title: UF833_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF833


title: UF846_Leaf-Rep1

status: Public on Feb 02 2010

type: RNA

city: Gainesville

first: Matias

last: Kirst

state: FL

country: USA

institute: University of Florida

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF846

hyb_protocol: 1.5ug labeled ds-cDNA was denatured at 95C for 5min and hybridized to custom in situ synthesized oligonucleotide microarrays (produced by NimbleGen, Madison, WI) at 42C overnight (16-20h).

scan_protocol: As described elsewhere (http://www.nimblegen.com/products/lit/exp_userguide_2008_05_21.pdf)

data_processing:
Raw intensity data was background corrected (Irizarry et al. 2003, Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264) and normalized using the Quantile normalization method (Bolstad et al. 2003, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193).
Data was quantile normalized using the Bioconductor Package (Gentleman et al. 2004, Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5: R80) in R programming environment (v. 2.4.1; www.r-project.org) and Log2 transformed.

molecule: total RNA

organism: Populus trichocarpa x Populus deltoides

source_name: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny, leaf tissue

label_protocol: RNA extracted from each individual in the progeny was converted to double-stranded (ds-) cDNA (SuperScript Double Strand cDNA Synthesis Kit, Invitrogen USA, Carlsbad, CA) with oligo-dT primer (Promega USA) according to the manufacturerâ??s protocol, except that synthesis of first and second strands were extended to 16h. Resultant ds-cDNA was labeled using cy3-tagged random 9mers and Klenow fragment for 2h at 37C.

extract_protocol: At harvest, the main plant organs (stems, roots, leaves and sylleptic branches) were collected separately. Stems were further dissected into secondary xylem tissue and phloem/bark/immature xylem. Leaf, secondary xylem, and root tissue from two biological replicates of each genotype were selected for gene expression analysis. All tissue was flash-frozen in liquid nitrogen immediately after harvest and stored at -80 Celsius (C) prior to lyophilization and subsequent RNA isolation. RNA was isolated by a standard protocol described previously (Chang S, J. Puryear, J. Cairney 1993, A simple and efficent method for isolating RNA from pine trees. Plant Mol Biol Rep 11: 113-116).

tag: strain

tag: tissue

value: leaf

tag: environmental conditions

value: 25mM supplemental N, long day conditions


title: UF844_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF844

value: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny


title: UF820_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF820


title: UF847_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF847


title: VEG replicate 3

city: Philadelphia

first: David

last: Roos

state: PA

address: 304B Carolyn Lynch Laboratories

department: Department of Biology

institute: University of Pennsylvania

hyb_protocol: Hybridization, washing, and scanning of arrays was performed using standard Affymetrix instrumentation and protocols for 11 micron, 169 format arrays.

data_processing: Biological triplicates were generated for each strain and expression values computed using the RMA implementation (default parameters) in the affy package from Bioconductor (Gentleman, Carey et al. 2004)

label: biotin

organism: Toxoplasma gondii

source_name: Tachyzoite stage, VEG strain

label_protocol: Labeled cRNA was created using the One-Cycle Labeling protocol in the Affymetrix GeneChip® IVT Labeling Kit (Santa Clara, CA).

growth_protocol: Prugniaud, RH, and VEG strain parasites were cultured in human foreskin fibroblast (HFF) cells as described in Roos, Donald et al. 1994.

extract_protocol: The resultant pellet was lysed with Buffer RLT from the Qiagen RNeasy Mini Kit (Valencia, CA) and RNA was extracted according to the manufacturer’s instructions.

treatment_protocol: Prior to host cell rupture, cells were scraped from the flask and spun at 300g for 9 min.

value: VEG

tag: developmental stage

value: Tachyzoite


title: VEG replicate 2

scan_protocol: Hybridization, washing, and scanning of arrays was performed using standard Affymetrix instrumentation and protocols for 11 micron, 169 format arrays.


title: PRU replicate 1

source_name: Tachyzoite stage, Prugniaud strain

value: Prugniaud


title: VEG replicate 1


title: UF824_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF824


title: UF840_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF840


title: PRU replicate 2


title: PRU replicate 3


title: UF816_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF816


title: UF813_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF813


title: UF819_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF819


title: UF807_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF807


title: RH replicate 3

source_name: Tachyzoite stage, RH strain

value: RH


title: UF814_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF814


title: UF806_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF806


title: C. coli test strain cco114_T

type: genomic

city: Ithaca

first: Michael

middle: J

last: Stanhope

state: NY

address: Schurman Hall

department: Population Medicine and Diagnostic Sciences

institute: Cornell University

description: CombiMatrix design #4649

hyb_protocol: Standard hybridization conditions for the biotinylated target included preblocking for 30 min at 50°C with 6x SSPE (1x SSPE is 0.18 M NaCl, 10 mM NaH2PO4, and 1 mM EDTA [pH 7.7]) containing 0.05% Tween 20, 5x Denhardt's solution, and 100ng/ul salmon sperm DNA followed by hybridization of the biotinylated target in hybridization solution (6x SSPE, 20-50ng/ul labeled DNA and 0.05% SDS) overnight at 50°C. The arrays were then washed once for at least 15 min with SSPE wash 1 (6x SSPE, 0.05% Tween-20) and then for 1 min with each of the following solutions:  SSPE wash 2 (3x SSPE, 0.05% Tween-20), SSPE wash 3 (0.5x SSPE, 0.05% Tween-20), and PBST wash (2x PBS, 0.1% Tween-20), followed by a final 2x PBS wash at room temperature. The hybridized array was then blocked with 5x casein-PBS buffer (BioFX Laboratories, Owings Mills, MD) for 15 min at room temperature and labeled for 30 min with Cy5-streptavidin (GE Healthcare, Amersham Biosciences, Piscataway, NJ) diluted 1:1,000 in 5x casein-PBS buffer. The arrays were scanned after they were washed twice with each of PBST and PBS solutions.

scan_protocol: Hybridized microarrays covered with the imaging solution and the coverslip were scanned with an Axon GenePix™ 4000B laser scanner (Axon Instruments, Union City, CA) using the following parameters:Wavelengths=635, ScanPower=100, FocusPosition=100, PixelSize=5.

data_processing: After scanning, the image was saved as a .tiff file from which the data were extracted using GenePix software.  The raw hybridization signal values, displayed in the GenePix Pro analysis Results (GPR) file, were log2-transformed to be used in subsequent analysis. Background intensity was estimated as the 75th percentile of all negative control probes, and subtracted on log2 scale from foreground Cy5 intensity of all spots on the array.  Such normalization made the magnitude of signal values of different arrays more comparable, with absent genes on each array centering around 0.  Expectation-maximization (EM) algorithm was then applied on the adjusted probe signals of each array to estimate the means and standard deviations of present genes and absent genes with the following parameters at initiation: mean and standard deviation for genes present and absent are 5.0 and 1.0; 0 and 0.5, respectively, percentage of absent genes at 10%. EM algorithm will run for 100 iterations or stop when the magnitude of change in mean estimate is less than 0.001 between iterations.  The EM algorithm fitted well-established Gaussian mixture model to the normalized signals of each array independently to distinguish the population of absent genes from present genes. It did not rely on comparison to signals of positive and negative control strains, so it was robust to technical processing variation in the array experiment. For each array, genes with spot signal below the lower 0.5 percentile of the estimated distribution of present genes were called absent, i.e. p < 0.005.  For C. coli strains tested on multiple arrays, a gene for a given probe was called present if it had a present call on at least one array.  For genes with multiple probes, a present call ratio, based on the total number of present calls out of the total number of probes for each gene, was used as a measurement of the divergence of the test strain again the reference strain.  The ratio will be in range 0-1, which reflects the gene divergence level (absent to present) in the test strain compared to the reference strain.  The present call ratio 0.4 was chosen as cutoff.  Present genes: ratio >0.4; absent and divergent genes: ratio <=0.4.

