title: Serum sample from colorectal cancer after surgical intervention group (X689)


title: blood patient with S. aureus bacteremia [CS127-D00256]

status: Public on Jan 11 2013

type: RNA

city: Durham

first: Sun Hee

last: Ahn

state: NC

address: Stead Bldg, RM 1546A

department: Medicine

country: USA

institute: Duke University

description: Enrollment protocol: Subjects were enrolled at Duke University Medical Center (DUMC; Durham, NC) as part of a prospective, NIH-sponsored study to develop novel diagnostic tests for severe sepsis and community-acquired pneumonia (ClinicalTrials.gov NCT00258869).  Enrolled patients had a known or suspected infection a exhibited two or more Systemic Inflammatory Response Syndrome criteria. Patients were excluded if they had an imminently terminal co-morbid condition, advanced AIDS (CD4 count < 50), were receiving antibiotics prior to enrollment, or were enrolled in another clinical trial. Subjects in the current report had culture-confirmed monomicrobial BSI due to S. aureus (n=26; median age 55 years; range 40-91) or E. coli (n=14; median age 51.5 years; range 25-91). Uninfected controls (n=44; median age 26 years; range 20-59) were enrolled at DUMC as part of study investigating the effect of aspirin on platelet function among healthy.

hyb_protocol: Target was prepared and hybridized according to the "Affymetrix Technical Manual". The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hours in a rotating oven at 60 rpm.  GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.

scan_protocol: Fluorescent images were detected in an GeneChip® Scanner 3000 and expression data was extracted using the GeneChip Operating System v 1.1 (Affymetrix).  All GeneChips were scaled to a median intensity setting of 500.

data_processing: Data processing was conducted using the Robust Multichip Average (RMA) generated by Affymetrix Expression Console software.   Microarray data was analyzed in two steps following the analysis strategy.  First, a Bayesian sparse factor model was fit to the expression data without regard to phenotype. Second, factors were then used as independent variables to build a penalized binary regression with variable selection model trained to identify S. aureus infection. In order to minimize issues with overfitting, batch was not included in the regression models. This approach also allows for model averaging, which properly accounts for uncertainty in the choice of predictors and typically outperforms the single best model in predictive accuracy. Genes were filtered for analysis using non-specific filtering for genes with high mean expression and high variance across samples. Samples with a high number of outlying genes were removed during the factor analysis. Mice were batched into discrete experiments with each experiment containing the relevant controls to avoid confounding. Using the same murine experimental data, another classifier was derived to classify methicillin-resistant vs. methicillin-sensitive S. aureus infection. The methodology was otherwise the same as that described above.  We fit a factor model on the human data independently from the mouse data. The factor model was fit to 8,892 genes after non-specific filtering to remove unexpressed and uniformly expressed genes. The factor model was trained on the 95 samples from three batches of expression data, and this resulted in 77 factors. These 77 factors were then projected onto the full data set with the goal of distinguishing S. aureus BSI from healthy controls or E. coli BSI. Leave-one-out cross-validation was utilized in order to control for overfitting of the penalized binary regression model. In order to minimize issues with overfitting, batch was not included in the regression models. Matlab scripts to perform these operations are available.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: blood patient with S. aureus bacteremia prior antibiotic treatment (Emergency Department)

label_protocol: The cDNA products were incubated with T7 RNA Polymerase and biotinylated ribonucleotides using an In Vitro Transcription kit (Affymetrix). The resultant cRNA product was purified using an RNeasy column (Qiagen) and quantified with a spectrophotometer. The cRNA target (20ug) was incubated at 94ºC for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc).  The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix).

extract_protocol: Total RNA was extracted from human blood using the PAXgene Blood RNA Kit (Qiagen, Valencia, CA) following the manufacturer’s recommended protocol including DNase treatment.  Following isolation, RNA quantity was determined using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). A set of four peptide nuleic acid (PNA) oligomers (Applied Biosystems, Foster City, CA) with sequences complimentary to globin mRNA were added to 2.5 ug of total RNA to reduce globin RNA transcription, then converted into cDNA using Reverse Transcriptase (Invitrogen) and a modified oligo(dT)24 primer that contains T7 promoter sequences (GenSet).   After first strand synthesis, residual RNA was degraded by the addition of RNaseH and a double-stranded cDNA molecule was generated using DNA Polymerase I and DNA Ligase. The cDNA was then purified and concentrated using a phenol:chloroform extraction followed by ethanol precipitation.

tag: ethnicity

value: Black

tag: host gender

value: Male

tag: host age (yr)

tag: pathogen

value: Staphylococcus aureus

tag: anatomic site of infection

value: urinary tract

tag: experimental batch


title: blood healthy control [DU09-01S01271.CEL]

source_name: blood human NOT infected

value: White

value: Female


title: blood healthy control [DU09-01S01091.CEL]


title: blood healthy control [DU09-01S01128.CEL]


title: blood healthy control [DU09-01S01235.CEL]


title: blood patient with S. aureus bacteremia [F02098]

value: Staphylococcus aureus and Streptococcus pneumoniae

value: lung


title: blood healthy control [DU09-01S01122.CEL]


title: blood healthy control [DU09-01S00735.CEL]


title: Serum sample from Advanced Adenoma after removal (X517)

city: Barcelona

first: María Dolores

last: Giráldez

state: Barcelona

address: Villarroel 170

department: Gastroenterology

country: Spain

institute: Hospital Clínic

description: Serum sample from Advanced Adenoma after removal group (X517)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor (v2.5) Lumi package.

label: biotin

source_name: serum plasma sample

label_protocol: Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

extract_protocol: 20 ml of whole blood from each participant were collected in EDTA tubes. Blood samples were left at 4ºC until plasma separation and plasma was frozen within 6 h of the blood draw. Briefly, samples were centrifuged at 1,600 x g for 10 min at 4 ºC to spin down blood cells, and plasma was transferred into new tubes, followed by further centrifugation at 16,000 x g for 10 minutes at 4ºC to completely remove cellular components. Plasma was then aliquoted and stored at -80°C until use.

tag: disease state

value: Advanced Adenoma after removal

tag: sample type

value: serum


title: blood healthy control [DU09-01S00995.CEL]

value: Unknown


title: blood healthy control [DU09-01S01246.CEL]

value: unknown


title: blood healthy control [DU09-01S01241.CEL]


title: blood healthy control [DU09-01S00822.CEL]


title: blood healthy control [DU09-01S00810.CEL]


title: blood patient with S. aureus bacteremia [F01541]

value: cardiac


title: Serum sample from colorectal cancer after surgical intervention group (X516)


title: Serum sample from colorectal cancer after surgical intervention group (X515)


title: blood healthy control [DU09-01S00588.CEL]


title: blood healthy control [DU09-01S00601.CEL]


title: Serum sample from Advanced Adenoma group (X514)

value: Advanced Adenoma


title: Serum sample from Advanced Adenoma group (X513)


title: Patient 1, Carcinoma_2

type: genomic

city: Richmond

first: Santanu

last: Dasgupta

state: VA

address: 1220 E Broad Street

institute: Virginia Commonwealth University

hyb_protocol: The biotinylated DNA was added to a hybridization solution and hybridized overnight at 49°C using standard Affymetrix protocol.

scan_protocol: Hybridized arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix Inc).

data_processing:
SNP 250K-NSpI array analysis: We used the 250K-Nsp I array platform from the Affymetrix 500K array set for genotyping each sample.  The genotype call was automatically detected by the Affymetrix’ Genotype Analysis (GTYPE) Software.  Data were analyzed with dChip using HMM model. Nexus program was also used in parallel.  Individual genes were identified based on the SNP ID.

Determination of loss of heterozygosity (LOH) and copy number variation (CNV): The resulting data was anlyzed using both dChip (www.dchip.org) and Nexus software package (http://www.snp-nexus.org) for the determination of LOH and CNV respectively. Intensity (.CEL) files was normalized and modeled using the PM-MM difference modeling method. Array normalization and quality control was performed as per the Affymetrix protocol and requirement. A region of "LOH" was designated when there was a consicutive loss of at least 10 SNPs. The Nexus program was utilized parallely to identify the copy neutral and copy number losses/gains as well as homozygous deletion based on the standard data interpretation criteria.

molecule: genomic DNA

source_name: surgical biopsy, Patient 1, Carcinoma_2

label_protocol: Two hundred fifty nanograms of genomic DNA was digested with Nsp I and ligated to adaptors that recognize the cohesive four base-pair (bp) overhangs. All fragments resulting from restriction enzyme digestion was then ligated using T4 ligase and PCR-amplified using an Applied Biosystems  Thermal Cycler I (9700) to achieve a size range of 200–1,100 bp. Amplified DNA was then pooled, concentrated and cleaned up. The amplified and cleaned product was fragmented using DNaseI (Affymetrix Inc.) and subsequently labeled and denatured using standard Affymetrix protocol.

growth_protocol: None, surgical biopsies

extract_protocol: Genomic DNA was extracted from surgical specimens following standard phenol/chloroform protocol

treatment_protocol: None, surgical biopsies

tag: patient

tag: age (years)

tag: gender

value: M

tag: tumor node metastisis (tnm)

tag: Stage

value: IA

tag: location

value: Right upper lobe

tag: diagnosis

value: MDSCC (moderately differentiated squamous cell carcinoma)

tag: smoking rate

value: 1-2 packs/day

tag: duration

value: 10 yrs

tag: tissue

value: Carcinoma


title: blood healthy control [DU09-01S00627.CEL]

tag: ethnicity

value: White

tag: host gender


title: blood healthy control [DU09-01S00798.CEL]

value: Male

tag: host age (yr)

tag: pathogen


title: blood healthy control [DU09-01S00652.CEL]

tag: anatomic site of infection

tag: experimental batch


title: InducedPluripotentStemCell_SSEA 1+/4+_LineB 29_rep1

city: jouy en josas

first: barbara

last: schmaltz-barbara

address: domaine de vilvert

country: France

institute: INRA

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a Rabbit Agilent Custom Gene Expression Oligo Microarrays (G4102A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107 and Grid: 037293_D_F_20111104). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Oryctolagus cuniculus

source_name: Induced Pluripotent Stem Cell SSEA 1+/4+ Line B 29

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol includes a DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell

value: Induced Pluripotent Stem Cell

tag: cell sub-population

value: SSEA 1+/4+ Line B 29


title: blood healthy control [DU09-01S01183.CEL]

value: Asian

value: Female


title: InducedPluripotentStemCell_SSEA 1+/4+_LineB 29_rep2


title: InducedPluripotentStemCell_SSEA 1+_line B 29_rep3

source_name: Induced Pluripotent Stem Cell SSEA 1+ line B 29

value: SSEA 1+ line B 29


title: blood healthy control [DU09-01S01065.CEL]


title: Serum sample from colorectal cancer group (X511)

tag: disease state

value: colorectal cancer

tag: sample type

value: serum


title: InducedPluripotentStemCell_SSEA 1+_line B 29_rep2


title: blood healthy control [DU09-01S01011.CEL]


title: blood healthy control [DU09-01S00835.CEL]


title: Serum sample from Advanced Adenoma after removal (X510)

description: Serum sample from Advanced Adenoma after removal group (X510)

value: Advanced Adenoma after removal


title: blood healthy control [DU09-01S01017.CEL]


title: Serum sample from colorectal cancer group (X508)


title: Serum sample from colorectal cancer after surgical intervention group (X506)


