title: SC_HaploidDeletionPool_AdaptH2O2_rep5

description: Haploid deletion mutant pool treated with 0.1 mM + 0.4 mM H2O2 and compared to cells treated with only 0.4 mM H2O2

hyb_protocol: DNA hybridization followed the protocol of Yuan et al. 2005. Slides were hybridized for 16h at 42 degree Celcius in a rotating oven, and washed.

data_processing: Following background-subtraction of individual spots, loess and two-dimensional spatial normalization are performed (default parameters within the R hoptage package). Value is log ratio of normalized intensities.

label_protocol: DNA labeling followed the protocol of Yuan et al. 2005. Briefly, asymmetric PCR was used to amplify unique tag sequences in the genomic DNA of the deletion strains. In each PCR reaction, 1 μg of gDNA was used for labeling.

extract_protocol: Genomic DNA was extracted from cell pellets using a glass bead preparation.

tag: A pool of the 4,831 viable haploid deletion strains was created from individual collections kept in glycerol stock and divided into 1 mL aliquots stored at -80° C. A single aliquot of pooled deletion strains was diluted in 15 mL YPD media and grown in a rotating wheel at 30° C to OD600 = 0.6. The sample was then split into two 6.5 mL portions. The aliquot corresponding to this channel was treated with 0.1 mM H2O2. After 45 minutes of continued growth at 30° C, the aliquotwas treated with a high dose (final concentration in media

value: 0.4 mM) of hydrogen peroxide. After 1 hour of treatment, the cells were harvested by centrifugation at 3000 rpm for 5 min and resuspended in 50 mL of YPD media. After 5 hours of growth, the cells were once again harvested by centrifugation and the pellets were immediately frozen in liquid nitrogen and stored at 80° C.

tag: A pool of the 4,831 viable haploid deletion strains was created from individual collections kept in glycerol stock and divided into 1 mL aliquots stored at -80° C. A single aliquot of pooled deletion strains was diluted in 15 mL YPD media and grown in a rotating wheel at 30° C to OD600 = 0.6. The sample was then split into two 6.5 mL portions. After 45 minutes of continued growth at 30° C, the aliquot corresponding to this channel was treated with a high dose (final concentration in media


title: Brain-SALS03-ArrayC-rep1

status: Public on Apr 23 2009

type: genomic

city: University of Sydney

first: Roger

last: Pamphlett

address: Blackburn Bld

country: Australia

institute: University of Sydney

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from SALS patient brain

hyb_protocol: Hybridization to Affymetrix GeneChip Human Tiling 2.0R arrays at 45 degrees overnight (Genpathway Inc.)

scan_protocol: Arrays were washed and scanned (Genpathway Inc.)

data_processing: Data processed using Affymetrix TAS software and Genpathway IP analysis software (Genpathway Inc.)

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: SALS Brain (Brodmann area 46)

label_protocol: Amplified DNAs were fragmented and labeled using the Affymetrix DNA Terminal Labeling Kit (Genpathway Inc.)

extract_protocol: Phenol chloroform extraction of human brain tissue. Genpathway Inc performed the following: DNA (12 ug) was precleared with protein G agarose beads (Invitrogen).  Methylated DNA was detected using a sheep polyclonal antibody against 5-methyl-cytosine.  After incubation at 4C overnight, protein G agarose beads were used to isolate the immune complexes.  Complexes were washed and eluted from the beads with SDS buffer.  IP’ed DNA was purified by phenol/chloroform extraction and ethanol precipitation.

tag: Gender

value: male

tag: Age

tag: Phenotype

value: SALS


title: Normal 7

type: RNA

city: Tromsø

first: Ruth

middle: Hracky

last: Paulssen

address: MH-Bygget Breivika

department: Institute of Clinical Medicine

country: Norway

institute: Universitetet i Tromsø

description: colon normal rep7

hyb_protocol: Ten micrograms of labelled DIG-cRNA was injected into each microarray hybridization chamber, hybridized at 55C for 16 hours, and visualized using the Applied Biosystems Chemiluniescence Detection Kit and as decribed bu the manufacturer's protocol.

scan_protocol: The signals were detected by the Applied Biosystems 1700 Chemiluninescent Microarray Analyzer. The Human Genome Survey Microarray v.2.0 (Applied Biosystems Inc., USA) with 32,878 probes for the interrogation of 29,098 genes was used for microarray analysis.

data_processing: The features were extracted from the arrays using the ABI1700 software. Normalization was carried out using quantile normalization (Bolstad et al. 2003).  For the purpose  of finding differentially expressed genes, we applied an empirical Bayes analysis using the LIMMA package (Smyth 2004), and significance was determined at the 0.05 level corrected for false discovery rate (FDR) using the Benjamini-Hochberg method (Benjamini & Hochberg 1995). Principal component analysis (PCA) and Partial least squares (PLS) and were carried out on the data in order to visualize the data structure and look for potential outlier samples (Gidsehaug et al. 2004).

label: DIG

molecule: total RNA

source_name: colon rectum

label_protocol: Total RNA samples were processed into digoxigenin (DIG)- labelled cRNA using the Applied Biosystems Chemiluminescent NanoAmp RT-IVT Labeling Kit (Applied Biosystems Inc., USA) and as described in the manufacturer's protocol.

growth_protocol: The patient group for this study consisted of 10 patients with an operable adenocarcinoma of the rectum. Tissue specimens were taken form both normal and tumor tissue of the rectum before and after  therapy and were kept in RNA storage buffer (RNA stabilization reagent, Qiagen GMBH, Germany) and stored at -70°C prior to downstream analyses.

extract_protocol: Disruption and homogenization of tissue specimens were performed in lysis buffer using the MagNa Lyser Instrument (Roche Applied Science, Germany) and according to the manufacturer’s protocol. Subsequently, total RNA was isolated with the MagNa Pure Compact Instrument and the MagNa Pure Compact RNA Isolation Kit (Roche Applied Science, Germany) as previously described (Paulssen et al. 2006). RNA was quantified by measuring absorbance at 260 nm, and RNA purity was determined by the ratios OD260nm/280nm and OD230/280nm using the NanoDrop instrument (NanoDrop® ND-1000, Wilmington, USA). The RNA integrity was determined by electrophoresis using the BioRad Experion Bioanalyzer (Data not shown). RNA samples with 16S/28S ratios of >1.4 were used for further analysis.

treatment_protocol: Each patient received 50 Gy (delivered as fractions of 2 Gy 25 times) during 5 weeks. In addition, patients received Capecitabine (Xeloda®, Roche) 2500 mg/ml daily during the whole period. Resection of the rectum was performed four to six weeks after preoperative radiation therapy.

tag: tissue

value: normal tissue

tag: treatment

value: non-irradiated


title: Tumour irradiated 2

description: colon tumour irradiated rep2

value: tumour tissue

value: irradiated


title: Normal 8

description: colon normal rep8


title: Gene expression in PLN vs ILN (FVB)

city: Stanford

first: Remi

middle: J

last: Creusot

state: CA

address: 269 Campus Dr, CCSR 2240

department: Medicine

country: USA

institute: Stanford University

description: No additional information.

hyb_protocol: Two color microarrays were performed using the whole mouse genome Oligo microarray kit (Agilent, series 2512694).  Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65C, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent) with the following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels.  Data was extracted using Feature Extraction software.

data_processing: Data was process using GeneSpring GX 7.3 Software. Data was imported using the enhanced Agilent FE Import setting. Spot information in Feature Extraction was used to flag data, and normalization was performed using "per spot and per chip: intensity dependent (Lowess) normalization".  Data obtained for the Cy5-labelled PLN sample were divided by the Cy3-labelled ILN sample to obtain ratios shown in the "PRE_VALUE" column.

organism: Mus musculus

source_name: FVB PLN

label_protocol: RNA was amplified, labeled with Cy5 and combined with spike B using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies). The amplified cRNA was purified using the RNeasy kit (Qiagen), and specific activity was determined with the NanoDrop 1000 spectrophotometer (Thermo Scientific).

extract_protocol: pancreatic lymph nodes were excised and immediately homogenized in Trizol Reagent.  RNA was extracted in Trizol and then purified using the RNeasy kit (Qiagen). RNA purity and quality was assessed using the NanoDrop 1000 spectrophotometer (Thermo Scientific), Agilent RNA 6000 Nano Reagents, RNA Nano chips, and the Agilent 2100 bioanalyzer (Agilent Technologies), according to manufacturer's instructions.

tag: strain

value: FVB

tag: sample

value: Pooled tissue from 5 mice

value: pancreatic lymph nodes

source_name: FVB ILN

label_protocol: RNA was amplified, labeled with Cy3 and combined with spike A using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies). The amplified cRNA was purified using the RNeasy kit (Qiagen), and specific activity was determined with the NanoDrop 1000 spectrophotometer (Thermo Scientific).

extract_protocol: inguinal lymph nodes were excised and immediately homogenized in Trizol Reagent.  RNA was extracted in Trizol and then purified using the RNeasy kit (Qiagen). RNA purity and quality was assessed using the NanoDrop 1000 spectrophotometer (Thermo Scientific), Agilent RNA 6000 Nano Reagents, RNA Nano chips, and the Agilent 2100 bioanalyzer (Agilent Technologies), according to manufacturer's instructions.

value: inguinal lymph nodes


title: Tumour irradiated 1

description: colon tumour irradiated rep1


title: SC_HaploidDeletionPool_AdaptH2O2_rep6

city: La Jolla

first: Ryan

last: Kelley

address: 9500 Gilman Drive

department: Bioinformatics

institute: UCSD

scan_protocol: Arrays were scanned using a GenePix 4000A or PerkinElmer Scanarray Lite microarray scanner at 10.0 uM and quantified with the GenePix 6.0 software package.

organism: Saccharomyces cerevisiae


title: Brain-CTRL02-ArrayC-rep1

description:
Affymetrix dsDNA terminal label (Genpathway Inc.)
MeDIP data from normal control brain

source_name: Control Brain (Brodmann area 46)

value: normal


title: Gene expression in PLN vs MLN (BALB/c)

description: No additional information.

data_processing: Data was process using GeneSpring GX 7.3 Software. Data was imported using the enhanced Agilent FE Import setting. Spot information in Feature Extraction was used to flag data, and normalization was performed using "per spot and per chip: intensity dependent (Lowess) normalization".  Data obtained for the Cy5-labelled PLN sample were divided by the Cy3-labelled MLN sample to obtain ratios shown in the "PRE_VALUE" column.

source_name: BALB/c PLN

value: BALB/c

source_name: BALB/c MLN

extract_protocol: mesenteric lymph nodes were excised and immediately homogenized in Trizol Reagent.  RNA was extracted in Trizol and then purified using the RNeasy kit (Qiagen). RNA purity and quality was assessed using the NanoDrop 1000 spectrophotometer (Thermo Scientific), Agilent RNA 6000 Nano Reagents, RNA Nano chips, and the Agilent 2100 bioanalyzer (Agilent Technologies), according to manufacturer's instructions.

