title: PPAR gamma siRNA rep3

status: Public on Jan 14 2009

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Gene expression data from 3T3-L1 adipocytes treated with PPAR gamma siRNA 14 days after initiation of differentiation.

hyb_protocol: Affymetrix arrays were hybridized according to standard Affymetrix protocols.

scan_protocol: Hybridized arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Scanned image files were analyzed for probe intensities and converted to tabular formats using the Microarray Suite Expression Analysis software from Affymetrix. Probe set intensitiy summarization and normalization were calculated using RMA implemented using the Bioconductor project in the software package R.  Present/Absent calls were calculated using the mas5calls function within the bioconductor affy package version 1.16.0.

source_name: day 14 adipocytes

label_protocol: cRNA labeling was done according to standard Affymetrix protocols.

growth_protocol: Murine 3T3-L1 cells were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (U.S. Bio-Technologies Inc, Parkerford, PA, USA), 100 U/ml penicillin, and 100 µg/ml streptomycin.  3T3 cells were grown to confluence and induced to differentiate 2 days after confluence with media containing 1 µM dexamethasone, 10 µg/ml bovine insulin, and 0.5 mM 3-isobutyl-1-methylxanthine (all Sigma, MO, USA) for 2 days and for an additional 2 days in insulin only. Adipocytes were considered mature after 8 days with at least 95% conversion into the adipocyte morphology.

extract_protocol: Total RNA was extracted and purified with the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturers directions.

treatment_protocol: 14 days after induction of differentiation, 3T3-L1 adipocytes were transfected by electroporation (Nucleofector II, AMAXA, Germany). Cells were detached from culture dishes with 0.25% trypsin and 0.5 mg collagenase/ml in PBS, washed twice, resuspended in electroporation buffer (solution V, AMAXA), mixed with 2 or 3nmol of control (non-targeting oligonucleotide, Dharmacon) or PPAR gamma siRNA oligonucleotides and seeded into 12-well plates after electroporation.

tag: 3T3-L1 cells


title: control siRNA rep2

type: RNA

city: Houston

state: TX

country: USA

description: Gene expression data from 3T3-L1 adipocytes treated with control siRNA 14 days after initiation of differentiation.

label: biotin

molecule: total RNA

organism: Mus musculus


title: preadipocyte rep2

description: Gene expression data from preadipocytes.

source_name: preadipocytes


title: PPAR gamma siRNA rep1


title: control siRNA rep1


title: control siRNA rep3


title: CIS patient No.14_Treated

status: Public on Jan 13 2009

city: Chapel Hill

first: Silva

last: Markovic-Plese

state: NC

address: 105 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

description: Gene expression of PBMCs from CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a

hyb_protocol: 15 ug of cRNA was used for gene array hybridization. Arrays were hybridized for 16 hours at 45oC in the GeneChip® Hybridization Oven 640.The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip® Fluidics Station 400.

scan_protocol: The arrays were scanned with the Hewlett Packard GeneArray Scanner.

data_processing: Affymetrix GeneChip® Microarray Suite 5.0 software

label: Biotin

organism: Homo sapiens

source_name: PBMCs from No.14 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA.

growth_protocol: PBMCs were seperated from 15 CIS patients and cultured in serum free medium.

extract_protocol: Total RNA was extracted using a Rneasy kit according to the manufacturer's instructions.

treatment_protocol: 10 million PBMCs per condition derived from 15 CIS patients were stimulated with plate-immobilized aCD3 and aCD28 mAb in the absence or presence of IFNb-1a for 24 h in serum-free medium.

tag: 107 PBMCs per condition derived from 15 CIS patients were stimulated with plate-immobilized αCD3 (1 μg/ml) and αCD28 (5 μg/ml) mAb (BD Biosciences) in the absence or presence of IFNβ-1a (1000 U/ml) (EMD Serono Inc) for 24 h in serum-free medium (Gibco).


title: CIS patient No.13_Treated

source_name: PBMCs from No.13 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: CD26+ cancer cell, replicate 2

city: Ribeirao Preto

first: Ricardo

last: Vêncio

state: SP

address: Av. Bandeirantes, 3900

department: Computing and Mathematics Department

country: Brazil

institute: Universidade de São Paulo

description: Primary tumor prostate cancer cells.

hyb_protocol: standard Affymetrix procedures.

scan_protocol: standard Affymetrix procedures.

data_processing: RMA of .cel files with SBEAMS (https://db.systemsbiology.net/projects/sbeams/)

source_name: prostate tumor Gleason 3

label_protocol: Approximately 200 ng of total RNA was processed to produce biotinylated cRNA.

extract_protocol: Prostate tumor tissue was MACS sorted for positive cells. Total RNA was extracted from the cell lysate.

tag: tissue

value: primary prostate tumor

tag: cell type

value: CD26+ MACS sorted cancer cells


title: CIS patient No.15_Treated

source_name: PBMCs from No.15 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: preadipocyte rep3


title: PPAR gamma siRNA rep2


title: preadipocyte rep1


title: CIS patient No.11_Treated

source_name: PBMCs from No.11 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: TEM4-18_1

status: Public on Jan 15 2009

city: Iowa City

first: Justin

last: Drake

state: IA

address: 6-509 Bowen Science Building

institute: The University of Iowa

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: MAS 5

label: According to Affymetrix protocol

source_name: TEM4-18 cell line, replicate 1

label_protocol: According to Affymetrix protocol

growth_protocol: DMEM/F12 with 10% FBS

extract_protocol: We used TRIzol reagent and RNeasy cleanup kit.  We followed both protocols according to manufacturer's instructions. RNA quality was assessed using the Agilent Model 2100 Bioanalyzer (Agilent Technologies).  Five micrograms of total RNA was processed for use on the microarray.

tag: A PC-3 cell line that was isolated after transendothelial migration across human microvascular endothelial cells from the lung.  These cells are derived from ATCC PC-3 cells and termed TEM4-18.  This cell line expresses luciferase.


title: CIS patient No.12_Treated

source_name: PBMCs from No.12 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: CIS patient No.9_Treated

source_name: PBMCs from No.9 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: CIS patient No.10_Treated

source_name: PBMCs from No.10 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: CIS patient No.8_Treated

source_name: PBMCs from No.8 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: CD26+ cancer cell, replicate 1

description: Primary tumor prostate cancer cells.


title: CIS patient No.7_Treated

source_name: PBMCs from No.7 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: CIS patient No.5_Treated

source_name: PBMCs from No.5 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: CIS patient No.2_Treated

source_name: PBMCs from No.2 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: CIS patient No.3_Treated

source_name: PBMCs from No.3 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: CIS patient No.15_Untreated

description: Gene expression of PBMCs from CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a

source_name: PBMCs from No.15 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: CIS patient No.1_Treated

source_name: PBMCs from No.1 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: CIS patient No.6_Treated

source_name: PBMCs from No.6 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: CIS patient No.10_Untreated

source_name: PBMCs from No.10 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: CIS patient No.9_Untreated

source_name: PBMCs from No.9 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: CIS patient No.6_Untreated

source_name: PBMCs from No.6 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: CIS patient No.14_Untreated

source_name: PBMCs from No.14 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: CIS patient No.11_Untreated

source_name: PBMCs from No.11 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: CIS patient No.8_Untreated

source_name: PBMCs from No.8 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: CIS patient No.4_Treated

source_name: PBMCs from No.4 CIS patient stimulated with aCD3+aCD28 mAb for 24h in presence of IFNb-1a


title: CIS patient No.13_Untreated

source_name: PBMCs from No.13 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: CIS patient No.5_Untreated

source_name: PBMCs from No.5 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: CIS patient No.12_Untreated

source_name: PBMCs from No.12 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: CIS patient No.2_Untreated

source_name: PBMCs from No.2 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: CIS patient No.7_Untreated

source_name: PBMCs from No.7 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: CIS patient No.1_Untreated

source_name: PBMCs from No.1 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: CIS patient No.4_Untreated

source_name: PBMCs from No.4 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: Met 20

city: Dresden

first: Wuttig

last: Daniela

address: Fetscherstr. 74

department: Department of Urology

country: Germany

institute: Dresden, University of Technology

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133 Plus 2.0. GeneChips were washed and stained in the Affymetrix GeneChip Fluidic Station.

scan_protocol: GeneChips were scanned using the GCS3000 7G Scanner (Affymetrix).

data_processing: Global background correction, quantile normalization and log2 transformation were carried out using the RMAExpress 4.1 software.

source_name: pulmonary metastasis of clear-cell renal cell carcinoma (laser resection)

label_protocol: Biotinylated cRNA were prepared according to the One-Cycle Target Labeling and Control Reagents Kit protocol (Affymetrix, Santa Clara, USA) from 2 - 2.5 ug total RNA.

extract_protocol:
Metastases were obtained during precise laser-based resection (1318 nm neodynium-YAG, Coswig Specialized Hospital).
Cryo-sections (4 um) of snap-frozen metastases were made and homogenized using QiaShredder (Qiagen, Hilden, Germany)
RNA was isolated with the RNeasy Mini Kit (Qiagen) with additional DNA digestion (RNase-Free DNase Set, Qiagen).

tag: gender

value: m

tag: Disease free interval (DFI) in  months

tag: no. of metastases


title: Met 23

value: f


title: Met 25


title: Met 14


title: HCT116-CDX1

city: Oxford

first: Carol

last: Chan

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Gene expression in 4 more cell lines that have been modified regarding the expression of CDX1. CDX1 is a homeobox protein that appears to be important to normal development of colorectal epithelium & our recent results indicate that at least a fifth of colorectal carcinoma (CRC) cell lines completely lack CDX1 mRNA expression. In addition, we have shown this loss of expression is exclusively mediated by methylation of the CDX1 promoter. This confirms that CDX1 represents a newly described oncosuppressor gene for colorectal carcinogenesis, although the mechanisms through which CDX1 acts as an oncosuppressor gene nonetheless remain unknown.

hyb_protocol: The protocols are taken from the Affymetrix GeneChip Expression analysis technical manual. http://www.affymetrix.com/support/technical/manual/expression_manual.affx

scan_protocol: Scanning is done in the Affymetrix GeneChip Scanner 3000 system with Autoloader.

data_processing: Gene expression data were normalized using the RMA algorithm.

source_name: colorectal cancer cell lines

label_protocol: Biotinylated cRNA was prepared from 2 microg total RNA using the Enzo BioArray High Yield Transcript Labelling Kit.

extract_protocol: RNA was extracted using the RNeasy Kit (Qiagen) according to the manufacturer's instructions.

tag: HCT116 stably transfected with CDX1 cDNA in the pRC/CMV expression vector


title: HCT116-Vec

tag: HCT116 stably transfected with pRC/CMV expression vector


title: Met 15


title: Met 13


title: LS174T-siVec

tag: LS174T stably transfected with CDX1 pSilencer vector


title: Met 18


title: Met 11


title: Met 17


title: CIS patient No.3_Untreated

source_name: PBMCs from No.3 CIS patient stimulated with aCD3+aCD28 mAb for 24h in absence of IFNb-1a


title: Met 16


title: LS174T-siCDX1

tag: LS174T stably transfected with CDX1 siRNA


title: Met 7


title: Met 1


title: Met 2


title: Met 6


title: Met 9


title: Met 4


title: Met 12


title: Met 8


title: Met 5


title: Met 3


title: Subcutaneous adipose tissue, SAT36

city: Seattle

first: Christopher

middle: L

last: Plaisier

state: Washington

address: 401 Terry Avenue North

institute: Institute for Systems Biology

description: Subcutaneous adipose tissue from 49 unrelated individuals.

hyb_protocol: The cRNA probes were then hybridized using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).