title: InducedPluripotentStemCell_SSEA 1+/4+_LineB 29_rep3


title: blood healthy control [DU09-01S01164.CEL]

value: Black


title: blood healthy control [DU09-01S00841.CEL]


title: blood healthy control [DU09-01S00671.CEL]


title: blood healthy control [DU09-01S00971.CEL]


title: blood healthy control [DU09-01S00946.CEL]


title: blood healthy control [DU09-01S00538.CEL]


title: Serum sample from colorectal cancer group (X503)


title: InducedPluripotentStemCell_SSEA 1+_line B 29_rep1


title: Serum sample from colorectal cancer group (X500)


title: Serum sample from colorectal cancer after surgical intervention group (X501)


title: blood healthy control [DU09-01S00928.CEL]


title: InducedPluripotentStemCell_SSEA 1-/4-_line B 29_rep2

source_name: Induced Pluripotent Stem Cell SSEA 1-/4- line B 29

value: SSEA 1-/4- line B 29


title: InducedPluripotentStemCell_SSEA 1-/4-_Line B 29_rep1


title: InducedPluripotentStemCell_SSEA 1-/4-_line B 29_rep3


title: InducedPluripotentStemCell_SSEA 1+/4+_line B 19_rep2

source_name: Induced Pluripotent Stem Cell SSEA 1+/4+ line B 19

value: SSEA 1+/4+ line B 19


title: blood healthy control [DU09-01S00779.CEL]


title: Serum sample from colorectal cancer group (X499)


title: blood healthy control [DU09-01S00633.CEL]


title: blood healthy control [DU09-01S00563.CEL]


title: blood healthy control [DU09-01S01046.CEL]


title: InducedPluripotentStemCell_SSEA 1+/4+_line B 19_rep1


title: Serum sample from colorectal cancer after surgical intervention group (X498)


title: Serum sample from colorectal cancer group (X496)


title: InducedPluripotentStemCell_SSEA 1+/4+_line B 19_rep3


title: Serum sample from colorectal cancer group (X495)


title: blood healthy control [DU09-01S00473.CEL]

value: unknown


title: blood healthy control [DU09-01S00427.CEL]


title: blood healthy control [DU09-01S00691.CEL]


title: InducedPluripotentStemCell_SSEA 1+_line B 19_rep3

source_name: Induced Pluripotent Stem Cell SSEA 1+ line B 19

value: SSEA 1+ line B 19


title: blood healthy control [DU09-01S00433.CEL]


title: blood healthy control [DU09-01S00785.CEL]


title: blood healthy control [DU09-01S00421.CEL]


title: InducedPluripotentStemCell_SSEA 1+_line B 19_rep2


title: InducedPluripotentStemCell_SSEA 1-/4-_line B 19_rep2

source_name: Induced Pluripotent Stem Cell SSEA 1-/4- line B 19

value: SSEA 1-/4- line B 19


title: InducedPluripotentStemCell_SSEA 1+_line B 19_rep1


title: InducedPluripotentStemCell_SSEA 1-/4-_line B 19_rep1


title: blood healthy control [DU09-01S00415.CEL]


title: InducedPluripotentStemCell_SSEA 1-/4-_line B 19_rep3


title: blood healthy control [DU09-01S00407.CEL]


title: Serum sample from colorectal cancer group (X451)


title: EmbryonicStemCell_TOT_Line8_rep3

source_name: Embryonic Stem Cell TOT Line8

value: Embryonic Stem Cell

value: TOT Line8


title: Serum sample from colorectal cancer group (X450)


title: blood healthy control [DU09-01S00446.CEL]

value: White


title: blood healthy control [DU09-01S00413.CEL]

value: Male


title: Serum sample from colorectal cancer group (X423)


title: Serum sample from colorectal cancer after surgical intervention group (X449)


title: Serum sample from colorectal cancer group (X470)


title: Serum sample from colorectal cancer after surgical intervention group (X452)


title: Serum sample from colorectal cancer group (X467)


title: blood patient with S. aureus bacteremia [002-0415ENRPAXGENE.CEL]

value: black

value: Staphylococcus aureus

value: vascular catheter


title: Serum sample from colorectal cancer group (X466)


title: blood patient with S. aureus bacteremia [V710.CEL]

value: Urinary tract


title: EmbryonicStemCell_SSEA1+_Line8_rep3

source_name: Embryonic Stem Cell SSEA1+ Line8

value: SSEA1+ Line8


title: Serum sample from colorectal cancer group (X422)

value: colorectal cancer

value: serum


title: blood patient with S. aureus bacteremia [002-0161PAXGENEENR.CEL]

value: Black

value: Bone


title: EmbryonicStemCell_TOT_Line8_rep1


title: EmbryonicStemCell_SSEA1-_Line8_rep2

source_name: Embryonic Stem Cell SSEA1- Line8

value: SSEA1- Line8


title: blood patient with S. aureus bacteremia [H2534.CEL]

value: white

value: Female

value: Vascular catheter


title: EmbryonicStemCell_SSEA1+_Line8_rep1

value: Embryonic Stem Cell


title: blood patient with S. aureus bacteremia [V738.CEL]


title: blood patient with S. aureus bacteremia [V674.CEL]


title: Serum sample from Advanced Adenoma after removal (X421)

description: Serum sample from Advanced Adenoma after removal group (X421)

value: Advanced Adenoma after removal


title: EmbryonicStemCell_TOT_Line8_rep2

value: TOT Line8


title: EmbryonicStemCell_SSEA1-_Line8_rep3


title: Serum sample from Advanced Adenoma group (X413)

value: Advanced Adenoma


title: blood patient with S. aureus bacteremia [002-040424HRSPAXGENE.CEL]

value: Male

value: Skin


title: EmbryonicStemCell_SSEA1-_Line8_rep1


title: Serum sample from Advanced Adenoma group (X570)


title: EmbryonicStemCell_SSEA1+_Line8_rep2


title: blood patient with S. aureus bacteremia [V943.CEL]

value: White

value: Staphylococcus aureus


title: EmbryonicStemCell_TOT_Line4_rep3

source_name: Embryonic Stem Cell TOT Line4

value: TOT Line4


title: Serum sample from Control group (X412)

description: Serum sample from Control group (X412)

value: Control


title: blood patient with S. aureus bacteremia [H4129.CEL]

value: Unknown

value: Lung


title: EmbryonicStemCell_TOT_Line4_rep2


title: Serum sample from colorectal cancer group (X411)

value: colorectal cancer

value: serum


title: EmbryonicStemCell_TOT_Line4_rep1


title: Serum sample from Control group (X409)

description: Serum sample from Control group (X409)


title: blood patient with S. aureus bacteremia [H3722.CEL]


title: blood patient with S. aureus bacteremia [H3229.CEL]

value: Black

value: Bone


title: Serum sample from Control group (X408)

description: Serum sample from Control group (X408)


title: large cell MALT lymphoma 23

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

country: Germany

institute: Ulm University

description: Hybridized to GenomeWide SNP 6.0 array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL-files were generated using Affymetrix Command console software
normalized raw data (lin scale) were generated using the R package aroma.affymetrix (H. Bengtsson, R. Irizarry, B. Carvalho & T.P. Speed, Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics 2008, 24, pp759-767)
CHP-files were generated using Affymetrix Genotyping console (BRLMM2)

source_name: large cell MALT lymphoma 23

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from freshly frozen tumor tissue using the QIAamp DNA Mini Kit (Qiagen). Content of tumor cells was at least 90%. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: stomach

tag: disease status

value: large cell MALT lymphoma

tag: sample id


title: large cell MALT lymphoma 27

description: Hybridized to GenomeWide SNP 6.0 array

source_name: large cell MALT lymphoma 27


title: EmbryonicStemCell_SSEA1+_Line4_rep2

source_name: Embryonic Stem Cell SSEA1+ Line4

value: Embryonic Stem Cell

value: SSEA1+ Line4


title: large cell MALT lymphoma 28

description: Hybridized to GenomeWide SNP 6.0 array

source_name: large cell MALT lymphoma 28


title: blood patient with S. aureus bacteremia [002-0216ENRPAXGENE1.CEL]

source_name: blood patient with S. aureus bacteremia prior antibiotic treatment (Emergency Department)


title: large cell MALT lymphoma 26

description: Hybridized to GenomeWide SNP 6.0 array

source_name: large cell MALT lymphoma 26

value: lung


title: large cell MALT lymphoma 21

description: Hybridized to GenomeWide SNP 6.0 array

source_name: large cell MALT lymphoma 21


title: Serum sample from Control group (X407)

description: Serum sample from Control group (X407)

source_name: serum plasma sample


title: EmbryonicStemCell_SSEA1+_Line4_rep1


title: large cell MALT lymphoma 24

description: Hybridized to GenomeWide SNP 6.0 array

source_name: large cell MALT lymphoma 24


title: large cell MALT lymphoma 22

description: Hybridized to GenomeWide SNP 6.0 array

source_name: large cell MALT lymphoma 22


title: Serum sample from Control group (X406)

description: Serum sample from Control group (X406)


title: large cell MALT lymphoma 25

description: Hybridized to GenomeWide SNP 6.0 array

source_name: large cell MALT lymphoma 25


title: blood patient with S. aureus bacteremia [H785.CEL]

value: Male


title: blood patient with S. aureus bacteremia [H638.CEL]


title: Serum sample from colorectal cancer group (X405)


title: EmbryonicStemCell_SSEA1-_Line4_rep1

source_name: Embryonic Stem Cell SSEA1- Line4

value: SSEA1- Line4


title: blood patient with S. aureus bacteremia [002-0159PAXGENEENR.CEL]

value: White


title: Serum sample from colorectal cancer group (X312)


title: EmbryonicStemCell_SSEA1-_Line4_rep2


title: EmbryonicStemCell_TOT_Line19_rep3

source_name: Embryonic Stem Cell TOT Line19

value: TOT Line19


title: large cell MALT lymphoma 20

description: Hybridized to GenomeWide SNP 6.0 array

source_name: large cell MALT lymphoma 20

value: illeocoecum


title: large cell MALT lymphoma 18

description: Hybridized to GenomeWide SNP 6.0 array

source_name: large cell MALT lymphoma 18


title: blood patient with S. aureus bacteremia [F00506.CEL]

value: Female

value: Staphylococcus aureus

value: Cardiac


title: EmbryonicStemCell_SSEA1+_Line4_rep3


title: large cell component composite MALT lymphoma 14

description: Hybridized to GenomeWide SNP 6.0 array


title: Serum sample from colorectal cancer group (X317)

value: colorectal cancer


title: blood patient with S. aureus bacteremia [F00520.CEL]

value: Skin


title: large cell component composite MALT lymphoma 15

description: Hybridized to GenomeWide SNP 6.0 array


title: large cell MALT lymphoma 16

description: Hybridized to GenomeWide SNP 6.0 array

source_name: large cell MALT lymphoma 16


title: Serum sample from Control group (X397)

description: Serum sample from Control group (X397)

value: Control

value: serum


title: EmbryonicStemCell_TOT_Line19_rep2


title: EmbryonicStemCell_TOT_Line19_rep1


title: large cell MALT lymphoma 19

description: Hybridized to GenomeWide SNP 6.0 array

source_name: large cell MALT lymphoma 19

value: stomach


title: large cell component composite MALT lymphoma 13

description: Hybridized to GenomeWide SNP 6.0 array

value: small intestine


title: blood patient with S. aureus bacteremia [CS475-D6291.CEL]

value: Black

value: Vascular catheter


title: Serum sample from Control group (X315)

description: Serum sample from Control group (X315)


title: blood patient with S. aureus bacteremia [F00611.CEL]


title: Serum sample from Control group (X394)

description: Serum sample from Control group (X394)


title: Serum sample from Advanced Adenoma group (X313)

value: Advanced Adenoma


title: blood patient with S. aureus bacteremia [CS453-D5936.CEL]


title: EmbryonicStemCell_SSEA1+_Line19_rep1

source_name: Embryonic Stem Cell SSEA1+ Line19

value: Embryonic Stem Cell

value: SSEA1+ Line19


title: EmbryonicStemCell_SSEA1+_Line19_rep2


title: large cell MALT lymphoma 17

description: Hybridized to GenomeWide SNP 6.0 array

source_name: large cell MALT lymphoma 17

value: large cell MALT lymphoma


title: A549 transfection with MMP19 full length cDNA in pCMV vector 4

city: Pittsburgh

first: Guoying

last: Yu

state: PA

address: 3500 Terrace St., W1200

department: Departmnet of Medicine

institute: University of Pittsburgh

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The gProcessed Signals, limit to Entrez Gene IDs, were log2-transformed and cyclic loess normalized.