value: mesenteric lymph nodes


title: Brain-SALS01-ArrayC-rep1


title: Gene expression in PLN vs MLN (FVB)

description: No additional information.

data_processing: Data was processed using GeneSpring GX 7.3 Software. Data was imported using the enhanced Agilent FE Import setting. Spot information in Feature Extraction was used to flag data, and normalization was performed using "per spot and per chip: intensity dependent (Lowess) normalization".  Data obtained for the Cy5-labelled PLN sample were divided by the Cy3-labelled MLN sample to obtain ratios shown in the "PRE_VALUE" column.

source_name: FVB MLN


title: Normal 6

description: colon normal rep6


title: Normal 5

description: colon normal rep5


title: Normal 4

description: colon normal rep4


title: SC_HaploidDeletionPool_AdaptH2O2_rep1


title: SC_HaploidDeletionPool_AdaptH2O2_rep4


title: SC_HaploidDeletionPool_AdaptH2O2_rep2


title: SC_HaploidDeletionPool_AdaptH2O2_rep3


title: Normal 3

description: colon normal rep3


title: SC_HaploidDeletionPool_AcuteH2O2_rep4

description: Haploid deletion mutant pool treated with 0.4 mM H2O2 and compared to untreated cells

source_name: Untreated

tag: A pool of the 4,831 viable haploid deletion strains was created from individual collections kept in glycerol stock and divided into 1 mL aliquots stored at -80° C. A single aliquot of pooled deletion strains was diluted in 15 mL YPD media and grown in a rotating wheel at 30° C to OD600 = 0.6. The sample was then split into two 6.5 mL portions. After 45 minutes of continued growth at 30° C, the aliquot corresponding to this channel was treated with a sham dose. After 1 hour of treatment, the cells were harvested by centrifugation at 3000 rpm for 5 min and resuspended in 50 mL of YPD media. After 5 hours of growth, the cells were once again harvested by centrifugation and the pellets were immediately frozen in liquid nitrogen and stored at 80° C.


title: Tumour 11

description: colon tumour rep11


title: Tumour 10

description: colon tumour rep10


title: Gene expression in GLN vs PDLN (NOD mouse #3)

description: No additional information.

hyb_protocol: Two color microarrays were performed using the whole mouse genome 4x44K Oligo microarray kit (Agilent, series 2514868).  Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65C, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

data_processing: Data was processed using GeneSpring GX 10 Software. Data was imported using the enhanced Agilent FE Import setting. Spot information in Feature Extraction was used to flag data, and normalization was performed using "per spot and per chip: intensity dependent (Lowess) normalization".  Data obtained for the Cy5-labelled GLN sample were divided by the Cy3-labelled PDLN sample to obtain ratios shown in the "PRE_VALUE" column of processed data. Raw data show log2 of ratio.

source_name: NOD GLN

extract_protocol: Gastric lymph node was excised and immediately homogenized in Trizol Reagent.  RNA was extracted in Trizol and then purified using the RNeasy kit (Qiagen). RNA purity and quality was assessed using the NanoDrop 1000 spectrophotometer (Thermo Scientific), Agilent RNA 6000 Nano Reagents, RNA Nano chips, and the Agilent 2100 bioanalyzer (Agilent Technologies), according to manufacturer's instructions.

value: gastric lymph node (left pancreatic lymph node)

value: NOD

tag: sex

value: female

tag: age

value: 12 wk old

source_name: NOD PDLN

extract_protocol: Pancreatico-duodenal lymph node was excised and immediately homogenized in Trizol Reagent.  RNA was extracted in Trizol and then purified using the RNeasy kit (Qiagen). RNA purity and quality was assessed using the NanoDrop 1000 spectrophotometer (Thermo Scientific), Agilent RNA 6000 Nano Reagents, RNA Nano chips, and the Agilent 2100 bioanalyzer (Agilent Technologies), according to manufacturer's instructions.

value: pancreatico-duodenal lymph node (right pancreatic lymph node)


title: Tumour 12

description: colon tumour rep12


title: SC_HaploidDeletionPool_AcuteH2O2_rep3

value: 0.4 mM) of hydrogen peroxide. After 1 hour of treatment, the cells were harvested by centrifugation at 3000 rpm for 5 min and resuspended in 50 mL of YPD media. After 5 hours of growth, the cells were once again harvested by centrifugation and the pellets were immediately frozen in liquid nitrogen and stored at 80° C.


title: Gene expression in GLN vs PDLN (NOD mouse #4)

description: No additional information.


title: Normal 1

description: colon normal rep1

value: normal tissue


title: Normal 2

description: colon normal rep2

value: non-irradiated


title: Tumour 13

description: colon tumour rep13

value: tumour tissue


title: Tumour 7

description: colon tumour rep7


title: Tumour 8

description: colon tumour rep8


title: W1118_2-3hs_vs_w1118_Stage_14_13145904

city: Mississauga

first: Zak

last: Razak

state: Ontario

address: 3359 Mississauga Rd

country: Canada

institute: Canadian Drosophila Microarray Centre

hyb_protocol: see flyarrays website

scan_protocol: as previously described (Neal et al., 2003), using a PerkinElmer/GSI ScanArray 4000 scanner and the ScanArray software. The 16 bit TIFF image files were quantified using QuantArray Version 3 (PerkinElmer) using the adaptive quantification algorithm (www.flyarrays.com)

data_processing: Quantified data was analyzed using GeneTraffic Duo 3.2 (Iobion Informatics/Stratagene) after normalization using rank-invariant Lowess extrapolation. Values represent normalized log2 ratios

label: Alexa Fluor 647

organism: Drosophila melanogaster

label_protocol: Followed Canadian Drosophila Microarray Centre indirect labelling protocol (www.flyarrays.com). Dye = Alexa Fluor 647

extract_protocol: Canadian Drosophila Microarray Centre (RNA isolation file - www.flyarrays.com)

tag: 60ug of RNA from 2-3hours embryos of W1118, Indirect labeling of total RNA for Microarray Hybridization protocol from CDMC, Dye Alexa Fluor647.

label: Alexa Fluor 555 (Cy3)

label_protocol: Followed Canadian Drosophila Microarray Centre indirect labelling protocol (www.flyarrays.com). Dye = Alexa Fluor 555

tag: Indirect label, Dye Alexa Fluor 555


title: W1118_2-3hs_vs_w1118_Stage_14_13145914


title: SC_HaploidDeletionPool_AcuteH2O2_rep2


title: Gene expression in GLN vs PDLN (NOD mouse #1)

description: No additional information.


title: W1118_2-3hs_vs_w1118_Stage_14_13145906


title: Tumour 5

description: colon tumour rep5


title: Gene expression in GLN vs PDLN (NOD mouse #2)

description: No additional information.


title: W1118_2-3hs_vs_w1118_Stage_14_13145912


title: SC_HaploidDeletionPool_AcuteH2O2_rep1


title: SMG_2-3hs_vs_w1118_Stage_14_13145917

source_name: SMGoverDf  2-3hs 60ug 647(Cy5)

tag: 60ug of RNA from 2-3hours embryos of SMG over Df. Indirect labeling of total RNA for Microarray Hybridization protocol from CDMC, Dye Alexa Fluor647.


title: Tumour 4

description: colon tumour rep4


title: Tumour 6

description: colon tumour rep6


title: Tumour 3

description: colon tumour rep3


title: SMG_2-3hs_vs_w1118_Stage_14_13145908


title: SMG_2-3hs_vs_w1118_Stage_14_13145915


title: Tumour 1

description: colon tumour rep1


title: SMG_2-3hs_vs_w1118_Stage_14_13145905


title: W1118_4-6hr_vs_W1118_Stage_14_12827385

data_processing: Quantified data was analyzed using GeneTraffic Duo 3.2 (Iobion Informatics/Stratagene) after normalization to the known stable transcripts for CG7939 and CG10122. Values represent normalized log2 ratios.

source_name: W1118 4-6hr unfertilized eggs

label_protocol: Followed Canadian Drosophila Microarray Centre direct labelling protocol (www.flyarrays.com)

extract_protocol: Trizol procedure, added extra steps suggested by Canadian Drosophila Microarray Centre (RNA isolation file - www.flyarrays.com)

source_name: w1118 stage 14


title: Tumour 2

description: colon tumour rep2


title: LEC - Lateral entorhinal cortex Replicate 3

status: Public on Apr 22 2009

city: Torrance

first: Stanislav

last: Karsten

address: 1124 Carson Street

department: Neurology

institute: Harbor-UCLA

description: Lateral entorhinal cortex Naglu-/- (affected) vs. Naglu+/- (unaffected). Biological replicate 3 of 3.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential according to manufacturer recommendations

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

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

source_name: neuronal bodies laser captured from lateral entorhinal cortex of Naglu-/-

label_protocol: Amplification and labeling of the RNA samples were performed using the Agilent Low RNA Input Linear Amplification Kit PLUS, and the quality of the labeled cRNA was checked using the Agilent 2100 Bioanalyzer.

extract_protocol:
Tissue Preparation: Mice were killed with excess pentobarbital, decapitated, and the brain removed as rapidly as possible. Hemispheres were briefly frozen in 2-methylbutane at -10 °C and stored at -80 °C until use. They were then cut sagittally on a cryostat to 12 um thickness onto noncharged slides. The slides were stored at -80 °C.
Microdissect Protocol: Immediately before use of the LCM, the slides were put through a series of washes in the following order: 75% ethanol, H2O, cresyl violet, a series of ethanol dehydration steps followed by xylene. Identification of MEC and LEC on the cresyl violet (Nissl)-stained slides was accomplished with the guidance of an anatomical atlas. Harvesting of MEC and LEC neurons was performed using optimized parameters for the PixCell IIe LCM System. 500 neurons were collected from each brain region.
Total RNA isolation for the LCM cells was performed using Qiagen RNeasy Micro kit with a slight modification of the manufacturer’s protocol for optimal yield. Up to 3 cap linings containing the cells were removed and placed in 75uL of RNALysis Tissue buffer (RLT, Qiagen) on ice until all cells were collected. Subsequently, 75 uL of RLT containing beta-mercaptoethanol were added before proceeding with the Qiagen protocol.

tag: gender

value: two months

value: Lateral entorhinal cortex neurons

value: C57BL/6 Naglu-/-

source_name: neuronal bodies laser captured from lateral entorhinal cortex of Naglu+/-

value: C57BL/6 Naglu+/-


title: W1118_4-6hr_vs_W1118_Stage_14_12663396


title: LEC - Lateral entorhinal cortex Replicate 3 dye-switch


title: LEC - Lateral entorhinal cortex Replicate 2 dye-switch

description: Lateral entorhinal cortex Naglu-/- (affected) vs. Naglu+/- (unaffected). Biological replicate 2 of 3.