scan_protocol: The chips were scanned using the GeneArray scanner (Affymetrix) to produce CEL files.

data_processing: CEL files were imported into R 2.6.0 using the justRMA function of the Affymetrix library in Bioconductor which does background subtraction and quantile normalization.

source_name: Subcutaneous adipose tissue

label_protocol: Samples were then converted to cRNA probes using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).

extract_protocol: Total RNA was extracted by first disrupting the tissue submerged in QIazol (Qiagen Cat. #79306) with a rotor stator homogenizer, layers were separated with Eppendorf Phase Lock gel 2ml tubes (Eppendorf) and the aqueous layer was then cleaned with the RNeasy Lipid Tissue Mini Kit (Qiagen). The integrity of the RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent).

tag: Subcutaneous adipose tissue


title: Subcutaneous adipose tissue, SAT41


title: Subcutaneous adipose tissue, SAT47


title: Subcutaneous adipose tissue, SAT46


title: Subcutaneous adipose tissue, SAT40


title: Subcutaneous adipose tissue, SAT49


title: Subcutaneous adipose tissue, SAT37


title: Subcutaneous adipose tissue, SAT39


title: Subcutaneous adipose tissue, SAT48


title: Subcutaneous adipose tissue, SAT31


title: Subcutaneous adipose tissue, SAT30


title: Subcutaneous adipose tissue, SAT42


title: Subcutaneous adipose tissue, SAT38


title: Subcutaneous adipose tissue, SAT44


title: Subcutaneous adipose tissue, SAT43


title: Subcutaneous adipose tissue, SAT33


title: Subcutaneous adipose tissue, SAT34


title: Subcutaneous adipose tissue, SAT32


title: Subcutaneous adipose tissue, SAT35


title: Subcutaneous adipose tissue, SAT29


title: Subcutaneous adipose tissue, SAT28


title: Subcutaneous adipose tissue, SAT26


title: Subcutaneous adipose tissue, SAT25


title: Subcutaneous adipose tissue, SAT45


title: Subcutaneous adipose tissue, SAT27


title: E13.5 male embryos_M19

first: Rui

last: Zhu

address: 1515 Holcombe Blvd.

department: Genetics

institute: UT MD Anderson Cancer Center

description: gene expression differences between 129/Sv and 129.MOLF-Chr19 strains

hyb_protocol: 1.Thaw 1 vial of the 20X eukaryotic hybridization controls and the vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) by heating the vials at 65C for 5 minutes. 2.Vortex the vials to ensure complete mixing and then briefly spin down the samples. 3.Prepare the hybridization cocktail as follows: Reagents Mini Array Midi Array Standard Array Fragmented cRNA 5mg 10mg 15 mg Control oligo B2 1.7ml 3.3ml 5ml 20X eukaryotic hybridization controls 5ml 10ml 15ml Herring sperm DNA 1ml 2ml 3ml Acetylated BSA 1ml 2ml 3ml 2X Hybridization buffer 50ml 100ml 150mul Water to 100ml to 200ml to 300ml 4.Equilibrate probe array to room temperature. 5.Heat the hybridization cocktail to 99C for 5 minutes, spin briefly and transfer to 45C for 5 minutes. 6.Spin hybridization/cocktail at maximum speed for 5 minutes to remove any insoluble material. 7.Wet the probe array by filling it through one of the septa with 1X hybridization buffer and incubate at 45C for 10 minutes with rotation. 8.Remove the buffer solution from the probe array and fill the probe array with the appropriate amount of the clarified hybridization cocktail. Hybridize overnight at 45C with rotation. Washing and Staining Probe Arrays Follow instructions for operation and usage of fluidics station as given in the Expression Analysis technical manual from Affymetrix.

scan_protocol: The arrays were stained with phycoerythrin-coupled avidin and scanned using a GeneArray Scanner 3000. The resultant output was analyzed using Affymetrix Microarray Suite software and examined for excessive background or evidence of RNA degradation. All microarray processing was performed in the Murine Microarray and Affymetrix Facility at the University of Texas M. D. Anderson Cancer Center.

data_processing: dChip (version 1.3) scaled. Normalized.

source_name: E13.5 male embryos 129.MOLF-Chr19

label_protocol:
Synthesis of Double Stranded cDNA from Total RNA (Using the Supercript Choice System by Gibco)
Use a starting amount of 5.0 – 40.0 mg total RNA.
First Strand cDNA Synthesis (using 5.0 mg of total RNA)
1.In a 1.5 mL microcentrifuge tube, combine the following: x mL of total RNA, 12- x mL of RNase/DNase free water and 1 mL of T7- (dT)24 primer.
2.Incubate at 70° C for 10 minutes. Centrifuge to collect contents at the bottom of the tube. Put on ice.
3.Add the following to the tube: 4 mL of 5X First strand cDNA buffer, 2 mL of 0.1 M DTT, and 1 mL of 10 mM dNTP mix.
4.Incubate at 42° C for 2 minutes.
5.Add to the tube 1 mL of Superscript II reverse transcriptase.
6.Incubate at 42° C for 1 hour. Centrifuge to collect contents at the bottom of the tube. Put on ice.
Second Strand cDNA Synthesis (using 5.0 mg of total RNA)
1.Add the following to the First Strand Synthesis tube: 91 mL of RNase/DNase free water, 30 mL of 5X Second strand reaction buffer, 3 mL of 10 mM dNTP mix, 1 mL of 10 U/mL DNA Ligase (E. coli), 4 mL of 10 U/mL DNA Polymerase I (E. coli), and 1 mL of 2 U/mL RNase H (E. coli).
2.Tap tube to mix. Centrifuge to collect contents at the bottom of the tube. Incubate at 16°C for 2 hours.
3.Add 2 mL [10 U] T4 DNA Polymerase.
4.Incubate at 16° C for 5 minutes.
5.Add 10 mL 0.5 M EDTA.
Cleanup of Double-Stranded cDNA
Phenol/Chloroform Extraction
1.Add 162 mL of (25:24:1) Phenol:chloroform:isoamyl alcohol. Vortex.
2.Centrifuge sample at maximum speed for 2 minutes.Transfer aqueous phase to fresh 1.5 mL microcentrifuge tube.
Ethanol Precipitation
1.Add 10 mg/mL of glycogen, 0.5 volumes of 7.5 M ammonium acetate, and 2.5 volumes of absolute ethanol to sample. Vortex.
2.Immediately spin at maximum speed for 20 minutes at room temperature.
3.Remove supernatant. Wash pellet with 500 mL of 80% ethanol. Spin at maximum speed for 5 minutes at room temperature.
4.Remove 80% ethanol. Wash again with 500 mL of 80% ethanol. Spin at maximum speed for 5 minutes at room temperature.
5.Air dry pellet.
6.Resuspend in 12 mL of RNase/Dnase free water. (You can store at -20°C. Save 1-2 mL aliquot to run on gel later.
Synthesis of Biotin-Labeled cRNA (Using In Vitro Transcription Reaction)
IVT Reaction (Using the ENZO BioArray High Yield RNA Transcript Labeling Kit)
1.Add the following to a fresh 1.5 mL microcentrifuge tube: x mL to give 1 mg double-stranded cDNA, 22 – x mL of RNase/Dnase free water, 4 mL of 10 X HY reaction buffer, 4 mL of 10 X Biotin labeled ribonucleotides, 4 mL of 10 X DTT, 4 mL of 10 X RNase inhibitor mix, and 2 mL of T7 RNA polymerase.
2.Incubate at 37°C for 4 – 5 hours, mixing tube every 30 – 45 minutes. (You can store at -20°C until ready to purify.
IVT Cleanup
-The preferred method for cRNA cleanup is by using RNeasy spin columns from Qiagen.
-The RNA elution step is performed twice to increase recovery.
-Ethanol precipitation (performed as described above) is performed following RNA elution and the RNA pellet is resuspended in 18 ml of water.
Quantifying the cRNA
1.Prepare 1:50 dilution of the RNA to a total of 100 ml.
2.Check OD at 260nm and 280 nm to determine sample concentration and purity. A 260/A280 ratio between 1.9 and 2.1 is acceptable.
3.The following formula is used to determine the cRNA yield.
Adjusted cRNA yield=RNA* - (total RNA#)($)
RNA* = amount of cRNA measured after IVT (mg)
total RNA# = sterting amount of total RNA (mg)
$ = fraction of cRNA reaction used in IVT
cRNA Fragmentation
1.To 20 mg of unadjusted cRNA 2 ml of 5X fragmentation buffer is added for every 8 ml of RNA and the total volume is adjusted to 40ml with water.
2.The fragmentation reaction is performed at 94C for 35 minutes and kept on ice post incubation.
3.An aliquot of cRNA is saved for gel analysis and the rest is stored at –20C until ready to perform hybridization.
Gel Electrophoresis
1.Run aliquots of purified cDNA (after ethanol precipitation), purified cRNA and fragmented cRNA on 1% agarose gel.
2.Mix RNA with loading dye and heat to 65C for 5 minutes before loading on the gel.

extract_protocol: 3 male embryos were pooled. RNA was isolated using Qiagen RNeasy mini kits. RNA was eluted in RNase free water and frozen at -80 degrees Celsius until sample quality could be assessed with the Agilent Bioanalyzer system.

tag: Background Srain

value: 129.MOLF-Chr 19

tag: Gender

value: male

tag: Tissue

value: whole embryos

tag: Age


title: E13.5 male embryos_129/Sv

source_name: E13.5 male embryos 129/Sv


title: Subcutaneous adipose tissue, SAT24


title: PN1 Mouse testis_M19

source_name: postnatal day 1 Mouse testis 129.MOLF-Chr19

extract_protocol: 25 pairs of PN1 testes were pooled. RNA was isolated using Qiagen RNeasy mini kits. RNA was eluted in RNase free water and frozen at -80 degrees Celsius until sample quality could be assessed with the Agilent Bioanalyzer system.

value: testis

value: postnatal day 1


title: Subcutaneous adipose tissue, SAT23


title: PN1 Mouse testis_129/Sv

source_name: postnatal day 1 Mouse testis 129/Sv

extract_protocol: 12 pairs of PN1 testes were pooled. RNA was isolated using Qiagen RNeasy mini kits. RNA was eluted in RNase free water and frozen at -80 degrees Celsius until sample quality could be assessed with the Agilent Bioanalyzer system.


title: Subcutaneous adipose tissue, SAT22


title: E13.5 Mouse testis_M19

source_name: E13.5 male genital ridges, 129.MOLF-Chr 19

extract_protocol: 20 pairs of testes were pooled. RNA was isolated using Qiagen RNeasy mini kits. RNA was eluted in RNase free water and frozen at -80 degrees Celsius until sample quality could be assessed with the Agilent Bioanalyzer system.


title: Subcutaneous adipose tissue, SAT18


title: Subcutaneous adipose tissue, SAT16


title: Subcutaneous adipose tissue, SAT21


title: Subcutaneous adipose tissue, SAT9


title: Subcutaneous adipose tissue, SAT8


title: Subcutaneous adipose tissue, SAT17


title: Subcutaneous adipose tissue, SAT11


title: Subcutaneous adipose tissue, SAT14


title: Subcutaneous adipose tissue, SAT13


title: Subcutaneous adipose tissue, SAT19


title: Subcutaneous adipose tissue, SAT15


title: Subcutaneous adipose tissue, SAT20


title: Subcutaneous adipose tissue, SAT5


title: Subcutaneous adipose tissue, SAT7


title: Subcutaneous adipose tissue, SAT12


title: Subcutaneous adipose tissue, SAT10


title: E13.5 Mouse testis_129/Sv

source_name: E13.5 male genital ridge 129/Sv


title: Subcutaneous adipose tissue, SAT3


title: Subcutaneous adipose tissue, SAT6


title: Subcutaneous adipose tissue, SAT4


title: Subcutaneous adipose tissue, SAT2


title: Subcutaneous adipose tissue, SAT1


title: MCF10a_MEK1_Vector_rep3

status: Public on Jan 12 2009

city: South San Francisco

first: Mark

last: Lackner

state: CA

address: 1 DNA Way

institute: Genentech

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133P 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with 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: MCF10a treated with MEK1 vector 24h