label: Biotin

molecule: genomic DNA

organism: Campylobacter coli

source_name: C. coli test strain from turkey

label_protocol: Purified fragments (1 to 2 ug) were labeled with biotin, using Mirus Label IT® µArray Biotin Labeling Kit  (Mirus Corp., Madison, WI) according to the manufacturer’s instructions, followed by removal of unincorporated dyes using QIAquick (Qiagen) columns.

extract_protocol: Genomic DNA was digested by sonication to sizes of 200-400bp, as visualized by agarose gel electrophoresis, then purified by using the Qiagen Qiaquick PCR purification kit.

tag: location

value: USA


title: C. coli test strain cco111_T

description: CombiMatrix design #4649


title: UF808_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF808


title: RH replicate 2


title: UF810_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF810


title: UF812_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF812


title: UF803_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF803


title: C. coli test strain cco107_T

description: CombiMatrix design #4649


title: C. coli test strain cco108_T

description: CombiMatrix design #4649


title: RH replicate 1


title: UF802_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF802


title: UF805_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF805


title: C. coli test strain cco105_T

description: CombiMatrix design #4649


title: C. coli test strain cco106_T

description: CombiMatrix design #4649


title: C. coli test strain cco104_T

description: CombiMatrix design #4649


title: C. coli test strain cco103_T

description: CombiMatrix design #4649


title: UF755_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF755


title: C. coli test strain cco100_C

description: CombiMatrix design #4649

source_name: C. coli test strain from chicken

value: Switzerland


title: C. coli test strain cco102_C

description: CombiMatrix design #4649


title: C. coli test strain cco093_H

description: CombiMatrix design #4649

source_name: C. coli test strain from human unspecified


title: UF743_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF743


title: C. coli test strain cco092_H

description: CombiMatrix design #4649


title: UF748_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF748


title: UF79_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF79


title: UF729_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF729


title: UF734_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF734


title: C. coli test strain cco091_H

description: CombiMatrix design #4649


title: C. coli test strain cco090_H

description: CombiMatrix design #4649


title: C. coli test strain cco088_H

description: CombiMatrix design #4649

value: Canada


title: UF723_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF723


title: UF724_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF724


title: UF716_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF716


title: UF718_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF718


title: UF722_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF722


title: C. coli test strain cco087_H

description: CombiMatrix design #4649

value: UK


title: C. coli test strain cco083_H

description: CombiMatrix design #4649

value: Belgium


title: C. coli test strain cco086_H

description: CombiMatrix design #4649


title: C. coli test strain cco082_H

description: CombiMatrix design #4649

value: Israel


title: UF715_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF715


title: UF710_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF710


title: UF706_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF706


title: UF720_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF720


title: C. coli test strain cco080_T

description: CombiMatrix design #4649

value: USA (CO)


title: C. coli test strain cco081_H

description: CombiMatrix design #4649

value: Sweden


title: UF881_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF881


title: UF703_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF703


title: UF705_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF705


title: C. coli test strain cco077_H

description: CombiMatrix design #4649

value: Bosnia Herzegovina


title: C. coli test strain cco079_H

description: CombiMatrix design #4649


title: C. coli test strain cco076_H

description: CombiMatrix design #4649

value: Slovenia


title: C. coli test strain cco070_H

description: CombiMatrix design #4649

value: Poland


title: C. coli test strain cco069_H

description: CombiMatrix design #4649


title: C. coli test strain cco071_H

description: CombiMatrix design #4649


title: C. coli test strain cco074_H

description: CombiMatrix design #4649


title: UF701_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF701

value: leaf

value: 25mM supplemental N, long day conditions


title: C. coli test strain cco067_B

description: CombiMatrix design #4649

source_name: C. coli test strain from bovine

value: USA (CA)


title: UF7_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF7

value: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny


title: C. coli test strain cco063_B

description: CombiMatrix design #4649


title: C. coli test strain cco062_B

description: CombiMatrix design #4649


title: C. coli test strain cco065_B

description: CombiMatrix design #4649


title: C. coli test strain cco061_B

description: CombiMatrix design #4649


title: UF590_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF590


title: UF700_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF700


title: C. coli test strain cco110_T

description: CombiMatrix design #4649


title: UF66_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF66


title: UF58_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF58


title: UF62_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF62


title: C. coli test strain cco060_B

description: CombiMatrix design #4649


title: UF565_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF565


title: UF61_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF61


title: UF585_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF585


title: UF579_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF579


title: C. coli test strain cco052_B

description: CombiMatrix design #4649

value: USA (WA)


title: UF561_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF561


title: UF546_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF546


title: UF547_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF547


title: C. coli test strain cco051_B

description: CombiMatrix design #4649


title: C. coli test strain cco055_B

description: CombiMatrix design #4649


title: UF541_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF541


title: UF544_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF544


title: UF539_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF539


title: C. coli test strain cco054_B

description: CombiMatrix design #4649


title: UF69_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF69


title: C. coli test strain cco027_B

description: CombiMatrix design #4649


title: C. coli test strain cco037_B

description: CombiMatrix design #4649


title: C. coli test strain cco049_B

description: CombiMatrix design #4649

value: USA (OR)


title: C. coli test strain cco025_B

description: CombiMatrix design #4649


title: UF534_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF534


title: UF533_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF533


title: C. coli test strain cco023_B

description: CombiMatrix design #4649


title: C. coli test strain cco020_B

description: CombiMatrix design #4649


title: C. coli test strain cco018_B

description: CombiMatrix design #4649


title: UF532_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF532


title: C. coli test strain cco019_B

description: CombiMatrix design #4649


title: C. coli test strain cco024_B

description: CombiMatrix design #4649


title: C. coli test strain cco016_C

description: CombiMatrix design #4649

value: USA (AL)


title: C. coli test strain cco017_C

description: CombiMatrix design #4649

value: USA


title: C. coli test strain cco014_C

description: CombiMatrix design #4649

value: USA (NC)


title: C. coli test strain cco013_C

description: CombiMatrix design #4649

value: USA (FL)


title: UF513_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF513


title: UF529_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF529


title: UF500_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF500


title: UF503_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF503


title: UF493_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF493


title: C. coli test strain cco015_C

description: CombiMatrix design #4649

value: USA (AR)


title: C. coli test strain cco012_S

description: CombiMatrix design #4649

source_name: C. coli test strain from swine


title: UF499_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF499


title: UF491_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF491


title: UF494_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF494


title: UF526_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF526


title: UF489_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF489


title: UF490_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF490


title: UF481_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF481


title: UF477_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF477


title: C. coli test strain cco009_C

description: CombiMatrix design #4649


title: C. coli test strain cco010_S

description: CombiMatrix design #4649


title: C. coli test strain cco007_S

description: CombiMatrix design #4649


title: C. coli test strain cco011_S

description: CombiMatrix design #4649


title: C. coli test strain cco008_S

description: CombiMatrix design #4649


title: C. coli test strain cco003_S

description: CombiMatrix design #4649


title: K562, BR1, 36hr

city: Oxford

first: Adam

last: Handel

address: Roosevelt Drive

department: Wellcome Trust Centre for Human Genetics

country: United Kingdom

institute: University of Oxford

description: K562 cells treated with 36 hours of vitamin D exposure

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 14.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria)