source_name: Human lung cancer Cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: A549 cells (American Type Culture Collection, Inc), were propagated in F12-K medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin, and 100 mg/ml streptomycin at 37°C in 5% CO2.

extract_protocol: RNA was prepared with Trizol (Qiagen, Valencia CA) following the manufacturer's instructions. The Total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Wild-type full length MMP19 cDNA with vector pCMV-sport6 was purchased from Openbiosystems. The constructs were transfected into A549 cells using the protocols of Lipofectamine 2000 (Invitrogen, Carlsbad, CA). Stable MMP19 expression and mock cell lines were generated with G418 (400 µg/ml) selection. MMP19 siRNA was purchased from Santa Cruz Biotechnology (Santa Cruz, CA).

value: Lung

tag: cell line

tag: transfection

value: MMP19 full length cDNA in pCMV vector


title: large cell component composite MALT lymphoma 12

description: Hybridized to GenomeWide SNP 6.0 array


title: Serum sample from Control group (X393)

description: Serum sample from Control group (X393)


title: blood patient with S. aureus bacteremia [CS445-D5781.CEL]

value: Male


title: EmbryonicStemCell_SSEA1+_Line19_rep3


title: Serum sample from Control group (X392)

description: Serum sample from Control group (X392)


title: blood patient with S. aureus bacteremia [CS439-D5657.CEL]

value: White

value: Staphylococcus aureus

value: Bone


title: A549 transfection with MMP19 full length cDNA in pCMV vector 3


title: large cell component composite MALT lymphoma 10

description: Hybridized to GenomeWide SNP 6.0 array


title: A549 transfection with MMP19 full length cDNA in pCMV vector 2


title: Serum sample from Control group (X391)

description: Serum sample from Control group (X391)


title: Serum sample from Control group (X390)

description: Serum sample from Control group (X390)


title: EmbryonicStemCell_SSEA1-_Line19_rep1

source_name: Embryonic Stem Cell SSEA1- Line19

value: SSEA1- Line19


title: EmbryonicStemCell_SSEA1-_Line19_rep3


title: blood patient with S. aureus bacteremia [CSD4396.CEL]

source_name: blood patient with S. aureus bacteremia prior antibiotic treatment (Emergency Department)


title: A549 mock transfection with pCMV vector 4

value: pCMV vector


title: EmbryonicStemCell_TOT_Line18_rep3

source_name: Embryonic Stem Cell TOT Line18

value: TOT Line18


title: large cell component composite MALT lymphoma 11

description: Hybridized to GenomeWide SNP 6.0 array

value: stomach


title: Serum sample from Control group (X389)

description: Serum sample from Control group (X389)

value: Control

value: serum


title: Serum sample from Advanced Adenoma group (X284)


title: large cell component composite MALT lymphoma 8_85

description: Hybridized to GenomeWide SNP 6.0 array


title: A549 transfection with MMP19 full length cDNA in pCMV vector 1


title: blood patient with S. aureus bacteremia [CS253-D3500.CEL]

value: Female

value: Skin


title: EmbryonicStemCell_TOT_Line18_rep2

value: Embryonic Stem Cell


title: blood patient with S. aureus bacteremia [CSD4620.CEL]

value: Cardiac-Endocarditis


title: A549 mock transfection with pCMV vector 3


title: Serum sample from Advanced Adenoma group (X277)

value: Advanced Adenoma


title: EmbryonicStemCell_TOT_Line18_rep1


title: blood patient with E. coli bacteremia [V355.CEL]

source_name: blood patient with E. coli bacteremia prior antibiotic treatment (Emergency Department)

value: Black

value: Escherichia coli

value: Urinary tract


title: A549 mock transfection with pCMV vector 2

value: Lung


title: EmbryonicStemCell_SSEA1+_Line18_rep3

source_name: Embryonic Stem Cell SSEA1+ Line18

value: SSEA1+ Line18


title: Serum sample from Advanced Adenoma group (X275)

source_name: serum plasma sample


title: large cell component composite MALT lymphoma 8_87

description: Hybridized to GenomeWide SNP 6.0 array


title: large cell component composite MALT lymphoma 9

description: Hybridized to GenomeWide SNP 6.0 array


title: EmbryonicStemCell_SSEA1+_Line18_rep1


title: Normal looking E243N

description: Normal looking area

hyb_protocol: 10mg of cRNA was hybridized to Codelink 55K Human Arrays

scan_protocol: Slides were scanned immediately after washing on the Genepix 4000B Scanner

data_processing: The Raw intensity Data is also called IOD - The Integrated Optical Density is calculated by CodeLink software. The IOD is determined from the average signal of each array feature multiplied by the number of pixels within that feature. Then this number has the local background subtracted. Since each pixel can have a maximum value of 60,000, this value can range from a thousand to millions of units. The data table value is the IOD divided by the median value on the array. This calculation is performed automatically by CodeLink Analysis and exported to the excel analysis sheet provided.

source_name: Human lung tissue

label_protocol: The 500ng senseRNA was used to start the manual target preparation protocol from Codelink Expression Bioarray System (Amersham Biosciences). Double stranded cDNA synthesis was performed with a T7oligo (dT) primer, containing a T7 RNA polymerase promoter site added to the 3’. The cDNA will is used as a template for in vitro transcription with biotin labeled nucleotides and the labeled cRNA will used for hybridization.

treatment_protocol: We used OCT embedded frozen lung samples from 4 IPF patients obtained from Pittsburgh Tissue bank, Department of Pathology, University of Pittsburgh. The preparation of the slides was done on temperature of -25°C, performing a cryostat cutting of 7-8 micron tick sections of the tissue, mounting them on foiled glass slides (Pen Membrane Slides 2.0 m-11505158 Leica) and storing on -80°C.  We used short staining protocol for Hematoxylin & Eosin Y (http://cgap-mf.nih.gov/Protocols/) in order to prevent degradation of RNA during the slide preparation. The slides were desiccated in 100%, 95%, 70% ethanol for 15 sec subsequently then washed in deionized water for 15 sec, dyed in Mayer’s Hematoxylin (Sigma MHS16)- 20 sec, rinsed twice for 15 sec in DNA-free water and put in 70% ethanol for 15 sec, followed by immersion in the second dye of Eosin Y (Sigma HT1101116) for 5 sec then dried out with 95%, 100% ethanol subsequently for 15 sec. To ensure dehydration of the section, the slides were submersed in Xylenes for 60-90 sec and air-dried for 2 minutes.  Under direct visualization, the targeted area was directly cut. In this protocol the laser beam cuts the foil and the cut area with the attached tissue falls directly into a tube with lysis buffer avoiding any other manipulation or contamination(68). Microdissection was performed in short time interval of limited to 10-15 minutes per slide in order to prevent degradation of RNA. The dissected tissue was immediately frozen and stored at -80°C with RNALater as a further step to prevent degradation of the RNA. This process was repeated for every target area for every patient

value: Lung tissue

tag: gender

value: male

tag: age

tag: area of lung near ipf

value: Normal looking


title: Hyperplastic E243C

description: Hyperplastic area

tag: tissue

value: Hyperplastic


title: A549 mock transfection with pCMV vector 1

value: pCMV vector


title: blood patient with E. coli bacteremia [CS593-D9156.CEL]

tag: ethnicity

value: White

tag: host gender


title: blood patient with E. coli bacteremia [F00210.CEL]

tag: host age (yr)

tag: pathogen


title: Serum sample from Advanced Adenoma group (X274)

value: serum


title: blood patient with S. aureus bacteremia [CSD4470.CEL]

value: Male

value: Staphylococcus aureus

tag: anatomic site of infection

tag: experimental batch


title: Serum sample from Control group (X269)

description: Serum sample from Control group (X269)

value: Control


title: EmbryonicStemCell_SSEA1+_Line18_rep2

tag: cell

value: Embryonic Stem Cell

tag: cell sub-population


title: Serum sample from Advanced Adenoma group (X270)

tag: disease state

value: Advanced Adenoma

tag: sample type


title: blood patient with E. coli bacteremia [D8414.CEL]

value: Black

value: Female


title: EmbryonicStemCell_SSEA1-_Line18_rep2

source_name: Embryonic Stem Cell SSEA1- Line18

value: SSEA1- Line18


title: Fibrotic foci E243F

description: Fibrotic foci

value: Fibrotic foci


title: small cell MALT lymphoma 6

description: Hybridized to GenomeWide SNP 6.0 array

source_name: small cell MALT lymphoma 6

value: stomach

tag: disease status

value: small cell MALT lymphoma

tag: sample id


title: EmbryonicStemCell_SSEA1-_Line18_rep3


title: Serum sample from Control group (X266)

description: Serum sample from Control group (X266)


title: blood patient with E. coli bacteremia [D5459.CEL]

value: Escherichia coli

value: Urinary tract


title: EmbryonicStemCell_SSEA1-_Line18_rep1


title: Hyperplastic E245C

description: Hyperplastic area

value: Lung tissue

value: male

value: Hyperplastic


title: blood patient with E. coli bacteremia [CS564-D8671.CEL]

value: White


title: Serum sample from Advanced Adenoma group (X264)

value: serum


title: small cell MALT lymphoma 8

description: Hybridized to GenomeWide SNP 6.0 array

source_name: small cell MALT lymphoma 8

value: large intestine


title: Normal looking E245N

description: Normal looking area

value: Normal looking


title: Serum sample from Control group (X251)

description: Serum sample from Control group (X251)

value: Control


title: Serum sample from Control group (X258)

description: Serum sample from Control group (X258)


title: small cell MALT lymphoma 7

description: Hybridized to GenomeWide SNP 6.0 array

source_name: small cell MALT lymphoma 7


title: small cell MALT lymphoma 3

description: Hybridized to GenomeWide SNP 6.0 array

source_name: small cell MALT lymphoma 3


title: Serum sample from Control group (X252)

description: Serum sample from Control group (X252)


title: blood patient with E. coli bacteremia [D2033.CEL]


title: small cell MALT lymphoma 5

description: Hybridized to GenomeWide SNP 6.0 array

source_name: small cell MALT lymphoma 5

value: lung


title: Fibrotic foci E245F

description: Fibrotic foci


title: Normal looking E488N

description: Normal looking area


title: Hyperplastic E488C

description: Hyperplastic area


title: blood patient with E. coli bacteremia [D2173.CEL]


title: Normal looking G044N

description: Normal looking area


title: small cell MALT lymphoma 2

description: Hybridized to GenomeWide SNP 6.0 array

source_name: small cell MALT lymphoma 2


title: Fibrotic foci E488F

description: Fibrotic foci


title: blood patient with E. coli bacteremia [D2341.CEL]

value: Black

value: Male


title: LckCre+;Hdac1L/L;Hdac2L/+ [383302A12]

city: Amsterdam

first: Jan-Hermen

last: Dannenberg

state: N-Holland

address: Plesmanlaan 121

country: Netherlands

institute: Antoni van Leeuwenhoek hospital

description:
LckCre+;Hdac1L/L;Hdac2L/+
aCGH of Hdac1/2 cKO lymphoma

hyb_protocol: Nimblegen protocol for mouse CGH 12x135 K whole genome tiling array

scan_protocol: Agilent Scanner (model G2505B) at a resolution of 2 micron double pass at 100% PMT for both channels

data_processing: Background correction and normalization was performed in the NimbleScan program according to manufacturer's protocol; probe annotation and corrected log2 ratios were imported into the R programming language from the NimbleScan output.