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

growth_protocol: Cells were grown in DMEM/F12 with 15 mM hepes buffer supplemented with 5% horse serum, 10 ug/ml insulin, 20 ng/ml EGF, 100 ng/ml choleratoxin, 0.5 ug/ml hydrocortisone pen/strep

extract_protocol: Qiagen Rneasy kit used for the extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were optimally transfected with  null, HRAS or MEK1 vectors.  Cells lysed 24h post-transfection

tag: MCF10a  immortalized, non-transformed human mammary epithelial cell-line overexpressing MEK


title: MCF10a_HRas_Vector_rep2

source_name: MCF10a treated with HRas vector 24h

tag: MCF10a  immortalized, non-transformed human mammary epithelial cell-line overexpressing RAS


title: MCF10a_MEK1_Vector_rep6


title: MCF10a_Null_Vector_rep4

source_name: MCF10a treated with null vector 24h

tag: MCF10a  immortalized, non-transformed human mammary epithelial cell-line overexpressing null vector


title: MCF10a_MEK1_Vector_rep5


title: breast cancer cell line_BT20

description: breast cancer cell line_BT20

source_name: Breast cancer

growth_protocol: Cell maintained in RPMI1640 or DMEM supplemented with 10% fetal bovine serum, non-essential amino acids and 2mmol/L L-glutamine

treatment_protocol: Cells untreated

value: Basal

value: Nonamplified


title: MCF10a_Null_Vector_rep2


title: MCF10a_HRas_Vector_rep1


title: Breast tumor tissue_HF-11383

description: Breast tumor tissue_HF-11383

tag: Luminal


title: breast cancer cell line_MDA-MB-134VI

description: breast cancer cell line_MDA-MB-134VI


title: MCF10a_Null_Vector_rep6


title: MCF10a_HRas_Vector_rep5


title: breast cancer cell line_KPL4

description: breast cancer cell line_KPL4

value: Luminal

value: Her2 amplified


title: Breast tumor tissue_HF-11385

description: Breast tumor tissue_HF-11385


title: MCF10a_HRas_Vector_rep3


title: Breast tumor tissue_HF-11255

description: Breast tumor tissue_HF-11255


title: MCF10a_Null_Vector_rep3


title: breast cancer cell line_HCC202

description: breast cancer cell line_HCC202


title: breast cancer cell line_MX1

description: breast cancer cell line_MX1


title: MCF10a_Null_Vector_rep1


title: MCF10a_Null_Vector_rep5


title: MCF10a_MEK1_Vector_rep4


title: MCF10a_HRas_Vector_rep4


title: Breast tumor tissue_HF-11392

description: Breast tumor tissue_HF-11392


title: MCF10a_MEK1_Vector_rep2


title: Breast tumor tissue_HF-11356

description: Breast tumor tissue_HF-11356


title: Breast tumor tissue_HF-11361

description: Breast tumor tissue_HF-11361

tag: Basal-like


title: MCF10a_MEK1_Vector_rep1


title: Breast tumor tissue_HF-11355

description: Breast tumor tissue_HF-11355


title: Breast tumor tissue_HF-11354

description: Breast tumor tissue_HF-11354


title: Breast tumor tissue_HF-11347

description: Breast tumor tissue_HF-11347


title: Breast tumor tissue_HF-11434

description: Breast tumor tissue_HF-11434


title: Breast tumor tissue_HF-11342

description: Breast tumor tissue_HF-11342


title: Breast tumor tissue_HF-11327

description: Breast tumor tissue_HF-11327


title: Breast tumor tissue_HF-11237

description: Breast tumor tissue_HF-11237


title: Breast tumor tissue_HF-11320

description: Breast tumor tissue_HF-11320


title: Breast tumor tissue_HF-11332

description: Breast tumor tissue_HF-11332


title: Breast tumor tissue_HF-11328

description: Breast tumor tissue_HF-11328


title: Breast tumor tissue_HF-11316

description: Breast tumor tissue_HF-11316


title: Breast tumor tissue_HF-11321

description: Breast tumor tissue_HF-11321


title: Breast tumor tissue_HF-11352

description: Breast tumor tissue_HF-11352


title: Breast tumor tissue_HF-11310

description: Breast tumor tissue_HF-11310


title: Breast tumor tissue_HF-11317

description: Breast tumor tissue_HF-11317


title: Breast tumor tissue_HF-11350

description: Breast tumor tissue_HF-11350


title: Breast tumor tissue_HF-11318

description: Breast tumor tissue_HF-11318


title: Breast tumor tissue_HF-11329

description: Breast tumor tissue_HF-11329


title: Breast tumor tissue_HF-11322

description: Breast tumor tissue_HF-11322


title: Breast tumor tissue_HF-11308

description: Breast tumor tissue_HF-11308


title: Breast tumor tissue_HF-11225

description: Breast tumor tissue_HF-11225


title: Breast tumor tissue_HF-11219

description: Breast tumor tissue_HF-11219


title: Breast tumor tissue_HF-11323

description: Breast tumor tissue_HF-11323


title: Breast tumor tissue_HF-11233

description: Breast tumor tissue_HF-11233


title: retina_normox_16h_3

status: Public on Jan 10 2009

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

country: France

institute: IGBMC

description: retina after 16 h normoxic treatment

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix).

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

data_processing: RMA

source_name: retina after 16 h normoxic treatment

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix)

growth_protocol: BALB/c mice were grown under standard conditons (ARVO).

extract_protocol: Retinas were isolated immediately, 0 h, 2 h, 4 h and 16 h after hypoxic preconditioning, frozen in liquid nitrogen and stored at -70°C, 3 retinas of 3 different mice were pooled and the procedure repeated 3 times to generate independent biological triplicates. RNA was extracted using the RNeasy isolation kit (Qiagen, Hilden, Germany), including a DNase treatment to digest residual genomic DNA.

treatment_protocol: After hypoxic preconditioning (6% O2 for 6 hours) reoxygenation was allowed in darkness for 0 h, 2 h, 4 h, 12 h and 16 h in normal room air in darkness. After reoxygenation BALB/c mice were exposed to 5'000 lux of white fluorescent light for 1 h and analyzed at the time points as indicated (Thiersch et al, BMC Genomics. 2008, 9:73).

tag: retina

tag: BALB/c


title: retina_hypox_16h_2

description: retina after 16 h hypoxic treatment

source_name: retina after 16 h hypoxic treatment


title: Oocyte_M2-16

city: Montpellier

first: John

last: De Vos

address: 80 av. Augustin Fliche

department: Institute for Research in Biotherapy

institute: University Hospital of Montpellier

description: Human embryonic stem cells (hESC) samples were compared to somatic tissues, human mature oocytes samples were compared to somatic tissues, then the hESC and the mature oocyte signatures were interesected to define an oocyte/hESC signature.

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

source_name: pooled, unfertilized mature human MII oocytes

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from about ∼4 ng total RNA.

extract_protocol: Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.

tag: Pooled, unfertilized MII oocytes (21 oocytes) collected after informed consent 44 hours post insemination or post microinjection by ICSI . All oocytes were from couples referred to our center for cIVF (tubal infertility) or for ICSI (male infertility).


title: retina_hypox_16h_1

description: retina after 16 h hypoxic treatment


title: retina_hypox_4h_3

description: retina after 4 h hypoxic treatment

source_name: retina after 4 h hypoxic treatment


title: Oocyte_M2-24


title: retina_normox_16h_2

description: retina after 16 h normoxic treatment


title: retina_hypox_4h_2

description: retina after 4 h hypoxic treatment


title: retina_normox_4h_2

description: retina after 4 h normoxic treatment

source_name: retina after 4 h normoxic treatment


title: retina_hypox_16h_3

description: retina after 16 h hypoxic treatment


title: retina_hypox_4h_1

description: retina after 4 h hypoxic treatment


title: HEPG2_1ug

source_name: hepatocellular carcinoma cell line HEPG2 (1ug)

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) 'standard protocol', starting from 1 microgram total RNA.

tag: subconfluent hepatocellular carcinoma cell line HEPG2. Sample labelling starting with  1 microgram total RNA.


title: retina_normox_4h_1

description: retina after 4 h normoxic treatment


title: retina_normox_4h_3

description: retina after 4 h normoxic treatment


title: retina_normox_2h_2

description: retina after 2 h normoxic treatment

source_name: retina after 2 h normoxic treatment


title: retina_normox_2h_3

description: retina after 2 h normoxic treatment


title: retina_normox_2h_1

description: retina after 2 h normoxic treatment


title: retina_normox_0h_3

description: retina after 0 h normoxic treatment

source_name: retina after 0 h normoxic treatment


title: retina_hypox_2h_3

description: retina after 2 h hypoxic treatment

source_name: retina after 2 h hypoxic treatment


title: retina_hypox_2h_1

description: retina after 2 h hypoxic treatment


title: retina_hypox_0h_1

description: retina after 0 h hypoxic treatment

source_name: retina after 0 h hypoxic treatment


title: retina_hypox_2h_2

description: retina after 2 h hypoxic treatment


title: retina_hypox_0h_2

description: retina after 0 h hypoxic treatment


title: retina_normox_0h_2

description: retina after 0 h normoxic treatment


title: retina_hypox_0h_3

description: retina after 0 h hypoxic treatment


title: T cell_Cycloheximide_4.5h_rep3

city: Livermore

first: Zhaoduo

last: Zhang

address: 7011 East Ave

department: Biosystems

institute: Sandia National Labs

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by cycloheximide treatment for 4.5 hours

hyb_protocol: Following fragmentation, 10 ?g of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix Gene-Chip scanner 3000.

data_processing: The data were analyzed with Affymetric GeneChip Operating Software (GCOS, version 1.3) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: T cells, IL-2 starved for 14 hours followed by cycloheximide treatment for 4.5 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ?g total RNA (GeneChip Expression Analysis, Technical Manual (701021 Rev. 5), 2005, Affymetrix).

growth_protocol: Mouse CTLL-2 cells was maintained in an incubator with 5% CO2 at 37oC in D10 medium (D10 = ATCC modified RPMI-1640 medium (10 mM HEPES, 2 mM L-glutamine, 1 mM Sodium pyruvate, 4.5 g/L glucose, 1.5 g/L sodium bicarbonate), supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 50 U/mL penicillin, 50 mg/mL streptomycin, 1 mM sodium pyruvate, 45 µM ?-mercaptoethanol), and 50 U/mL human rIL-2 (Chiron).

extract_protocol: Cells was collected and washed with PBS, resuspended in PBS before adding RNAlater RNA stabilization solution (Qiagen). Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by treatment with cycloheximide (20 ?g/mL) for 4.5 hours at 37oC with 5% CO2.

tag: Cytotoxic T lymphocyte cell line CTLL-2, derived from a C57BL/6 mouse, dependent upon IL-2 for growth


title: Oocyte_M2-21

hyb_protocol: hybridization and washing was carried out on a GeneChip (Affymetrix) station, washing  according to the manufacturer’s protocol.

scan_protocol: Scann carried out on a GeneChip (Affymetrix) station (7G Scanner) according to the manufacturer’s protocol.