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA)

data_processing: The quantified signals were background corrected (Normexp with offset value 10 [21]) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm

organism: Homo sapiens

label_protocol: 400 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer

growth_protocol: We used nine cell lines (Hep-G2, HL60, K562, AG09309, AG09319, GM15084, GM12878, GM07348 and GM07019).  These were cultured in RPMI-1640 supplemented with 10% fetal bovine serum, 0.2 mM L-glutamine at 37 oC in 5% humidified CO2

extract_protocol: After harvesting, cells were lysed in 500 uL of lysis buffer (Promega).  Homogenised samples were immediately stored at -80 oC

treatment_protocol: We stimulated cells with 0.1 microM calcitriol for 0 hours, 8 hours or 36 hours

tag: cell line

tag: vitamin d exposure

source_name: Common reference (S1-S54)

value: Common reference (S1-S54)


title: C. coli test strain cco004_S

description: CombiMatrix design #4649


title: C. coli test strain cco006_S

description: CombiMatrix design #4649


title: K562, BR2, 36hr

source_name: K562 cells treated with 36 hours of vitamin D exposure


title: UF468_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF468


title: C. coli test strain cco001_S

description: CombiMatrix design #4649


title: K562, BR1, 8hr

description: K562 cells treated with 8 hours of vitamin D exposure


title: K562, BR2, 8hr

source_name: K562 cells treated with 8 hours of vitamin D exposure


title: C. coli test strain cco002_S

description: CombiMatrix design #4649


title: C. coli reference strain RM2228

description: CombiMatrix design #4649

source_name: C. coli reference strain from chicken


title: C. coli test strain cco114_T

description: CombiMatrix design #5543

label_protocol: Purified fragments (1 to 2 ug) were labeled with biotin, using Mirus Label IT® µAArray Biotin Labeling Kit  (Mirus Corp., Madison, WI) according to the manufacturer's instructions, followed by removal of unincorporated dyes using QIAquick (Qiagen) columns.


title: K562, BR2, 0hr

description: K562 cells not treated with vitamin D

source_name: K562 cells not treated with vitamin D


title: C. coli test strain cco005_S

description: CombiMatrix design #4649


title: C. coli test strain cco111_T

description: CombiMatrix design #5543


title: K562, BR1, 0hr

description: K562 cells not treated with vitamin D


title: UF453_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF453


title: UF452_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF452


title: UF456_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF456


title: UF441_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF441


title: UF436_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF436


title: UF435_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF435


title: HL60, BR2, 36hr

description: HL60 cells treated with 36 hours of vitamin D exposure


title: UF457_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF457


title: UF437_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF437


title: UF419_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF419


title: C. coli test strain cco108_T

description: CombiMatrix design #5543


title: C. coli test strain cco107_T

description: CombiMatrix design #5543


title: C. coli test strain cco106_T

description: CombiMatrix design #5543


title: C. coli test strain cco105_T

description: CombiMatrix design #5543


title: HL60, BR2, 8hr

description: HL60 cells treated with 8 hours of vitamin D exposure


title: HL60, BR1, 36hr

source_name: HL60 cells treated with 36 hours of vitamin D exposure


title: C. coli test strain cco103_T

description: CombiMatrix design #5543


title: C. coli test strain cco110_T

description: CombiMatrix design #5543


title: C. coli test strain cco104_T

description: CombiMatrix design #5543


title: C. coli test strain cco102_C

description: CombiMatrix design #5543

value: Switzerland


title: C. coli test strain cco092_H

description: CombiMatrix design #5543


title: HL60, BR2, 0hr

description: HL60 cells not treated with vitamin D

source_name: HL60 cells not treated with vitamin D


title: HL60, BR1, 0hr

description: HL60 cells not treated with vitamin D


title: C. coli test strain cco091_H

description: CombiMatrix design #5543


title: C. coli test strain cco090_H

description: CombiMatrix design #5543


title: HL60, BR1, 8hr

source_name: HL60 cells treated with 8 hours of vitamin D exposure


title: UF409_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF409

source_name: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny, leaf tissue


title: C. coli test strain cco100_C

description: CombiMatrix design #5543


title: C. coli test strain cco087_H

description: CombiMatrix design #5543

value: UK


title: UF406_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF406


title: C. coli test strain cco086_H

description: CombiMatrix design #5543

value: Canada


title: C. coli test strain cco093_H

description: CombiMatrix design #5543


title: UF407_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF407


title: UF401_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF401


title: UF402_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF402


title: C. coli test strain cco088_H

description: CombiMatrix design #5543


title: Ag09309, BR2, 36hr

description: Ag09309 cells treated with 36 hours of vitamin D exposure


title: C. coli test strain cco082_H

description: CombiMatrix design #5543

value: Israel


title: UF40_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF40


title: C. coli test strain cco081_H

description: CombiMatrix design #5543

value: Sweden


title: Ag09309, BR2, 8hr

description: Ag09309 cells treated with 8 hours of vitamin D exposure


title: Ag09309, BR1, 8hr

source_name: Ag09309 cells treated with 8 hours of vitamin D exposure


title: C. coli test strain cco080_T

description: CombiMatrix design #5543

value: USA (CO)


title: C. coli test strain cco076_H

description: CombiMatrix design #5543

value: Slovenia


title: C. coli test strain cco074_H

description: CombiMatrix design #5543

value: Poland


title: C. coli test strain cco077_H

description: CombiMatrix design #5543

value: Bosnia Herzegovina


title: Ag09309, BR1, 36hr

source_name: Ag09309 cells treated with 36 hours of vitamin D exposure


title: Ag09309, BR1, 0hr

description: Ag09309 cells not treated with vitamin D


title: C. coli test strain cco079_H

description: CombiMatrix design #5543

value: Belgium


title: UF396_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF396

value: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny

value: leaf

value: 25mM supplemental N, long day conditions


title: C. coli test strain cco071_H

description: CombiMatrix design #5543


title: Ag09309, BR2, 0hr

source_name: Ag09309 cells not treated with vitamin D


title: UF383_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF383


title: UF392_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF392


title: GM18054, BR2, 36hr

description: GM18054 cells treated with 36 hours of vitamin D exposure


title: C. coli test strain cco069_H

description: CombiMatrix design #5543


title: C. coli test strain cco067_B

description: CombiMatrix design #5543

value: USA (CA)


title: GM18054, BR1, 36hr

source_name: GM18054 cells treated with 36 hours of vitamin D exposure


title: C. coli test strain cco063_B

description: CombiMatrix design #5543


title: GM18054, BR2, 8hr

description: GM18054 cells treated with 8 hours of vitamin D exposure


title: C. coli test strain cco070_H

description: CombiMatrix design #5543


title: C. coli test strain cco062_B

description: CombiMatrix design #5543


title: GM18054, BR1, 8hr

source_name: GM18054 cells treated with 8 hours of vitamin D exposure


title: UF381_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF381


title: UF380_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF380


title: UF372_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF372


title: C. coli test strain cco060_B

description: CombiMatrix design #5543


title: GM18054, BR2, 0hr

description: GM18054 cells not treated with vitamin D


title: C. coli test strain cco055_B

description: CombiMatrix design #5543


title: C. coli test strain cco061_B

description: CombiMatrix design #5543


title: C. coli test strain cco065_B

description: CombiMatrix design #5543


title: UF368_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF368


title: UF36_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF36


title: UF352_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF352


title: C. coli test strain cco052_B

description: CombiMatrix design #5543

value: USA (WA)


title: C. coli test strain cco051_B

description: CombiMatrix design #5543


title: C. coli test strain cco083_H

description: CombiMatrix design #5543

source_name: C. coli test strain from human unspecified


title: UF35_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF35


title: GM18054, BR1, 0hr

source_name: GM18054 cells not treated with vitamin D


title: C. coli test strain cco037_B

description: CombiMatrix design #5543

source_name: C. coli test strain from bovine


title: C. coli test strain cco049_B

description: CombiMatrix design #5543

value: USA (OR)


title: C. coli test strain cco027_B

description: CombiMatrix design #5543


title: GM07348, BR2, 36hr

description: GM07348 cells treated with 36 hours of vitamin D exposure

source_name: Common reference (S1-S54)

value: Common reference (S1-S54)


title: C. coli test strain cco025_B

description: CombiMatrix design #5543


title: GM07348, BR1, 36hr

source_name: GM07348 cells treated with 36 hours of vitamin D exposure


title: UF328_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF328


title: UF337_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF337


title: GM07348, BR2, 8hr

description: GM07348 cells treated with 8 hours of vitamin D exposure


title: C. coli test strain cco024_B

description: CombiMatrix design #5543


title: C. coli test strain cco020_B

description: CombiMatrix design #5543


title: C. coli test strain cco023_B

description: CombiMatrix design #5543


title: UF320_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF320


title: C. coli test strain cco019_B

description: CombiMatrix design #5543


title: UF32_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF32


title: GM07348, BR2, 0hr

description: GM07348 cells not treated with vitamin D


title: GM07348, BR1, 0hr

source_name: GM07348 cells not treated with vitamin D


title: C. coli test strain cco015_C

description: CombiMatrix design #5543

source_name: C. coli test strain from chicken

value: USA (AR)