organism: Mus musculus

source_name: normal genomic tail DNA from LckCre+;Hdac1L/L;Hdac2L/+ mice

label_protocol: Dual Color labeling kit from Nimblegen

extract_protocol: genomic DNA was isolated from approx. 100 mg lymphoma tissue and corresponding normal tail tissue using the  Puregene genomic DNA isolation kit from Qiagen

value: normal tail

tag: strain

value: mixed background FVB/C57/B6

source_name: genomic DNA from LckCre+;Hdac1L/L;Hdac2L/+ tumor

value: tumor


title: LckCre+;Hdac1L/L;Hdac2L/+ [425030A10]


title: LckCre+;Hdac1L/+;Hdac2L/L [470365A03]

description:
LckCre+;Hdac1L/+;Hdac2L/L
aCGH of Hdac1/2 cKO lymphoma

source_name: normal genomic tail DNA from LckCre+;Hdac1L/+;Hdac2L/L mice

source_name: genomic DNA from LckCre+;Hdac1L/+;Hdac2L/L tumor


title: Serum sample from Control group (X239)

description: Serum sample from Control group (X239)


title: LckCre+;Hdac1L/L;Hdac2L/+ [425030A06]


title: blood patient with E. coli bacteremia [CSD5036.CEL]

value: Female


title: small cell MALT lymphoma 4

description: Hybridized to GenomeWide SNP 6.0 array

source_name: small cell MALT lymphoma 4

value: stomach

value: small cell MALT lymphoma


title: In vitro-differentiated human Th2 cells

city: San Francisco

first: Andrea

middle: J

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description:
Raw data file:
252372310006_S01_miRNA-v1_95_May07_2_2.txt

hyb_protocol: Cy3-labelled RNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent UCSF custom 8x15K miRNA arrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent scanner immediately after washing.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.6 (Agilent) using default parameters)
All replicates of human miR probes have been collapsed and median signal intensity extracted.

source_name: Human Th2 polarized cells

label_protocol: Total RNA was labeled with Cy3-CTP using the miRCURY LNA microRNA power labeling kit (Exiqon, Inc, Woburn, MA), according to manufacturers protocol

extract_protocol: The total RNA extraction was performed using the miRNeasy kit from Qiagen (including theoptional on column-DNAseI treatment). RNA quantity was measure by OD spectrophotometry (Nanodrop).

treatment_protocol: Blood derived primary CD4+ T-cells were differentiated in vitro into a TH2 phenotype (Sandig et al. 2007. Human th2 cells selectively express the orexigenic peptide, pro-melanin-concentrating hormone. Proc Natl Acad Sci U S A 104: 12440-12444)

tag: cell type

value: in vitro Th2 cells (derived from blood CD4 T-cells)


title: LckCre+;Hdac1L/L [470365A01]

description:
LckCre+;Hdac1L/L
aCGH of Hdac1/2 cKO lymphoma

source_name: normal genomic tail DNA from LckCre+;Hdac1L/L;Hdac2+/+ mice

source_name: genomic DNA from LckCre+;Hdac1L/L;Hdac2+/+ tumor


title: LckCre+;Hdac1L/L;Hdac2L/+ [425030A09]


title: Hyperplastic G044C

description: Hyperplastic area

value: Lung tissue

tag: gender

value: male

tag: age


title: blood patient with E. coli bacteremia [D887.2.CEL]

source_name: blood patient with E. coli bacteremia prior antibiotic treatment (Emergency Department)

value: White

value: Escherichia coli

value: Urinary tract


title: blood patient with E. coli bacteremia [D5294.CEL]


title: blood patient with E. coli bacteremia [CS101-D00649.CEL]


title: HF-15598-(1)_hind

status: Public on Jan 10 2013

city: South San Francisco

first: Peter

last: Haverty

address: 1 DNA Way

department: Bioinformatics

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 ratio  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. Data were then segmented  using  the GLAD algorithm (PMID:15381628).

source_name: NSCLC tumor

label_protocol: Affymetrix 100K protocol

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

tag: tissue

value: NSCLC tumor

tag: kras mutation status


title: small cell MALT lymphoma 1

description: Hybridized to GenomeWide SNP 6.0 array

source_name: small cell MALT lymphoma 1


title: WT vs. Hfq mutant

city: Taichung

first: Yichyi

last: Lai

address: No.110, Sec. 1 Jianguo N. Road

department: Microbiology and Immunology

country: Taiwan

institute: Chung Shan Medical University

description: Total RNA were harvested from log-phase cultures of S5 and H0201 grown in LB medium.

hyb_protocol: Hybridization was performed with the addition of Gex hybridization buffer HI-RPM (Agilent) in an Agilent microarray hybridization chamber for 17h at 60 degree celcius. After hybridization, the slides were washed in Gene expression Wash buffer (Agilent).

scan_protocol: Agilent microarray scanner at 535nm for Cy3 and 625nm for Cy5.

data_processing:
Feature extraction 9.5.3 and image analysis software was used to locate and delineate every spot in the array, to integrate each spot's intensity, and to normalize data using the rank-consistency-filtering lowess method.
The data points which had flag value of non-zero or a signal-to-noise ratio smaller than 2.6 were masked. All the data were log2 transformed.

organism: Klebsiella pneumoniae

source_name: WT

label_protocol: cDNA was synthesized from one microgram of enriched mRNA with Cyscribe 1st-strand cDNA labeling kit (GE), and labeled with Cy3 or Cy5 (CyDye, PerkinElmer).

growth_protocol: K. pneumoniae WT strain or hfq mutant were grown in LB medium without the supplement of any antibiotics

extract_protocol: Total RNA were isolated from log-phase cultures by using Tri-Reagent (Molecular Research Center), and purified by Qiagen Rneasy cleanup kit.

source_name: Hfq mutant


title: HF-15563-(1)_hind


title: HF-15576-(1)_hind


title: HF-15558-(1)_hind


title: HF-15559-(1)_hind


title: HF-15560-(1)_hind


title: EmbryonicStemCell_SSEA1-_Line19_rep2

source_name: Embryonic Stem Cell SSEA1- Line19

value: Embryonic Stem Cell

value: SSEA1- Line19


title: Fibrotic foci G044F

description: Fibrotic foci

source_name: Human lung tissue

tag: area of lung near ipf

value: Fibrotic foci


title: HF-15604-(1)_hind


title: HF-15561-(1)_hind


title: HF-15545-(1)_hind


title: HF-15589-(1)_hind


title: HF-15523-(1)_hind


title: HF-15547-(1)_hind


title: HF-15549-(1)_hind


title: HF-15546-(1)_hind


title: HF-15505-(1)_hind


title: HF-15570-(1)_hind


title: HF-15519-(1)_hind


title: HF-15541-(1)_hind


title: HF-15535-(1)_hind


title: HF-15526-(1)_hind


title: HF-15539-(1)_hind


title: HF-15533-(1)_hind


title: HF-15534-(1)_hind


title: HF-15228_hind


title: HF-15520-(1)_hind


title: HF-11769-(2)_hind


title: HF-15525-(1)_hind


title: HF-15515-(1)_hind


title: HF-15238-(1)_hind


title: HF-15506-(1)_hind


title: HF-11775-(2)_hind


title: HF-15213_hind


title: HF-15516-(1)_hind


title: HF-15527-(1)_hind


title: HF-15511-(1)_hind


title: HF-15512-(1)_hind


title: HF-11757-(2)_hind


title: HF-15217_hind


title: HF-15358-(1)_hind


title: HF-15355-(1)_hind


title: Serum sample from Control group (X240)

description: Serum sample from Control group (X240)

source_name: serum plasma sample

value: Control

value: serum


title: HF-15235-(1)_hind


title: HF-15233-(1)_hind


title: HF-15237-(1)_hind


title: HF-15231-(1)_hind


title: blood patient with E. coli bacteremia [CSD2575.CEL]

tag: ethnicity

tag: host gender

tag: host age (yr)


title: HF-15218-(1)_hind


title: HF-15220-(1)_hind


title: HF-15227-(1)_hind


title: HF-15224-(1)_hind


title: HF-15212-(1)_hind


title: HF-3705-(1)_hind


title: HF-3711-(1)_hind


title: HF-15215-(1)_hind


title: HF-5171_hind


title: HF-8025_hind


title: HF-9233-(1)_hind


title: HF-2130_hind


title: HF-3718-(1)_hind


title: HF-3703-(1)_hind


title: Serum sample from Advanced Adenoma group (X245)

value: Advanced Adenoma


title: HF-4810-(1)_hind


title: HF-7980-(1)_hind


title: HF-11744_hind


title: HF-9390-(1)_hind


title: HF-5158-(1)_hind


title: HF-3043-(1)_hind


title: HF-11731_hind


title: HF-8890-(1)_hind


title: HF-11743_hind


title: HF-11783_hind


title: HF-11734_hind


title: HF-11737_hind


title: HF-11739_hind


title: HF-11732_hind


title: HF-11730_hind


title: HF-11780_hind


title: HF-4527-(1)_hind


title: HF-11767_hind


title: HF-11763_hind


title: HF-11771_hind


title: HF-11782_hind


title: HF-11785_hind


title: HF-11758_hind


title: HF-15240-(1)_hind


title: HF-11751_hind


title: HF-15567-(1)_hind


title: HF-11776_hind


title: HF-11772_hind


title: HF-11766_hind


title: HF-11770_hind


title: HF-11756_hind


title: HF-11752_hind


title: HF-15576-(1)_xba


title: HF-15559-(1)_xba


title: HF-15589-(1)_xba


title: HF-15547-(1)_xba


title: HF-11754_hind


title: HF-15598-(1)_xba


title: HF-11765_hind


title: HF-15561-(1)_xba


title: HF-15560-(1)_xba


title: HF-15523-(1)_xba


title: HF-15545-(1)_xba


title: HF-15558-(1)_xba


title: HF-15546-(1)_xba


title: HF-15519-(1)_xba


title: HF-15505-(1)_xba


title: HF-15570-(1)_xba


title: HF-15549-(1)_xba


title: HF-15604-(1)_xba


title: HF-15567-(1)_xba


title: HF-15541-(1)_xba


title: HF-15533-(1)_xba


title: HF-15563-(1)_xba


title: HF-15539-(1)_xba


title: HF-15535-(1)_xba


title: HF-15525-(1)_xba


title: HF-15512-(1)_xba


title: HF-15217_xba


title: HF-15526-(1)_xba


title: HF-15516-(1)_xba


title: HF-15527-(1)_xba


title: HF-15511-(1)_xba


title: HF-15515-(1)_xba


title: HF-11775-(2)_xba


title: HF-15213_xba


title: HF-11757-(2)_xba


title: HF-15355-(1)_xba


title: HF-15240-(1)_xba


title: HF-15227-(1)_xba


title: HF-15520-(1)_xba


title: HF-15235-(1)_xba


title: HF-15238-(1)_xba


title: HF-15237-(1)_xba


title: HF-15231-(1)_xba


title: HF-15218-(1)_xba


title: HF-15220-(1)_xba


title: HF-11769-(2)_xba


title: HF-15358-(1)_xba


title: HF-15233-(1)_xba


title: HF-15215-(1)_xba


title: HF-8025_xba


title: HF-15212-(1)_xba


title: HF-5171_xba


title: HF-15224-(1)_xba


title: HF-9233-(1)_xba


title: HF-2130_xba


title: HF-3703-(1)_xba


title: U251 FAT1 siRNA#2 replicate 1

city: New York

first: Luc

middle: GT

last: Morris

state: NY

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: RMA normalized with Partek Genomics Suite version 6.6