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from total RNA, about ∼4 ng for a pooled oocytes sample

extract_protocol: Total RNA was isolated using RNeasy mini kits (Qiagen, Courtaboeuf, France) and quantified using a NanoDrop spectrophotometer (Thermo Fischer,Wilmington, Delaware, USA).

tag: pooled, unfertilized MII oocytes (21 oocytes) collected after informed consent 44 hours post insemination or post microinjection by ICSI . All oocytes were from couples

tag: referred to our center for cIVF (tubal infertility) or for ICSI (male infertility).


title: retina_normox_0h_1

description: retina after 0 h normoxic treatment


title: T cell_Cycloheximide_4.5h_rep4


title: T cell_Cycloheximide_4.5h_rep2


title: 05-WH-028: MSI

status: Public on Jan 08 2009

city: Parkville

first: Oliver

last: Sieber

state: Victoria

address: 6th floor, Centre for Medical Research,  Royal Melbourne Hospital,  Royal Parade

department: Melbourne Tumour Biology Branch

country: Australia

institute: Ludwig Institute for Cancer Research

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: The simpleaffy package in R/Bioconductor was used to calculate MAS5.0 calls. These values are not normalized. Normalization was performed by quantile normalization with respect to a defined reference set.

source_name: primary colorectal adenocarcinoma

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Surgically isolated colorectal cancers were immediately frozen in liquid nitrogen. Total RNA was extracted from cancer tissue using Trizol reagent (Invitrogen).

tag: MSI


title: 05-WH-052: MSI


title: 04-TB-124: MSS

tag: MSS


title: 04-TB-058: MSS


title: 05-WH-018: MSS


title: 04-TB-021: MSS


title: 04-TB-077: MSS


title: 05-WH-027: MSS


title: T cell_IL-2_Cycloheximide_4 hour_rep4

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by cycloheximide for 30min prior to IL-2 stimulation for 4 hours

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software (GCOS, version 1.3) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: T cells, IL-2 starved for 14 hours followed by cycloheximide for 30min prior to IL-2 stimulation for 4 hours

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by treatment with cycloheximide (20 ?g/mL) for 30min prior to human rIL-2 (100 U/mL, Chiron) stimulation for 4 hours at 37oC with 5% CO2.


title: 04-TB-007: MSS


title: T cell_Cycloheximide_4.5h_rep1


title: T cell_IL-2_Cycloheximide_4 hour_rep2


title: 05-WH-067: MSS


title: 05-WH-057: MSS


title: 04-TB-155: MSS


title: 04-TB-138: MSS


title: 04-TB-061: MSS


title: 04-TB-075: MSS


title: T cell_Cycloheximide_30min_rep3

description: Gene expression data from T cells cultured without IL-2 for 14 hours followed by cycloheximide for 30min

source_name: T cells, IL-2 starved for 14 hours followed by cycloheximide for 30min

treatment_protocol: Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by treatment with cycloheximide (20 ?g/mL) for 30min at 37oC with 5% CO2.


title: T cell_Cycloheximide_30min_rep4


title: T cell_IL-2_Cycloheximide_4 hour_rep1


title: 04-TB-076: MSS


title: T cell_Cycloheximide_30min_rep2


title: T cell_IL-2_Cycloheximide_4 hour_rep3


title: 04-TB-015: MSS


title: 03-TB-108: MSS


title: 03-TB-102: MSS


title: 03-TB-083: MSS


title: 03-TB-096: MSS


title: retina_normox_16h_1

description: retina after 16 h normoxic treatment


title: 03-TB-040: MSI


title: 03-TB-078: MSS


title: 03-TB-066: MSS


title: 03-TB-032: MSS


title: 03-TB-036: MSS


title: 03-TB-061: MSS


title: 03-TB-009: MSS


title: 03-TB-021: MSI


title: 03-TB-031: MSS


title: 03-TB-030: MSS


title: 03-TB-003: MSS


title: 03-TB-024: MSS


title: 03-TB-022: MSI


title: 03-TB-019: MSS


title: 03-TB-014: MSS


title: 03-TB-012: MSS


title: 02-TB-073: MSI


title: 02-TB-085: MSS


title: 02-TB-079: MSS


title: 03-TB-008: MSS


title: 03-TB-005: MSS


title: 02-TB-062: MSS


title: 02-TB-084: MSI


title: 02-TB-088: MSS


title: 02-TB-056: MSS


title: 02-TB-064: MSI


title: 02-TB-087: MSS


title: 02-TB-059: MSS


title: 02-TB-061: MSS


title: 02-TB-050: MSS


title: 02-TB-074: MSI


title: 02-TB-038: MSS


title: 01-TB-035: MSS


title: 02-TB-052: MSS


title: 02-TB-060: MSS


title: T cell_Cycloheximide_30min_rep1


title: 02-TB-045: MSS


title: 02-TB-055: MSS


title: 01-TB-037: MSS


title: nTreg-1

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

description: Total cellular RNA from either isolated naïve and natural Treg cells or cells cultured under Th1, Th2, Th17, and iTreg conditions was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Approximately 10 µg of RNA was labeled and hybridized to GeneChip Mouse Genome 430 2.0 arrays (Affymetrix) according to the manufacturer's protocols. Expression values were determined using GeneChip Operating Software (GCOS) v1.1.1 software. All data analysis was performed using GeneSpring software GX 7.3.1 (Agilent Technologies).

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: MAS5 processed

source_name: CD25hiCD4+ T cells

label_protocol: Standard Affymetrix

extract_protocol: Trizal reagent, standard protocol

tag: CD25hiCD4+ T cells


title: 02-TB-042: MSS


title: 02-TB-040: MSS


title: 02-TB-035: MSS


title: nTreg-2


title: iTreg-2

source_name: CD4+ T cells cultured in vitro for 10 days


title: 02-TB-016: MSS


title: iTreg-1

tag: CD4+ T cells cultured in vitro for 10 days


title: 01-TB-032: MSS


title: Naive-2

source_name: Naive CD4+ T cells

tag: Naive CD4+ T cells


title: 01-TB-034: MSS


title: 02-TB-018: MSS


title: 01-TB-008: MSS


title: 01-TB-024: MSI


title: 01-TB-030: MSS


title: 01-TB-019: MSS


title: 00-TB-005: MSS


title: Th1-1


title: Th17-2


title: Naive-1

source_name: Freshly isolated naive CD4+ T cells

tag: Freshly isolated naive CD4+ T cells


title: 01-TB-006: MSS


title: Th1-2


title: Th17-1


title: Th2-1

source_name: CD4+ T cells cultured for 10 days

tag: CD4+ T cells cultured for 10 days


title: Th2-2


title: SMRTmRID 3T3-MEFs, technical replicate 1

status: Public on Jan 07 2009

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description:
Gene expression data from SMRTmRID 3T3-MEFs
Undifferentiated 3T3-MEFs were harvested upon reaching confluency.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with MG430 2.0 arrays, washed and processed in accordance with standard Affymetrix protocols.

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

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

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

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

tag: SMRTmRID 3T3-MEFs

tag: undifferentiated cells


title: SMRTmRID 3T3-MEFs, technical replicate 2


title: 00-TB-002: MSI


title: mouse 3T3_TNF_0.5h

city: PASADENA

first: Shengli

last: Hao

address: 1200 E. California Blvd,

department: Biology Division

institute: California Institute of Technology

description: standard Affymetrix procedures

hyb_protocol: Standard protocol for GeneChip Expression Analysis from Affymetrix Technical Manual.

data_processing: Affymetrix STATISTICAL_ALGORITHM_TYPE

source_name: mouse embryonic 3T3 fibroblasts stimulated with TNF for 0.5h

label_protocol: 8 µg of total RNA was analysed for integrity and labeled for microarray analysis using the Affymetrix Mouse Genome 430 2.0 array. cDNA generated using Alternative Protocol for One-Cycle cDNA synthesis from Total RNA.

growth_protocol: Mouse embryonic immortal 3T3 fibroblast cell lines were maintained at less than 90% confluence in DMEM medium supplemented with 10% bovine calf serum (Hyclone), Penicillin/Streptomycin.

extract_protocol: Total RNA was isolated using Qiagen RNeasy MINI kit.

treatment_protocol: For experiments, cells were cultured for 24 hours in low density with normal culture medium and were then maintained overnight with 0.5% serum before stimulation with TNF 10ng/ml for 0.5h and then harvesting for RNA

tag: mouse embryonic 3T3 fibroblasts


title: Wild-type 3T3-MEFs, technical replicate 1

description:
Gene expression data from wild-type 3T3-MEFs
Undifferentiated 3T3-MEFs were harvested upon reaching confluency.

tag: wild-type 3T3-MEFs


title: mouse 3T3_TNF_2h

description: standard Affymetrix procedures

source_name: mouse embryonic 3T3 fibroblasts stimulated with TNF for 2h

treatment_protocol: For experiments, cells were cultured for 24 hours in low density with normal culture medium and were then maintained overnight with 0.5% serum before harvesting for RNA (basal expression).


title: mouse 3T3_TNF_12h

description: standard Affymetrix procedures

source_name: mouse embryonic 3T3 fibroblasts stimulated with TNF for 12h

treatment_protocol: For experiments, cells were cultured for 24 hours in low density with normal culture medium and were then maintained overnight with 0.5% serum before stimulation with 10 ng/ml TNF for 12 hours and then harvesting for RNA .


title: large airways, smoker 159

status: Public on Jan 06 2009

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: Comparison of gene expression in large airway epithleium of normal non-smokers and normal smokers

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HuGeneFL, HG-U133A or HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneArray 2500 for HuGeneFL and the GeneChip Scanner 3000 7G for HG-U133A and HG-U133 Plus 2.0.

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

source_name: large airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA for HuGeneFL and HG-U133A or 2 microg total RNA for HG-U133 Plus 2.0 (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

value: F

tag: Ethnic group

value: black

tag: Smoking status

value: smoker, 3.8 pack-years


title: large airways, smoker 127

value: M

value: smoker, 11.5 pack-years


title: large airways, smoker 134

value: white

value: smoker, 20 pack-years


title: large airways, smoker 151

value: hispanic

value: smoker, 12.5 pack-years


title: large airways, smoker 169

value: smoker, 47 pack-years


title: mouse 3T3_Basal

description: standard Affymetrix procedures

source_name: mouse embryonic 3T3 fibroblasts


title: Wild-type 3T3-MEFs, technical replicate 2


title: large airways, smoker 141

value: hispnaic

value: smoker, 13 pack-years


title: large airways, smoker 040

value: smoker, 24 pack-years


title: large airways, smoker 161

value: smoker, 5 pack-years


title: large airways, smoker 155

value: smoker, 7.6 pack-years


title: large airways, smoker 136

value: smoker, 26 pack-years


title: large airways, smoker 125

value: smoker, 19 pack-years


title: large airways, smoker 129

value: smoker, 11 pack-years


title: large airways, smoker 130

value: smoker, 12 pack-years


title: large airways, smoker 090

value: smoker, 10 pack-years


title: large airways, smoker 122

value: M

value: smoker, 3 pack-years


title: large airways, non-smoker 066

value: black

value: non-smoker


title: large airways, non-smoker 072

value: F


title: large airways, non-smoker 006


title: large airways, smoker 087

value: hispanic

value: smoker, 30 pack-years


title: large airways, non-smoker 071


title: large airways, non-smoker 078

value: white


title: large airways, non-smoker 050


title: large airways, non-smoker 045


title: large airways, non-smoker 065


title: large airways, non-smoker 041


title: large airways, non-smoker 059


title: large airways, smoker 120


title: OBF-1 overexpression BCS-3 (Large PreB)

status: Public on Jan 05 2009

city: Basel

first: Edward

middle: James

last: Oakeley

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Large PreB from an OBF-1 overexpressing mouse