title: C. coli test strain cco016_C

description: CombiMatrix design #5543

value: USA (AL)


title: C. coli test strain cco017_C

description: CombiMatrix design #5543

value: USA


title: GM07019, BR2, 36hr

description: GM07019 cells treated with 36 hours of vitamin D exposure


title: GM07348, BR1, 8hr

source_name: GM07348 cells treated with 8 hours of vitamin D exposure


title: UF298_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF298


title: C. coli test strain cco012_S

description: CombiMatrix design #5543

source_name: C. coli test strain from swine


title: C. coli test strain cco014_C

description: CombiMatrix design #5543

value: USA (NC)


title: GM07019, BR1, 36hr

source_name: GM07019 cells treated with 36 hours of vitamin D exposure


title: C. coli test strain cco018_B

description: CombiMatrix design #5543


title: UF325_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF325


title: C. coli test strain cco013_C

description: CombiMatrix design #5543

value: USA (FL)


title: UF300_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF300


title: UF293_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF293


title: UF309_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF309


title: C. coli test strain cco011_S

description: CombiMatrix design #5543


title: C. coli test strain cco008_S

description: CombiMatrix design #5543


title: C. coli test strain cco009_C

description: CombiMatrix design #5543


title: GM07019, BR2, 8hr

description: GM07019 cells treated with 8 hours of vitamin D exposure


title: C. coli test strain cco010_S

description: CombiMatrix design #5543


title: C. coli test strain cco007_S

description: CombiMatrix design #5543


title: UF290_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF290


title: GM07019, BR1, 8hr

source_name: GM07019 cells treated with 8 hours of vitamin D exposure


title: C. coli test strain cco005_S

description: CombiMatrix design #5543


title: GM07019, BR1, 0hr

description: GM07019 cells not treated with vitamin D


title: UF292_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF292

source_name: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny, leaf tissue


title: C. coli test strain cco004_S

description: CombiMatrix design #5543


title: C. coli test strain cco006_S

description: CombiMatrix design #5543


title: GM07019, BR2, 0hr

source_name: GM07019 cells not treated with vitamin D


title: C. coli test strain cco002_S

description: CombiMatrix design #5543


title: C. coli test strain cco003_S

description: CombiMatrix design #5543


title: C. coli test strain cco001_S

description: CombiMatrix design #5543


title: C. coli reference strain RM2228

description: CombiMatrix design #5543

source_name: C. coli reference strain from chicken


title: GM12878, BR1, 36hr

description: GM12878 cells treated with 36 hours of vitamin D exposure


title: GM12878, BR2, 8hr

description: GM12878 cells treated with 8 hours of vitamin D exposure


title: GM12878, BR2, 36hr

source_name: GM12878 cells treated with 36 hours of vitamin D exposure


title: UF285_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF285


title: con_1554

city: San Francisco

first: Sajeev

last: Batra

state: CA

institute: UCSF

hyb_protocol: Cy5 labeled sample was hybridized to the HEEBO array in 3x SSC at 65C 16 hours.

scan_protocol: HEEBO arrays were scanned with an Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and gridded using the Spotreader program (Niles Scientific, Portola Valley, CA. USA)

data_processing: Spot analysis was performed with Spotreader and stored in a relational database (Acuity). Data were ratio normalized, and control and poor-quality features (as determined by both visual examination and application of quantitative filters for saturation, feature diameter, and variance) were removed. Data were further filtered for spots that did not exhibit signal in any of the sample channels (based on the percentage of pixels in the feature above background and feature intensity) and for excessive missing data. The ratio of medians of the remaining data was transformed to log2 space, median centered by array, and median centered by gene.

source_name: Amplified RNA from recto-sigmoid biopsy from HIV infected individual

label_protocol: RNA extracted from the samples was amplified using Amino Allyl MessageAmp II aRNA kit from Ambion. The amplified material was then coupled to Cy5.

extract_protocol: Trizol reagent and Invitrogen Purelink RNA purification system

value: recto-sigmoid

source_name: Amplified reference colon RNA from an uninfected healthy individual obtained during surgery.

value: Colon


title: GM12878, BR1, 8hr

source_name: GM12878 cells treated with 8 hours of vitamin D exposure


title: GM12878, BR1, 0hr

description: GM12878 cells not treated with vitamin D


title: con_1545


title: con_1560


title: UF280_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF280


title: UF284_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF284


title: con_1518


title: UF266_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF266


title: UF272_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF272


title: noncon_1515


title: Ag09319, BR2, 36hr

description: Ag09319 cells treated with 36 hours of vitamin D exposure


title: con_1504


title: GM12878, BR2, 0hr

source_name: GM12878 cells not treated with vitamin D


title: UF287_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF287


title: con_1529


title: noncon_1292


title: UF270_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF270


title: Ag09319, BR1, 36hr

source_name: Ag09319 cells treated with 36 hours of vitamin D exposure


title: noncon_1265


title: noncon_1259


title: noncon_1298


title: UF247_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF247


title: UF269_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF269


title: noncon_1246


title: Ag09319, BR2, 8hr

description: Ag09319 cells treated with 8 hours of vitamin D exposure

source_name: Common reference (S1-S54)


title: UF254_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF254


title: Ag09319, BR1, 8hr

source_name: Ag09319 cells treated with 8 hours of vitamin D exposure


title: UF246_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF246


title: noncon_1254


title: con_1198


title: Ag09319, BR2, 0hr

description: Ag09319 cells not treated with vitamin D


title: noncon_1217


title: con_1256


title: Ag09319, BR1, 0hr

source_name: Ag09319 cells not treated with vitamin D


title: Hep-G2, BR2, 36hr

description: Hep-G2 cells treated with 36 hours of vitamin D exposure


title: Hep-G2, BR1, 36hr

source_name: Hep-G2 cells treated with 36 hours of vitamin D exposure


title: UF240_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF240


title: con_1139


title: noncon_1094


title: Hep-G2, BR1, 8hr

description: Hep-G2 cells treated with 8 hours of vitamin D exposure


title: UF241_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF241


title: noncon_1080


title: noncon_1190


title: UF237_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF237


title: UF231_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF231


title: Hep-G2, BR1, 0hr

description: Hep-G2 cells not treated with vitamin D

source_name: Hep-G2 cells not treated with vitamin D


title: UF228_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF228


title: Hep-G2, BR2, 8hr

source_name: Hep-G2 cells treated with 8 hours of vitamin D exposure


title: UF217_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF217


title: UF229_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF229


title: UF223_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF223


title: Hep-G2, BR2, 0hr

description: Hep-G2 cells not treated with vitamin D


title: UF224_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF224


title: UF215_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF215


title: melanoma short-term culture M980928

status: Public on Feb 01 2010

city: Cambridge

last: Berger

state: MA

address: 7 Cambridge Center

department: Cancer Program

institute: The Broad Instititute

description: gene expression data, microarray-derived

hyb_protocol: cRNA were hybridized according to the standard Affymetrix protocol

scan_protocol: data were scanned according to standard protocols

data_processing: data were processed using the aroma.affymetrix package in Bioconductor. RMA (robust multichip average) was applied in combination with quantile normalization to generate gene centric expression values.

source_name: melanoma short-term culture M980928

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

growth_protocol: Cell lines and short-term cultures were grown as described in Lin et al, Cancer Research (2008), 68:664-673

