

extract_protocol: Total RNA was isolated from 20 corneas (10 mice) with Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA) and purified with the Rneasy Mini Kit Qiagen, Valencia, CA).

tag: Strain

tag: Age

value: 14 day

tag: Gender

value: Mixed


title: Human_Control3

description: FEV1:1.98, Ratio:78, Diagnosis: NSC Adeno, ArrayID:610L

value: Caucasian, Age:71, Gender:Female, Height:63


title: Human_Control4

description: FEV1:2.59, Ratio:74, Diagnosis: NSC Adeno, ArrayID: 610M

tag: Race:Caucasian, Age

value: 68, Gender:Female, Height:65in


title: Human_Lung_Unclassified2

description: FEV1:1.45, Ratio:73, Diagnosis: NSC Adeno, ArrayID: 610H

value: 77, Gender:Female,Height:63in.


title: B6 WT_Rep2


title: B6 WT_Rep1


title: Dstncorn1-2J_Rep3

description: Gene expression data from corneas of 14 day old of C57BL/6JSmn-Dstncorn1-2J/J  (Dstncorn1-2J)


title: Human_Lung_Unclassified1

description: FEV1:2.51, Ratio:80.96, Diagnosis: NSC Adeno, ArrayID: 610D

tag: Race

value: Caucasian, Age:46, Gender:Male, Height:66in.


title: Human_Control2

description: FEV1:2.72, Ratio:74, Diagnosis: NSC Squamo, ArrayID: 610F

value: Caucasian, Age:60, Gender:Female, Height:64in.


title: Human_COPD_Case2

description: FEV1:1.41, Ratio:51, Diagnosis: NSC Adeno, ArrayID: 610C

value: AfricanAmerican, Gender:Female, Age:65, Height:66in.


title: Human_COPD_Case1

description: FEV1:2.54, Ratio:58, Diagnosis: NSC Squamous, ArrayID: 610A

value: Caucasian, Age:63, Gender:Male, Height:72in.


title: Human_COPD_Case3

description: FEV1:1.64, Ratio:57, Diagnosis: NSC Adeno, ArrayId: 610E

value: Caucasian, Age:53, Gender:Female, Height:65in.


title: Dstncorn1-2J_Rep1


title: Dstncorn1-2J_Rep2


title: Dstncorn1_Rep3

description: Gene expression data from corneas of 14 day old of A.BY-H2bc H2-T18f/SnJ-Dstncorn1/J (Dstncorn1)

value: A.BY-H2bc H2-T18f/SnJ-Dstncorn1/J


title: A.BY WT_Rep3

description: Gene expression data from corneas of 14 day old of A.BY-H2bc H2-T18f/SnJ (A. BY wild-type)

value: A.BY-H2bc H2-T18f/SnJ


title: A.BY WT_Rep2


title: Dstncorn1_Rep2


title: SG_P{hsGAL4}X1_14APF_rep3

status: Public on May 29 2008

city: Fayetteville

first: Michael

last: Lehmann

state: AR

address: SCEN 601

department: Biological Sciences

institute: University of Arkansas

description: Salivary glands from animals carrying two copies of P{hs-GAL4}X1, heat shocked at 9 hours after puparium formation, and dissected at 14 hours after puparium formation.

hyb_protocol: Hybridization was performed following the instructions provided in the Affymetrix Manual (Section 2), using a Fluidics Station 450 and the Midi_euk2 v3 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip 3000 Scanner 7G and Genechip Operation Software (GCOS) v. 1.4.

data_processing: The data were processed and normalized using dChip 2006. The median intensity of the baseline assay used for normalization was 145.

organism: Drosophila melanogaster

source_name: salivary glands expressing GAL4 from P{hs-GAL4}X1, heat shocked, dissected 14 hours APF

label_protocol: Biotin-labeled cRNA was produced using the One-Cycle Eukaryotic Target Labeling Assay recommended by Affymetrix. Labeling was carried out exactly as specified in the instructions manual, section 2 (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

growth_protocol: Animals were kept at 25 °C, except during heat shock period.

extract_protocol: Salivary glands were dissected on ice and directly transferred to TRIzol Reagent (Invitrogen, Carlsbad, California). To support lysis of the tissue, the mixture was subjected to vigorous vortexing. Total RNA was isolated according to the instructions of the manufacturer. As a last step of the extraction procedure, the RNA was purified using an RNeasy Minikit (Quiagen, Hilden, Germany).

treatment_protocol: Animals were subjected to a 30-min heat shock treatment at 37 °C at 9 hours after puparium formation. Salivary glands were dissected for RNA extraction at 14 hours after puparium formation.

tag: Salivary glands from animals carrying two copies of P{hs-GAL4}X1, dissected at 14 hours after puparium formation.


title: SG_w1118(2)_14APF_rep1

description: Salivary glands from w1118 animals heat shocked at 9.5 hours after puparium formation and dissected at 14 hours after puparium formation.

source_name: salivary glands, heat shocked, dissected 14 hours APF

treatment_protocol: Animals were subjected to a 30-min heat shock treatment at 37 °C at 9.5 hours after puparium formation. Salivary glands were dissected for RNA extraction at 14 hours after puparium formation.