hyb_protocol: RNA was hybridised using the standard Affymetrix hybridisation protocol as per manufacturer's instructions (45°C over night)

scan_protocol: The chips were scanned using an Affymetrix genechip scanner as per manufacturer's instructions

data_processing: Expression values were estimated using the GCRMA algorithm implemented in Genedata's Refiner 4.5. Further data anaylsis was performed using Genedata's Analyst 4.5

source_name: Large PreB

label_protocol: RNA was amplified and labelled using the Affymetrix 1-cycle 3'IVT protocol

growth_protocol: Mice were grown for seven weeks in our mouse facility

extract_protocol: RNA was purified using the Qiagen RNA easy protocol according to the manufacturer's insructions

treatment_protocol: EPLM and Large PreB cells were FACS sorted

tag: Strain

value: B6CF1 x C57BL/6, Tissue:Bone marrow, Age:7 weeks


title: large airways, smoker 167

value: smoker, 43 pack-years


title: large airways, non-smoker 040

value: black/hispanic


title: OBF-1 overexpression BCS-4 (Large PreB)


title: large airways, non-smoker 038

value: asian


title: large airways, non-smoker 047

tag: Smoking status:smoker, 1 pack-years


title: large airways, non-smoker 036

value: hispnaic


title: OBF-1 overexpression BCS-2 (Large PreB)


title: OBF-1 overexpression BCS-1 (Large PreB)


title: WT-4 (Large PreB)

description: Control EPLM


title: WT-3 (Large PreB)

description: Control EPLM


title: WT-2 (Large PreB)

description: Control EPLM


title: Vehicle-Control 24 hours set 1

city: Boston

first: dimitrios

last: Spentzos

state: MA

address: 330 Brookilne Ave CLS 541

department: Department of medicine

institute: Beth ISrael Deaconess Medical center

description: Gene expression data from 36M2 trated with Vehicle-Control for 24hrs

hyb_protocol: cDNA synthesis and hybridization on oligonucleotide microarrays (U133 Plus 2.0 Array GeneChip, Affymetrix, Inc., Santa Clara, CA) containing approximately 54,700 transcripts were carried out using standard protocols.

scan_protocol: The chips were scanned in an HIP chip scanner (Affymetrix)

data_processing: Robust Multi-Array (RMA)

source_name: 36M2 cell line from ovarian serous carcinoma cells

growth_protocol: Cells were grown in RPMI 1640 media with L-glutamine, 10% fetal bovine serum and 1% of penicillin/streptomycin.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen Valencia, CA, USA) according to manufacturer’s instructions

treatment_protocol: we treated the 36M2 cell line with carboplatin 100μM or vehicle-control for 24hrs and cells were harvested and processed for RNA isolation at 24, 30 and 36hrs after treatment.

tag: Vehicle-Control

tag: Vehicle-Control 24 hours set 1


title: Carboplatin 36 hours set 1

description: Gene expression data from 36M2 trated with Carboplatin for 36hrs

label_protocol: cDNA synthesis and hybridization on oligonucleotide microarrays (U133 Plus 2.0 Array GeneChip, Affymetrix, Inc., Santa Clara, CA) containing approximately 54,700 transcripts were carried out using standard protocols.

tag: Carboplatin

tag: Carboplatin 36 hours set 1


title: Carboplatin 36 hours set 2

tag: Carboplatin 36 hours set 2


title: Vehicle-Control 30 hours set 2

description: Gene expression data from 36M2 trated with Vehicle-Control for 30hrs

tag: Vehicle-Control 30 hours set 2


title: Vehicle-Control 36 hours set 2

description: Gene expression data from 36M2 trated with Vehicle-Control for 36hrs

tag: Vehicle-Control 36 hours set 2


title: Carboplatin 24 hours set 2

description: Gene expression data from 36M2 trated with Carboplatin for 24hrs

tag: Carboplatin 24 hours set 2


title: Vehicle-Control 30 hours set 1

tag: Vehicle-Control 30 hours set 1


title: Vehicle-Control 24 hours set 2

tag: Vehicle-Control 24 hours set 2


title: Vehicle-Control 36 hours set 1

tag: Vehicle-Control 36 hours set 1


title: 01-TB-020: MSS

tag: MSS


title: Carboplatin 30 hours set 2

description: Gene expression data from 36M2 trated with Carboplatin for 30hrs

tag: Carboplatin 30 hours set 2


title: Carboplatin 24 hours set 1

tag: Carboplatin 24 hours set 1


title: skin_IFNARKO_salineinjected_24hours_rep2

status: Public on Jan 02 2009

first: Barbara

last: Burleigh

address: 665 Huntington Ave

department: Immunology and Infectious Diseases

institute: Harvard School of Public Health

description: Gene expression date for control (saline injected) IFNAR-/- mice

hyb_protocol: Following fragmentation of 20ug of cRNA, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Genepattern Software v2.0 (43) and normalized using ExpressionFileCreator under default settings to do RMA with quartile normalization, background correction and median scaling.

source_name: skin, IFNARKO, saline injected, 24 hours.

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

growth_protocol: Trypomastigotes harvested from culture supernatants were washed twice in sterile 0.9 % saline prior to injection

extract_protocol: 24 hours post-injection skin surrounding the injection site was excised and snap frozen in liquid nitrogen.  Frozen tissue was mixed with Trizol reagent and homogenized using the OMNI tissue homogenizer or Lysing Martrix D (QBiogene) and the FP120 machine (Savant). RNA was extracted from homogenized tissue using Trizol reagent (Invitrogen) according to manufacturer’s RNA isolation protocol. The RNA was then purified using the RNAeasy Kit (Qiagen) according to the RNA cleanup protocol.

treatment_protocol: mice were shaved an injected intradermally on the side flank with 100uL of saline vehicle or 10^6 T. cruzi split between 2 adjacent sites

tag: 129-ifnar-/-, female, 16-18g, tissue:skin, saline injected


title: skin_129_Ystraininfected_24hours_rep2

description: Gene expression data for Y strain infected 129 mice

source_name: skin, Y strain infected, 24 hours

tag: 129, female, 16-18g, tissue:skin, Y strain infected


title: skin_IFNARKO_Ystraininfected_24hours_rep1

description: Gene expression date for Y strain infected IFNAR-/- mice

source_name: skin, IFNARKO, Y strain infected, 24 hours.

tag: 129-ifnar-/-, female, 16-18g, tissue:skin, Y strain infected


title: skin_129_Ystraininfected_24hours_rep1


title: skin_IFNARKO_Ystraininfected_24hours_rep2


title: skin_IFNARKO_salineinjected_24hours_rep1


title: skin_129_salineinjected_24hrs_rep3

description: Gene expression data for control (saline injected) 129 mice

source_name: skin, saline injected, 24 hours.

tag: 129, female, 16-18g, tissue:skin, saline injected


title: skin_IFNgKO_Ystraininfected_24hrs_rep1

description: Gene expression data for Y strain infected IFNg-/- mice

source_name: skin, IFNgKO, Y strain infected, 24 hours

tag: C.129S7(B6)-Ifngtm1Ts/J, female, 16-18g, tissue:skin, Y strain infected


title: skin_129_salineinjected_24hrs_rep1


title: skin_Balb/c_gstraininfected_24hours_rep3

description: Gene expression data for G strain infected Balb/c mice

source_name: skin, G strain infected, 24 hours

tag: Balb/c, female, 16-18g, tissue:skin, G strain infected


title: skin_IFNARKO_Ystraininfected_24hours_rep3


title: skin_129_salineinjected_24hrs_rep2


title: skin_IFNARKO_salineinjected_24hours_rep3


title: skin_Balb/c_brazilstraininfected_24hours_rep2

description: Gene expression data for Brazil strain infected Balb/c mice

source_name: skin, Brazil strain infected, 24 hours

tag: Balb/c, female, 16-18g, tissue:skin, Brazil strain infected


title: skin_IFNgKO_salineinjected_24hrs_rep2

description: Gene expression data for control (saline injected) IFNg-/- mice

source_name: skin, IFNgKO, saline injected, 24 hours

tag: C.129S7(B6)-Ifngtm1Ts/J, female, 16-18g, tissue:skin, saline injected


title: skin_Balb/c_gstraininfected_24hours_rep1


title: skin_Balb/c_gstraininfected_24hours_rep2


title: skin_Balb/c_Ystraininfected_24hours_rep3

description: Gene expression data for Y strain infected Balb/c mice

tag: Balb/c, female, 16-18g, tissue:skin, Y strain infected


title: skin_IFNgKO_salineinjected_24hrs_rep1


title: skin_Balb/c_Nkcelldep_salineinjected_24hours_rep1

description: Gene expression data for control (saline injected) Balb/c mice after NK cell depletion

source_name: skin, NK cell depleted, saline injected, 24 hours.

tag: Balb/c, female, 16-18g, tissue:skin, NK cell depleted, saline injected


title: skin_Balb/c_Nkcelldep_Ystraininfected_24hours_rep1

description: Gene expression data for Y strain infected Balb/c mice after NK cell depletion

source_name: skin, NK cell depleted, Y strain infected, 24 hours.

tag: Balb/c, female, 16-18g, tissue:skin, NK cell depleted, Y strain infected


title: skin_Balb/c_brazilstraininfected_24hours_rep1


title: skin_IFNgKO_Ystraininfected_24hrs_rep2


title: skin_Balb/c_Ystraininfected_24hours_rep1


title: Carboplatin 30 hours set 1

tag: Carboplatin

tag: Carboplatin 30 hours set 1


title: skin_Balb/c_salineinjected_24hrs_rep7

description: Gene expression data for control (saline injected) Balb/c mice

tag: Balb/c, female, 16-18g, tissue:skin, saline injected


title: skin_Balb/c_salineinjected_24hrs_rep6


title: skin_Balb/c_Ystraininfected_24hours_rep2


title: skin_Balb/c_salineinjected_24hrs_rep5


title: skin_Balb/c_salineinjected_24hrs_rep4


title: skin_Balb/c_salineinjected_24hrs_rep2


title: skin_Balb/c_salineinjected_24hrs_rep3


title: DMSO-2

status: Public on Jan 01 2009

city: Charlestown

first: Othon

last: Iliopoulos

address: Bldg 149, 13th Street

department: Cancer Center

institute: Massachusetts General Hospital

description: Gene expression values less than a minimum threshold of 20 or a maximum threshold of 16000 were set to 20 and 16000, respectively. Genes with minimal variation across the dataset were discarded (maximum/minimum < 3 or maximum – minimum < 100).

hyb_protocol: Labeled cRNA was prepared and hybridized to Affymetrix U133_Plus_2.0 microarrays according to the manufacturer’s protocols.

scan_protocol: Scans were processed using Affymetrix MAS5 software and median scaled.

source_name: Human Clear Cell Renal Carcinoma cell line

extract_protocol: RNA was harvested using TRI-Reagent LS (Molecular Research Center, TS 120), treated with RNase-free DNaseI (Worthington) to remove contaminating genomic DNA and purified over RNeasy Mini Kit columns (Qiagen, 74104).

tag: 786-O cells treated with DMSO, replicate 2


title: skin_129_Ystraininfected_24hours_rep3


title: skin_Balb/c_salineinjected_24hrs_rep1


title: WT8-1

label_protocol: Labeled cRNA was prepared and hybridized to Affymetrix U133_Plus_2.0 microarrays according to the manufacturer’s protocols.