title: LEC - Lateral entorhinal cortex Replicate 1

description: Lateral entorhinal cortex Naglu-/- (affected) vs. Naglu+/- (unaffected). Biological replicate 1 of 3.


title: LEC - Lateral entorhinal cortex Replicate 2


title: W1118_4-6hr_vs_W1118_Stage_14_12663395

tag: 8120.6 ugperml


title: MEC - Medial entorhinal cortex Replicate 2 dye-switch

description: Medial entorhinal cortex Naglu-/- (affected) vs. Naglu+/- (unaffected). Biological replicate 2 of 3.

source_name: neuronal bodies laser captured from medial entorhinal cortex of Naglu+/-

value: Medial entorhinal cortex neurons

source_name: neuronal bodies laser captured from medial entorhinal cortex of Naglu-/-


title: MEC - Medial entorhinal cortex Replicate 1

description: Medial entorhinal cortex Naglu-/- (affected) vs. Naglu+/- (unaffected). Biological replicate 1 of 3.


title: MEC - Medial entorhinal cortex Replicate 2


title: LEC - Lateral entorhinal cortex Replicate 1 dye-switch


title: MEC - Medial entorhinal cortex Replicate 1 dye-switch


title: MEC - Medial entorhinal cortex Replicate 3

description: Medial entorhinal cortex Naglu-/- (affected) vs. Naglu+/- (unaffected). Biological replicate 3 of 3.


title: Tumour 9

description: colon tumour rep9

source_name: colon rectum


title: IL13.S6wt.6

city: San Francisco

first: Andrea

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description:
10Mm_223.gpr
Transgenic mice expressing IL-13 under the control of a Clara cell–specific promoter, mice were 6–8 wks of age, rep 5

hyb_protocol: Samples were hybridized for 20h at 63 degrees in a solution containing 2.8  SSC,0.025 M HEPES pH7.0,0.2% SDS,1 μg/μL yeast tRNA,and 0.6 μg/μL human Cot-1 DNA

scan_protocol: Scanned on an Axon 4000AB scanner. Images were quantified using GenePix 6.0 software.

data_processing: LOWESS normalized, no background subtraction was used

source_name: Mouse pooled whole lung lung reference

label_protocol: cDNA  reverse transcribed and indirectly labelled with amino-allyl Cy3 or Cy5

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions

value: whole lung

tag: type

value: pooled reference RNA

source_name: whole lung


title: MEC - Medial entorhinal cortex Replicate 3 dye-switch


title: HCC38_xba

city: South San Francisco

first: Peter

last: Haverty

address: 1 DNA Way

institute: Genentech, Inc.

hyb_protocol: Affymetrix 100K protocol

scan_protocol: Affymetrix 100K protocol

data_processing: Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization.  Ninety normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=100k) and analyzed at the same time.  One CEL file for each set (Xba and Hind) with the median signal intensity across the set was selected as the reference array.   The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows.  For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set.  The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment.

source_name: Neoplastic breast tissue

label_protocol: Affymetrix 100K protocol

growth_protocol: All cell lines were grown in DMEM or RPMI-1640 supplemented with 10% FBS

extract_protocol: Qiagen DNA extraction kit was used according to the manufacturer's instructions

tag: breast cancer cell line


title: HCC-1569_xba


title: HCC2218_xba


title: CAL-148_xba


title: MFM-223_xba


title: HCC70_xba


title: HCC1395_xba


title: HCC1428_xba


title: HCC1419_xba


title: UACC893_xba


title: ZR7530_xba


title: CAL851_xba


title: HCC1187_xba


title: EVSA-T_xba


title: CAL51_xba


title: EFM192A_xba


title: HCC1954_xba


title: HCC1937_xba


title: HCC202_xba


title: CAL120_xba


title: UACC812_xba


title: KPL1_xba


title: EFM19_xba


title: ZR751_xba


title: HCC1143_xba


title: T47D_xba


title: HCC1500_xba


title: SKBR3_xba


title: MDAMB453_xba


title: MCF7_xba


title: CD19+ B cells from healthy donor (BC CD19+ 20 11)

city: Rome

first: Sabina

last: Chiaretti

address: Via Benevento, 6

department: Cellular Technologies and Hematology

country: Italy

institute: Division of Hematology

description: no additional information

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on the HGU133A.2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GCS300 scanner (AFFYMETRIX).

data_processing: The data were analyzed with dChip software. For normalization, model based expressions were computed for each array and probe set, using the PM-MM model

label: Biotin

source_name: peripheral blood of  healthy donor

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

extract_protocol: Trizol extraction after CD19 enrichment of total RNA was performed according to the manufacturer's instructions.

value: peripheral blood


title: BT483_xba


title: CD19+ B cells from healthy donor (BC CD19+ 14 11)

description: no additional information

source_name: peripheral blood of healthy donor


title: CAMA1_xba


title: MDA231_xba


title: DU4475_xba


title: MDA436_xba


title: BT549_xba


title: MDA175_xba


title: UACC893_hind


title: CD19+ B cells from healthy donor (BC CD19+ 26 01)

description: no additional information


title: CLL spontaneous regression (DIBCLL4)

description: no additional information

source_name: peripheral blood of a CLL patient with spontaneous regression

treatment_protocol: CD19 enrichment was performed

tag: ighv status

value: mutated

tag: zap-70 status

value: negative

tag: cd38 status


title: HCC1806_xba


title: ZR7530_hind


title: AU5_65_xba


title: BT474_xba


title: MFM-223_hind


title: HS578T_xba


title: MDA415_xba


title: HCC38_hind


title: CAL-148_hind


title: HCC-1569_hind


title: MB468_xba


title: CLL progressive disease (PGCLL19)

description: no additional information

source_name: peripheral blood of a CLL patient with progressive disease

tag: tissue


title: CLL spontaneous regression (RMCLL20)

description: no additional information


title: CLL spontaneous regression (MUCLL18)

description: no additional information


title: HCC1395_hind


title: CLL stable disease (SFCLL21)

description: no additional information

source_name: peripheral blood of a CLL patient with stable disease

value: positive


title: HCC1500_hind


title: HCC1143_hind


title: HCC70_hind


title: HCC2218_hind


title: CLL stable disease (MKCLL14)

description: no additional information

value: not performed


title: CLL stable disease (LOCLL13)

description: no additional information


title: CLL stable disease (GUCLL12)

description: no additional information


title: HCC202_hind


title: CLL progressive disease (MMCLL16)

description: no additional information


title: CLL progressive disease (MCCLL15)

description: no additional information

value: germline


title: CLL progressive disease (GFCLL11)

description: no additional information


title: CLL stable disease (MMCLL17)

description: no additional information


title: KPL1_hind


title: HCC1937_hind


title: HCC1187_hind


title: HCC1954_hind


title: CLL progressive disease (GPCLL10)

description: no additional information


title: HCC1419_hind


title: EVSA-T_hind


title: HCC1428_hind


title: CLL stable disease (FGCLL9)

description: no additional information


title: CLL stable disease (DMCLL5)

description: no additional information

value: Not performed


title: CLL progressive disease (CACLL3)

description: no additional information


title: CLL progressive disease (ARCLL2)

description: no additional information


title: EFM192A_hind


title: CLL progressive disease (FMCLL7)

description: no additional information


title: CLL progressive disease (DCCLL6)

description: no additional information


title: CLL stable disease (AECLL1)

description: no additional information

value: Mutated


title: T47D_hind


title: ZR751_hind


title: EFM19_hind


title: CLL progressive disease (FDTRCLL8)

description: no additional information


title: CAL120_hind


title: CAL51_hind


title: SKBR3_hind


title: Late cells_L_rep3

city: Jerusalem

first: Alexander

last: Levitzki

address: Givat Ram

department: Department of Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

description: Human  U133A 2.0

hyb_protocol: Standard Affymetrix hybridization protocol for gene expression profile ( carried out in the microarray unit of the Weizmann institute)

scan_protocol: Standard Affymetrix protocol for gene expression profile ( carried out in the microarray unit of the Weizmann institute)

data_processing: The gene expression data were analyzed using the Microarray Suite (MAS) 5.0 algorithm. For each probe, a CHP output file contained a signal quantitative metric, which represents the relative level of expression of a transcript, and a “detection” classification of each signal as present, marginal, or absent.

label_protocol: Standard Affymetrix probe synthesis for gene expression profile ( carried out in the microarray unit of the Weizmann institute)

growth_protocol: Cells were maintained in Keratinocyte Growth Medium (KGM): DMEM, 25% Nutrient mixture F-12 (HAM), 10% fetal bovine serum, 5 µg/ml insulin, 0.4 µg/ml hydrocortisone, 10−10 M cholera toxin, 10 ng/ml epidermal growth factor, 1.8×10−4 M adenine, 5 µg/ml transferrin, 2×10−9 M T3, 100,000 U/L penicillin, 100 µg/L streptomycin, 0.1 mg/ml amphotericin.

extract_protocol: Three independent cultures of Late cells were grown. RNA was isolated using RNeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The HPV16-immortalized keratinocytes had been transfected with a plasmid carrying the genome of the human papillomavirus, HPV16 (Mitrani-rosenbaum et al., 1992, Intervirology33: 76-85).Late passage (passage 270, L) represents cells that underwent about 1000 doublings.

tag: cell line

value: HF1 - HPV16-immortalized forskin keratinocytes


title: CLL spontaneous regression (TCCLL22)

description: no additional information


title: BP cells_BP_rep1

description: Human  U133A 2.0

source_name: benzo[a]pyrene treated HPV16-immortalized keratinocytes

extract_protocol: Three independent cultures of BP cells were grown. RNA was isolated using RNeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: BP cells were derived from L HF1 cells  (Mitrani-rosenbaum et al., 1992, Intervirology33: 76-85) by benzo[a]pyrene treatment, as follows: L cells were treated with the carcinogen, benzo[a]pyrene (5µM) for 30 days to establish a clone able to form colonies in soft agar. The established clone was suspended in soft agar for 2 weeks and selected colonies were grown and then further cultured in soft agar for additional selection (BP).


title: Late cells_L_rep2

description: Human  U133A 2.0


title: BP cells_BP_rep2

description: Human  U133A 2.0


title: MB468_hind


title: MDAMB453_hind


title: UACC812_hind


title: BP cells_BP_rep3

description: Human  U133A 2.0


title: MDA435_hind


title: MDA436_hind


title: Late cells_L_rep1

description: Human  U133A 2.0

value: HF1- HPV16-immortalized forskin keratinocytes


title: MDA415_hind


title: Early cells_E_rep2

description: Human  U133A 2.0

extract_protocol: Three independent cultures of Early cells were grown. RNA was isolated using RNeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The HPV16-immortalized keratinocytes had been transfected with a plasmid carrying the genome of the human papillomavirus, HPV16 (Mitrani-rosenbaum et al., 1992, Intervirology33: 76-85). Early passage (passage 20, E) represents cells that underwent about 50 doublings after transfection.