tag: Salivary glands of strain w1118, dissected at 14 hours after puparium formation.


title: A.BY WT_Rep1


title: SG_P{hsGAL4}89_14APF_rep1

description: Salivary glands from animals carrying two copies of P{GAL4-Hsp70.PB}89-2-1, heat shocked at 9 hours after puparium formation, and dissected at 14 hours after puparium formation.

source_name: salivary glands expressing GAL4 from P{hs-GAL4}89, heat shocked, dissected 14 hours APF

tag: Salivary glands of animals carrying two copies of P{GAL4-Hsp70.PB}89-2-1, heat shocked, dissected at 14 hours after puparium formation.


title: SG_sens_14APF_rep3

description: Salivary glands from animals carrying one copy of P{GAL4-Hsp70.PB}89-2-1 and one copy of UAS-sens, heat shocked at 9 hours after puparium formation, and dissected at 14 hours after puparium formation.

data_processing: The data were processed and normalized using dChip 2006. The median intensity of the baseline assay used for normalization was 150.

source_name: sens-expressing salivary glands, heat shocked, dissected 14 hours APF

tag: Salivary glands from animals carrying one copy of P{GAL4-Hsp70.PB}89-2-1 and one copy of UAS-sens, heat shocked, dissected at 14 hours after puparium formation.


title: SG_P{hsGAL4}X1_14APF_rep1


title: SG_sens_14APF_rep1

tag: Salivary glands of animals carrying one copy of P{GAL4-Hsp70.PB}89-2-1 and one copy of UAS-sens, heat shocked, dissected at 14 hours after puparium formation.


title: SG_P{hsGAL4}X1_14APF_rep2

source_name: salivary glands expressing GAL4 from P{hs-GAL4}X1, heat shocked, dissect 14 hours APF


title: SG_sens_14APF_rep2

source_name: sens-expressing salivary glands, heat shocked, dissected at 14 hours APF


title: SG_w1118(2)_14APF_rep2


title: E13.5 embryo head sample B63E6K

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description:
Analysis of mouse brain proteome and transcriptome rearrangement during early embryonic development
D. Hartl1*, M. Irmler2*, I. Römer1, M. Mader2, L. Mao1, C. Zabel1, M. Hrabé de Angelis2, J. Beckers2, J.  Klose1

hyb_protocol: Affymetrix Expression protocol

scan_protocol: Affymetrix Expression protocol

source_name: Embryonic tissue at day 13.5

label_protocol: MessageAmp II-Biotin Enhanced (Ambion, 1791)

extract_protocol: RNeasy Lipid Tissue Mini kit (Qiagen)

tag: C57Bl/6 embryonic day 13.5


title: E13.5 embryo head sample B63E7K


title: HSC-wildtype-1

city: Tokyo

first: Susumu

last: Goyama

address: 7-3-1 Hongo, Bunkyo-ku

department: Hematology

institute: Tokyo University

description: Lineage(-), Sca-1(+), c-Kit(+) cells derived from Evi-1(flox/flox) mice were transduced with GFP  (control) or Cre-GFP expressing retroviruses. Total RNA was prepared from sorted GFP(+) cells.

hyb_protocol: Following fragmentation, Biotin-labeled cDNA was hybridized to the Mouse Genome 430 2.0 Array® (Affymetrix®) for 16 h at 45°C as recommended by the manufacturer. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.

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

data_processing: Expression data were extracted from image files produced on Affymetrix® GeneChip Operating Software 1.0® (GCOS®).

source_name: hematopoietic stem cells transduced with control

label_protocol: Biotin-labeled cDNA probes were prepared using the NuGen Ovation Biotin labeling system (NuGEN Technologies, Inc.), according to the manufacturer's protocol.

extract_protocol: RNA was extracted from sorted cells using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instruction.

tag: Age:8 weeks


title: HSC-Evi1-KO-2

description: Lineage(-), Sca-1(+), c-Kit(+) cells derived from Evi-1(flox/flox) mice were transduced with GFP (control) or Cre-GFP expressing retroviruses. Total RNA was prepared from sorted GFP(+) cells.

source_name: hematopoietic stem cells transduced with Cre


title: Hippocampus wt sample 15

description: Interlocking transcriptomics, proteomics and toponomics technologies for brain tissue analysis in hippocampus Schubert et al

data_processing: normalised RMA data

source_name: Complete hippocampus (left side)

extract_protocol: RNeasy Lipid Rich Tissue Mini kit (Qiagen), DNase treated (Ambion turbo-DNase)

tag: C57Bl/6J, male, 3 months, wild type


title: Hippocampus wt sample 17


title: Hippocampus wt sample 11

description:
Interlocking transcriptomics, proteomics and toponomics technologies for brain tissue analysis in hippocampus
Schubert et al


title: E9.5 embryo head sample 24

source_name: Embryonic tissue at day 9.5

label_protocol: GeneChip® IVT Labeling Kit (one-cycle kit, Affymetrix)

tag: C57Bl/6 embryonic day 9.5


title: Hippocampus wt sample 13


title: E13.5 embryo head sample B62E7K


title: HSC-wildtype-2


title: E13.5 embryo head sample B63E5K


title: HSC-Evi1-KO-1


title: E13.5 embryo head sample B62E6K


title: SG_1P{hsGAL4}89_14APF_rep1

description: Salivary glands from animals carrying one copy of P{GAL4-Hsp70.PB}89-2-1, heat shocked at 9 hours after puparium formation, and dissected at 14 hours after puparium formation.