tag: VHL reconstituted 786-O cells (WT8), replicate 1


title: PRC3-3

tag: Vector only 786-O cells (PRC3), replicate 3


title: WT8-3

tag: VHL reconstituted 786-O cells (WT8), replicate 3


title: 76-2

tag: Compound 76 treated 786-O cells, replicate 2


title: 76-3

tag: Compound 76 treated 786-O cells, replicate 3


title: cells transfected with siHX

city: Hangzhou

first: Qiaoyi

last: Liang

state: Zhejiang

address: 88 Jiefang Road

department: Zhejiang University

country: China

institute: Cancer Insititute

hyb_protocol: Use the GeneChip® Hybridization, Wash and Stain Kit (Affymetrix, P/N 900720) following manufacturer's instructions

scan_protocol: Scan on a GeneChip® Scanner 3000

data_processing: GCOS (GeneChip® Operating Software) was used.

source_name: colon cancer HT29 cells

label_protocol: Use the One-Cycle Target Labeling and Control Reagents (Affymetrix, P/N 900493) following manufacturer's instructions

growth_protocol: Colon cancer HT29 cells were cultured in RPMI 1640 medium supplemented with 10% FCS

extract_protocol: Total RNA extracted using Trizol, followed by purification with QIAGEN RNeasy® Kit

treatment_protocol: Cells were transfected with siRNAs. In the test group, the human endogeous retrovirus HERV-HX was evaluated to be knocked down.

tag: HERV-HX knock-down


title: cells of control

tag: control


title: 40-2

tag: Compound 40 treated 786-O cells, replicate 2


title: 77-2

tag: Compound 77 treated 786-O cells, replicate 2


title: 77-1

tag: Compound 77 treated 786-O cells, replicate 1


title: 40-3

tag: Compound 40 treated 786-O cells, replicate 3


title: Blk-2

tag: 786-O cells treated with medium only, replicate 2


title: Blk-3

tag: 786-O cells treated with medium only, replicate 3


title: WT8-2

tag: VHL reconstituted 786-O cells (WT8), replicate 2


title: PRC3-1

tag: Vector only 786-O cells (PRC3), replicate 1


title: DMSO-3

tag: 786-O cells treated with DMSO, replicate 3


title: PRC3-2

tag: Vector only 786-O cells (PRC3), replicate 2


title: 77-3

tag: Compound 77 treated 786-O cells, replicate 3


title: 41-3

tag: Compound 41 treated 786-O cells, replicate 3


title: 41-2

tag: Compound 41 treated 786-O cells, replicate 2


title: 41-1

tag: Compound 41 treated 786-O cells, replicate 1


title: 76-1

tag: Compound 76 treated 786-O cells, replicate 1


title: pTV

tag: shRNA vector only control 786-O cells (pTV)


title: DMSO1

tag: 786-O cells treated with DMSO, replicate 1


title: Blk-1

tag: 786-O cells treated with medium only, replicate 1


title: 40-1

tag: Compound 40 treated 786-O cells, replicate 1


title: pTR

tag: HIF-2a shRNAi in 786-O cells (pTR)


title: ASPS_Patient_7_Array_1

city: Frederick

first: Luke

middle: Hunter

last: Stockwin

address: Ft. Detrick

department: DTP

institute: NCI Frederick

description: Data from arrays hybridized to tumor RNA was analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome.

hyb_protocol: The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc).  The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix).  The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm.  GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.

scan_protocol: Fluorescent images were detected in an GeneChip® Scanner 3000

data_processing: Expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix).  All GeneChips were scaled to a median intensity setting of 500.

source_name: ASPS Tumor

label_protocol: Target was prepared and hybridized according to the Affymetrix Technical Manual.  Total RNA (10 ug) was converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).

growth_protocol: Not Applicable

extract_protocol: Rneasy (Qiagen) total RNA extraction

treatment_protocol: RNA samples were isolated immediately following surgery.

tag: Confirmed primary or metastatic ASPS

tag: Patient 7


title: ASPS_Patient_4_Array_1

tag: Patient 4


title: ASPS_Patient_7_Array_2


title: ASPS_Patient_1_Array_2

tag: Patient 1


title: ASPS_Patient_6_Array_2

tag: Patient 6


title: ASPS_Patient_1_Array_1


title: ASPS_Patient_2_Array_2

tag: Patient 2


title: ASPS_Patient_2_Array_1


title: ASPS_Patient_4_Array_2


title: ASPS_Patient_3_Array_2

tag: Patient 3


title: ASPS_Patient_5_Array_2

tag: Patient 5


title: Univ_RNA_Array_1

source_name: Universal RNA

treatment_protocol: Not applicable.

tag: Universal RNA (Promega)


title: ASPS_Patient_5_Array_1


title: 721_Empty_vector

city: Madison

first: Bill

last: Sugden

state: WI

address: 1400 University Avenue

department: Oncology

institute: University of Wisconsin-Madison

description: Empty Vector

hyb_protocol: Following fragmentation, cRNA was hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays according to protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 according to protocols provided by the manufacturer.

data_processing: The data was processed with GCOS software using the MAS5 algorithm, with a target signal value set to 1000.

source_name: 721 lymphoblastoid cells, empty retroviral vector

label_protocol: cDNA was synthesized from total RNA (with an oligo-dT primer containing a T7 promoter sequence) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, Carlsbad, CA). Biotinlyated cRNA was then prepared from the cDNA using the BioArray High Yield RNA Transcript Labeling Kit-T7 (Enzo, Farmingdale, NY).

growth_protocol: Cells were grown in RPMI-1640 supplemented with 10% fetal bovine serum, 200 U of penicillin, and 200 μg of streptomycin sulfate per mL

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

treatment_protocol: The EBV-positive lymphoblastoid cell line 721 was transduced with a retroviral vector encoding Bcl-XL (Bcl-XL IRES mRFP) and sorted for efficient mRFP expression on FACS-Vantage SE with the FACS-DIVA option. The forced expression of Bcl-XL overcomes apoptosis induced by the loss of EBV when DomNeg1 is expressed. These sorted cells were subsequently transduced with either an empty retroviral vector (IRES GFP) or DomNeg1-expressing retroviral vector (DomNeg1 IRES GFP), sorted for efficient expression of GFP 4 days post-transduction, and lysed in TRIzol for total RNA extraction.

tag: EBV-positive lymphoblastoid cell line, overexpresses Bcl-XL


title: ASPS_Patient_6_Array_1


title: ASPS_Patient_3_Array_1


title: U251_Enza_18h_2

first: Yuri

last: Kotliarov

address: 4 Memorial Dr., room 134

department: CHI

institute: NHLBI

description: standard glioma cell lines

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix GCOS 1.2 with default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: U251 cell line treated with Enzastaurin for 18 hours

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

growth_protocol: U251 cells were cultured in RPMI media supplemented with 5% serum.


title: U251_Enza_18h_3

description: standard glioma cell lines

tag: U251 cell line treated with Enzastaurin for 18 hours


title: 721_DomNeg1_vector

description: DomNeg1 Vector

source_name: 721 lymphoblastoid cells, DomNeg1-encoding retroviral vector


title: U251_Enza_18h_1

description: standard glioma cell lines


title: Univ_RNA_Array_2


title: U251_Enza_10h_3

description: standard glioma cell lines

source_name: U251 cell line treated with Enzastaurin for 10 hours


title: U251_Enza_10h_2

description: standard glioma cell lines

tag: U251 cell line treated with Enzastaurin for 10 hours


title: U251_Enza_04h_3

description: standard glioma cell lines

source_name: U251 cell line treated with Enzastaurin for 4 hours


title: U251_Enza_04h_1

description: standard glioma cell lines

tag: U251 cell line treated with Enzastaurin for 4 hours


title: U251_DMSO_18h_2

description: standard glioma cell lines

source_name: U251 cell line treated with DMSO for 18 hours


title: U251_DMSO_10h_3

description: standard glioma cell lines

source_name: U251 cell line treated with DMSO for 10 hours


title: U251_Enza_10h_1

description: standard glioma cell lines


title: U251_DMSO_10h_1

description: standard glioma cell lines

tag: U251 cell line treated with DMSO for 10 hours


title: FL cells, at 22 h after exposure to 0.05 µM BPDE, biological rep2

first: Lu

last: XiangYun

address: 388 Yuhangtang Road

institute: Zhejiang University School of Medicine

description: Gene expression data from FL cells exposed to 5 nM BPDE

hyb_protocol: The biotinlyated cRNAs were fragmented and hybridized to the microarrays at 45°C for 16 h in the Hybridization Oven 640 rotating at 60 rpm. Following hybridization, the microarrays were washed and stained with streptavidin-phycoerythrin in the Fluidics Station 400,

scan_protocol: Based on the Affymetrix Microarray Suite 5.0 platform, GeneChips were scanned using the GeneChip Scanner 3000, and original Affymetrix .dat proprietary output files were generated.

data_processing: The probe level data was manipulated using MAS5.0 algorithm, and the average intensity of each array was globally scaled to a target of 500. Data normalization and differential expression analysis using ANOVA (analysis of variation) statistical method was performed in Gene Spring 7.0 software. A probe set was delimited as differentially expressed if it had “Present” detection calls and exhibited p value <0.05 across the comparison of three controls and three treatments.

source_name: FL cells exposed to 0.05 µM BPDE for 2 h, and subsequently recovered for additional 22 h

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

growth_protocol: Human amnion epithelial FL cells were grown as monolayers in minimal essential medium (MEM, Gibco-Invitrogen, Carlsbad, CA) supplemented with 10% newborn bovine serum (Gibco-Invitrogen), 100 U/mL penicillin, and 100 µg/mL streptomycin in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated with Trizol reagents (Invitrogen), and further purified using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturers’ protocols. Isolated total RNA was analyzed on an Agilent Bioanalyzer 2100 to verify that the starting material was of good quality.

treatment_protocol: At the logarithmic growth phase, the cultures were exposed to vehicle control (0.1%, V/V) and a low concentration (0.05 µM) BPDE for 2 h in a culture medium that did not contain 10% newborn bovine serum, followed by additional growth for 1, 10 and 22 h, respectively, in a fresh medium containing 10% newborn bovine serum. The cultures were rinsed twice with phosphate buffer solution before change of the medium.

tag: human amnion epithelial FL cells

tag: Gender

value: female


title: U251_Enza_04h_2

description: standard glioma cell lines


title: FL cells, at 10 h after exposure to 0.05 µM BPDE, biological rep2

source_name: FL cells exposed to 0.05 µM BPDE for 2 h, and subsequently recovered for additional 10 h


title: FL cells, at 22 h after exposure to 0.05 µM BPDE, biological rep3


title: U251_DMSO_04h_3

description: standard glioma cell lines

source_name: U251 cell line treated with DMSO for 4 hours


title: U251_DMSO_10h_2

description: standard glioma cell lines


title: FL cells, at 22 h after exposure to 0.05 µM BPDE, biological rep1


title: U251_DMSO_18h_1

description: standard glioma cell lines

tag: U251 cell line treated with DMSO for 18 hours


title: FL cells, at 22 h after exposure to DMSO vehicle control, biological rep2

description: Gene expression data from FL cells exposed to DMSO vehicle control

source_name: FL cells exposed to DMSO vehicle control for 2 h, and subsequently recovered for additional 22 h


title: FL cells, at 10 h after exposure to 0.05 µM BPDE, biological rep1


title: FL cells, at 1 h after exposure to 0.05 µM BPDE, biological rep3

source_name: FL cells exposed to 0.05 µM BPDE for 2 h, and subsequently recovered for additional 1 h


title: FL cells, at 10 h after exposure to DMSO vehicle control, biological rep3

source_name: FL cells exposed to DMSO vehicle control for 2 h, and subsequently recovered for additional 10 h


title: FL cells, at 22 h after exposure to DMSO vehicle control, biological rep1


title: FL cells, at 10 h after exposure to 0.05 µM BPDE, biological rep3


title: U251_DMSO_04h_2

description: standard glioma cell lines

tag: U251 cell line treated with DMSO for 4 hours


title: FL cells, at 22 h after exposure to DMSO vehicle control, biological rep3


title: FL cells, at 1 h after exposure to DMSO vehicle control, biological rep3

source_name: FL cells exposed to DMSO vehicle control for 2 h, and subsequently recovered for additional 1 h


title: FL cells, at 1 h after exposure to DMSO vehicle control, biological rep2


title: FL cells, at 1 h after exposure to 0.05 µM BPDE, biological rep1


title: FL cells, at 10 h after exposure to DMSO vehicle control, biological rep1


title: FL cells, at 1 h after exposure to DMSO vehicle control, biological rep1


title: FL cells, at 1 h after exposure to 0.05 µM BPDE, biological rep2


title: U251_DMSO_04h_1

description: standard glioma cell lines


title: U251_DMSO_18h_3

description: standard glioma cell lines


title: FL cells, at 10 h after exposure to DMSO vehicle control, biological rep2


title: Mucositis-BREN32

city: Charlotte

first: Jean-Luc

middle: C

last: Mougeot

address: 1542 Garden Terrace

department: Internal Medicine

institute: Carolinas Medical Center

description: Gene expression data from AML patients two days following induction chemotherapy