title: Keratinocytes_K_rep2

description: Human  U133A 2.0

source_name: keratinocytes from biopsy specimens

extract_protocol: Three independent cultures of keratinocytes were grown. RNA was isolated using RNeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Growth according to standard protocol

value: skin


title: 43°C vs. 37°C_exp3

city: Geneva

first: Pierre

middle: E

last: Vaudaux

address: 24 rue Micheli-du-Crest

department: Infectious Diseases

country: Switzerland

institute: Geneva University Hospital

description:
Biological replicate 3 of 3
ISP_37/43 rep3

hyb_protocol: Agilent standard protocol:17h at 60°C; Agilent proprietary buffers

scan_protocol: Agilent scanner, 100% PMT. Extraction using Agilent's Feature Extraction Software

data_processing: Lowess on background subtracted values using Feature Extraction Software

organism: Staphylococcus aureus

label_protocol: Direct labelling of 10 ug total RNA using SUPERSCRIPT II H- Reverse Transcriptase (Invitrogen)

growth_protocol: Bacterial cultures were prepared by growing 100-fold dilutions of overnight cultures in 15 ml MHB for 5h at 37°C (without shaking), to an OD540 of 0.6. Then the pre-culture were transfered either to 43°C or 48°C or left at 37°C for 10 min

extract_protocol: RNeasy extraction kit from Qiagen

treatment_protocol: Immediately after the heat shock, all cultures were directly transfered to RNAprotect Bacteria Reagent (Qiagen)

tag: Culture maintained at 37°C (CTL)

tag: Culture shifted to 43°C


title: MDAMB361_xba


title: Keratinocytes_K_rep3

description: Human  U133A 2.0


title: MDAMB361_hind


title: Early cells_E_rep1

description: Human  U133A 2.0


title: Early cells_E_rep3

description: Human  U133A 2.0


title: DU4475_hind


title: MCF7_hind


title: MDA231_hind


title: MDA175_hind


title: CAMA1_hind


title: MDA435_xba


title: 43°C vs. 37°C_exp2

description:
Biological replicate 2 of 3
ISP_37/43 rep2


title: HS578T_hind


title: 48°C vs. 37°C_exp3

description:
Biological replicate 3 of 3
ISP_37/48 rep3

tag: Culture shifted to 48°C


title: 48°C vs. 37°C_exp2

description:
Biological replicate 2 of 3
ISP_37/48 rep2


title: 43°C vs. 37°C_exp1

description:
Biological replicate 1 of 3
ISP_37/43 rep1


title: Keratinocytes_K_rep1

description: Human  U133A 2.0


title: BT483_hind


title: BT549_hind


title: BT474_hind


title: AU5_65_hind


title: HCC1806_hind


title: Patient_20_day_70

status: Public on Apr 21 2009

city: Bloomington

first: Milton

middle: W

last: Taylor

state: IN

address: 343 Jordan Hall

department: Biology

institute: Indiana University

description: Gene expression data from PBMC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on HGU133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Affymetrix Gene Chip Operating Software (GCOS) using the MAS 5.0 algorithm using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix, 2004).

extract_protocol: Whole blood collected in heparin tubes. PBMCs separated using Ficol-Hypaque gradient. RNA extracted from PBMC with Trizol (Invitrogen) followed by Rneasy (Qiagen).

tag: Patient id

tag: Caucasian

tag: Male

tag: Time Point (day)