source_name: salivary glands expressing GAL4 from one copy of P{GAL4-Hsp70.PB}89-2-1, heat shocked, dissected 14 hours APF

tag: Salivary glands from animals carrying one copy of P{GAL4-Hsp70.PB}89-2-1, dissected at 14 hours after puparium formation.


title: E9.5 embryo head sample 22


title: E11.5 embryo head sample 36

source_name: Embryonic tissue at day 11.5

tag: C57Bl/6 embryonic day 11.5


title: E11.5 embryo head sample 52


title: E13.5 embryo head sample B62E8K


title: E11.5 embryo head sample 33


title: E11.5 embryo head sample 51


title: E9.5 embryo head sample 16


title: E9.5 embryo head sample 19


title: E9.5 embryo head sample 15


title: Dstncorn1_Rep1


title: 100nM elesclomol + 5mM NAC treated cells at time 6h, technical rep2.

city: Lexington

first: Jane

middle: Frances

last: Kepros

state: MA

address: 45 Hartwell Ave

department: Biology

institute: Synta Pharmaceuticals Corp.

description: Gene expression data from drug treated cells

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

source_name: cryopreserved cells ordered from ATCC.org

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells acquired from ATCC.  Grown in vitro in 10% serum DMEM media.

extract_protocol: QIAGEN Rneasy Mini Kit (#74106) was used for extraction according to the manufacturers instructions.

treatment_protocol: 3x10^6 cells/treatment were plated at a density of approx. 17,637cells/cm^2 and incubated for 3h prior to treatment.  Pretreated with 5mM NAC for 30 min, as appropriate.  Harvested after 6 h of treatment.

tag: Hs 294T cell line

tag: Human Melanoma

tag: passage 11


title: 100nM elesclomol + 5mM NAC treated cells at time 6h, technical rep1.


title: 5mM NAC treated cells at time 6h, technical rep2.


title: E9.5 embryo head sample13


title: E14 cortex GFPhigh cells sample 2

description: Prospective isolation of radial glia subtypes – lineage and transcriptom analysis Luisa Pinto1, Michael Mader1, Martin Irmler2, Marco Gentilini3, Federico Santoni4, Vassiliki Nikoletopoulou5, Steven Pollard6, Alessandro Bulfone3, Yves Barde5, Johannes Beckers2, and Magdalena Götz1,7,8

data_processing: Mas 5.0

source_name: FACS-sorted cells from cortex of E14 embryos of hGFAP eGFP mice

label_protocol: GeneChip® IVT Labeling Kit (single round, Affymetrix)

extract_protocol: RNeasy Mini kit (Qiagen) with on column DNase treatment

tag: Selected by FACS for positive staining for GFP


title: 100nM elesclomol + 250nM paclitaxel treated cells at time 6h, technical rep2

treatment_protocol: 3x10^6 cells/treatment were plated at a density of approx. 17,637cells/cm^2 and incubated for 3h prior to treatment.

tag: passage 6


title: E14 cortex GFPhigh Prominin+ cells, sample S2

tag: Selected by FACS for positive staining for prominin and GFP


title: E14 cortex GFPlow cells sample 2


title: 100nM elesclomol treated cells at time 6h, technical rep1.


title: E14 cortex GFPhigh cells sample 3


title: 100nM elesclomol treated cells at time 6h, technical rep2.


title: E14 cortex GFPhigh Prominin+ cells, sample S1


title: 0.01% DMSO treated cells at time 6h, technical rep2.

description: Gene expression data from vehicle treated, healthy cells


title: E14 cortex GFPhigh cells sample 1


title: 250nM paclitaxel treated cells at time 6h, technical rep1


title: E14 cortex GFPhigh Prominin+ cells, sample S4


title: E14 cortex GFPlow cells sample 3


title: 5mM NAC treated cells at time 6h, technical rep1.


title: E14 cortex GFPhigh Prominin+ cells, sample S3


title: E14 cortex GFPlow cells sample 1


title: 100nM elesclomol treated cells at time 6h, technical rep2


title: 250nM paclitaxel treated cells at time 6h, technical rep2


title: E14 cortex GFPlow Prominin+ cells, sample S3


title: 0.01% DMSO treated cells at time 6h, technical rep1.