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

scan_protocol: Each array was scanned twice using the Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA).

data_processing: The non-normalized signal data acquired in GCOS v1.2 were saved as a pivot file into Excel. The pivot file was formatted and imported into dCHIP2005. The default invariant set method in dCHIP2005 was used to normalize the data. The median array was BREN52. Only signal intensities and present or absent calls of dCHIP2005 normalized data were used in the analysis (e.g. no detection p value). Pre-filtering of data was performed in dCHIP2005 to select for genes whose expression varied across the samples with SD/mean between 0.1 and 10 and called present in more than 20% of total samples. Further filtering was utilized to remove genes with background level of expression or variations as defined by Max-Min absolute values <200. The resulting dataset exported without array outliers (e.g. replaced by null values in dCHIP2005), was further processed using TM4/TMEV3.1 program (http://www.tigr.org).

source_name: Buccal mucosa biopsy, AML patient two days post-chemotherapy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Samples were processed at the microarray facility at Carolinas Medical Center, Charlotte, NC, mainly as described by Meyer, RA et al. (2004). Briefly, buccal mucosa specimens were homogenized in TRIzol (Invitrogen Life Technologies, Carlsbad, CA) with a Brinkman Polytron tissue homogenizer. RNA was extracted, precipitated, purified with RNeasy columns (Qiagen, Valencia, CA) and quantified by UV absorbance. Total RNA integrity for microarray analysis was determined by electrophoresis at 100 volts for 45 minutes in ethidium bromide containing 1% agarose gels. Antisense biotinylated cRNA target probes were synthesized from total RNA according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

treatment_protocol: Patients with acute myeloid leukemia AML were treated with induction chemotherapy: Ara-C (cytarabine) 100 mg/m2 for 7 days and daunorubicin 45-60 mg/m2 qd x 3 days. Immediately prior to induction chemotherapy and two days following initiation of chemotherapy, buccal mucosa biopsy specimens, 3x2 mm in size, were collected. In addition, buccal mucosa specimens were collected from 3 healthy control subjects. All tissues were placed in an RNAlater solution (Ambion, Austin, TX) and stored at -80C.

tag: BREN32, two days post-chemotherapy


title: Mucositis-BREN52

tag: BREN52, two days post-chemotherapy


title: Mucositis-BREN11

description: Gene expression data from AML patient the same day before induction chemotherapy

source_name: Buccal mucosa biopsy, AML patient pre-chemotherapy

tag: BREN11, pre-chemotherapy


title: Mucositis-BREN22

tag: BREN22, two days post-chemotherapy


title: Mucositis-BRENC3

description: Gene expression data from healthy control subjects

source_name: Buccal mucosa biopsy, healthy control subject

tag: BRENC3, healthy control


title: Mucositis-BRENC1

tag: BRENC1, healthy control


title: Mucositis-BRENC2

tag: BRENC2, healthy control


title: Mucositis-BREN51

tag: BREN51, pre-chemotherapy


title: Mucositis-BREN41

tag: BREN41, pre-chemotherapy


title: Mucositis-BREN42

tag: BREN42, two days post-chemotherapy


title: Mucositis-BREN21

tag: BREN21, pre-chemotherapy


title: MERLION_X04K00321

city: Villejuif

first: Philippe

last: Broët

address: 16 Ave Paul Vaillant Couturier

department: Faculty of Medicine

institute: University Paris-Sud

hyb_protocol: According to the manufacturer's protocol (Affymetrix, Santa Clara, CA).

data_processing: The expression microarray data were standardized and normalized using the robust multi-array average (RMA) procedure [22]. Genes whose maximum expression did not exceed the median value of expression or whose interquartile range (IQR) did not exceed the first quartile of the IQR distribution were excluded. A total of 37,771 probe sets were considered for analysis.

source_name: Lung cancer, pT2N0, male, age=68, state=0

extract_protocol: Total RNA was extracted from frozen (–80°C) tumor samples using a standard Trizol procedure. Frozen samples were shattered in liquid nitrogen and homogenized in 1 ml TRIzol (Invitrogen, Carlsbad, USA). Extraction was performed using a standard chloroform/isopropanol method. RNA pellets were resuspended in RNase-free water, subjected to a Qiagen clean up step and stored at -80°C.

tag: pT2N0, male, age=68, state=0


title: MERLION_X03K05904

scan_protocol: According to the manufacturer's protocol (Affymetrix, Santa Clara, CA).

source_name: Lung cancer, pT2N0, male, age=74, state=1

tag: pT2N0, male, age=74, state=1


title: MERLION_X02K04518

source_name: Lung cancer, pT2N0, female, age=61, sate=0

label_protocol: According to the manufacturer's protocol (Affymetrix, Santa Clara, CA).