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

treatment_protocol: cells were grown under standard conditions (no treatment)

tag: melanoma type

value: patient-derived short-term culture M980928


title: melanoma short-term culture M990514

source_name: melanoma short-term culture M990514

value: patient-derived short-term culture M990514


title: UF209_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF209

source_name: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny, leaf tissue


title: melanoma short-term culture M990802

source_name: melanoma short-term culture M990802

value: patient-derived short-term culture M990802


title: melanoma short-term culture M000921

source_name: melanoma short-term culture M000921

value: patient-derived short-term culture M000921


title: UF214_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF214

value: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny

value: leaf


title: UF22_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF22

value: 25mM supplemental N, long day conditions


title: MCF-7_10 nM E2 (6h)_SRA siRNA_rep2

city: Houston

first: Charles

middle: E

last: Foulds

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Affymetrix HG U133+2 data

hyb_protocol: 15 ug of the labeled cRNA was fragmented and re-checked for concentration.  A hybridization cocktail containing Affymetrix spike-in controls and labeled cRNA was loaded onto a GeneChip® HG U133 Plus 2.0 Array.  The array was hybridized overnight at 45 C with rotation at 60 rpm then washed and stained with a strepavidin, R-phycoerythrin conjugate stain.  Signal amplification was done using biotinylated anti-streptavidin.

scan_protocol: The stained array was scanned on an Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control (QC) metrics recorded using Affymetrix GCOS software version 1.4.

data_processing: We used the following software packages for data QC and statistical analysis: Affymetrix Expression Console (www.affymetrix.com) for data QC (all three triplicates of the three experiments showed good quality), BRB Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) for statistical analysis, and dChip (www.dchip.org) for clustering pictures. Expressions were estimated with BRB Array Tools using the RMA method. We used for the analysis ~ 40,000 probesets present in at least 25-30% of all arrays for each of the cell lines. Since our sample size was equal to three for each of the groups, we performed t-tests with the Random Variance Model (RVM), which is designed for small sample size experiments. The method of Benjamini and Hochberg was used for estimation of FDR. The cutoffs for differentially expressed genes were FDR < 0.05 and fold change > 1.2 for the entire datasets.

source_name: MCF-7 cells 10 nM E2 (6h), SRA siRNA

label_protocol: RNAs were labeled using the standard Affymetrix T7 oligo(dT) primer protocol. Five ug of total RNA was reverse transcribed to produce double-stranded cDNA.  The cDNA product was used as a template for an in vitro transcription reaction, producing biotin-labeled cRNA.  The labeled cRNA was quantified using the NanoDrop spectrophotometer.

growth_protocol: HeLa cells were grown in high-glucose DMEM containing 10% FBS, 1% pencillin-streptomycin, and L-glutamine. MCF-7 cells were grown in phenol-red free high-glucose DMEM containing 5% charcoal-stripped FBS, 1% pencillin-streptomycin, and L-glutamine.

extract_protocol: Trizol (Invitrogen) was used to isolate total RNA, which was then further purified by RNeasy columns (Qiagen), prior to cRNA labeling.

treatment_protocol: Cells were transiently transfected with either 25 nM siRNA pools (for HeLa cells) or 50 nM siRNA pools (for MCF-7 cells) using Mirus Trans-It-TKO. HeLa cells were harvested after 3 days. After 2.5d, MCF-7 cells were further treated with fresh stripped media (minus E2) or with media containing 10 nM E2 for six hours before harvesting.

value: MCF-7 cancer cell line

tag: tissue origin of cancer cell

value: breast

tag: protocol

value: siRNA-mediated SRA depletion

tag: agent

value: estradiol


title: MCF-7_10 nM E2 (6h)_SRA siRNA_rep1

description: Affymetrix HG U133+2 data


title: melanoma short-term culture M000216

source_name: melanoma short-term culture M000216

value: patient-derived short-term culture M000216


title: MCF-7_minus E2_SRA siRNA_rep1

description: Affymetrix HG U133+2 data

source_name: MCF-7 cells minus E2, SRA siRNA

value: no estradiol


title: MCF-7_minus E2_SRA siRNA_rep3

description: Affymetrix HG U133+2 data


title: MCF-7_10 nM E2 (6h)_SRA siRNA_rep3

description: Affymetrix HG U133+2 data


title: UF201_Leaf-Rep1

description: Gene expression measured from RNA extracted from leaf samples collected from individual UF201


title: MCF-7_minus E2_NT siRNA_rep3

description: Affymetrix HG U133+2 data

source_name: MCF-7 cells minus E2,control

value: control siRNA


title: melanoma short-term culture M010403

source_name: melanoma short-term culture M010403

value: patient-derived short-term culture M010403


title: melanoma short-term culture M980409

source_name: melanoma short-term culture M980409

value: patient-derived short-term culture M980409


title: MCF-7_10 nM E2 (6h)_NT siRNA_rep2

description: Affymetrix HG U133+2 data

source_name: MCF-7 cells 10 nM E2 (6h),control


title: MCF-7_10 nM E2 (6h)_NT siRNA_rep1

description: Affymetrix HG U133+2 data


title: MCF-7_minus E2_NT siRNA_rep2

description: Affymetrix HG U133+2 data


title: MCF-7_minus E2_SRA siRNA_rep2

description: Affymetrix HG U133+2 data


title: HeLa_SRA siRNA_rep3

description: Affymetrix HG U133+2 data

source_name: HeLa cells, SRA siRNA

value: HeLa cancer cell line

value: cervix


title: St286b

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

description: no additional information

hyb_protocol: Agilent (Agilent, Santa Clara, USA) 8x15K CGH protocol, 65°C for 18-20 h.

scan_protocol: GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm, line average 2

data_processing: Image analysis with GenePix Pro 6.0, data preprocessing in R with limma package: background subtraction with "normexp" and offset 50. Two-component Gaussian mixture model decomposition was applied to log2-intensities (probes included whose names started with '_pai' or '_scab') separately for each array. Classification boundary between the two components was calculated analytically and it defined an array specific threshold for signals 0 (low-intensity) and 1 (high-intensity).

organism: Streptomyces scabiei

source_name: potato scab lesion

label_protocol: A 500 ng sample was labelled according BioPrime labelling kit's (Invitrogen, Carlsbad, CA) instruction.

growth_protocol: Bacteria were grown on potato dextrose agar (Sigma, Steinheim, Germany) at 28°C 7 days.

extract_protocol: Lysis aided with SDS, phenol-chloroform extraction and precipitation with ethanol.

tag: growth replicate

value: B


title: St266b

description: no additional information


title: St286a

description: no additional information

value: A


title: MCF-7_minus E2_NT siRNA_rep1

description: Affymetrix HG U133+2 data


title: HeLa_SRA siRNA_rep2

description: Affymetrix HG U133+2 data


title: melanoma short-term culture M970109

source_name: melanoma short-term culture M970109

value: patient-derived short-term culture M970109


title: HeLa_NT siRNA_rep2

description: Affymetrix HG U133+2 data

source_name: HeLa cells,control


title: S.ret

description: no additional information

organism: Streptomyces reticuliscabiei


title: HeLa_SRA siRNA_rep1

description: Affymetrix HG U133+2 data


title: HeLa_NT siRNA_rep1

description: Affymetrix HG U133+2 data


title: St266a

description: no additional information


title: St250a

description: no additional information


title: St250b

description: no additional information


title: St300Ba

description: no additional information


title: St255b

description: no additional information

organism: Streptomyces turgidiscabies


title: St300Bb

description: no additional information


title: HeLa_NT siRNA_rep3

description: Affymetrix HG U133+2 data


title: St255a

description: no additional information


title: St300b

description: no additional information


title: St368b

description: no additional information


title: St304b

description: no additional information


title: St342b

description: no additional information


title: St368a

description: no additional information


title: St300a

description: no additional information


title: St32b

description: no additional information


title: St304a

description: no additional information


title: St261b

description: no additional information


title: St323a

description: no additional information


title: St32a

description: no additional information


title: St261a

description: no additional information


title: St287a

description: no additional information


title: St287b

description: no additional information


title: St323b

description: no additional information


title: Ss53

description: no additional information


title: BMDM control 1 6h

status: Public on Jan 19 2010

city: Marseille

first: Benoit

last: Desnues

address: 27 boulevard Jean Moulin

department: URMITE UMR CNRS 6236

country: France

institute: Faculté de Médecine de la Timone

description: Gene expression after 6 hours incubation of uninfected BMDM

hyb_protocol: 1.65 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 Mouse Genome Oligo Microarrays (G4122F) 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 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 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014868_D_20060807mouse) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mus musculus

source_name: BMDM, 6h, control, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 300 ng 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.