title: 100nM elesclomol + 250nM paclitaxel treated cells at time 6h, technical rep1


title: 100nM elesclomol treated cells at time 6h, technical rep1


title: E14 cortex GFPlow Prominin+ cells, sample S2


title: 0.01% DMSO treated cells at time 6h, technical rep2


title: E14 cortex GFPlow Prominin+ cells, sample S1


title: 0.01% DMSO treated cells at time 6h, technical rep1


title: untreated cells at 0h, technical rep1

description: Gene expression data from untreated, healthy cells


title: E18 cortex GFP+ Prominin+ cells, sample S2

description:
Prospective isolation of radial glia subtypes – lineage and transcriptom analysis
Luisa Pinto1, Michael Mader1, Martin Irmler2, Marco Gentilini3, Federico Santoni4, Vassiliki Nikoletopoulou5, Steven Pollard6, Alessandro Bulfone3, Yves Barde5, Johannes Beckers2, and Magdalena Götz1,7,8

source_name: FACS-sorted cells from cortex of E18 embryos of hGFAP eGFP mice


title: E18 cortex GFP+ Prominin+ cells, sample S4


title: E18 cortex GFP+ Prominin+ cells, sample S5


title: E18 cortex GFP+ Prominin+ sample S3

source_name: Facs-sorted cells from cortex of E18 embryos of hGFAP eGFP mice


title: untreated cells at 0h, technical rep2


title: Subject DP, 6h

status: Public on May 28 2008

city: Copenhagen N

first: Ole

middle: Hartvig

last: Mortensen

address: Panum 6.5.28, Blegdamsvej 3

department: Department of Biomedical Sciences

country: Denmark

institute: University of Copenhagen

description: Human skeletal muscle biopsy from vastus lateralis of musculus quadriceps muscle from a male subject.

hyb_protocol: After fragmentation at 94 C for 35 min in fragmentation buffer (40 mM Tris, 30 mM MgOAc, 10 mM KOAc), the labeled cRNA was hybridized for 16 h to Affymetrix HG-U133 Plus 2.0 (Affymetrix Inc., Santa Clara, CA, USA).After hybridization the array was washed and stained with streptavidin phycoerythrin solution using the Fluidics Station 400 (Affymetrix Inc.).

scan_protocol: Finally the arrays were scanned using the GeneChip Scanner 3000 (Affymetrix Inc.) to obtain non-normalized expression levels.

data_processing: Affymetrix CEL-files were normalized using gcRMA (Wu et al., 2004) available in the Bioconductor package version 1.7 (http://www.bioconductor.org) for the statistical software package R version 2.21 (R Development Core Team, 2005).

source_name: Human skeletal muscle biopsy from a 3h IL-6 infusion

label_protocol: Total RNA was synthesized to double-strand cDNA using Superscript Choice System (Invitrogen, Carlsbad, CA, USA) with an oligo-dT primer containing a T7 RNA polymerase promoter (GenSet, Evry, France). The cDNA was used as a template for in vitro transcription reaction to synthesize biotin-labeled antisense cRNA (BioArray High Yield RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY, USA)

extract_protocol: Trizol, followed by RNEasy (Qiagen) purification of total RNA

treatment_protocol: IL-6 infusion from 0h to 3h

tag: Subject

value: DP

tag: Timepoint

tag: Sex

value: Male


title: Subject CO, 6h

value: CO


title: Subject DP, 3h


title: Subject HH, 3h

value: HH


title: Subject CO, 3h


title: Subject HH, 6h


title: Subject HH, 0h


title: Subject CO, 0h


title: Group 3, Normal Skin, N7598J

city: Tampa

first: Sean

last: Yoder

state: FL

address: 12902 Magnolia Dr.

department: Molecular Genomics Core Facility

institute: Moffitt Cancer Center & Research Institute

description: Gene expression data from flash frozen surgically resected tissue from Normal Skin

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip 133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 Scanner.

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: Normal Skin

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

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

tag: Group 3

tag: Normal Skin


title: Group 3, Primary Melanoma, T6950A

description: Gene expression data from flash frozen surgically resected tissue from Primary Melanoma

source_name: Melanoma Tumor Tissue

tag: Primary Melanoma


title: Group 3, Primary Melanoma, T6516I


title: Group 3, Metastatic Melanoma, T8647A

description: Gene expression data from flash frozen surgically resected tissue from Metastatic Melanoma

tag: Metastatic Melanoma


title: Group 3, Metastatic Melanoma, T8122A


title: Subject DP, 0h


title: Group 3, Metastatic Melanoma, T7859A


title: Group 3, Metastatic Melanoma, T8486D


title: Group 3, Normal Skin, N7288C


title: Group 3, Metastatic Melanoma, T8268A


title: Group 3, Normal Skin, N7600G


title: Group 3, Metastatic Melanoma, T8032D


title: Group 3, normal human epidermal melanocytes, NHEM

description: Gene expression data from normal Human melanocytes cultured in vitro

source_name: cultured normal human epidermal melanocytes purchased from Cambrex BioScience

tag: normal human epidermal melanocytes


title: Group 3, Metastatic Melanoma, T8248C


title: Group 3, Metastatic Melanoma, T8244A


title: Group 3, Metastatic Melanoma, T8202A


title: Group 3, Metastatic Melanoma, T7851A


title: Group 3, Metastatic Melanoma, T7533A


title: Group 3, Metastatic Melanoma, T6952B


title: Group 3, Metastatic Melanoma, T7711A


title: Group 3, Metastatic Melanoma, T7126D


title: Group 3, Metastatic Melanoma, T6435A


title: Group 3, Metastatic Melanoma, T6950B


title: Group 3, Metastatic Melanoma, T7223A


title: Group 3, Metastatic Melanoma, T7746D


title: Group 3, Metastatic Melanoma, T6851A


title: Group 3, Metastatic Melanoma, T7336A


title: Group 3, Metastatic Melanoma, T6829A


title: Group 2, Squamous cell carcinoma, 8300-36

description: Gene expression data from flash frozen surgically resected tissue from Squamous cell carcinoma