source_name: U251 cell line

label_protocol: Affymetrix protocol

extract_protocol: Trizol

tag: cell line

tag: sirna

value: FAT1 siRNA #2


title: HF-9390-(1)_xba


title: U251 FAT1 siRNA#2 replicate 2


title: HF-5158-(1)_xba


title: HF-4527-(1)_xba


title: HF-7980-(1)_xba


title: HF-8890-(1)_xba


title: HF-3705-(1)_xba


title: HF-3711-(1)_xba


title: U251 FAT1 siRNA#1 replicate 2

value: FAT1 siRNA #1


title: HF-4810-(1)_xba


title: HF-3718-(1)_xba


title: HF-11744_xba


title: HF-3043-(1)_xba


title: HF-15228_xba


title: U251 FAT1 siRNA#1 replicate 1


title: HF-11732_xba


title: HF-11739_xba


title: HF-15534-(1)_xba


title: HF-11743_xba


title: HF-11734_xba


title: HF-11737_xba


title: HF-11731_xba


title: HF-11780_xba


title: U87 FAT1 siRNA#2 replicate 1

source_name: U87 cell line


title: U251 scramble siRNA replicate 2

value: scramble


title: U87 FAT1 siRNA#1 replicate 2


title: HF-11730_xba


title: U251 scramble siRNA replicate 1


title: HF-11763_xba


title: HF-11783_xba


title: U87 FAT1 siRNA#2 replicate 2


title: IHA FAT siRNA#1 replicate 1

source_name: immortalized human astrocyte cell line

value: immortalized human astrocytes


title: U87 scramble siRNA replicate 2


title: HF-11758_xba


title: HF-11767_xba


title: IHA FAT siRNA#2 replicate 1


title: IHA FAT siRNA#1 replicate 2


title: HF-11785_xba


title: U87 FAT1 siRNA#1 replicate 1


title: IHA scramble siRNA replicate 2


title: HF-15506-(1)_xba


title: U87 scramble siRNA replicate 1


title: HF-11782_xba


title: HF-11751_xba


title: HF-11776_xba


title: HF-11772_xba


title: HF-11771_xba


title: IHA FAT siRNA#2 replicate 2


title: HF-11752_xba


title: HF-11754_xba


title: IHA scramble siRNA replicate 1


title: HF-11770_xba


title: WT 30 min_exp1

city: Seoul

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

description: Ctr vs WT 30 min_exp1; set1-30min

hyb_protocol: Microarray Hybridization and Washing.  A C. neoformans serotype D 70-mer microarray slide containing 7,936 probes (Duke University) was pre-hybridized at 42°C in 60 ml of pre-hybridization buffer (42.4 ml sterile distilled water, 2 ml 30% BSA (Sigma), 600 µl 10% SDS, 15 ml 20x SSC (Saline-Sodium Citrate, 3 M NaCl, 0.3 M Na-citrate, pH 7.0)), washed with distilled water and isopropanol, and dried by brief centrifugation (1000rpm, 2 min).  The Cy3- and Cy5-labeled cDNA samples were combined, concentrated through a Microcon30 filter, and vacuum-dried.  The dried cDNA samples were resuspended with 24 µl of 1x hybridization buffer (250 µl 50% formamide, 125 µl 20x SSC, 5 µl 10% SDS, 120 µl dH2O, total 500 µl), added with 1 µl polyA tail DNA (Sigma), further incubated at 100°C for 3 min and allowed to cool for 5 min at room temperature.  The microarray slides were aligned into the hybridization chamber (DieTech), removed of any dust, and covered by Lifterslips (Erie Scientific).  The Cy3/Cy5-labeled cDNA samples were applied in between Lifterslips and slides.  To prevent slides from drying, 5 ml of 3x SSC buffer was applied into the hybridization chamber, which were subsequently incubated for 16 hr at 42°C.  After incubation, the microarray slides were washed with three different washing buffers (wash buffer 1 (10 ml 20x SSC, 600 µl 10% SDS, 189.4 ml dH2O, preheated at 42°C), wash buffer 2 (3.5 ml 20x SSC, 346.5 ml dH2O), wash buffer 3 (0.88 ml 20x SSC, 349.12 ml dH2O)) for 2, 5, and 5 min, respectively, on an orbital shaker.  Three independent DNA microarrays with 3 independent biological replicates were performed.

scan_protocol: After hybridization and washing, the microarray slides were scanned with a GenePix 4100A scanner (Axon Instrument) and the signals were analyzed with GenePix Pro (Ver. 4.0) and gal file (http://genome.wustl.edu/activity/ma/cneoformans).

data_processing: Since total RNAs isolated from serotype A C. neoformans strains were hybridized on the microarray slides printed with the serotype D 70-mer oligonucleotide sequences, the serotype A gene sequences were mapped to those of the serotype D using BLASTN.  C. neoformans H99 gene sequences that were updated at 24 November 2008 were downloaded from Broad institute (http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans).  The serotype D C. neoformans JEC21 gene sequences that were updated 27 April 2005 were downloaded from JCVI (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/c_neoformans/).  The functional category of each C. neoformans H99 gene was assigned using the NCBI KOG database (http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi).  Using the serotype A gene sequence, each S. cerevisiae gene name or ID listed in the supplementary Tables was identified by blastp search (e-value cut-off: e-6). We downloaded Homo sapiens and Cryptococcus neoformans genomes from independent database. Homo sapiens genome was downloaded at NCBI genome ftp (ftp://ftp.ncbi.nih.gov/genomes) and Cryptococcus neoformans genome was downloaded at BROAD institute database (www.broadinstitute.org/annotation/genome/cryptococcus_neoformans), July of 2011. A public orthologs detecting program, Inparanoid (ver. 4.1) and NCBI Blast were implemented to identify orthologous genes. For hierarchical and statistical analysis, data transported from GenePix software were analyzed with Acuity (Axon) by employing Lowess normalization (Lowess M log ratio (F532 Mean - B532, F635 Mean - B635)), reliable gene filtering, clustering (standard correlation and average linkage) and zero-transformation, and ANOVA analysis (P<0.05), and Microsoft Excel software (Microsoft).

organism: Cryptococcus neoformans H99

source_name: WT_GE_30 min

label_protocol: For cDNA synthesis, the total RNA concentration was adjusted to 1 µg/µl with DEPC-treated water, and 15 µl of the total RNA (15 µg) was added to 1 µl of 5 µg/µl oligo dT (5’-TTTTTTTTTTTTTTTTTTTTV-3’)/pdN6 (Amersham, 1:1 mixture of 10 µg/µl, respectively), incubated at 70°C for 10 min, and place on ice for 10 min.  Then 15 µl of cDNA synthesis mixture (3 µl 0.1 M DTT, 0.3 µl RNase inhibitor (Intron), 1.2 µl aa-dUTP (5-(3-aminoallyl)-2’-deoxyuridine 5’-triphosphate)/dNTPs (a mixture of 6 µl dTTP (100 mM), 4 µl aa-dUTP (100 mM), 10 µl dATP (100 mM), 10 µl dCTP (100 mM), 10 µl dGTP (100 mM). 40 µl DEPC-treated water), 1.5 µl RevertAidTM H Minus M-MuLV Reverse Transcriptase (Fermentas), 6 µl RevertAidTM H Minus M-MuLV Reverse Transcriptase buffer, 3 µl DEPC-treated water) was added and incubated at 42°C for 2 hrs.  Then 10 µl of 1 N NaOH and 10 µl of 0.5 M EDTA (pH 8.0) were added and incubated at 65°C for 15 min.  After incubation, 25 µl of 1 M HEPES buffer (pH 8.0) and 450 µl of DEPC-treated water were added, and the whole mixture was concentrated through a Microcon30 filter (Millipore) and vacuum-dried for 1 hr. For Cy3 and Cy5 (Amersham) labeling of the prepared cDNA, Cy3 and Cy5 were dissolved in 10 µl DMSO and 1 µl of each dye was aliquoted into separate tubes.  The cDNAs prepared as described above were added to 9 µl of 0.05 M Na-bicarbonate (pH 8.0) and incubate at room temperature for 15 min.  The cDNAs prepared from pooled reference RNAs were mixed with Cy5 as a control and the cDNAs prepared from each test RNA (each experimental condition) were mixed with Cy3. Each mixture was further incubated at room temperature for 1 hr in the dark and purified by QIAquick PCR purification kit (QIAGEN).

growth_protocol: The wild-type H99 strain was grown in 50 ml YPD (yeast extract-peptone-dextrose) medium at 30°C for 16 hr. 10 milliliter of the overnight culture was inoculated into a 200 ml fresh YPD medium and further incubated for 4-5 hr at 30°C until it approximately reaches to the 1.0 of optical density (OD) at 600 nm (OD600nm = 1.0). For short-term exposure to Gromwell extract, the culture were added with GE at a final concentration of 6.4 mg/ml and further incubated at 30°C for 60 min. At each time point (0, 10, 30, or 60 min), a portion of cells (50 ml culture) was sampled.

extract_protocol: For total RNA isolation, the lyophilized cell pellets were added to 3 ml volume of sterile 3 mm glass bead (SIGMUND LINDER), homogenized by shaking, added to 4 ml of TRizol reagent (Tri reagent, Molecular Research Center), and allowed to incubate at room temperature for 5 min.  Then 800 µl of chloroform was added, incubated for 3 min at room temperature, transferred to 14 ml round-bottom tubes (SPL), and centrifuged by 10,000 rpm at 4°C for 15 min. 750 ul of the supernatant was transferred to a new round-bottom tube, 2 ml isopropanol was added, inverted several times, and allowed to incubate for 10 min at room temperature.  Then the mixture was re-centrifuged at 10,000 rpm at 4°C for 10 min, and the pellet was washed with 4 ml of 75% ethanol diluted with diethylpyrocarbonate (DEPC)-treated water and centrifuged at 8,000 rpm at 4°C for 5 min.  The pellet was dried and resuspended with 500 µl DEPC-treated water.  Concentration and purity of total RNA samples were calculated by measuring OD260nm and gel-electrophoresis, respectively.  For control total RNA, all total RNAs prepared from WT cells grown in conditions described above were pooled (pooled reference RNAs).