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

treatment_protocol: BMDM were infected with T. whipplei (MOI 50) or left untreated in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated for 6 at 37 ºC in a humidified incubator with 5% CO2.

tag: cell type

value: Bone-marrow derived macrophages


title: IHP vs ILP rep2 dye swap_LPHP5repB79F

status: Public on Jan 14 2010

city: Urbana

first: Stephen

middle: Patrick

last: Moose

state: IL

address: 1201 W Gregory

department: Crop Sciences

institute: University of Illinois at Urbana-Champaign

hyb_protocol: Hybridizations were performed overnight in custom designed cassettes in 42 degree water bath, followed by 3 washes.

scan_protocol: Scanned on a Genepix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA). Used GenePix Pro 6.0 (Molecular Devices Corporation) for spotfinding.

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

organism: Zea mays

source_name: ILP

label_protocol: The Amino Allyl MessageAmp™ II aRNA Amplification kit (Ambion, Austin, TX) with Cyanine-3 and -5 (GE Healthcare Bio-Sciences Corp., Piscataway, NJ) dyes were used to amplify and label samples.

extract_protocol: Total RNA was isolated using LS TRIzol (Invitrogen, Carlsbad, CA), digested by DNAse,  then Rneasy purification kit (Qiagen, Valencia, CA).

tag: protein line

value: ILP

tag: age

value: 16 DAP

tag: tissue type

value: seed

source_name: IHP

value: IHP


title: IRLP  vs ILP rep1_B219

source_name: IRLP

value: IRLP


title: BMDM control 2 6h

source_name: BMDM, 6h, control, replicate 2


title: BMDM Tw 1 6h

description: Gene expression after 6 hours infection with T. whipplei of BMDM

source_name: BMDM, 6h, T. whipplei, replicate 1


title: IHP vs ILP rep3_LPHP3repB84F


title: IHP vs ILP rep2 _LPHP4repB77F


title: IHP vs ILP rep3_LPHP3repA76F


title: IHP vs ILP rep1 _LPHP1repB85F


title: IHP vs ILP rep1 dye swap_LPHP2repA75F


title: IRLP  vs ILP rep2_B221


title: ILP vs IRLP rep2 dye swap_B222


title: BMDM Tw 2 6h

source_name: BMDM, 6h, T. whipplei, replicate 2


title: MCF-7_10 nM E2 (6h)_NT siRNA_rep3

description: Affymetrix HG U133+2 data

value: MCF-7 cancer cell line

value: breast

value: estradiol


title: IRHP vs IHP rep2 dye swap_B224

source_name: IRHP

value: IRHP


title: BMDM Tw 3 6h

source_name: BMDM, 6h, T. whipplei, replicate 3


title: IHP vs ILP rep2 dye swap_LPHP5repA74F


title: IHP vs ILP rep1 dye swap_LPHP2repB83F


title: IHP vs IRHP rep1_B177


title: IRHP vs IHP rep1 dye swap_B223


title: ILP vs IRLP rep1 dye swap_B220


title: IHP vs IRHP rep2_B178


title: St342a

description: no additional information


title: IHP vs ILP rep2 _LPHP4repA73F


title: BMDM control 3 6h

source_name: BMDM, 6h, control, replicate 3


title: IRHP vs IHP rep2 dye swap_A290


title: IHP vs IRHP rep2_A286


title: P90_1_(5)

status: Public on Dec 01 2009

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: separated prostate lobes, postnatal day P90, pool 1 of 3

hyb_protocol: Experimental and reference probes were combined and competitively hybridized to microarrays under a coverslip for 16 h at 63°C.

scan_protocol: Fluorescent array images were collected for Cy3 and Cy5 emissions using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA). Image intensity data were extracted and analyzed using GenePix 4.1 software.

data_processing: Log2-ratios were normalized using a print-tip specific intensity-based scatter plot smoother using robust locally linear fits to capture the dependence of the log-ratios on overall log-spot intensities

label_protocol: cDNA probe pairs were prepared by amino-allyl reverse transcription using 2 μg of amplified RNA and labeling with Cy3-dCTP or Cy5-dCTP fluorescent dyes (Amersham Bioscience, Piscataway, NJ.)

extract_protocol: Whole male UGS (E14.5, E15.5, E16.5, E17.5, and E18.5) or separated prostate lobes (P7, P30, and P90) were dissected from C57BL6/J mice and snap frozen in liquid nitrogen. For each biological replication, we pooled 3 to 10 mice representing one or two litters. RNA from pools of UGS or specific prostate lobes (vp, ap, and dlp) was prepared using the Qiagen RNeasy Mini kit. We included an on-column DNaseI treatment to remove contaminating DNA. Before RNA amplification, we combined equal quantities of RNA from vp, ap, and dlp for the postnatal prostate samples. We amplified 1 ug of total RNA from each sample through one round using the Arcturus RiboAmp kit. For the E14.5 UGS reference sample, a second round of amplification was done to provide enough RNA for all microarrays.

tag: gender

value: male

value: separated prostate lobe (vp, ap, and dlp) pool

tag: arna

value: one round aRNA

source_name: E14.5 UGS reference

value: whole UGS pool

value: two round aRNA


title: P90_2_(5)

description: separated prostate lobes, postnatal day P90, pool 2 of 3

tag: strain

tag: tissue


title: P90_2_(3)

tag: developmental stage


title: IHP vs IRHP rep1_A195


title: IRLP vs ILP rep2_A279


title: IRLP vs ILP rep1_A277


title: ILP  vs IRLP rep2 dye swap_A280


title: P90_3_(3)

description: separated prostate lobes, postnatal day P90, pool 3 of 3


title: IRHP vs IHP rep1 dye swap_A289


title: IFNAR S.t.

status: Public on Dec 31 2009

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: IFNAR S.t.

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

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: Signal Intensities were calculated using RMA algorithm and for statistical analysis we applied GeneSpring GX 10 software suite (Agilent Technologies, Waldbronn, Germany).

source_name: Bone marrow

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

growth_protocol: with MCSF

extract_protocol: Qiagen RNAeasy

treatment_protocol: 6 hours with S.typhimurium MOI: 5

tag: genetic modification

value: IFNAR knockout

value: bone marrow

value: macrophages


title: IHP vs ILP rep1_LPHP1repA77F

value: ILP


title: P90_3_(5)


title: IFNAR L.m.

description: IFNAR L.m.

treatment_protocol: 6 hours with L.monocytogenes MOI: 5


title: MC VSV-AV2

description: MC VSV-AV2

growth_protocol: with IL-3

treatment_protocol: 6 hours with VSV-AV2 MOI: 2

value: mast cells


title: wt O cntr

description: wt O cntr

treatment_protocol: Untreated control


title: ILP  vs IRLP rep1 dye swap_A278

value: 16 DAP

value: seed


title: IFNAR O cntr

description: IFNAR O cntr


title: MC cntr

description: MC cntr


title: MC S.t.

description: MC S.t.

treatment_protocol: 6 hours with S.typhimurium MOI: 50


title: wt O L.m.

description: wt O L.m.


title: wt O S.t.

description: wt O S.t.


title: wt O VSV-AV2

description: wt O VSV-AV2


title: MC L.m.

description: MC L.m.