tag: Group 2

tag: Squamous cell carcinoma


title: Group 2, Squamous cell carcinoma, 8298-34


title: Group 2, Squamous cell carcinoma, 8299-35


title: Group 2, Squamous cell carcinoma, 8289-25


title: Group 3, Metastatic Melanoma, T6519A1


title: Group 3, Metastatic Melanoma, T7133B


title: Group 3, Metastatic Melanoma, T6807A


title: Group 3, Metastatic Melanoma, T6425A


title: Group 2, Squamous cell carcinoma, 8284-20


title: Group 2, Primary Melanoma, 8033G-17


title: Group 3, Metastatic Melanoma, T7784A


title: Group 2, Squamous cell carcinoma, 8287-23


title: Group 2, Primary Melanoma, 7156B-29


title: Group 2, Primary Melanoma, 7062A-3


title: Group 2, Primary Melanoma, 7288B-21


title: Group 2, Primary Melanoma, 6924A-18


title: Group 2, Primary Melanoma, 7682B-31


title: Group 2, Primary Melanoma, 7327A-7


title: Group 2, Primary Melanoma, 6705A-12

tag: 5 mm


title: Group 2, Primary Melanoma, 7838A-15


title: Group 2, Metastatic Melanoma, 7510A-30


title: Group 2, Metastatic Melanoma, 7129A-11


title: Group 2, Metastatic Melanoma, 7838D-2


title: Group 2, Metastatic Melanoma, 7051B-27


title: Group 2, Metastatic Melanoma, 7322B-24


title: Group 2, Basal cell carcinoma, 8297-33

description: Gene expression data from flash frozen surgically resected tissue from Basal cell carcinoma

tag: Basal cell carcinoma


title: Group 2, Basal cell carcinoma, 8295-31


title: Group 2, Basal cell carcinoma, 8296-32


title: MEFs expressing Oct4, Sox2, Klf4, c-Myc (Day 8, replicate 1)

city: Cambridge

first: Tarjei

middle: S

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

description: Neo(r) MEFs derived from chimeric mice generated from Nanog-GFP iPS cells with inducible lentivirus expressing Oct4, Klf4, Sox2 and c-Myc

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

source_name: MEF

label_protocol: Standard Affymetrix protocol

extract_protocol: Standard Affymetrix protocol

tag: Day 8 of Dox induction


title: Group 2, Basal cell carcinoma, 8291-27


title: Oct4-iPS cell line MCV8.1 (replicate 1)

description: Oct4-GFP positvie iPS cell line generated by subcloning Es-like colonies from cell line MCV8

tag: Oct4-GFP positive


title: MEFs expressing Oct4, Sox2, Klf4, c-Myc (Day 16, replicate 2)

tag: Day 16 of Dox induction


title: Group 2, Basal cell carcinoma, 8288-24


title: Oct4-iPS cell line MCV8.1 (replicate 2)


title: Group 2, Basal cell carcinoma, 8290-26


title: MEFs expressing Oct4, Sox2, Klf4, c-Myc (Day 12, replicate 2)

tag: Day 12 of Dox induction


title: Group 2, Basal cell carcinoma, 8294-30


title: Group 2, Basal cell carcinoma, 8292-28


title: Activated B lymphocytes expressing Oct4, Sox2, Klf4, c-Myc (replicate 1)

description: Activated B lymphocytes generated from chimeric mice generated from Nanog-GFP iPS cells with inducible lentivirus

source_name: Adult peripheral blood

tag: Day 4 of Dox induction


title: Group 2, Metastatic Melanoma, 6933A-10


title: Activated B lymphocytes expressing Oct4, Sox2, Klf4, c-Myc (replicate 2)


title: Group 2, Basal cell carcinoma, 8293-29


title: Activated B lymphocytes (replicate 1)

tag: No Dox


title: Group 2, Basal cell carcinoma, 8286-22


title: MEFs expressing Oct4, Sox2, Klf4, c-Myc (Day4, replicate 1)


title: B-iPS replicate 2

description: B lymphocyte-derived iPS cell line (Nanog-GFP)

source_name: B lymphocyte derived iPS line

tag: Nanog GFP positive


title: MEFs expressing Oct4, Sox2, Klf4, c-Myc (Day4, replicate 2)


title: Group 2, Basal cell carcinoma, 8285-21


title: Group 1, Squamous cell carcinoma, 7842_14

tag: Group 1


title: B-iPS replicate 1


title: MEFs expressing Oct4, Sox2, Klf4, c-Myc (Day 12, replicate 1)


title: MEFs expressing Oct4, Sox2, Klf4, c-Myc (Day 16, replicate 1)

tag: Dox 16 of Dox induction


title: MEFs expressing Oct4, Sox2, Klf4, c-Myc (Day 8, replicate 2)


title: Activated B lymphocytes (replicate 2)


title: Group 1, Normal Skin, 6611 A5

tag: Normal Skin


title: Group 1, Squamous cell carcinoma, 7796_7


title: Group 1, Primary Melanoma, 7838 A

tag: Primary Melanoma


title: Group 1, Squamous cell carcinoma, 7794_5


title: Partially reprogrammed cell line BIV1 (Dox-) replicate 1

description: B lymphocyte-derived partially reprogrammed cell line cultured after withdrawal of Dox.