title: Patient_19_day_3

description: Gene expression data from PBMC


title: Patient_20_day_3

description: Gene expression data from PBMC


title: Patient_19_day_10

description: Gene expression data from PBMC


title: Patient_20_day_10

description: Gene expression data from PBMC


title: Patient_19_day_6

description: Gene expression data from PBMC


title: Patient_20_day_6

description: Gene expression data from PBMC


title: Patient_18_day_70

description: Gene expression data from PBMC


title: Patient_20_day_0

description: Gene expression data from PBMC


title: Patient_19_day_70

description: Gene expression data from PBMC


title: Patient_18_day_13

description: Gene expression data from PBMC


title: Patient_20_day_42

description: Gene expression data from PBMC


title: Patient_20_day_13

description: Gene expression data from PBMC


title: Patient_19_day_27

description: Gene expression data from PBMC


title: Patient_20_day_27

description: Gene expression data from PBMC


title: Patient_18_day_42

description: Gene expression data from PBMC


title: Patient_19_day_42

description: Gene expression data from PBMC


title: Patient_18_day_3

description: Gene expression data from PBMC


title: 48°C vs. 37°C_exp1

description:
Biological replicate 1 of 3
ISP_37/48 rep1


title: Patient_18_day_6

description: Gene expression data from PBMC


title: Patient_18_day_10

description: Gene expression data from PBMC


title: Patient_18_day_27

description: Gene expression data from PBMC


title: Patient_18_day_0

description: Gene expression data from PBMC


title: Patient_17_day_42

description: Gene expression data from PBMC


title: Patient_19_day_13

description: Gene expression data from PBMC


title: Patient_17_day_27

description: Gene expression data from PBMC


title: Patient_19_day_0

description: Gene expression data from PBMC


title: CAL851_hind


title: Patient_17_day_70

description: Gene expression data from PBMC


title: Patient_15_day_27

description: Gene expression data from PBMC

tag: Female


title: Patient_16_day_0

description: Gene expression data from PBMC


title: Patient_17_day_0

description: Gene expression data from PBMC


title: Patient_17_day_13

description: Gene expression data from PBMC


title: Patient_16_day_13

description: Gene expression data from PBMC


title: Patient_16_day_3

description: Gene expression data from PBMC


title: Patient_16_day_42

description: Gene expression data from PBMC


title: Patient_17_day_3

description: Gene expression data from PBMC


title: Patient_16_day_70

description: Gene expression data from PBMC


title: Patient_16_day_27

description: Gene expression data from PBMC


title: Patient_17_day_10

description: Gene expression data from PBMC


title: Patient_15_day_13

description: Gene expression data from PBMC


title: Patient_16_day_10

description: Gene expression data from PBMC


title: Patient_16_day_6

description: Gene expression data from PBMC


title: Patient_17_day_6

description: Gene expression data from PBMC


title: Patient_15_day_70

description: Gene expression data from PBMC


title: Patient_15_day_6

description: Gene expression data from PBMC


title: Patient_14_day_27

description: Gene expression data from PBMC


title: Patient_14_day_42

description: Gene expression data from PBMC


title: Patient_14_day_6

description: Gene expression data from PBMC


title: Patient_15_day_0

description: Gene expression data from PBMC


title: Patient_14_day_70

description: Gene expression data from PBMC


title: Patient_14_day_3

description: Gene expression data from PBMC


title: Patient_15_day_10

description: Gene expression data from PBMC


title: Patient_15_day_3

description: Gene expression data from PBMC


title: Patient_14_day_13

description: Gene expression data from PBMC


title: Patient_14_day_10

description: Gene expression data from PBMC


title: Patient_15_day_42

description: Gene expression data from PBMC


title: Patient_13_day_70

description: Gene expression data from PBMC


title: Patient_13_day_42

description: Gene expression data from PBMC


title: Patient_14_day_0

description: Gene expression data from PBMC


title: Patient_13_day_10

description: Gene expression data from PBMC


title: Patient_13_day_0

description: Gene expression data from PBMC


title: Patient_13_day_27

description: Gene expression data from PBMC


title: Patient_13_day_13

description: Gene expression data from PBMC


title: Patient_13_day_6

description: Gene expression data from PBMC


title: Patient_12_day_0

description: Gene expression data from PBMC

tag: African American


title: Patient_12_day_27

description: Gene expression data from PBMC


title: Patient_12_day_3

description: Gene expression data from PBMC


title: Patient_12_day_42

description: Gene expression data from PBMC


title: Patient_12_day_10

description: Gene expression data from PBMC


title: Patient_11_day_27

description: Gene expression data from PBMC


title: Patient_12_day_70

description: Gene expression data from PBMC


title: Patient_12_day_6

description: Gene expression data from PBMC


title: Patient_12_day_13

description: Gene expression data from PBMC


title: Patient_11_day_70

description: Gene expression data from PBMC


title: Patient_10_day_27

description: Gene expression data from PBMC


title: Patient_13_day_3

description: Gene expression data from PBMC


title: Patient_11_day_10

description: Gene expression data from PBMC


title: Patient_11_day_42

description: Gene expression data from PBMC


title: Patient_11_day_6

description: Gene expression data from PBMC


title: Patient_11_day_13

description: Gene expression data from PBMC


title: Patient_10_day_42

description: Gene expression data from PBMC


title: Patient_10_day_70

description: Gene expression data from PBMC


title: Patient_10_day_13

description: Gene expression data from PBMC


title: Patient_9_day_42

description: Gene expression data from PBMC


title: Patient_9_day_70

description: Gene expression data from PBMC


title: Patient_11_day_0

description: Gene expression data from PBMC


title: Patient_10_day_6

description: Gene expression data from PBMC


title: Patient_10_day_0

description: Gene expression data from PBMC


title: Patient_9_day_13

description: Gene expression data from PBMC


title: Patient_9_day_10

description: Gene expression data from PBMC


title: Patient_10_day_3

description: Gene expression data from PBMC


title: Patient_9_day_27

description: Gene expression data from PBMC


title: Patient_10_day_10

description: Gene expression data from PBMC


title: Patient_9_day_6

description: Gene expression data from PBMC


title: Patient_8_day_13

description: Gene expression data from PBMC


title: Patient_7_day_42

description: Gene expression data from PBMC


title: Patient_8_day_0

description: Gene expression data from PBMC


title: Patient_8_day_70

description: Gene expression data from PBMC


title: Patient_9_day_0

description: Gene expression data from PBMC


title: Patient_7_day_27

description: Gene expression data from PBMC


title: Patient_7_day_70

description: Gene expression data from PBMC


title: Patient_7_day_10

description: Gene expression data from PBMC


title: Patient_7_day_13

description: Gene expression data from PBMC


title: Patient_8_day_3

description: Gene expression data from PBMC


title: Patient_8_day_42

description: Gene expression data from PBMC


title: Patient_8_day_10

description: Gene expression data from PBMC


title: Patient_8_day_6

description: Gene expression data from PBMC


title: Patient_8_day_27

description: Gene expression data from PBMC


title: Patient_9_day_3

description: Gene expression data from PBMC


title: Patient_7_day_3

description: Gene expression data from PBMC


title: Patient_6_day_27

description: Gene expression data from PBMC


title: Patient_6_day_70

description: Gene expression data from PBMC


title: Patient_7_day_0

description: Gene expression data from PBMC


title: Patient_7_day_6

description: Gene expression data from PBMC


title: Patient_6_day_0

description: Gene expression data from PBMC


title: Patient_6_day_13

description: Gene expression data from PBMC


title: Patient_5_day_42

description: Gene expression data from PBMC


title: Patient_6_day_42

description: Gene expression data from PBMC


title: Patient_5_day_70

description: Gene expression data from PBMC


title: Patient_5_day_27

description: Gene expression data from PBMC


title: Patient_6_day_3

description: Gene expression data from PBMC


title: Patient_6_day_10

description: Gene expression data from PBMC


title: Patient_5_day_13

description: Gene expression data from PBMC


title: Patient_5_day_3

description: Gene expression data from PBMC


title: Patient_5_day_10

description: Gene expression data from PBMC


title: Patient_4_day_42

description: Gene expression data from PBMC


title: Patient_4_day_70

description: Gene expression data from PBMC


title: Patient_3_day_6

description: Gene expression data from PBMC


title: Patient_3_day_42

description: Gene expression data from PBMC


title: Patient_4_day_13

description: Gene expression data from PBMC


title: Patient_4_day_3

description: Gene expression data from PBMC


title: Patient_3_day_27

description: Gene expression data from PBMC


title: Patient_4_day_0

description: Gene expression data from PBMC


title: Patient_3_day_70

description: Gene expression data from PBMC


title: Patient_4_day_27

description: Gene expression data from PBMC


title: Patient_3_day_10

description: Gene expression data from PBMC


title: Patient_2_day_27

description: Gene expression data from PBMC


title: Patient_1_day_10

description: Gene expression data from PBMC


title: Patient_1_day_42

description: Gene expression data from PBMC


title: Patient_1_day_70

description: Gene expression data from PBMC


title: Patient_2_day_6

description: Gene expression data from PBMC


title: Patient_1_day_3

description: Gene expression data from PBMC


title: Patient_1_day_27

description: Gene expression data from PBMC


title: Patient_2_day_70

description: Gene expression data from PBMC


title: Patient_2_day_42

description: Gene expression data from PBMC


title: Patient_2_day_0

description: Gene expression data from PBMC


title: Patient_3_day_0

description: Gene expression data from PBMC


title: Patient_3_day_3

description: Gene expression data from PBMC


title: Patient_2_day_10

description: Gene expression data from PBMC


title: Pseudomonas aeruginosa (pMUM3) (1)

city: Amsterdam

first: Marian

last: Llamas

address: van der Boechorststraat 7

department: Medical Microbiology

country: Netherlands

institute: VU Medical Center

data_processing: Target hybridization, washing, staining and scanning were performed by the Affymetrix Core Facility using a GeneChip® hybridization oven, a Fluidics station and MICROARRAY SUITE software (Affymetrix). Genes were considered differentially regulated if the relative change (n-fold) was >2.5 and the P value was <0.05.

label: biotin-ddUTP

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa (pMUM3) (1)

label_protocol: Enzo BioArrayTM Terminal Labeling kit (Affymetrix)

growth_protocol: Grown in 300 mL Erlenmeyer flask with 30 mL LB and 25 µg/ml piperacillin at 37°C and 200 revolutions per min.

extract_protocol: Total RNA was isolated by the hot phenol method using the Tri Reagent® LS (Molecular Research Center, Inc.). Contaminating DNA was eliminated by Dnase I (Amersham) treatment, and RNA was isolated by phenol-chloroform extraction and precipitation with 2.5 x volume 100% (vol/vol) ethanol and 0.1 x volume 3 M sodium acetate pH 4.8. An additional RNA purification step was performed using the RNeasy columns (Qiagen). RNA quantity was assessed by UV absorption at 260 nm in a ND-1000 Spectrophotometer (NanoDrop Technologies, USA). RNA quality was monitored by 1.5% (wt/vol) agarose gel electrophoresis containing 2,2 M formaldehyde as denaturing agent.

tag: strain

value: Pseudomonas aeruginosa PAO25 containing the plasmid pMUM3


title: Patient_5_day_0

description: Gene expression data from PBMC


title: Pseudomonas aeruginosa (pMUM3) (2)

description: Target hybridization, washing, staining and scanning were performed by the Affymetrix Core Facility using a GeneChip® hybridization oven, a Fluidics station and MICROARRAY SUITE software (Affymetrix)

label: Enzo BioArrayTM Terminal Labeling kit (Affymetrix)

source_name: Pseudomonas aeruginosa (pMUM3) (2)


title: Patient_1_day_6

description: Gene expression data from PBMC


title: CD4-Hg CD25+ (anti CD3, CD28) HG-U133B

status: Public on Apr 20 2009

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: CD4-Hg CD25+ (anti CD3, CD28)

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 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 150.

source_name: CD4-Hg CD25+ (anti CD3, CD28) HG-U133B

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: anti CD3 plate bound, 1µg/ml, 1µg/µl anti CD28

extract_protocol: Rneasy

tag: genetic modification:

value: Blood


title: CD4-Hg CD25- (anti CD3, CD28) HG-U133B

description: CD4-Hg CD25- (anti CD3, CD28)

source_name: CD4-Hg CD25- (anti CD3, CD28) HG-U133B


title: MPO CD4+CD25- (naive) I A unstimulated HG-U133B

description: MPO CD4+CD25- (naiv) I A

growth_protocol: no stimulation


title: Patient_1_day_0

description: Gene expression data from PBMC


title: THU CD4+ CD25+  II A unstimulated HG-U133B

description: THU CD4+ CD25+  II A


title: CD4-Hg CD25+ (anti CD3) HG-U133B

description: CD4-Hg CD25+ (anti CD3)

source_name: CD4-Hg CD25+ (anti CD3) HG-U133B

growth_protocol: anti CD3 plate bound, 1µg/ml TR66 + 100U/µl IL-2 (rec_human)


title: MPO CD4+CD25+ I B unstimulated HG-U133B

description: MPO CD4+CD25+ I B

source_name: MPO CD4+CD25+ I B unstimulated HG-U133B


title: FoxP3 d3

description: FoxP3 d3

source_name: FoxP3 d3

value: T-cells


title: THU CD4+ CD25- (naive) II A unstimulated HG-U133B

description: THU CD4+ CD25- (naiv) II A


title: Patient_2_day_3

description: Gene expression data from PBMC


title: Garp d3

description: Garp d3

source_name: Garp d3


title: Triplicate data of THP-1 72h after PMA stimulated

status: Public on Apr 19 2009

city: Yokohama

first: Piero

last: Carninci

department: Center for Life Science Technologies

country: Japan

institute: RIKEN

hyb_protocol: The RNA samples were reverse transcribed to produce cDNA and then subjected to quantitative PCR using SYBR Green (Molecular Probes) using the ABI Prism 7900HT system (Applied Biosystems, Foster City, CA, USA) with a 384-well amplification plate; genes for each sample were assayed in triplicate. Reactions were carried out in 20μL volumes in 384-well plates; each reaction contained: 0.5 U of HotStar Taq DNA polymerase (Qiagen) and the manufacturer’s 1× amplification buffer adjusted to a final concentration of 1mM MgCl2, 160μM dNTPs, 1/38000 SYBR Green I (Molecular Probes), 7% DMSO, 0.4% ROX Reference Dye (Invitrogen), 300 nM of each primer (forward and reverse), and 2μL of 40-fold diluted first-strand cDNA synthesis reaction mixture (12.5ng total RNA equivalent). Polymerase activation at 95ºC for 15 min was followed by 40 cycles of 15 s at 94ºC, 30 s at 60ºC, and 30 s at 72ºC.

scan_protocol: The dissociation curve analysis, which evaluates each PCR product to be amplified from single cDNA, was carried out in accordance with the manufacturer’s protocol. Expression levels were reported as Ct values.

data_processing: The large number of genes assayed and the replicates measures required that samples be distributed across multiple amplification plates, with an average of twelve plates per sample. Because it was envisioned that GAPDH would serve as a single-gene normalization control, this gene was included on each plate. All primer pairs were replicated in triplicates. Raw qPCR expression measures were quantified using Applied Biosystems SDS software and reported as Ct values. The Ct value represents the number of cycles or rounds of amplification required for the fluorescence of a gene or primer pair to surpass an arbitrary threshold. The magnitude of the Ct value is inversely proportional to the expression level so that a gene expressed at a high level will have a low Ct value and vice versa. Replicate Ct values were combined by averaging, with additional quality control constraints imposed by a standard filtering method developed by the RIKEN group for the preprocessing of their qPCR data. Briefly this method entails:   1.  Sort the triplicate Ct values in ascending order: Ct1, Ct2, Ct3. Calculate differences between consecutive Ct values: difference1 = Ct2 – Ct1 and difference2 = Ct3 – Ct2  2.  Four regions are defined (where Region4 overrides the other regions):    Region1: difference ≦ 0.2  Region2: 0.2 < difference ≦ 1.0 Region3: 1.0 < difference    If difference1 and difference2 fall in the same region, then the three replicate Ct values are averaged to give a final representative measure. If difference1 and difference2 are in different regions, then the two   replicate Ct values that are in the small number region are averaged instead.   - Quantile normalization Algorithm   Quantile normalization proceeds in two stages. First, if samples are distributed across multiple plates, normalization is applied to all of the genes assayed for each sample to remove plate-to-plate effects by enforcing the same quantile distribution on each plate. Then, an overall quantile normalization is applied between samples, assuring that each sample has the same distribution of expression values as all of the other samples to be compared. A similar approach using quantile normalization has been previously described in the context of microarray normalization. Briefly, our method entails the following steps:    1.  qPCR data from a single RNA sample are stored in a matrix M of dimension k (maximum number of genes or primer pairs on a plate) rows by p (number of plates) columns. Plates with differing numbers of genes are made equivalent by padded plates with missing values to constrain M to a rectangular structure.    2.  Each column is sorted into ascending order and stored in matrix M’. The sorted columns correspond to the quantile distribution of each plate. The missing values are placed at the end of each ordered column. All calculations in quantile normalization are performed on non-missing values.      3.  The average quantile distribution is calculated by taking the average of each row in M’. Each column in M’ is replaced by this average quantile distribution and rearranged to have the same ordering as the original row order in M. This gives the within-sample normalized data from one RNA sample.   4.  Steps analogous to 1 – 3 are repeated for each sample. Between-sample normalization is performed by storing the within-normalized data as a new matrix N of dimension k (total number of genes, in our example k = 2,396) rows by n (number of samples) columns. Steps 2 and 3 are then applied to this matrix.    - Rank-Invariant Set Normalization Algorithm   1.  qPCR data from all samples are stored in matrix R of dimension g (total number of genes or primer pairs used for all plates) rows by s (total number of samples).    2.  We first select gene sets that are rank-invariant across a single sample compared to a common reference. The reference may be chosen in a variety of ways, depending on the experimental design and aims of the experiment. As described in Tseng et al., the reference may be designated as a particular sample from the experiment (e.g. time zero in a time course experiment), the average or median of all samples, or selecting the sample which is closest to the average or median of all samples. Genes are considered to be rank-invariant if they retain their ordering or rank with respect to expression across the experimental sample versus the common reference sample. We collect sets of rank-invariant genes for all of the s pairwise comparisons, relative to a common reference. We take the intersection of all s sets to obtain the final set of rank-invariant genes that is used for normalization.   3.  Let  αj represent the average expression value of the rank-invariant genes in sample j. (α1, …, αs) then represents the vector of rank-invariant average expression values for all conditions 1 to s.    4.  We calculate the scale factor  βj for sample j where βj represents the ratio of the rank-invariant average expression value in the first sample versus sample j, i.e. β 1 =  α1/ αj  =   for j = 1 to s.  5.  Finally, we normalize the raw data by multiplying each column j of R by the scale factor  βj for j = 1 to s.