treatment_protocol: 6 hours with L.monocytogenes, MOI: 50


title: P90_1_(3)


title: E18_3_(5)

description: Whole male UGS embryonic day 17.5, pool 3 of 3


title: P7_1_(5)

description: separated prostate lobes, postnatal day P7, pool 1 of 3


title: P30_3_(3)

description: separated prostate lobes, postnatal day P30, pool 3 of 3


title: P30_2_(5)

description: separated prostate lobes, postnatal day P30, pool 2 of 3


title: P7_1_(3)


title: P30_2_(3)


title: P30_1_(5)

description: separated prostate lobes, postnatal day P30, pool 1 of 3


title: P7_3_(5)

description: separated prostate lobes, postnatal day P7, pool 3 of 3


title: E17_3_(5)

description: Whole male UGS embryonic day 16.5, pool 3 of 3


title: E17_1_(3)

description: Whole male UGS embryonic day 16.5, pool 1 of 3


title: P30_3_(5)


title: E17_2_(5)

description: Whole male UGS embryonic day 16.5, pool 2 of 3


title: E17_3_(3)


title: P7_2_(3)

description: separated prostate lobes, postnatal day P7, pool 2 of 3


title: E17_2_(3)


title: E17_1_(5)


title: E18_1_(3)

description: Whole male UGS embryonic day 17.5, pool 1 of 3


title: P7_2_(5)


title: E18_1_(5)


title: E18_3_(3)


title: E18_2_(5)

description: Whole male UGS embryonic day 17.5, pool 2 of 3


title: P30_1_(3)


title: E18_2_(3)


title: melanoma short-term culture M990802

description: hybridized to Affy SNP 6.0

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing:
Probe-level intensities were scaled so that the sample-specific median value is 1000.
For further data processing details, please see: The Cancer Genome Atlas Research Network (2008) Nature, 455:1061-1068.

source_name: melanoma short-term culture M990802

label_protocol: Standard Affymetrix protocol.

growth_protocol: melanoma cell lines and short-term cultures were grown as described in Lin et al, Cancer Research (2008), 68:664-673

extract_protocol: DNA was extracted from melanomas as described in Lin et al, Cancer Research (2008), 68:664-673. DNA from HapMap normal samples was obtained from Coriell cell repository

treatment_protocol: cells were grown under standard conditions

tag: disease status

value: melanoma

value: patient-derived short-term culture M990802


title: P7_3_(3)


title: melanoma short-term culture M000921

description: hybridized to Affy SNP 6.0

source_name: melanoma short-term culture M000921

value: patient-derived short-term culture M000921


title: E16_3_(5)

description: Whole male UGS embryonic day 15.5, pool 3 of 3


title: E16_3_(3)


title: E16_2_(5)

description: Whole male UGS embryonic day 15.5, pool 2 of 3


title: E15_1_(5)

description: Whole male UGS embryonic day 14.5, pool 1 of 3


title: E16_2_(3)


title: E15_1_(3)


title: E15_3_(5)

description: Whole male UGS embryonic day 14.5, pool 3 of 3


title: E16_1_(3)

description: Whole male UGS embryonic day 15.5, pool 1 of 3


title: E15_2_(5)

description: Whole male UGS embryonic day 14.5, pool 2 of 3


title: E16_1_(5)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 80)

status: Public on Jun 25 2009

city: Rochester

first: LIANG

last: WANG

state: MN

address: 200 FIRST ST SW

department: LAB MED PATH

institute: MAYO CLINIC

description: cell line from a patient with prostate cancer

scan_protocol: Illumina BeadArray reader

data_processing: We first transformed raw data generated from BeadStudio (Illumina, San Diego, CA) using a variance stabilization transformation algorithm and then normalized them using quantile normalization implemented in Bioconductor (www.bioconductor.org).

label_protocol: 500ng of total RNA was labled using Illumina human-6 V2 BeadChip standard protocol

growth_protocol: We then grew all transformed cell lines in RPMI 1640 media supplemented with 15% fetal bovine serum, and 1% penicillin/streptomycin at 37°C in humidified incubators in an atmosphere of 5% CO2. Experimental series were set up by seeding 5-ml cultures in T25 flasks. Each culture was fed with 5ml of fresh media twice a week until the cell number reached ~106 in a T75 flask. The cells were harvested and suspended in 500 l of RNAlater and stored at -80°C for further processing.

extract_protocol: We extracted total RNA from each cell culture using miRNeasy Mini Kit (QIAGEN) under the manufacturer’s guidelines. This protocol could effectively recover both mRNA and miRNA. The integrity of these total RNAs was assessed using an Agilent 2100 Bioanalyzer.

treatment_protocol: Natural grown cell lines without any treatment

tag: cell line

tag: pathological grade

value: high grade


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 83)

hyb_protocol: Illumina human-6 V2 BeadChip standard protocol


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 86)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 89)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 88)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 85)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 87)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 90)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 77)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 79)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 84)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 82)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 76)


title: Patient 12

status: Public on Nov 09 2009

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

description: Array CGH analysis of a female patient with pleomorphic/necrotic lobular intraepithelial neoplasia (LIN3).

hyb_protocol: Hybridization was done overnight at 42degC  in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned at 10 um resolution using an Agilent scanner. PMT settings: 100/100

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005).Background intensities were not subtracted. Signal intensities were normalized by subgridd LOWESS. Aberrations were defined by Circular Binary Segmentation in combination with log2 ratio threshold of 0.15 and -0.15, respectively.

label: Alexa Fluor 3

source_name: test - DNA isolated from laser captured microdissected formalin-fixed, paraffin-embedded tissue.

label_protocol: DNA was labelled by random priming according Invitrogens recommendation (Invitrogen BioPrime Total Genomic Labeling System).Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: Sections of formalin-fixed paraffin-embedded (FFPE) specimens cut at 7-8um were mounted on special foil-coated slides (Molecular Devices, San Diego, USA). The sections were then deparaffinized with Xylene, processed in decreasing concentrations of ethanol and stained with haematoxylin. Lasercapture microdissection for both lesions was performed at multiple sites using Veritas Arcturus. Cells were digested in 10ul TE, pH 9, and 0.5ul proteinase K (20mg/ml) for 48h at 55degC . After inactivation of proteinase K at 99degC  for 10min, the digest was stored at -20degC .  Without any further purification, the complete digest was used for whole genome amplification by means of the WGA (Whole Genome Amplification) kit from Sigma.

treatment_protocol: Whole genome amplification by GenomePlex (Sigma).

value: female

value: lobular intraepithelial neoplasia grade 3 (LIN3)

label: Alexa Fluor 5

source_name: reference - DNA pool isolated from laser captured microdissected formalin-fixed, paraffin-embedded healthy tissue.

value: mammary tissue without histomorphological changes obtained from reduction mammoplasty specimens


title: E15_3_(3)

value: male

value: one round aRNA


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 71)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 73)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 78)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 74)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 70)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 81)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 67)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 75)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 72)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 68)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 65)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 64)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 66)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 69)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 63)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 52)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 60)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 62)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 56)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 54)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 58)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 51)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 61)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 57)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 59)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 55)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 53)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 44)

value: low grade


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 47)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 49)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 46)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 43)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 48)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 41)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 50)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 40)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 37)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 38)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 39)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 42)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 35)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 34)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 36)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 27)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 33)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 28)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 29)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 32)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 30)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 25)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 26)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 23)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 31)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 22)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 21)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 24)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 17)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 18)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 19)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 20)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 15)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 88)

label_protocol: 250ng of total RNA was labled using Illumina HumanMI microRNA assay standard protocol


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 89)

hyb_protocol: HumanMI microRNA assay standard protocol


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 12)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 9)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 11)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 14)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 90)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 13)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 5)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 4)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 1)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 6)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 8)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 10)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 16)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 2)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 86)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 87)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 3)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 7)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 81)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 82)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 79)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 83)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 85)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 78)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 77)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 80)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 76)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 74)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 73)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 71)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 67)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 84)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 72)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 68)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 65)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 66)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 63)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 62)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 69)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 58)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 57)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 55)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 54)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 56)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 59)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 53)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 52)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 51)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 64)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 50)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 49)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 60)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 70)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 48)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 61)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 47)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 45)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 44)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 43)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 42)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 46)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 37)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 39)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 40)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 36)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 32)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 38)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 41)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 31)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 30)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 33)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 34)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 27)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 29)


title: EBV transformed lymphoblastoid cell line (mRNA, Sample 45)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 23)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 25)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 21)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 28)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 35)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 24)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 12)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 19)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 22)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 17)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 18)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 20)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 15)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 26)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 14)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 13)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 11)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 10)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 9)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 7)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 6)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 8)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 16)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 4)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 3)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 2)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 5)