title: Partially reprogrammed cell line MCV6 replicate 1

description: MEF-derived partially reprogrammed cell line expression Oct4, Klf4, c-Myc and Sox2 from constitutive retrovirus

tag: GFP negative, SSEA1 negative, AP negative


title: Group 1, Metastatic Melanoma, 6685 A

tag: Metastatic Melanoma


title: Partially reprogrammed cell line BIV1 (Dox+) replicate 1

description: B lymphocyte-derived partially reprogrammed cell line expressing Oct4, Klf4, c-Myc and Sox2 from lentivirus induced by Dox.

tag: Induced with Dox


title: Group 1, Metastatic Melanoma, 6685 B


title: Group 1, Squamous cell carcinoma, 7844_16

tag: Squamous cell carcinoma


title: Partially reprogrammed cell line MCV6 replicate 2


title: Partially reprogrammed cell line BIV1 (Dox-) replicate 2


title: Group 1, Metastatic Melanoma, 7838 D


title: Group 1, Metastatic Melanoma, 7838 B


title: Group 1, Squamous cell carcinoma, 7798_9


title: Partially reprogrammed cell line MCV8 (Medium MHC) replicate 2

description: MEF-derived partially reprogrammed cell line expressing Oct4, Klf4, c-Myc and Sox2 from constitutive retrovirus. Medium MHC expression (by FACS).

tag: MHC medium, GFP negative


title: Group 1, Metastatic Melanoma, 6611 B


title: Group 1, Metastatic Melanoma, 6611 A2


title: Partially reprogrammed cell line BIV1 (Dox+) replicate 2


title: Group 1, Metastatic Melanoma, 6611 A3


title: Partially reprogrammed cell line MCV8 (High MHC) replicate 1

description: MEF-derived partially reprogrammed cell line expressing Oct4, Klf4, c-Myc and Sox2 from constitutive retrovirus. High MHC expression (by FACS).

tag: MHC high, GFP negative


title: Partially reprogrammed cell line MCV8 (High MHC) replicate 2


title: Partially reprogrammed cell line MCV8 (low MHC) replicate 2

description: MEF-derived partially reprogrammed cell line expressing Oct4, Klf4, c-Myc and Sox2 from constitutive retrovirus. Low MHC expression (by FACS).

tag: MHC low, GFP negative


title: Group 1, Primary Melanoma, 7840_12


title: Partially reprogrammed cell line MCV8 (SSEA-) replicate 2

description: MEF-derived partially reprogrammed cell line expressing Oct4, Klf4, c-Myc and Sox2 from constitutive retrovirus. SSEA1 negative (by FACS).

tag: SSEA1 negative, GFP negative


title: Partially reprogrammed cell line MCV8 (medium MHC) replicate 1


title: Partially reprogrammed cell line MCV8 (Low MHC) replicate 1


title: Group 1, Primary Melanoma, 7790_1


title: Group 1, Metastatic Melanoma, 6611 A1


title: Group 1, Melanoma in situ, 7795_6

description: Gene expression data from flash frozen surgically resected tissue from Melanoma in situ

tag: Melanoma in situ


title: Group 1, Melanoma in situ, 7846_18


title: Partially reprogrammed cell line MCV8 (SSEA+) replicate 2

description: MEF-derived partially reprogrammed cell line expressing Oct4, Klf4, c-Myc and Sox2 from constitutive retrovirus. SSEA1 positive (by FACS).

tag: SSEA1 positive, GFP negative


title: RGA-GR-DEX-REP1

city: Singapore

first: Hao

last: Yu

address: Lower Kent Ridge Road

country: Singapore

institute: National University of Singapore

hyb_protocol: According to the manufacturer's instructions (Affymetrix, Santa Clara, California, USA)

data_processing: GeneChip® Scanner was used to scan the probe arrays and signals were obtained by GeneChip® Operating Software (GCOS). The GCOS generated data files (.CEL file) were imported into GeneSpring GX 7.3.1 (Agilent) to do further analysis.

source_name: Arabidopsis inflorescence without flowers later than stage 12, dex treated, 4h

extract_protocol: Total RNAs were extracted by using RNeasy Plant Mini Kit (Qiagen)

tag: Ecotype Lansberg erecta


title: Group 1, Basal cell carcinoma, 7800_11

tag: Basal cell carcinoma


title: RGA-GR-MOCK-REP3

scan_protocol: According to the manufacturer's instructions (Affymetrix, Santa Clara, California, USA)

source_name: Arabidopsis inflorescence without flowers later than stage 12, mock treated, 4h


title: Group 1, Basal cell carcinoma, 7843_15


title: Partially reprogrammed cell line MCV8 (SSEA-) replicate 1


title: Group 1, Basal cell carcinoma, 7845_17


title: Partially reprogrammed cell line MCV8 (SSEA+) replicate 1


title: ES_wt_rep2

description: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

data_processing: GCOS version 1.4, default parameters

source_name: V6.5 murine ES cells

growth_protocol: ES cells were cultivated in 5% CO2 at 37º on irradiated MEFs in DMEM containing 15% FCS, leukemia-inhibiting factor, penicillin/streptomycin, L-glutamine, nonessential amino acids and 2-mercaptoethanol. Cells were subject to at least two to three passages on 0.2% gelatin under feeder-free conditions to exclude feeder contamination.