label: Sybr Green

source_name: THP-1 after PMA stimulated 72h

label_protocol: not applicable

growth_protocol: The THP-1 cell line was sub-cloned and one clone (#5) was selected for its ability to differentiate relatively homogeneously in response to phorbol 12-myristate-13-acetate (PMA) (Sigma). THP-1.5 was used for all subsequent experiments. THP-1.5 cells were cultured in RPMI, 10% FBS, Penicillin/Streptomycin, 10mM HEPES, 1mM Sodium Pyruvate, 50uM 2-Mercaptoethanol.

extract_protocol: Total RNA was purifed from TRIzol lysates according to manufacturer’s instructions.

treatment_protocol: THP-1.5 were treated with 30ng/ml PMA over a time-course of 96h. Total cell lysates were harvested in TRIzol reagent at 1, 2, 4, 6, 12, 24, 48, 72, 96 hours, including an undifferentiated control.

tag: tissue type

tag: cell type

value: monocyte

value: 1 year infant

tag: sex

value: male


title: Triplicate data of THP-1 48h after PMA stimulated

source_name: THP-1 after PMA stimulated 48h

value: peripheral blood


title: Triplicate data of THP-1 96h after PMA stimulated

source_name: THP-1 after PMA stimulated 96h


title: CD4-Hg CD25- (anti CD3) HG-U133B

description: CD4-Hg CD25- (anti CD3)

source_name: CD4-Hg CD25- (anti CD3) HG-U133B


title: CD4-245 (CD25-, CD3) HG-U133B

description: CD4-245 (CD25-, CD3)


title: CD4-245 (CD25+, CD3 u. CD28) HG-U133B

description: CD4-245 (CD25+, CD3 u. CD28)


title: GFP d3

description: GFP d3

source_name: GFP d3


title: CD4-245 (CD25+, CD3) HG-U133B

description: CD4-245 (CD25+, CD3)


title: H1-ES_sample3

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: cell pellet in Trizol

data_processing:
Raw CEL files were processed using Affymetrix Expression Console Software using RMA-Core-DABG

pgf-file = HuEx-1_0-st-v2.r2.pgf
clf-file = HuEx-1_0-st-v2.r2.clf
bgp-file = HuEx-1_0-st-v2.r2.antigenomic.bgp
meta-ps-file = HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label_protocol: 1ug of total RNA was labeled according to Standard Affymetrix WT protocol for Exon 1.0 STarrays

growth_protocol:
http://encodewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines#Cell_phenotype_study
Human H1 human male ES cells cultured on TESR/Matrigel and split one to six using dispase. Karyotypically normal, 95% Oct4 positive, differentiable into mesodermal, endodermal and ectodermal lineages

extract_protocol: total RNA was extracted from cell pellets using Trizol protocol

treatment_protocol: cells were supplied as pellets in trizol

value: embryonic stem (H1_ES)


title: Triplicate data of THP-1 2h after PMA stimulated

source_name: THP-1 after PMA stimulated 2h


title: Triplicate data of THP-1 4h after PMA stimulated

source_name: THP-1 after PMA stimulated 4h


title: H1-ES_sample4

description: cell pellet in Trizol

hyb_protocol: Standard Affymetrix WT protocol for Exon 1.0 STarrays


title: Triplicate data of THP-1 6h after PMA stimulated

source_name: THP-1 after PMA stimulated 6h


title: Triplicate data of THP-1 12h after PMA stimulated

source_name: THP-1 after PMA stimulated 12h


title: CD4-245 (CD25-, CD3 u. CD28) HG-U133B

description: CD4-245 (CD25-, CD3 u. CD28)


title: Triplicate data of THP-1 1h after PMA stimulated

source_name: THP-1 after PMA stimulated 1h


title: Triplicate data of THP-1 24h after PMA stimulated

source_name: THP-1 after PMA stimulated 24h


title: Triplicate data of THP-1 0h after PMA stimulated

description: PMAControlHR

source_name: THP-1 after PMA stimulated 0h


title: Treg THU d3

description: Treg THU d3

source_name: Treg THU d3


title: Functional characterization of P-cadherin in invasive breast cancer cells (clone B)

status: Public on Apr 18 2009

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description: Human breast cell line mda-mb-231 (control and clones), cultured in DMEM with Glutamax-1 supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 0.4% fungizone. Passaged by trypsinization.

hyb_protocol: Hybridization was performed in 4x standard saline citrate, 1x bovine serum albumin, 2 µg/ml DNAs, and 0.1% sodium dodecyl sulphate at 42°C for 15 hours.

scan_protocol: Slides were washed, dried and then scanned in a Scanarray 5000 XL scanner (GSI Lumonics Kanata, Ontario, Canada) at wavelengths of 635 and 532 nm for Cy5 and Cy3 dyes, respectively.

data_processing: To obtain 10-m resolution images, which were quantified using the Scanarray 5000 XL scanner (GSI Lumonics)

source_name: MDA-MB-231 overexpressing CDH3_B + dexamethasone

extract_protocol: Total RNA was isolated using Rneasy Midi Kit (Qiagen, Hilden, Germany) as indicated by the manufacturer

tag: cells

value: MDA-MB-231 overexpressing CDH3_B

source_name: MDA-MB-231 control cells + dexamethasone

value: MDA-MB-231 control cells


title: Functional characterization of E-cadherin in invasive breast cancer cells (clone B3_2)

source_name: MDA-MB-231 overexpressing CDH1_B3 + dexamethasone

label_protocol: Hybridization was performed in 4x standard saline citrate, 1x bovine serum albumin, 2 µg/ml DNAs, and 0.1% sodium dodecyl sulphate at 42°C for 15 hours.

value: MDA-MB-231 overexpressing CDH1_B3


title: Functional characterization of P-cadherin in invasive breast cancer cells (clone A_2)

source_name: MDA-MB-231 overexpressing CDH3_A + dexamethasone (experiment 2)

value: MDA-MB-231 overexpressing CDH3_A

source_name: MDA-MB-231 control cells + dexamethasone (experiment 2)


title: Functional characterization of E-cadherin in invasive breast cancer cells (clone B3).

source_name: MDA-MB-231 overexpressing CDH1_B3 + dexamethasone (experiment 2)


title: EDC_679

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

description: Gene expression data from MCF-7 cells treated with Estrogen dendrimer conjugate for 4 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Array Set HG-U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS 3000.

data_processing: The data were analyzed with  GCOS2.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: MCF-7 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7 cells were maintained in MEM media with 5% Calf serum

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

treatment_protocol: MCF-7 cells were treated in phenol free MEM media with 5% CD-Calf serum with the ligands for four hours

tag: disease

value: Breast adenocarcinoma

value: MCF-7 cells

tag: agent

value: Estrogen dendrimer conjugate


title: Functional characterization of E-cadherin in invasive breast cancer cells (clone B1).

source_name: MDA-MB-231 overexpressing CDH1_B1 + dexamethasone

value: MDA-MB-231 overexpressing CDH1_B1


title: CLL patient ZAP70 low, biological rep5

city: Bruxelles

first: Basile

last: Stamatopoulos

address: Bd de Waterloo n°121

department: Experimental Hematology

country: Belgium

institute: Jules Bordet Institute

description: Gene expression data from CLL patient expressing low level of ZAP70 measured by real time PCR

hyb_protocol: Following fragmentation, 16 µg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix gENESHIP Fluidics Station 450 regarding Affymetrix protocol (www.affymetrix.com)

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

data_processing: Image analysis and probe quantification were done with Affymetrix software, which produced raw probe intensity data in the Affymetrix CEL files. Normalization was done with the RMA method, which processed a group of CEL files simultaneously using BRB arrays tools.

source_name: CD19+ purified cells from CLL patient ZAP70 low, biological rep5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (www.affymetrix.com)

extract_protocol:
Peripheral Blood Mononuclear Cells (PBMC) were obtained from blood of Chronic lymphocytic leukemia patients.
PBMC were isolated by density-gradient centrifugation and B cells were purified with a CD19+ magnetic-bead system.
Total RNA was extracted from purified CD19+ cells in a single step using TriPure Isolation Reagent

tag: Binet Stage:B

tag: Mutational status

value: M

tag: ZAP70 -

tag: LPL -


title: CLL patient ZAP70 low, biological rep7

source_name: CD19+ purified cells from CLL patient ZAP70 low, biological rep7

tag: Binet Stage:A


title: Functional characterization of P-cadherin in invasive breast cancer cells (clone B_2).

source_name: MDA-MB-231 overexpressing CDH3_B + dexamethasone (experiment 2)


title: CLL patient ZAP70 low, biological rep4

source_name: CD19+ purified cells from CLL patient ZAP70 low, biological rep4

tag: LPL +


title: EDC_677

tag: cell line


title: CLL patient ZAP70 low, biological rep2

source_name: CD19+ purified cells from CLL patient ZAP70 low, biological rep2


title: CLL patient ZAP70 high, biological rep7

description: Gene expression data from CLL patient expressing high level of ZAP70 measured by real time PCR

source_name: CD19+ purified cells from CLL patient ZAP70 high, biological rep7

value: UM

tag: ZAP70 +


title: CLL patient ZAP70 low, biological rep6

source_name: CD19+ purified cells from CLL patient ZAP70 low, biological rep6


title: E2_672

description: Gene expression data from MCF-7 cells treated with 17-beta estradiol for 4 hours

value: 17-beta estradiol


title: E2_673


title: E2_671


title: CLL patient ZAP70 low, biological rep3

source_name: CD19+ purified cells from CLL patient ZAP70 low, biological rep3


title: CLL patient ZAP70 high, biological rep6

source_name: CD19+ purified cells from CLL patient ZAP70 high, biological rep6

tag: Binet Stage:C


title: CLL patient ZAP70 low, biological rep1

source_name: CD19+ purified cells from CLL patient ZAP70 low, biological rep1


title: CLL patient ZAP70 high, biological rep5

source_name: CD19+ purified cells from CLL patient ZAP70 high, biological rep5


title: CLL patient ZAP70 high, biological rep4

source_name: CD19+ purified cells from CLL patient ZAP70 high, biological rep4


title: EDC_678


title: Functional characterization of P-cadherin in invasive breast cancer cells (clone A)

source_name: MDA-MB-231 overexpressing CDH3_A + dexamethasone

source_name: MDA-MB-231 control cells + dexamethasone


title: Ctrl_675

description: Gene expression data from MCF-7 cells treated with empty dendrimer for 4 hours

value: empty dendrimer


title: Ctrl_676


title: Functional characterization of E-cadherin in invasive breast cancer cells (clone B1_2).