tag: pT2N0, female, age=61, sate=0


title: MERLION_X03K05402

source_name: Lung cancer, pT2N0, female, age=70, state=0

tag: pT2N0, female, age=70, state=0


title: MERLION_X03K05815

source_name: Lung cancer, pT2N0, female, age=75, state=0

tag: pT2N0, female, age=75, state=0


title: MERLION_X03K03296

source_name: Lung cancer, pT2N0, male, age=60, state=0

tag: pT2N0, male, age=60, state=0


title: MERLION_X03K04513

source_name: Lung cancer, pT2N0, female, age=65, state=0

tag: pT2N0, female, age=65, state=0


title: MERLION_X03K05471

source_name: Lung cancer, pT2N0, male, age=79, state=1

tag: pT2N0, male, age=79, state=1


title: MERLION_X03K05419

source_name: Lung cancer, pT2N0, male, age=67, state=0

tag: pT2N0, male, age=67, state=0


title: MERLION_X03K00419

source_name: Lung cancer, pT2N0, male, age=65, state=0

tag: pT2N0, male, age=65, state=0


title: MERLION_X03K00958

source_name: Lung cancer, pT2N0, male, age=79, state=0

tag: pT2N0, male, age=79, state=0


title: MERLION_X03K00420

source_name: Lung cancer, pT2N0, male, age=75, state=0

tag: pT2N0, male, age=75, state=0


title: MERLION_X03K02711

source_name: Lung cancer, pT2N0, male, age=7O, state=0

tag: pT2N0, male, age=7O, state=0


title: MERLION_X03K01466

source_name: Lung cancer, pT2N0, male, age=64, state=1

tag: pT2N0, male, age=64, state=1


title: MERLION_X03K02235

source_name: Lung cancer, pT2N0, male, age=72, state=1

tag: pT2N0, male, age=72, state=1


title: MERLION_X03K00525

source_name: Lung cancer, pT2N0, male, age=52, state=0

tag: pT2N0, male, age=52, state=0


title: MERLION_03K001632

source_name: Lung cancer, pT2N0, male, age=53, sate=0

tag: pT2N0, male, age=53, sate=0


title: MERLION_X03K04174

source_name: Lung cancer, pT2N0, male, age=57, state=0

tag: pT2N0, male, age=57, state=0


title: MERLION_X03K00615


title: MERLION_X02K05193

source_name: Lung cancer, pT2N0, male, age=70, state=0

tag: pT2N0, male, age=70, state=0


title: MERLION_X02K04465

source_name: Lung cancer, pT2N0, male, age=47, state=1

tag: pT2N0, male, age=47, state=1


title: MERLION_X02K02220

source_name: Lung cancer, pT2N0, male, age=50, state=1

tag: pT2N0, male, age=50, state=1


title: MERLION_X02K03250

source_name: Lung cancer, pT2N0, male, age=58, state=0

tag: pT2N0, male, age=58, state=0


title: MERLION_X02K01914

source_name: Lung cancer, pT2N0, male, age=49, state=0

tag: pT2N0, male, age=49, state=0


title: MERLION_X02K03253

source_name: Lung cancer, pT2N0, male, age=59, state=0

tag: pT2N0, male, age=59, state=0


title: MERLION_X02K05529

source_name: Lung cancer, pT2N0, male, age=54, state=1

tag: pT2N0, male, age=54, state=1


title: MERLION_X02K05993


title: MERLION_X02K01675

source_name: Lung cancer, pT2N0, male, age=57, state=1

tag: pT2N0, male, age=57, state=1


title: MERLION_X03K00095

source_name: Lung cancer, pT2N0, female, age=51, state=0

tag: pT2N0, female, age=51, state=0


title: MERLION_X02K02039

source_name: Lung cancer, pT2N0, male, age=62, state=NA

tag: pT2N0, male, age=62, state=NA


title: MERLION_X02K02911

source_name: Lung cancer, pT2N0, male, age=77, state=1

tag: pT2N0, male, age=77, state=1


title: MERLION_X02K01279

source_name: Lung cancer, pT2N0, male, age=68, state=1

tag: pT2N0, male, age=68, state=1


title: MERLION_X03K03232

source_name: Lung cancer, pT2N0, male, age=55, state=1

tag: pT2N0, male, age=55, state=1


title: MERLION_X02K01203


title: MERLION_X02K00932


title: MERLION_X02K04866

source_name: Lung cancer, pT2N0, female, age=48, state=0

tag: pT2N0, female, age=48, state=0


title: MERLION_X02K00389

source_name: Lung cancer, pT2N0, male, age=50, state=0

tag: pT2N0, male, age=50, state=0


title: MERLION_X02K02285

source_name: Lung cancer, pT2N0, male, age=76, state=1

tag: pT2N0, male, age=76, state=1


title: MERLION_X01K04841


title: MERLION_X02K02472

source_name: Lung cancer, pT2N0, male, age=63, state=0

tag: pT2N0, male, age=63, state=0


title: MERLION_X02K00985

source_name: Lung cancer, pT2N0, male, age=42, state=0

tag: pT2N0, male, age=42, state=0


title: MERLION_X02K00438

source_name: Lung cancer, pT2N0, female, age=84, state=1

tag: pT2N0, female, age=84, state=1


title: MERLION_X02K00864

source_name: Lung cancer, pT2N0, female, age=42, state=0

tag: pT2N0, female, age=42, state=0


title: MERLION_X02K00554

source_name: Lung cancer, pT2N0, female, age=42, state=1

tag: pT2N0, female, age=42, state=1


title: WE 13.5 _Replicate2

city: Cambridge

first: Mitchell

last: Guttman

address: 7 Cambridge Center

institute: Broad Institute

description: lincRNA Paired Samples

hyb_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

data_processing: RMA

source_name: Whole Embryo E13.5

extract_protocol: Trizol

tag: Embryonic Tissue


title: MERLION_X03K03389

source_name: Lung cancer, pT2N0, male, age=67, state=1

tag: pT2N0, male, age=67, state=1


title: MERLION_X01K04994

source_name: Lung cancer, pT2N0, male, age=73, state=1

tag: pT2N0, male, age=73, state=1


title: WE 10.5 _Replicate2

description: lincRNA Paired Samples

scan_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

source_name: Whole Embryo E10.5


title: MERLION_X01K05045

source_name: Lung cancer, pT2N0, female, age=44, state=0

tag: pT2N0, female, age=44, state=0


title: MERLION_X01K04005

source_name: Lung cancer, pT2N0, male, age=56, state=1

tag: pT2N0, male, age=56, state=1


title: HL 13.5 _Replicate2

description: lincRNA Paired Samples

source_name: Hindlimb E13.5

label_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array


title: WE 9.5 _Replicate2

description: lincRNA Paired Samples

source_name: Whole Embryo E9.5


title: MERLION_X01K05273

source_name: Lung cancer, pT2N0, male, age=57, state=0

tag: pT2N0, male, age=57, state=0


title: MERLION_X01K04097

source_name: Lung cancer, pT2N0, male, age=47, state=0

tag: pT2N0, male, age=47, state=0


title: HL 10.5 _Replicate2

description: lincRNA Paired Samples

source_name: Hindlimb E10.5


title: MERLION_X01K03697

source_name: Lung cancer, pT2N0, female, age=62, state=NA

tag: pT2N0, female, age=62, state=NA


title: MERLION_X01K03555

source_name: Lung cancer, pT2N0, female, age=65, state=0

tag: pT2N0, female, age=65, state=0


title: MERLION_X01K02786

source_name: Lung cancer, pT2N0, male, age=81, state=0

tag: pT2N0, male, age=81, state=0


title: FL 13.5 _Replicate2

description: lincRNA Paired Samples

source_name: Forelimb E13.5


title: FL 10.5 _Replicate2

description: lincRNA Paired Samples

source_name: Forelimb E10.5


title: WE 13.5 _Replicate1

description: lincRNA Paired Samples


title: MERLION_X02K01226

source_name: Lung cancer, pT2N0, male, age=66, state=1

tag: pT2N0, male, age=66, state=1


title: FL 9.5 _Replicate2

description: lincRNA Paired Samples

source_name: Forelimb E9.5


title: WE 9.5 _Replicate1

description: lincRNA Paired Samples


title: WE 10.5 _Replicate1

description: lincRNA Paired Samples


title: MERLION_X01K02059

source_name: Lung cancer, pT2N0, male, age=77, state=1

tag: pT2N0, male, age=77, state=1


title: HL 13.5 _Replicate1

description: lincRNA Paired Samples


title: FL 10.5 _Replicate1

description: lincRNA Paired Samples


title: MERLION_X01K02265


title: HL 10.5 _Replicate1

description: lincRNA Paired Samples


title: FL 9.5_Replicate1

description: lincRNA Paired Samples


title: FL 13.5 _Replicate1

description: lincRNA Paired Samples


title: MERLION_X00K06478

source_name: Lung cancer, pT2N0, female, age:54, state:0

tag: pT2N0, female, age:54, state:0


title: MERLION_X00K01639

source_name: Lung cancer, pT2N0, male, age:52, state:0

tag: pT2N0, male, age:52, state:0


title: MERLION_X00K06181

source_name: Lung cancer, pT2N0, male, age:50, state:1

tag: pT2N0, male, age:50, state:1


title: MERLION_X00K06227

source_name: Lung cancer, pT2N0, male, age:49, state:0

tag: pT2N0, male, age:49, state:0


title: MERLION_X00K06157

source_name: Lung cancer, pT2N0, male, age:72, state:0

tag: pT2N0, male, age:72, state:0


title: MERLION_X00K06057

source_name: Lung cancer, pT2N0, male, age:77 , state:0

tag: pT2N0, male, age:77 , state:0


title: MERLION_X01K02349

source_name: Lung cancer, pT2N0, female, age=48, state=1

tag: pT2N0, female, age=48, state=1


title: MERLION_X00K05250

source_name: Lung cancer, pT2N0, male, age:68, state:1

tag: pT2N0, male, age:68, state:1


title: Mouse lung Fibroblasts R1

description: lincRNA Paired Samples

source_name: MLF

tag: MLF


title: MERLION_X00K05009

source_name: Lung cancer, pT2N0, male, age:78, state:1

tag: pT2N0, male, age:78, state:1


title: MERLION_X01K00208

source_name: Lung cancer, pT2N0, female, age:79, state:0

tag: pT2N0, female, age:79, state:0


title: MERLION_X01K01501

source_name: Lung cancer, pT2N0, male, age=53, state=0

tag: pT2N0, male, age=53, state=0


title: MERLION_X00K05435

source_name: Lung cancer, pT2N0, male, age:60, state:0

tag: pT2N0, male, age:60, state:0


title: MERLION_X00K04955

source_name: Lung cancer, pT2N0, female, age:68, state:0

tag: pT2N0, female, age:68, state:0


title: MERLION_X02K03683

source_name: Lung cancer, pT2N0, male, age=78, state=0

tag: pT2N0, male, age=78, state=0


title: Mouse lung Fibroblasts R2

description: lincRNA Paired Samples


title: No injection, rep2-3

status: Public on Dec 31 2008

city: Stanford

first: Bokyung

last: Choi

address: 318 Campus Drive

department: Applied physics

institute: Stanford University

description: Uninjected control embryos processed and cultured in parallel with embryos from Sample 11.

hyb_protocol: Fragmented, labeled, ssDNA samples were submitted to Stanford University PAN Core Facility for hybridization to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix), and laser scanning.

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed with dChip 2007 with the default setting. The mask file for normalization control was used.

source_name: No injection, rep2-3

label_protocol: Direct biotin labeling and fragmentation were performed (FL-Ovation cDNA Biotin Module (Nugen).

extract_protocol: Samples containing 20 pooled injected or control mouse embryos were washed through 3 drops of PBS/PVP and collected for total RNA extraction and isolation (Picopure Total RNA Isolation Kit, Molecular Devices Corp.), to yield 10 μL of total RNA.  5 μL of total RNA, or the equivalent of 10 mouse embryos, was subjected to two rounds of amplification (WT-Ovation Pico system, Nugen) according to manufacturer’s instructions.   The quality of ssDNA resulting from the second round amplification was tested on the Bioanalyzer 2100 (Agilent), and a typical yield of 5-8 μg per sample was quantitated by the ND-1000 UV spectrophotometer (Nanodrop Technologies).

treatment_protocol: 3-5 week old wild type F1 (C57BL6xDBA/2) females (Charles River) were superovulated by intraperitonial injections of 5 IU of pregnant mare’s serum gonadotropin (Sigma) followed by 5 IU of human chorionic gonadotropin (Sigma) 48 hours later, and mated overnight with wild type males. Mice were sacrificed by cervical dislocation 17 hours after hCG injection, and 1-cell embryos were released from oviducts. Cumulus cells were removed by hyaluronidase (Sigma) treatment and pipetting. Pre-implantation embryos at the two pronuclei stage were recovered, pooled from 3-6 females in M2 media (Chemicon International), followed by immediate cytoplasmic microinjection of gene-specific antisense morpholino oligonucleotides and culture in Human Tubal Fluid with 10% serum supplement (In-Vitro Fertilization, Inc.) microdrops under mineral oil (Sigma) in mixed gas (90% nitrogen, 5% oxygen, 5% carbon dioxide; Praxair) at 37°C, and cultured at ten embryos per 20 μL drop. Uninjected control embryos derived from the same embryo pool, and were placed in identical conditions in parallel, except that they were not injected.

tag: Embryos were collected at the mid-2-cell stage at 43 hours post-human chorionic gonadotropin injection.


title: MERLION_X01K01544

source_name: Lung cancer, pT2N0, male, age 48, state 0

tag: pT2N0, male, age 48, state 0


title: No injection, rep2-2

description: Uninjected control embryos processed and cultured in parallel with embryos from Sample 9.

source_name: No injection, rep2-2


title: Ccna2-MO injected, rep2-3

description: 1-cell stage mouse embryos (see treatment protocol below) were injected with 0.6 mM of antisense morpholino oligonucleotide which was designed to specifically target the 5'UTR of Ccna2.

source_name: Ccna2-MO injected, rep2-3


title: AC61-pLXSB-Rb

city: Kyoto

first: Chiaki

last: Takahashi

state: Kyoto

address: Yosida-Knoe-cho, Sakyo-ku,

department: Molecular Oncology

country: Japan

institute: Kyoto University Graduate School of Medicine

hyb_protocol: According to Affymetrix's instructions.

scan_protocol: According to Affymetrix's instructions.

data_processing: According to Affymetrix's instructions. ExpressionStat 5.0

label_protocol: According to Affymetrix's instructions.

extract_protocol: According to Kurabo's instructions. http://www.kurabo.co.jp/bio/English/na24.html

tag: C-cell adenocarcinoma derived from Rb+/-N-ras-/- mice and transfected with pLXSB-Rb.


title: Oct4-MO injected, rep1-3

description: 1-cell stage mouse embryos (see treatment protocol below) were injected with 0.6 mM of antisense morpholino oligonucleotide which was designed to specifically target the translational start site of Oct4.

source_name: Oct4-MO injected, rep1-3


title: Ccna2-MO injected, rep2-2

source_name: Ccna2-MO injected, rep2-2


title: AC61-pLXSB

tag: C-cell adenocarcinoma derived from Rb+/-N-ras-/- mice and transfected with pLXSB


title: No injection, rep2-1

description: Uninjected control embryos processed and cultured in parallel with embryos from Sample 7.

source_name: No injection, rep2-1


title: No injection, rep1-2

description: Uninjected control embryos processed and cultured in parallel with embryos from Sample 3.

source_name: No injection, rep1-2


title: Ccna2-MO injected, rep2-1

source_name: Ccna2-MO injected, rep2-1


title: No injection, rep1-1

description: Uninjected control embryos processed and cultured in parallel with embryos from Sample 1.

source_name: No injection, rep1-1


title: Scrambled BMEL 5

city: Philadelphia

first: Joshua

last: Friedman

state: PA

address: ARC 1007B, 3615 Civic Center Blvd.

department: Pediatrics

institute: University of Pennsylvania School of Medicine

description: BMEL gene expression data

hyb_protocol: The hybridization was performed according to the Affymatrix manual using a Tecan HS4800 hybridization station (Tecan, Austria)

scan_protocol: Slides were scanned by a ScanArray 4000 XL scanner (Packard Biochip Technologies, USA)

data_processing: Image analysis was carried out using the ImaGene 6.1.0 software (BioDiscovery, Inc., USA)

source_name: BMELs, transfected with LNA oligo

label_protocol: 100ng of total RNA per sample was amplified and biotinylated using the MessageAmp Premier kit (Ambion)

growth_protocol: Grown under growth conditions as described in PMID: 12297826

extract_protocol: mirVana™ miRNA Isolation Kit (Ambion)

treatment_protocol: Oligofectamine transfection

tag: Cell line derived from fetal mouse liver

tag: BMELs grown under growth conditions


title: Scrambled BMEL 2

description: BMEL gene expression data


title: ASO-30a BMEL 3

description: BMEL gene expression data


title: MERLION_X00K03912

source_name: Lung cancer, pT2N0, male, age:70, state:1

tag: pT2N0, male, age:70, state:1


title: ASO-30a BMEL 5

description: BMEL gene expression data