extract_protocol: Trizol according to the manufacturer's recommendations

tag: Genotype 129SvJae x C57BL/6; male; passages 10–15


title: MEF_wt_rep2

hyb_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

source_name: Mouse embryonic fibroblasts

growth_protocol: DMEM with 10% fetal bovine serum and penicillin/streptomycin at 37º, 5% CO2.

tag: Genotype 129SvJae x C57BL/6; male; d13.5; passages 4-6


title: RGA-GR-DEX-REP2

source_name: Arabidopsis inflorescence without flowers later than stage 12, dexamethasone treated, 4h

label_protocol: According to the manufacturer's instructions (Affymetrix, Santa Clara, California, USA)


title: MEF_wt_rep1

scan_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array


title: Nontransgenic(ga1-3rgargl2)-DEX-REP3


title: Nontransgenic(ga1-3rgargl2)-DEX-REP2


title: RGA-GR-DEX-REP3


title: Nontransgenic(ga1-3rgargl2)-DEX-REP1


title: RGA-GR-MOCK-REP1


title: RGA-GR-MOCK-REP2


title: CH2 of C. kokaiensis in ATH1

status: Public on May 27 2008

city: Fukuoka

first: Shin-Ichi

last: Morinaga

state: Fukuoka

address: 6-10-1, Hakozaki

department: Department of Biology

institute: Kyushu University

description: This data was calibrated by gDNA hybridization of Accession no. GSM246369 in GEO.

hyb_protocol: According to the manufacturer's instructions (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

data_processing: Data analysis was conducted according to Hammond et al. (2005).

organism: Cardamine sp. SIM-2007

source_name: Chasmogamous flower

extract_protocol: A primordium of a first inflorescence with primordia of the first to eighth flowers was collected from each plant when the first flower primordium was visible. We collected 160 inflorescence primordia and placed them in the same microtube. The total RNA of sample was extracted using Isogen (Nippon Gene, Japan). The quality and quantity of total RNA were checked using an RNA Nano Labchip and 2100 Bioanalyzer (Agilent Technologies, USA).

tag: Cardamine kokaiensis Yahara (Brassicaceae) is an annual cleistogamous herb that grows only near the Kokai River, Ibaraki Prefecture, Japan (36°1' N, 140°0' E). This plant was discovered by T. Yahara (Kyushu University, Japan) and has not been described yet. However, this plant will be described this species name in the near future (Yahara in preparation). After the plants were self-pollinated and cultivated for four generations, the single descendant seeds were used in experiments. The chilling treatments were performed at 4°C in darkness after germination for 14 days. The first flowers of plants produced CH flowers.


title: Group 1, Basal cell carcinoma, 7797_8

tag: Group 1


title: INT2 of C. kokaiensis in ATH1

scan_protocol: According to the manufacturer's instructions (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

source_name: Intermediate flower

tag: Cardamine kokaiensis Yahara (Brassicaceae) is an annual cleistogamous herb that grows only near the Kokai River, Ibaraki Prefecture, Japan (36°1' N, 140°0' E). This plant was discovered by T. Yahara (Kyushu University, Japan) and has not been described yet. However, this plant will be described this species name in the near future (Yahara in preparation). After the plants were self-pollinated and cultivated for four generations, the single descendant seeds were used in experiments. The chilling treatments were performed at 4°C in darkness after germination for 28 days. The first flowers of plants produced INT flowers.


title: INT1 of C. kokaiensis in ATH1

source_name: Intermadiate flower

label_protocol: According to the manufacturer's instructions (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

tag: Cardamine kokaiensis Yahara (Brassicaceae) is an annual cleistogamous herb that grows only near the Kokai River, Ibaraki Prefecture, Japan (36°1' N, 140°0' E). This plant was discovered by T. Yahara (Kyushu University, Japan) and has not been described yet. However, this plant will be described this species name in the near future (Yahara in preparation). After the plants were self-pollinated and cultivated for four generations, the single descendant seeds were used in experiments. The chilling treatments were performed at 4°C in darkness after germination for 14 days. The first flowers of plants produced INT flowers.


title: ES_wt_rep3

label_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array


title: ES_wt_rep1


title: CH1 of C. kokaiensis in ATH1


title: gDNA of C. kokaiensis in ATH1

type: genomic

description: gDNA hybridyzation data was used to calibration of cross-species microarray

hyb_protocol: The labeling DNA hybridized to Affymetrix ATH1 arrays according to the manufacturer's instructions (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

data_processing: Because CEL file was used to calibration of cross-species microarray, data processing was not conducted

molecule: genomic DNA

source_name: gDNA

label_protocol: Genomic DNA (1ug) was labeled by 500 ng using the BioPrime DNA Labeling System (Invitrogen, Paisley, UK) according to Hammond et al. (2005). The Total labeled DNA from 1ug purified Nucleotide Removal kit (QIAGEN Ltd).