source_name: MDA-MB-231 overexpressing CDH1_B1 + dexamethasone (experiment 2)

source_name: MDA-MB-231 control cells + dexamethasone (experiment 2)


title: CLL patient ZAP70 high, biological rep3

source_name: CD19+ purified cells from CLL patient ZAP70 high, biological rep3


title: Ctrl_674

source_name: MCF-7 cells


title: CLL patient ZAP70 high, biological rep2

source_name: CD19+ purified cells from CLL patient ZAP70 high, biological rep2


title: TE06 (I6) - replicate 3 - mAdbID:94795

status: Public on Apr 17 2009

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 94795

hyb_protocol: Hybridization Protocol Other: Hybridization: Combine Cy3 and Cy5 labeled target (adjust the color to purple) and complete dry the sample by speed vacuum . Add 37ul of the following mixture to the dried target (for 20x40mm slide): 1ul 50x Denhardt’s blocking solution (Sigma Cat# 2532) 1ul poly dA (8mg/ml Pharmacia Cat# 27-7988-01) 1ul yeast tRNA (4mg/ml Sigma Cat# R8759) 10ul Human Cot I DNA (1mg/ml Gibco BRL Cat# 15279-011) 3ul 20X SSC 1ul 10% SDS 20ul of DEPC H2O Heat for 2 min at 99oC and Cool to RT. Apply target mixture to array slide, add coverslip, place in humidified hyb chamber, and hybridize at 65oC over night.

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 5.04 Temperature: 26.66

data_processing:
BRB ArrayTool Data Processing
Calculation Method: Analyzed using BRBArrayTools developed by the Biometric Research Branch, National Cancer Institute (http://linus.nci.nih.gov/BRB-ArrayTools.html ). Briefly, the raw data set was filtered according to standard procedure to exclude spots with minimum intensity that arbitrarily was set to an intensity parameter of 200 for in both fluorescence channels. If the fluorescence intensity of one channel was great than 200 and that of the other but was below 200, the fluorescence of the low intensity channel was arbitrarily set to 200. Spots with diameters < 20ìm and flagged spots were also excluded from the analyses. Then, the filtered data were normalized using Lowess Smoother for gene expression microarray.

source_name: Pooled Normal Donor PBMC

label_protocol:
Cy3 Labeling Protocol
Other: Labeled using ULS aRNA Fluorescent Labeling kit (Kreatech).

extract_protocol:
Trizol Extraction Protocol
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturers instructions. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using nanodrop with A260/A280 ratios > 2.0 after dilution in DEPC water.

tag: Tissue

value: blood

tag: Cell type

value: PBMC

label_protocol:
Cy5 Labeling Protocol
Other: Labeled using ULS aRNA Fluorescent Labeling kit (Kreatech).

tag: Cell line

value: Human embryonic stem cell line


title: CLL patient ZAP70 high, biological rep1

source_name: CD19+ purified cells from CLL patient ZAP70 high, biological rep1


title: HUVEC treated with Non-sense SiRNA , biological rep1

city: Boston

last: Oettgen

state: MA

address: Harvard Institutes of Medicine, 4 Blackfan Circle

department: Department of Medicine

institute: Beth Israel Deaconess Medical Center

description: Gene expression data from HUVEC treated with Non-sense SiRNA.

hyb_protocol: standard Affymetrix protocole

scan_protocol: GeneChips were scanned using the Affymetrix standrad scanner..

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

source_name: cell lines HUVEC (human umbilical vein EC)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: HUVEC


title: HUVEC treated with Non-sense SiRNA  biological rep2


title: HUVEC treated with ERG SiRNA , biological rep2

description: HUVEC treated with ERG SiRNA


title: WA 09 (H9) - differentiation-day 7 - mAdbID:94295

description: mAdb experiment ID: 94295

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.28;; 4.73 Temperature: 32.95

source_name: WA09 (H9) - differentiation day 7

treatment_protocol:
Treatment time: Day 7
In-vivo treatment: For embryonic body (EB) differentiation, hES cells were detached with collagenase IV and the cell aggregates were briefly triturated and cultured in ultra low attachment plates (Corning Inc, Corning, NY) for 7 days in maintenance medium without bFGF. The medium was changed every three days.


title: HUVEC treated with ERG SiRNA , biological rep1

description: HUVEC treated with ERG SiRNA


title: WA09 (H9) - replicate 3 - mAdbID:94794

description: mAdb experiment ID: 94794

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.18;; 4.21 Temperature: 28.07


title: NHA - mAdbID:94294

description: mAdb experiment ID: 94294

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.28;; 4.75 Temperature: 33.04

source_name: NHA

value: Normal human astrocytes


title: WA 09 (H9) - differentiation-day 10 - mAdbID:94290

description: mAdb experiment ID: 94290

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.28;; 4.82 Temperature: 33.41

source_name: WA09 (H9) - differentiation day 10

treatment_protocol:
Treatment time: Day 10
In-vivo treatment: For embryonic body (EB) differentiation, hES cells were detached with collagenase IV and the cell aggregates were briefly triturated and cultured in ultra low attachment plates (Corning Inc, Corning, NY) for 10 days in maintenance medium without bFGF. The medium was changed every three days.


title: TE06 (I6) - replicate 1 - mAdbID:94281

description: mAdb experiment ID: 94281

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.27;; 4.66 Temperature: 32.55


title: BG01v - replicate 2 - mAdbID:94278

description: mAdb experiment ID: 94278

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.37 Temperature: 31.3


title: BG01v - replicate 3 - mAdbID:94279

description: mAdb experiment ID: 94279

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.28;; 4.72 Temperature: 32.89


title: HUVEC - mAdbID:94292

description: mAdb experiment ID: 94292

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.28;; 4.79 Temperature: 33.22

source_name: HUVEC

value: umbilical cord

value: Human umbilical vein endothelial cells


title: WA 09 (H9) - differentiation-day 4 - mAdbID:94288

description: mAdb experiment ID: 94288

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.28;; 4.85 Temperature: 33.56

source_name: WA09 (H9) - differentiation day 4

treatment_protocol:
Treatment time: Day 4
In-vivo treatment: For embryonic body (EB) differentiation, hES cells were detached with collagenase IV and the cell aggregates were briefly triturated and cultured in ultra low attachment plates (Corning Inc, Corning, NY) for 4 days in maintenance medium without bFGF. The medium was changed every three days.


title: WA09 (H9) - replicate 1 - mAdbID:94280

description: mAdb experiment ID: 94280

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.28;; 4.7 Temperature: 32.8


title: UASMC - mAdbID:94287

description: mAdb experiment ID: 94287

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.29;; 4.87 Temperature: 33.62

source_name: UASMC

value: Umbilical Artery Smooth Muscle Cells


title: HMVEC - mAdbID:94291

description: mAdb experiment ID: 94291

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.28;; 4.81 Temperature: 33.35

source_name: HMVEC

value: Human microvascular endothelial cells


title: BG01v - replicate 1 - mAdbID:94284

description: mAdb experiment ID: 94284

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.29;; 4.88 Temperature: 33.68


title: TE06 (I6) - replicate 2 - mAdbID:94282

description: mAdb experiment ID: 94282

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.27;; 4.63 Temperature: 32.46


title: ZFXcko_B cell_12hr_rep2

city: New York

first: Teresita

last: Arenzana

department: Microbiology Department

institute: Columbia University

hyb_protocol: Labeled RNA samples (10 ug/array) were hybridized in duplicate to Mouse Genome 430 2.0 arrays (Affymetrix) at the Columbia University Microarray Project core facility according to the manufacturer's instructions.

scan_protocol: Array scanning was done using GCOS 1.4 software (Affymetrix).

data_processing: Raw data processing was done using GCOS 1.4 software (Affymetrix).

label: Biotin-16-UTP, Biotin-11-CTP

source_name: ZFXcko B cell, a-IgM, 12 hr

label_protocol: 100 ng of each RNA sample were used for reverse transcription and two rounds of linear antisense RNA amplification/labeling (Ambion). The aRNA was amplified without labeling in the first round, and then labeled with Biotin-16-UTP(Roche Applied Sciences) and Biotin-11-CTP (PerkinElmer Life Sciences) in the second round. Labeled aRNA was fragmented in RNA Fragmentation Buffer (QIAGEN) prior to hybridization.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen).

tag: Strain

value: 129SvEv, Gender:Male, Age:8wk, Cell type:Splenic follicular B cell


title: WA09 (H9) - replicate 2 - mAdbID:94793

description: mAdb experiment ID: 94793

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.25 Temperature: 27.73


title: ZFXcko_B cell_2hr_rep2

source_name: ZFXcko B cell, a-IgM, 2 hr


title: LFB - mAdbID:94275

description: mAdb experiment ID: 94275

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.25;; 4.43 Temperature: 31.55

source_name: LFB

value: Lung fibroblasts


title: ZFXcko_B cell_12hr_rep1


title: ZFXwt_B cell_12hr_rep2

source_name: ZFXwt B cell, a-IgM, 12 hr


title: granulosa cells_FOXOA3 adenovirus_FSH

city: Houston

first: JoAnne

middle: S

last: Richards

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: no additional information

hyb_protocol: Labeled cRNA were hybridized on Affymetrix GeneChip Rat Genome 230 2.0 Array using Hybridization Oven 640 with the GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner 3000 according to standard Affymetrix protocols

data_processing: Scanned images were processed using Affymetrix Microarray Suite Expresson Analysis software.

organism: Rattus norvegicus

source_name: granulosa cells from immature rat, infected with FOXOA3 adenovirus, treated with FSH

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 mg total RNA.

growth_protocol: Primary granulosa cells from estradiol-treated rats were plated in defined medium (serum-free DMEM-F12) in 12-well cultures dishes that were precoated with 1% serum.

extract_protocol: Total RNA extraction by RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Granulosa cells were infected with adenoviral vectors expressing GFP (control), constitutively active FOXO1 (FOXOA3), or a DNA-binding mutant (FOXOA3-mDBD) for 4h. The cells were then washed and cultured in the presence or absence of hormones [FSH (100 ng/ml)] for 24 h.