treatment_protocol: 50 ml culture was rapidly frozen in liquid nitrogen and lyophilized overnight. The lyophilized cells were subsequently used for total RNA isolation.  As biological replicates for DNA microarrays, three independent cultures for each strain were prepared for total RNA isolation.

tag: treated with

value: 6.4 mg/ml Gromwell extract for 30 min

source_name: pooled total RNA from all strain all treatment

value: reference (Ctr)


title: WT 10 min_exp3

description: Ctr vs WT 10 min_exp3; set3-10min

source_name: WT_GE_10 min

value: 6.4 mg/ml Gromwell extract for 10 min


title: BRCA2 mutation carrier 3

city: jerusalem

first: tamar

last: zahavi

address: Ein-Kerem

department: Oncology

country: Israel

institute: Hadassah

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133A 2.0 Array GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: Data analysis was done using GeneSpring GX software (Agilent technologies).   Background adjustment, quantile normalization and summarization were done using RMA methodology. The relative expression data for each probe set then generated by normalizing each gene to the median of its own expression intensities across the entire experiment set (per gene normalization). Control probes and genes whose expressions were not changed across the experiment were removed from the list before statistical analysis was performed. Differentially expressed genes were analyzed by One-way Welch ANOVA, with p-value cutoff of 0.05 after Benjamini and Hochberg False Discovery Rate multiple testing correction

source_name: Lymphocytes, BRCA2-mutation carrier

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

growth_protocol: Fresh blood samples were obtained from proven BRCA1 and BRCA2 mutation carriers and mutation-negative women

extract_protocol: RNA was extracted using EZ RNA kit (Biological Industries, Israel) according to manufacturer's instruction

treatment_protocol: Lymphocytes were collected from fresh blood samples using LymphoPrep kit (Sigma) and short-term cultured for 6 days in RPMI 16/40 with L-Glutamine (Biological Industries, Israel), supplemented with 1% Hepes, 16% Fetal Calf Serum, Penicillin+Streptomycin, and IL-2. Cells were γ-irradiated with 8 Gray (Gy) at a high dose rate (0.86 Gy/min, Ortovoltage X-ray machine).

value: Lymphocytes

tag: mutation


title: WT 30 min_exp2

description: Ctr vs WT 30 min_exp2; set2-30min

tag: sample type


title: WT 60 min_exp2

description: Ctr vs WT 60 min_exp2; set2-60min

source_name: WT_GE_60 min

value: 6.4 mg/ml Gromwell extract for 60 min


title: HF-11766_xba


title: HF-11756_xba


title: WT 30 min_exp3

description: Ctr vs WT 30 min_exp3; set3-30mim


title: WT 60 min_exp3

description: Ctr vs WT 60 min_exp3; set3-60min


title: WT 0 min_exp3

description: Ctr vs WT 0 min_exp3; set3-0time

source_name: WT_GE_0 min


title: WT 10 min_exp1

description: Ctr vs WT 10 min_exp1; set1-10min


title: WT 10 min_exp2

description: Ctr vs WT 10 min_exp2; set2-10min


title: BRCA2 mutation carrier 7


title: BRCA1 mutation carrier 6

source_name: Lymphocytes, BRCA1-mutation carrier


title: BRCA2 mutation carrier 1


title: BRCA2 mutation carrier 8


title: HF-11765_xba

source_name: NSCLC tumor


title: BRCA1 mutation carrier 9


title: BRCA2 mutation carrier 6


title: WT 0 min_exp2

description: Ctr vs WT 0 min_exp2; set2-0time


title: BRCA2 mutation carrier 5


title: BRCA1 mutation carrier 8


title: BRCA1 mutation carrier 7


title: BRCA2 mutation carrier 4


title: WT 60 min_exp1

description: Ctr vs WT 60 min_exp1; set1-60min


title: BRCA2 mutation carrier 2


title: BRCA1 mutation carrier 4


title: BRCA1 mutation carrier 5


title: WT 0 min_exp1

description: Ctr vs WT 0 min_exp1; set1-0time


title: BRCA1 mutation carrier 3


title: Basque Extensive sample Replicate 9

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

description: Basque Extensif sample Replicate 9 of 10

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 300 ng of cyanine 3-labeled cRNA sample and 300 ng of cyanine 5-labeled reference sample per hybridization. The hybridization reactions were performed at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. Slides were disassembled and washed for 1 minute at room temperature in SSPE wash solution 1 (6x SSPE + 0.005% Sarcosine) and in SSPE wash solution 2 (0.06x SSPE + 0.005% Sarcosine) for one minute at room temperature. The microarrays were then treated with Agilent Stabilization and Drying Solution at room temperature for 30 seconds.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: median normalized data obtained from log2 of processed Green signal/processed Red reference signal. Limma package and the Rquantile normalizeWithinArrays procedure were used.

organism: Sus scrofa

source_name: Longissimus muscle of BE pig

label_protocol: Total RNA (350 ng) from each animal was labeled individually with Cy3 by using the Quick-Amp Labeling Kit  following the manufacturer’s instructions.

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

treatment_protocol: Thirty minutes after slaughter, a sample of Longissimus muscle was taken (last rib level), cut in small pieces parallel to the muscle fibres axis, restrained on flat sticks, promptly frozen in liquid nitrogen and stored at -80°C.

value: skeletal muscle

tag: pig live weight

tag: breed

value: Basque

tag: rearing conditions

value: Extensive

source_name: reference pool composed of an equal amount of total RNA isolated from all 50 samples


title: Basque Extensive sample Replicate 10

description: Basque Extensif sample Replicate 10 of 10


title: BRCA1 mutation carrier 2


title: Basque Extensive sample Replicate 7

description: Basque Extensif sample Replicate 7 of 10


title: Basque Extensive sample Replicate 8

description: Basque Extensif sample Replicate 8 of 10


title: Basque Extensive sample Replicate 6

description: Basque Extensif sample Replicate 6 of 10


title: non carrier 9

source_name: Lymphocytes, mutation-negative

value: non-carrier


title: non carrier 3


title: Basque Extensive sample Replicate 5

description: Basque Extensif sample Replicate 5 of 10


title: non carrier 7


title: Basque Extensive sample Replicate 2

description: Basque Extensif sample Replicate 2 of 10


title: non carrier 6


title: non carrier 5


title: Basque Extensive sample Replicate 3

description: Basque Extensif sample Replicate 3 of 10


title: Basque Extensive sample Replicate 4

description: Basque Extensif sample Replicate 4 of 10


title: Basque Extensive sample Replicate 1

description: Basque Extensif sample Replicate 1 of 10


title: non carrier 4


title: BRCA1 mutation carrier 1


title: Large White Alternative sample replicate 6

description: Large White Alternatif sample Replicate 6 of 10

source_name: Longissimus muscle of LWA pig

value: Large White

value: Alternative


title: Large White Alternative sample replicate 7

description: Large White Alternatif sample Replicate 7 of 10


title: Large White Alternative sample replicate 8

description: Large White Alternatif sample Replicate 8 of 10


title: sevS11_eye_disc_Rep2

city: barcelona

first: Natalia

last: Mora

state: barcelona

address: avd. Diagonal 643

department: Genetics

institute: University of Barcelona

description: Total RNA from w1118;+;+ wing imaginal discs was pooled and used as a common reference against sevd2 and sevS11. Three microarrays were hybridized for sevS11 experiment in biological replicate, such that the total RNA from the sample used as a starting material came from two different extractions. Two arrays were hybridized with the same amplified RNA from extraction 1 and common reference (obtained using the Amino-Allyl Messageamp II aRNA Amplification Kit from Ambion, Inc) but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account. From extraction 2 another array was hybridized without dye swap.

hyb_protocol: Samples were diluted in 2X Hybridization Buffer #5185-5973(Agilent Technologies) and hybridization was carried out at 60ºC for 18 hours with a G2534A SureHyb Chamber in a G2545A Hybridization Oven (Agilent Technologies).

scan_protocol: GenePix Results (GPR) data files were obtained for each microarray with an Axon 4000B scanner and GenePix Pro 6 (Axon Instruments, Inc).

data_processing: GPR files were analyzed with Limma package from BioConductor (Gentleman et al., 2004; Genome Biol 5, R80; Smyth, 2004; Statistical Applications in Genetics and Molecular Biology 3, Article 3) using the same criteria. Data was background corrected with the "normexp" method and normalized with OLIN (Futschik and Crompton, 2005; Bioinformatics 21, 1724-1726). Spots not fulfilling the quality thresholds (based on spot size, foreground versus background signals, saturation, coincidence between differently calculated ratio measures and R2 of regression ratio) were eliminated from further analysis.

organism: Drosophila melanogaster

source_name: eye_discs_sevS11_(EXTRACTION 1)

label_protocol: 1.5ug total RNA were amplified and indirectly labelled with Amino-Allyl Messageamp II aRNA Amplification Kit (Ambion, Inc). Fragmentation was done with RNA Fragmentation Reagents #8740(Ambion, Inc).

growth_protocol: All Drosophila strains and crosses were kept on standard media with 0.025% bromophenol blue at 25ºC.

extract_protocol: Eye imaginal discs were dissected in PBS and kept in RNAlater prior to extraction with RNeasy Protect Mini Kit (QIAGEN Inc.). Quality was assessed in all samples using the Eukaryote Total RNA Nano Assay on a 2100 Bioanalyzer (Agilent Technologies). Total RNA from w1118;+;+ eye imaginal discs was pooled and used as a common reference against sevd2 and sevS11

tag: strain

tag: Stage

value: third instar larvae (bromophenol blue staged)

value: eye imaginal discs

tag: genetic background

value: w1118;+;+ isogenic wt strain (Ryder, E., 2004; Genetics 167, 797-813).


title: Large White Alternative sample replicate 10

description: Large White Alternatif sample Replicate 10 of 10

tag: tissue


title: sevS11_eye_disc_Rep1

extract_protocol: Eye imaginal discs were dissected in PBS and kept in RNAlater prior to extraction with RNeasy Protect Mini Kit (QIAGEN Inc.). Quality was assessed in all samples using the Eukaryote Total RNA Nano Assay on a 2100 Bioanalyzer (Agilent Technologies).


title: non carrier 8


title: non carrier 2


title: sevd2_eye_disc_Rep4

description: Description 	Total RNA from w1118;+;+ wing imaginal discs was pooled and used as a common reference against sevd2 and sevS11. Four microarrays were hybridized for sevd2 experiment in biological replicate pairs, such that the total RNA from the sample used as a starting material came from different extractions. Both arrays from each pair were hybridized with the same amplified RNA from sample and common reference (obtained using the Amino-Allyl Messageamp II aRNA Amplification Kit from Ambion, Inc) but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account.