extract_protocol: Total genomic DNA was extracted from 100mg of C. kokaiensis leaf tissue no chilling treatment using a DNeasy Plant mini kit (QIAGEN Ltd, Crawley, UK).

tag: Cardamine kokaiensis Yahara (Brassicaceae) is an annual cleistogamous herb that grows only near the Kokai River, Ibaraki Prefecture, Japan (36°1' N, 140°0' E). This plant was discovered by T. Yahara (Kyushu University, Japan) and has not been described yet. However, this plant will be described this species name in the near future (Yahara in preparation). After the plants were self-pollinated and cultivated for four generations, the single descendant seed were used in experiment.


title: bleo/Neo_polysomal_Rep5

status: Public on May 25 2008

type: other

first: Hartmut

last: Land

address: 601 Elmwood Avenue, Box 633

department: Biomedical Genetics

description: Refer to submitted paper, McMurray et al.

hyb_protocol: The cRNA yield was fragmented and hybridization cocktails were prepared using Affymetrix standard protocol for eukaryotic target hybridization.  Targets were hybridized to Affymetrix Mouse Genome 430 2.0 Expression Arrays at 45°C for 16 hours, washed and stained using Affymetrix Fluidics protocol EukGE-WS2v4_450 in the Fluidics Station 450.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 3000.

data_processing: Expression values from the 50 microarrays processed were obtained using the RMA procedure with background correction in Bioconductor (http://www.bioconductor.org).

molecule: other

source_name: bleo/Neo vector cells, polysomal RNA

label_protocol: Five micrograms of RNA was reverse transcribed and labeled using the mAMP kit (Ambion), with the 1x amplification protocol.

growth_protocol: Four polyclonal cell populations, control (Bleo/Neo), mp53 (p53175H/Neo), Ras (Bleo/RasV12) and mp53/Ras (p53175H/RasV12) were derived by retroviral infection of low-passage polyclonal young adult mouse colon (YAMC) cells.  YAMC cells (a gift from R. Whitehead and A.W. Burgess) derived from the Immorto-mouse (aka H-2Kb/tsA58 transgenic mouse) expressing temperaturesensitive simian virus 40 large T (tsA58) under the control of an interferon γ-inducible promoter were maintained at the permissive temperature (33°C) for large T in the presence of interferon γ to support conditional immortalization in vitro. This permits expansion of the cells in tissue culture. In contrast, exposure of YAMC cells to the non-permissive temperature for large T (39°C) in the absence of interferon γ leads to growth arrest followed by cell death, indicating the absence of spontaneous immortalizing mutations in the cell population. The cells were cultured on Collagen IV-coated dishes (1μg/cm2 for 1.5 hr at room temp; Sigma) in RPMI 1640 medium (Invitrogen) containing 10% (v/v) fetal bovine serum (FBS) (Hyclone), 1×ITS-A (Invitrogen), 2.5 μg/ml gentamycin (Invitrogen), and 5 U/ml interferon γ (R&D Systems). All experiments testing the effects of RasV12 and p53175H were carried out at the non-permissive temperature for large T function (39°C) and in the absence of interferon γ.

extract_protocol: Polysomal RNA was harvested from YAMC, bleo/neo, mp53/neo, bleo/Ras and mp53/Ras cells to obtain gene expression profiles reflective of protein synthesis rates.  Cells were lysed in Extraction Buffer (50 mM MOPS, 15 mM MgCl, 150 mM NaCl, 0.5% Triton X-100 with 100 ug/mL cycloheximide, 1 mg/mL heparin, 200U RNAsin (2 uL/mL of buffer), 2mM PMSF).  Supernatants were applied to 10-50% sucrose gradients, centrifuged at 36,000 rpm for 2 hr at 4°C and fractions were collected using an ISCO gradient fractionator reading absorbance at 254 nm.  Polysome containing fractions were pooled and RNA was purified using the RNeasy Mini Kit (Qiagen) following the standard protocol for animal cells, except that sucrose fractions were mixed with 3.5 volumes Buffer RLT before binding to the RNeasy column.  RNA was on-column DNase digested as part of the RNeasy RNA extraction protocol.

treatment_protocol: RNA was harvested from ten replicates for each cell population grown in non-permissive conditions for 48 hr, followed by 24 hr in media with 0% FBS to maximize the contribution of oncogenic signaling to gene expression.  RNA was collected while cells were sub-confluent and all cell populations were actively cycling.

tag: Refer to Whitehead, R. H., VanEeden, P. E., Noble, M. D., Ataliotis, P. & Jat, P. S. Establishment of conditionally immortalized epithelial cell lines from both colon and small intestine of adult H-2Kb-tsA58 transgenic mice. Proc Natl Acad Sci U S A 90, 587-91 (1993) and Xia, M. & Land, H. Tumor suppressor p53 restricts Ras stimulation of RhoA and cancer cell motility. Nat Struct Mol Biol 14, 215-23 (2007).