tag: infection

value: FOXOA3 adenovirus

value: FSH

tag: strain

value: Sprague-Dawley

tag: gender

value: female

tag: age


title: ZFXcko_B cell_0hr_rep2

source_name: ZFXcko B cell, a-IgM, 0 hr


title: granulosa cells_FOXOA3-mDBD adenovirus_FSH

description: no additional information

source_name: granulosa cells from immature rat, infected with FOXOA3-mDBD adenovirus, treated with FSH

value: FOXOA3-mDBD adenovirus

tag: agent


title: ZFXwt_B cell_0hr_rep1

source_name: ZFXwt B cell, a-IgM, 0 hr


title: ZFXcko_B cell_0hr_rep1


title: ZFXwt_B cell_2hr_rep1

source_name: ZFXwt B cell, a-IgM, 2 hr


title: granulosa cells_GFP adenovirus_FSH

description: no additional information

source_name: granulosa cells from immature rat, infected with GFP adenovirus, treated with FSH

value: GFP adenovirus


title: ZFXcko_B cell_2hr_rep1


title: ZFXwt_B cell_0hr_rep2


title: ZFXwt_B cell_2hr_rep2


title: Brain_BVi_1

city: Singapore

first: Jerome

last: Boulaire

address: 31 Biopolis Way

department: Gene Delivery

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

description: GeneSpring processed/normalized data not provided by submitter

hyb_protocol: Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the GeneChip Rat Genome 230 2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions.

scan_protocol: Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software

data_processing: Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 3 out of 4 brain samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition

source_name: Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of inactivated baculovirus vectors (5E7 viral particles)

label_protocol: One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)

extract_protocol: Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer

treatment_protocol: Inactivated baculovirus vectors were obtained by placing 200 µl of purified baculovirus (at 107pfu/ µl) on ice at a distance of 5 cm and subjected to short wavelength UV radiation (254nm UV) for 1 hour using a HL-2000 Hybrilinker (UVP, LLC Upland, CA). The inactivation of infectivity was verified by infecting U87 glioma cells. The inactivated baculoviruses (5ul, 5E07 viral particles) were injected stereotaxically into the striatum at two injection sites (AP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis.

value: Wistar

value: Male

tag: weight

tag: tissue

value: Brain

value: Inactivated baculovirus vectors


title: granulosa cells_GFP adenovirus_vehicle

description: no additional information

source_name: granulosa cells from immature rat, infected with GFP adenovirus, treated with vehicle

value: vehicle (control)


title: Brain_PBSi_3

source_name: Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of PBS

treatment_protocol: 5 ul of Phosphate buffered saline (PBS) were injected stereotaxically into the striatum at two injection sites (AP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis.

value: PBS


title: Cy5-Animal (a4.2+b4.2) & Cy3-Vegetal (A4.1+B4.1)

city: Toba

first: Lixy

last: Yamada

state: Mie

address: 429-63 Sugashima

department: Graduate School of Science,

institute: Nagoya University

hyb_protocol: A set of 1µg fluorescent-labeled cRNA targets from each sample was assembled into a hybridization reaction on the Ciona intestinalis Oligoarray ver.1 (GPL4556), using In Situ Hybridization Kit Plus (Agilent Tech.).  Hybridized microarrays were washed according to the manufacture’s protocol.

scan_protocol: Scanned on an Agilent G2565BA Microarray Scanner System.

data_processing: Intensity of probes per array was extracted from scanned microarray images using Feature Extraction software (Agilent Tech. ver.A.7.5.1), which performs background subtraction and dye normalization using the Linear & LOWESS method.  All algorithms and parameters used in this analysis were the default condition of the software.  The Local Background Subtraction Method was used for background subtractions and the Locally Weighted Linear Regression Method (Linear & LOWESS method) for normalization.

organism: Ciona intestinalis

source_name: Vegetal (A4.1+B4.1) blastomeres

label_protocol: Aliquots of total RNA were labeled with either Cy-3 CTP or Cy-5 CTP (Perkin-Elmer/NEN Life Sci.) by two-round linear amplification using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent Tech.) as specified by the manufacture. The quality and size distribution of targets were determined by RNA 6000 Nano Lab-on-chip Assay (Agilent Tech.), and quantification was determined using a NanoDrop microscale spectrophotometer (NanoDrop Technologies).

growth_protocol: Adults of Ciona intestinalis were cultivated at the Maizuru Fisheries Research Station of Kyoto University, the Marine Field of Field Science Center.

extract_protocol: Total RNA extracted from each isolated blastmares using Trizol following manufacturer's instructions

treatment_protocol: Eggs and sperm were obtained surgically from the gonoduct.  After insemination, embryos were dechorionated and reared at about 18°C in Millipore-filtered seawater (MFSW) containing 50 μg/ml streptomycin sulfate. Four pairs of blastomere, namely anterior-animal a4.2, posterior-animal b4.2, anterior-vegetal A4.1, and posterior-vegetal B4.1 were isolated with a fine glass needle under a stereomicroscope during 8-cell stage.  Isolated blastomeres were collected and treated for RNA extraction before next cell division starts.

tag: stages

value: 8-cell stage embryos

source_name: Animal (a4.2+b4.2) blastomeres


title: Brain_PBSi_2


title: Cy3-A4.1+a4.2+b4.2 & Cy5-B4.1

source_name: A4.1+a4.2+b4.2 blastomeres

source_name: B4.1 blastomeres


title: Cy5-A4.1+a4.2+b4.2 & Cy3-B4.1


title: Brain_BVi_3


title: TE06 (I6) - replicate 3 - mAdbID:94652

description: mAdb experiment ID: 94652

hyb_protocol: Sample Hybridization Protocol Other: The samples and the reference were co-hybridized to the miRNA array at room temperature over night. Both the processed cDNA and the miRNA array slides were scanned by GenePix scanner Pro 4.0 (Axon, Sunnyvale, CA, USA).

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.18;; 5.16 Temperature: 25.84

data_processing:
miRNA Data Processing
Calculation Method: The signal intensities were exported by R-based package mArray; the background-substracted intensities were normalized by variance stabilization normalization (VSN)and imported into BRRArray Tools.

source_name: EBV-infected lymphcytes

label_protocol:
Cy3 Labeling Protocol
Other: 4 µg total RNA was directly labeled with miRCURY™ LNA Array Power Labeling Kit (Exiqon, Woburn, MA) according to manufacture’s procedure.

value: Lymphoblastoid cells transfected with Epstein-Barr virus (EBV)

label_protocol:
Cy5 Labeling Protocol
Other: 4 µg total RNA was directly labeled with miRCURY™ LNA Array Power Labeling Kit (Exiqon, Woburn, MA) according to manufacture’s procedure.

value: Human embryonic stem cell line


title: Brain_PBSi_4


title: Brain_BVi_4


title: Brain_BVi_2

label_protocol:
One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)^SAMPLE = GSM361860
One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)


title: ZFXwt_B cell_12hr_rep1

value: 129SvEv, Gender:Male, Age:8wk, Cell type:Splenic follicular B cell


title: Cy3-Animal (a4.2+b4.2) & Cy5-Vegetal (A4.1+B4.1)


title: Brain_PBSi_1


title: LFB - mAdbID:94651

description: mAdb experiment ID: 94651

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 5.1 Temperature: 26.69

value: lung

value: Lung fibroblast


title: H9-EB-day14 - mAdbID:94650

description: mAdb experiment ID: 94650

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.2;; 4.25 Temperature: 29.04

source_name: WA09 (H9) - differentiation day 14

treatment_protocol:
Treatment time: day 14
In-vivo treatment: For embryonic body (EB) differentiation, hES cells were detached with collagenase IV and the cell aggregates were briefly triturated and cultured in ultra low attachment plates (Corning Inc, Corning, NY) for 14 days in maintenance medium without bFGF. The medium was changed every three days.


title: H9-EB-day7 - replicate 2 - mAdbID:94649

description: mAdb experiment ID: 94649

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.2;; 4.76 Temperature: 27.21

source_name: WA09 (H9) - differentiation day 7

treatment_protocol:
Treatment time: day 7
In-vivo treatment: For embryonic body (EB) differentiation, hES cells were detached with collagenase IV and the cell aggregates were briefly triturated and cultured in ultra low attachment plates (Corning Inc, Corning, NY) for 7 days in maintenance medium without bFGF. The medium was changed every three days.


title: TE06 (I6) - replicate 2 - mAdbID:93545

description: mAdb experiment ID: 93545

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4.15 Temperature: 28.74


title: TE06 (I6) - replicate 4 - mAdbID:94643

description: mAdb experiment ID: 94643

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.22;; 4.12 Temperature: 29.78


title: H9-EB-day10 - replicate 2 - mAdbID:94648

description: mAdb experiment ID: 94648

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.62 Temperature: 27.61

source_name: WA09 (H9) - differentiation day 10

treatment_protocol:
Treatment time: day 10
In-vivo treatment: For embryonic body (EB) differentiation, hES cells were detached with collagenase IV and the cell aggregates were briefly triturated and cultured in ultra low attachment plates (Corning Inc, Corning, NY) for 10 days in maintenance medium without bFGF. The medium was changed every three days.


title: BG01v - replicate 3 - mAdbID:94645

description: mAdb experiment ID: 94645

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.22;; 4.11 Temperature: 29.35


title: WA09 (H9)- replicate 3 - mAdbID:94640

description: mAdb experiment ID: 94640

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.49 Temperature: 28.1


title: BG01v - replicate 2 - mAdbID:94642

description: mAdb experiment ID: 94642

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 10 LaserPower: 3.22;; 4.12 Temperature: 29.96


title: H9-EB-day4 - mAdbID:93533

description: mAdb experiment ID: 93533

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 4.1 Temperature: 29.68

source_name: WA09 (H9) - differentiation day 4

treatment_protocol:
Treatment time: day 4
In-vivo treatment: For embryonic body (EB) differentiation, hES cells were detached with collagenase IV and the cell aggregates were briefly triturated and cultured in ultra low attachment plates (Corning Inc, Corning, NY) for 4 days in maintenance medium without bFGF. The medium was changed every three days.


title: WA09 (H9)- replicate 2 - mAdbID:94641

description: mAdb experiment ID: 94641

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.21;; 4.55 Temperature: 27.82


title: WA09 (H9)- replicate 1 - mAdbID:93534

description: mAdb experiment ID: 93534

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.24;; 4.1 Temperature: 29.53


title: BG01v - replicate 1 - mAdbID:93540

description: mAdb experiment ID: 93540

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.23;; 4.25 Temperature: 27.79


title: HMVEC - mAdbID:93263

description: mAdb experiment ID: 93263

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.21;; 3.55 Temperature: 30.02

source_name: HMVEC

value: Human microvascular endothelial cells


title: TE06 (I6) - replicate 1 - mAdbID:93261

description: mAdb experiment ID: 93261

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.66 Temperature: 29.35


title: HUVEC - mAdbID:93260

description: mAdb experiment ID: 93260

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.22;; 4.6 Temperature: 29.47

source_name: HUVEC

value: umbilical cord

value: Human umbilical endothelial cells