source_name: eye_discs_sevd2_(EXTRACTION 2)


title: non carrier 1


title: sevS11_eye_disc_Rep3

source_name: eye_discs_sevS11_(EXTRACTION 2)


title: Large White Alternative sample replicate 9

description: Large White Alternatif sample Replicate 9 of 10


title: Large White Alternative sample replicate 4

description: Large White Alternatif sample Replicate 4 of 10


title: Large White Alternative sample replicate 5

description: Large White Alternatif sample Replicate 5 of 10


title: Large White Alternative sample replicate 3

description: Large White Alternatif sample Replicate 3 of 10


title: Large White Conventional sample replicate 10

description: Large White Conventional sample Replicate 10 of 10

source_name: Longissimus muscle of LWC pig

value: Conventional


title: Large White Alternative sample replicate 2

description: Large White Alternatif sample Replicate 2 of 10


title: Large White Conventional sample replicate 9

description: Large White Conventional sample Replicate 9 of 10


title: Large White Alternative sample replicate 1

description: Large White Alternatif sample Replicate 1 of 10


title: sevd2_eye_disc_Rep3


title: sevd2_eye_disc_Rep2

source_name: eye_discs_sevd2_(EXTRACTION 1)


title: Large White Conventional sample replicate 6

description: Large White Conventional sample Replicate 6 of 10


title: Large White Conventional sample replicate 4

description: Large White Conventional sample Replicate 4 of 10


title: Large White Conventional sample replicate 7

description: Large White Conventional sample Replicate 7 of 10


title: Large White Conventional sample replicate 8

description: Large White Conventional sample Replicate 8 of 10


title: Basque Alternative sample Replicate 10

description: Basque Alternatif sample Replicate 10 of 10

source_name: Longissimus muscle of BA pig


title: Large White Conventional sample replicate 1

description: Large White Conventional sample Replicate 1 of 10


title: Large White Conventional sample replicate 3

description: Large White Conventional sample Replicate 3 of 10


title: Basque Alternative sample Replicate 8

description: Basque Alternatif sample Replicate 8 of 10


title: Basque Alternative sample Replicate 2

description: Basque Alternatif sample Replicate 2 of 10


title: Basque Alternative sample Replicate 7

description: Basque Alternatif sample Replicate 7 of 10


title: Large White Conventional sample replicate 5

description: Large White Conventional sample Replicate 5 of 10


title: Large White Conventional sample replicate 2

description: Large White Conventional sample Replicate 2 of 10


title: Basque Alternative sample Replicate 4

description: Basque Alternatif sample Replicate 4 of 10


title: Basque Alternative sample Replicate 3

description: Basque Alternatif sample Replicate 3 of 10


title: Basque Alternative sample Replicate 1

description: Basque Alternatif sample Replicate 1 of 10


title: Basque Alternative sample Replicate 9

description: Basque Alternatif sample Replicate 9 of 10


title: Basque Alternative sample Replicate 6

description: Basque Alternatif sample Replicate 6 of 10


title: sevd2_eye_disc_Rep1

description: Description 	Total RNA from w1118;+;+ wing imaginal discs was pooled and used as a common reference against sevd2 and sevS11. Four microarrays were hybridized for sevd2 experiment in biological replicate pairs, such that the total RNA from the sample used as a starting material came from different extractions. Both arrays from each pair were hybridized with the same amplified RNA from sample and common reference (obtained using the Amino-Allyl Messageamp II aRNA Amplification Kit from Ambion, Inc) but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account.


title: Basque Conventional sample Replicate 6

description: Basque Conventional sample Replicate 6 of 10

source_name: Longissimus muscle of BC pig


title: Basque Conventional sample Replicate 5

description: Basque Conventional sample Replicate 5 of 10


title: Basque Conventional sample Replicate 7

description: Basque Conventional sample Replicate 7 of 10


title: Basque Alternative sample Replicate 5

description: Basque Alternatif sample Replicate 5 of 10


title: Longissimus sample Replicate 89

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 300 ng of cyanine 3-labeled cRNA sample per hybridization. The hybridization reactions were performed at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. Slides were disassembled and washed in Gene Expression Wash Buffer 1 for 1 minute at room temperature and then in Gene Expression Wash Buffer 2 for 1 minute at 32°C.

data_processing: Raw data from 15198 probes fluorescent hybridization signal intensities were log transformed and centered within sample by subtraction of sample median from all raw values.

source_name: skeletal muscle

label_protocol: Total RNA (500 ng) from each animal was labeled individually with Cy3 by using the Quick-Amp Labeling Kit  following the manufacturer’s instructions.

tag: pig

tag: muscle type

value: Longissimus

tag: ChIP


title: Basque Conventional sample Replicate 2

description: Basque Conventional sample Replicate 2 of 10


title: Basque Conventional sample Replicate 3

description: Basque Conventional sample Replicate 3 of 10


title: Basque Conventional sample Replicate 8

description: Basque Conventional sample Replicate 8 of 10


title: Basque Conventional sample Replicate 4

description: Basque Conventional sample Replicate 4 of 10


title: Basque Conventional sample Replicate 9

description: Basque Conventional sample Replicate 9 of 10


title: Longissimus sample Replicate 90


title: HD5 MONOCYTES

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

country: Italy

institute: University of Modena and Reggio Emilia

description:
US22502667_251485068846_S01_GE1_107_Sep09_1_1
Gene expression data from monocytes purified from peripheral blood

hyb_protocol: Cy3-labeled cRNAs (1.65 ug) were fragmented to an average size of 50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent). Samples were hybridized for 17 hours at 65°C on 4x44K Whole Human Genome Microarray (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Fluorescence data were analyzed with Feature Extraction Software v.10.5 (Agilent Technologies) an QC Chart tool v.1.3 to obtain background subtracted, spatially detrended Processed Signal intensities and quality control analyses.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral blood, normal monocytes, replicate 5

label_protocol: High quality RNAs were amplified and Cy3-labeled using Low Input Quick Amp Labeling kit (Agilent Technologies, Palo alto, CA, USA). Agilent RNA One-Color Spike-In was added in each sample to provide positive controls for monitoring the microarray workflow from sample amplification and labelling to microarray processing. It contains 10 in vitro synthesized, polyadenylated transcripts derived from the Adenovirus E1A transcriptome that are premixed at various ratios. All cRNA products were purified using RNeasy columns (QIAGEN). Dye incorporation and cRNA yield were checked with InfiniteM200 (Tecan).Samples had to contain at least 6 pmole of cyanine dye/ug of cRNA to be considered suitable for subsequent hybridization.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation (Ficoll, Pharmacia LKB Biotechnology, Piscataway, NY, USA). To enrich for peripheral blood monocytes, PBMCs were incubated with CD14-specific Microbeads and separated by AutoMACS throughout passage on two subsequent columns (Miltenyi Biotech, Auburn, CA, USA), obtaining a purity >97% in normal controls and >90% in CLL patients as assessed by flow cytometry using APC-conjugated mAb specific for CD14 (Miltenyi Biotech). For gene expression analyses, further monocyte selection was performed seeding cells onto plastic for 2 hours into a humidified 37°C incubator with 5%CO2 before RNA collection.

extract_protocol: total RNAs were extracted from purified CD14+ cells using RNeasy Midi kit Plus (QIAGEN, Valencia, CA, USA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNAs were quantified using InfiniteM200 (Tecan)

tag: cell type

value: Purified CD14+monocytes

value: periferal blood

tag: disease status

value: healthy donor (HD)


title: Basque Conventional sample Replicate 1

description: Basque Conventional sample Replicate 1 of 10


title: HD2 MONOCYTES

description:
US22502667_251485068845_S01_GE1_107_Sep09_1_2
Gene expression data from monocytes purified from peripheral blood

source_name: Peripheral blood, normal monocytes, replicate 2


title: Longissimus sample Replicate 88


title: HD3 MONOCYTES

description:
US22502667_251485068845_S01_GE1_107_Sep09_1_3
Gene expression data from monocytes purified from peripheral blood

source_name: Peripheral blood, normal monocytes, replicate 3


title: Basque Conventional sample Replicate 10

description: Basque Conventional sample Replicate 10 of 10


title: HD4 MONOCYTES

description:
US22502667_251485068845_S01_GE1_107_Sep09_1_4
Gene expression data from monocytes purified from peripheral blood

source_name: Peripheral blood, normal monocytes, replicate 4


title: Longissimus sample Replicate 87


title: Longissimus sample Replicate 85


title: Longissimus sample Replicate 80


title: Longissimus sample Replicate 78


title: Longissimus sample Replicate 77


title: Longissimus sample Replicate 82


title: Longissimus sample Replicate 83


title: Longissimus sample Replicate 84


title: Longissimus sample Replicate 76


title: Longissimus sample Replicate 75


title: CLL4 MONOCYTES

description:
US22502667_251485068847_S01_GE1_107_Sep09_1_1
Gene expression data from monocytes purified from peripheral blood

source_name: Peripheral blood, CLL-derived monocytes, replicate 4

value: CLL patient


title: HD1 MONOCYTES

description:
US22502667_251485068845_S01_GE1_107_Sep09_1_1
Gene expression data from monocytes purified from peripheral blood

source_name: Peripheral blood, normal monocytes, replicate 1


title: CLL5 MONOCYTES

description:
US22502667_251485068847_S01_GE1_107_Sep09_1_2
Gene expression data from monocytes purified from peripheral blood

source_name: Peripheral blood, CLL-derived monocytes, replicate 5


title: CLL3 MONOCYTES

description:
US22502667_251485068846_S01_GE1_107_Sep09_1_4
Gene expression data from monocytes purified from peripheral blood

source_name: Peripheral blood, CLL-derived monocytes, replicate 3


title: CLL1 MONOCYTES

description:
US22502667_251485068846_S01_GE1_107_Sep09_1_2
Gene expression data from monocytes purified from peripheral blood

source_name: Peripheral blood, CLL-derived monocytes, replicate 1


title: Longissimus sample Replicate 86


title: CLL2 MONOCYTES

description:
US22502667_251485068846_S01_GE1_107_Sep09_1_3
Gene expression data from monocytes purified from peripheral blood

source_name: Peripheral blood, CLL-derived monocytes, replicate 2


title: Semimembranosus sample Replicate 89

value: Semimembranosus


title: Longissimus sample Replicate 74


title: Semimembranosus sample Replicate 84


title: Longissimus sample Replicate 73


title: Semimembranosus sample Replicate 88


title: Longissimus sample Replicate 70


title: Longissimus sample Replicate 72


title: Semimembranosus sample Replicate 81


title: Longissimus sample Replicate 71


title: Longissimus sample Replicate 79


title: Semimembranosus sample Replicate 86


title: Longissimus sample Replicate 81


title: Semimembranosus sample Replicate 78


title: Semimembranosus sample Replicate 87


title: Semimembranosus sample Replicate 90


title: Semimembranosus sample Replicate 67


title: Semimembranosus sample Replicate 68


title: Semimembranosus sample Replicate 69


title: Semimembranosus sample Replicate 77


title: Semimembranosus sample Replicate 64


title: Semimembranosus sample Replicate 65


title: Semimembranosus sample Replicate 66


title: Semimembranosus sample Replicate 63


title: Semimembranosus sample Replicate 58


title: Semimembranosus sample Replicate 57


title: Semimembranosus sample Replicate 62


title: Semimembranosus sample Replicate 59


title: Semimembranosus sample Replicate 60


title: Semimembranosus sample Replicate 54


title: Semimembranosus sample Replicate 52


title: Semimembranosus sample Replicate 40


title: Semimembranosus sample Replicate 55


title: Semimembranosus sample Replicate 47


title: Semimembranosus sample Replicate 36


title: Semimembranosus sample Replicate 38


title: Semimembranosus sample Replicate 39


title: Semimembranosus sample Replicate 35


title: Semimembranosus sample Replicate 34


title: Semimembranosus sample Replicate 61


title: Semimembranosus sample Replicate 9


title: Semimembranosus sample Replicate 31


title: Semimembranosus sample Replicate 32


title: Semimembranosus sample Replicate 33


title: Semimembranosus sample Replicate 11


title: Semimembranosus sample Replicate 16


title: Semimembranosus sample Replicate 10


title: Semimembranosus sample Replicate 7


title: Semimembranosus sample Replicate 37


title: Semimembranosus sample Replicate 4


title: Semimembranosus sample Replicate 2


title: Semimembranosus sample Replicate 6


title: Semimembranosus sample Replicate 56


title: Semimembranosus sample Replicate 1


title: Semimembranosus sample Replicate 5


title: Semimembranosus sample Replicate 8


title: Semimembranosus sample Replicate 3


title: Semimembranosus sample Replicate 83


title: Semimembranosus sample Replicate 85


title: Semimembranosus sample Replicate 82


title: Semimembranosus sample Replicate 73


title: Semimembranosus sample Replicate 75


title: Semimembranosus sample Replicate 76


title: Semimembranosus sample Replicate 79


title: Semimembranosus sample Replicate 71


title: Semimembranosus sample Replicate 72


title: Semimembranosus sample Replicate 53


title: Semimembranosus sample Replicate 70


title: Semimembranosus sample Replicate 51


title: Semimembranosus sample Replicate 48


title: Semimembranosus sample Replicate 49


title: Semimembranosus sample Replicate 80


title: Semimembranosus sample Replicate 50


title: Semimembranosus sample Replicate 74


title: Semimembranosus sample Replicate 45


title: Semimembranosus sample Replicate 46


title: Semimembranosus sample Replicate 41


title: Semimembranosus sample Replicate 44


title: Semimembranosus sample Replicate 25


title: Semimembranosus sample Replicate 42


title: Semimembranosus sample Replicate 30


title: Semimembranosus sample Replicate 29


title: Semimembranosus sample Replicate 26


title: Semimembranosus sample Replicate 23


title: Semimembranosus sample Replicate 21


title: Semimembranosus sample Replicate 27


title: Semimembranosus sample Replicate 20


title: Semimembranosus sample Replicate 22


title: Semimembranosus sample Replicate 43


title: Semimembranosus sample Replicate 28


title: Semimembranosus sample Replicate 19


title: Semimembranosus sample Replicate 24


title: Semimembranosus sample Replicate 18


title: Semimembranosus sample Replicate 17


title: 252665513003-4

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

hyb_protocol: Agilent : 1650.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction software version 10.7.3.1

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Chomzynski

tag: genotype/variation

value: B splenocytes

tag: amount in (µg)

tag: rin number


title: Longissimus sample Replicate 69


title: Longissimus sample Replicate 67


title: Semimembranosus sample Replicate 13


title: 252665513003-2


title: Semimembranosus sample Replicate 14


title: Longissimus sample Replicate 68


title: 252665513003-3


title: Semimembranosus sample Replicate 15


title: Semimembranosus sample Replicate 12


title: Chicken Embryonic Fibroblasts, biological rep1

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

institute: Seoul National University

description: Gene expression data from chicken embryonic fibroblasts cultured until passage 2.

hyb_protocol: The biotin-labeled, in vitro-transcribed RNA was then fragmented and hybridized to the chicken genome GeneChip array at 45°C for 16 h.

scan_protocol: After hybridization, the arrays were washed in a GeneChip Fluidics Station 450 with a nonstringent washing buffer. The arrays were stained with a streptavidin–phycoerythrin complex. After staining, intensities were determined with a GeneChip scanner controlled by GeneChip Operating Software (Affymetrix).

data_processing: Gene expression data analysis was conducted using Microarray Suite 5.0 software (Affymetrix) and GenPlex v1.8 software (ISTECH, Inc., Goyang, South Korea). Global saline normalization using a GCOS algorithm was conducted, after which the normalized data were log2-transformed. Then fold changes and Welch’s t-test were applied for the selection of highly significant transcripts, maintaining a fold-change cutoff of 4.0; the significance level was set a P ≤ 0.05.

organism: Gallus gallus

source_name: Embryonic fibroblasts from E6.5 chicken embryos

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

growth_protocol: Freshly laid eggs were incubated with intermittent rocking at 37.5°C under 50–60% relative humidity until sample collection.

extract_protocol: Total RNA was extracted from PGCs and CEFs with a Qiagen RNeasy kit. DNA traces from the total RNA were degraded with RQ1 RNase-Free DNase before gene-expression analysis on an Affymetrix GeneChip Chicken Genome Array

treatment_protocol: About 2 µL blood cells retrieved from the dorsal aorta of embryos at E2.5 were cultured in knockout DMEM medium with essential components, and 10 ng•mlˉ1 human bFGF as growth inducing factor. PGCs were cultured in a 5% CO2 atmosphere at 37°C. For CEF culture, all internal organs and limbs were removed from the embryos at E6.5. Then the remaining embryonic body was dissociated using trypsin-EDTA at 37°C for 20 min. Then the cells were cultured in DMEM containing 10% FBS and 1% antibiotic-antimycotic in a 5% CO2 atmosphere at 37°C.

value: Embryonic fibroblasts

tag: cell pluripotency

value: Somatic cells

tag: developmental stage

value: Embryonic developmental days 6.5


title: Chicken Embryonic Fibroblasts, biological rep2


title: Longissimus sample Replicate 64


title: Longissimus sample Replicate 66


title: Longissimus sample Replicate 65


title: Longissimus sample Replicate 63


title: 252665513003-1


title: Longissimus sample Replicate 62


title: wild type shoot, biological rep1

city: Murcia

first: Pedro

last: Diaz-Vivancos

address: Campus Universitario de Espinardo, 25

department: Plant Breeding

institute: CEBAS-CSIC

description:
WT.S1
Columbia-0 replicate comprised 30 shoots.

hyb_protocol: Hybridization was performed as described in the Agronomics1 Standard Operating procedures.

scan_protocol: Scanning was performed as described in the Agronomics1 Standard Operating procedures.

data_processing: The Robust Multiarray Averaging (RMA) method of microarray normalization and summarization was used.

organism: Arabidopsis thaliana

source_name: shoot from 7-day-old wild type seedlings grown on vertical plates

label_protocol: Labeling was performed as described in the Agronomics1 Standard Operating Procedures.

growth_protocol: Arabidopsis thaliana Columbia-0 ecotype (Col0) and the root meristemless1 (rml1) mutant were grown on vertical plates containing PANG2 medium (1 mM KNO3; 150 µM CaCl2; 100 µM NaH2PO4; 20 µM MgSO4, micronutrients; 0.5 g.L-1 0.5 % sucrose and MES buffer pH 5.7) under an irradiance of 150 µmol*m-2*s-1 with a 16 h photoperiod and a temperature of 20ºC with 50 % relative humidity for 7 days.

extract_protocol: Plants of the rml1 and Columbia-0 ecotype were harvested, separated into roots and shoots, immediately frozen in liquid nitrogen and stored at -80ºC until RNA extraction was performed. Total RNA was extracted from frozen shoots and roots using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

tag: ecotype

value: wild type

value: shoot

tag: age

value: 7 days


title: rml1 root

description:
RML.R
rml1 root sample comprised 234 roots.

source_name: root from 7-day-old rml1 seedlings grown on vertical plates

value: root meristemless 1 (rml1) mutant

value: root


title: wild type root

description:
WT.R
Columbia-0 ecotype comprised 90 roots.

source_name: root from 7-day-old wild type seedlings grown on vertical plates


title: Chicken Embryonic Fibroblasts, biological rep3


title: wild type shoot, biological rep3

description:
WT.S3
Columbia-0 replicate comprised 30 shoots.


title: rml1 shoot, biological rep3

description:
RML.S3
rml1 replicate comprised 108 shoots.

source_name: shoot from 7-day-old rml1 seedlings grown on vertical plates


title: Blood Primordial germ cells, biological rep2

description: Gene expression data from chicken blood primordial germ cells cultured with the presence of bFGF.

source_name: Primordial germ cells from blood of E2.5 chicken embryos

value: Primordial germ cells from blood

value: Reproductive cells

value: Embryonic developmental days 2.5


title: Blood Primordial germ cells, biological rep1


title: rml1 shoot, biological rep2

description:
RML.S2
rml1 replicate comprised 65 shoots.


title: rml1 shoot, biological rep1

description:
RML.S1
rml1 replicate comprised 61 shoots.


title: Blood Primordial germ cells, biological rep3


title: Longissimus sample Replicate 60

source_name: skeletal muscle

value: Longissimus


title: Longissimus sample Replicate 59


title: Longissimus sample Replicate 61


title: wild type shoot, biological rep2

description:
WT.S2
Columbia-0 replicate comprised 30 shoots.


title: Longissimus sample Replicate 56


title: Longissimus sample Replicate 54


title: Longissimus sample Replicate 52


title: Longissimus sample Replicate 55


title: Longissimus sample Replicate 53


title: Longissimus sample Replicate 48


title: Longissimus sample Replicate 49


title: Longissimus sample Replicate 47


title: Longissimus sample Replicate 51


title: Longissimus sample Replicate 46


title: Longissimus sample Replicate 57


title: Longissimus sample Replicate 44


title: Longissimus sample Replicate 45


title: Longissimus sample Replicate 58


title: Longissimus sample Replicate 36


title: Longissimus sample Replicate 37


title: Longissimus sample Replicate 39


title: Longissimus sample Replicate 50


title: Longissimus sample Replicate 38


title: Longissimus sample Replicate 43


title: Longissimus sample Replicate 40


title: Longissimus sample Replicate 41


title: Longissimus sample Replicate 34


title: Longissimus sample Replicate 42


title: Longissimus sample Replicate 35


title: Longissimus sample Replicate 33


title: Longissimus sample Replicate 31


title: Longissimus sample Replicate 32


title: Longissimus sample Replicate 27


title: Longissimus sample Replicate 25


title: Longissimus sample Replicate 26


title: Longissimus sample Replicate 24


title: Longissimus sample Replicate 28


title: Longissimus sample Replicate 30


title: Longissimus sample Replicate 29


title: Longissimus sample Replicate 22


title: Longissimus sample Replicate 21


title: Longissimus sample Replicate 23


title: BALB.BB10Chr16

city: Salt Lake City

first: Thai

last: Cao

state: UT

address: 30 North 1900 East, SOM5C402

institute: University of Utah

description: Hybridized to Mouse Diversity Genotyping Array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

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

data_processing: CEL files were analyzed using R MouseDivGeno software by the JAX Mouse Diversity Genotyping Array Service (Jackson Laboratory).

source_name: BALB.B10Chr16 Consomic

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: DNA was extracted from liver of consomic mice maintained in our breeding colony at the University of Utah.

extract_protocol: DNA was extracted from proteinase-K digested liver DNA using DNeasy Tissue Kit (Qiagen).

tag: consomic line

tag: parental strain

value: liver


title: B10.BALBChr16

source_name: B10.BALBChr16 Consomic


title: mRNA Abundance Untreated 3

city: Stanford

first: Jamie

middle: Geier

last: Bates

address: 279 Campus Dr.

department: Biochemistry

institute: Stanford U.

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/94429.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

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

source_name: Mouse Reference

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: universal mouse reference RNA

source_name: lysate

value: wildtype v-Abl transformed pre-B cells

tag: compound based treatment


title: Longissimus sample Replicate 17

institute: INRA


title: Longissimus sample Replicate 19


title: mRNA Abundance +Rap 3

description:
Simple annotation: Leukemia/Lymphoma Cell Lines, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/94435.gif

value: RAP