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 1)


title: A1 hnRNP-siRNA versus control replicate 3

status: Public on Aug 20 2008

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description:
HeLa transfection set biological replicate 2 of 2. Technical replicate 1 of 1. A1 hnRNP-siRNA versus control comparsion.
12456631_A1med_ICO.gpr

hyb_protocol: Two biological replicate experiments (for A1, FUS and H) or three (for p68) were performed, each comparing siRNA versus control. For each biological replicate the pair of labelled samples was co-hybridized once on a single microarray. Thus, two A1 hnRNP, two FUS, two H hnRNP and three p68-CDX5 RNA interference versus control hybridizations were processed, totalling 9 array datasets.

scan_protocol: Fluorescent images were obtained using a Scanarray 5000 XL (GSI Lumonics, Kanata, ON, Canada) scanner -for A1 and FUS- or a Genetic Microsystems 418 (Affymetrix, Santa Clara, CA, USA) scanner -for H and p68- at different combinations of laser power and gain settings that allowed balancing of image intensities and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA, USA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization using 0.3 as the span parameter with reduced weights in control and poor quality spots, followed by scaling across chips. Target genes were considered as differentially expressed when above 95% rank of the B empirical Bayes statistic. All quantitative and statistical analyses were performed using using Limma package in the R. environment (Smyth 2004).

label_protocol: Twenty micrograms of total RNA were labelled using the indirect dye labelling method. The Atlas Glass Array labelling kit (Clontech, Beckton Dickinson) was used following the manufacturers instructions, except that the aminoallyl-dUTP incorporation reaction was performed for 2 hours using Superscript II reverse transcriptase (Invitrogen) in the presence of Rnasin Rnase inhibitor (Promega), and that crosslinking to NHS-Cyanine dye esters of Cy3 and Cy5 (Amersham) was carried for 3 hours. Glass microarrays holding 19200 features representing the whole genome of H. sapiens spotted in as single spots onto CMT-GAPS slides (Corning) by the microarray facility at University Health Network (Toronto, Canada) were preblocked in 1% BSA, 0.5% SDS 45 min. at 42ºC and hybridized to labelled samples in the presence of blocking agents (20 ug tRNA, 4 ug salmon sperm DNA and 20 ug poly-dA -1:1 60mer:40mer) in  DigEasyHyb (Roche) at 37ºC, for 16 hours. After hybridization they were washed in 1X SSC at room temperature, followed by 1X SSC, 0.1% SDS at 50ºC with a final rinse at room temperature in 0.1X SSC and dried by centrifugation 5 minutes at 1000 rpm.

growth_protocol: HeLa cells were cultured in DMEM medium supplemented with 10% FBS and penicillin (10.000U/ml) and streptomycin (10 mg/ml), at 37ºC and 5% CO2 and 100% humidity. For RNA interference experiments, approximately 8x10E6 HeLa cells were electroporated at 250 V and 960 uF with 15 ug of plasmid, obtaining approximately 90% transfection efficiency.

extract_protocol: RNA was extracted using standard total RNA extraction protocol (Nucleospin)

value: human HeLa

tag: transfection vector

value: A1 hnRNP-interfering RNAi in pSuper

source_name: pSuper

value: empty pSuper


title: FUS-siRNA versus control replicate 3

description:
HeLa transfection set biological replicate 2 of 2. Technical replicate 1 of 1. FUS-siRNA versus control comparsion.
12456063_FUS_medICO.gpr

source_name: pSuper-RNAi-FUS

value: FUS-interfering RNAi in pSuper


title: FUS-siRNA versus control replicate 2

description:
HeLa transfection set biological replicate 1 of 2. Technical replicate 1 of 1. FUS-siRNA versus control comparsion.
12455590_FUS_medICO.gpr


title: p68-DDX5-siRNA versus control replicate 2

description:
HeLa transfection set biological replicate 2 of 3. Technical replicate 1 of 1. p68-DDX5-siRNA versus control comparsion.
12455788p68-2Cy5VsC-2Cy3_med.gpr

value: p68-DDX5-interfering RNAi in pSuper


title: A1 hnRNP-siRNA versus control replicate 2

description:
HeLa transfection set biological replicate 1 of 2. Technical replicate 1 of 1. A1 hnRNP-siRNA versus control comparsion.
12456607_A1med_ICO.gpr


title: H hnRNP-siRNA versus control replicate 1

description:
HeLa transfection set biological replicate 1 of 2. Technical replicate 1 of 1. H hnRNP-siRNA versus control comparsion.
12455578H-3Cy5VsC-3Cy3_med.gpr

source_name: pSuper-RNAi-H

value: H-hnRNP-interfering RNAi in pSuper


title: p68-DDX5-siRNA versus control replicate 1

description:
HeLa transfection set biological replicate 1 of 3. Technical replicate 1 of 1. p68-DDX5-siRNA versus control comparsion.
12455490p68-3Cy5VsC-3Cy3_med.gpr

value: p68 DDX5-interfering RNAi in pSuper


title: p68-DDX5-siRNA versus control replicate 3

description:
HeLa transfection set biological replicate 3 of 3. Technical replicate 1 of 1. p68-DDX5-siRNA versus control comparsion.
12456017p68-1Cy5VsC-1Cy3_med.gpr


title: Gene expression profiles of HL-60 cells exposed to o-xylene (IC50) [sample 2]

status: Public on Aug 08 2008

city: Seoul

first: Sailendra

middle: Nath

last: Sarma

address: P.O. Box 131, Cheongryang

country: South Korea

institute: Korea Institute of Science and Technology

description: HL-60 cells were treated with 0.84 mM o-xylene for 3 h, and the RNA was subjected to microarray analysis.

hyb_protocol: Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). This was followed by the coupling of the Cy3 dye for the controls (DMSO) or Cy5 dye for the treated samples. Hybridization was performed in a hybridization oven at 62℃ for 12 h. After washing (2× SSC/0.1% SDS for 2 min at 58℃, 1× SSC for 2 min at RT and 0.2× SSC for 3 min at RT), the slide was dried by centrifugation at 800 rpm for 3 min at RT.

scan_protocol: Hybridization images on the slides were scanned by ScanArray Lite (PerkinElmer Life Sciences, USA). Scanned images were analyzed with GenePix 3.0 software (Axon Instruments, USA) to obtain gene expression ratios.

data_processing: The fluorescent intensity of each spot was calculated by local median background subtraction. The robust scatter-plot smoother LOWESS function was used to perform intensity dependent normalization for the gene expression. Scatter plot analysis was made by Microsoft Excel 2003. Significance Analysis of Microarray (SAM) was performed for the selection of the genes with significant gene expression changes (Tusher et al., 2001). Computing a p-value for each gene assessed the statistical significance of the differential expression of genes. To determine the p-value, a permutation procedure was used and for each permutation, two-sample t statistics were computed for each gene. Genes were considered differentially expressed when logarithmic gene expression ratios in three independent hybridizations were more than 1.5 or less than 0.66, i.e., 1.5-fold difference in expression level, and when the p-values were less than 5.

source_name: HL-60 cells treated with DMSO for 3 h

label_protocol: Gene expression analysis was conducted on the RNA samples using 35 K whole human genome microarray (Operon Biotechnologies, Inc. Germany). Triplicate analysis was performed for each chemical, simultaneously. Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). Cy3 dye for the controls (DMSO).

extract_protocol: Total RNA was extracted from the HL-60 cells treated to DMSO for 3 h using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).

value: human promyelocytic leukemia cells

tag: treatment

value: DMSO

tag: treatment time

value: 3 h

source_name: HL-60 cells treated with o-xylene (IC50) for 3 h

label_protocol: Gene expression analysis was conducted on the RNA samples using 35 K whole human genome microarray (Operon Biotechnologies, Inc. Germany). Triplicate analysis was performed for each chemical, simultaneously. Labeling and hybridization were performed by instruction of Platinum Biochip Reagent Kit (GenoCheck Co. Ltd., Korea). Cy5 dye for the treated samples.

extract_protocol: Total RNA was extracted from the HL-60 cells treated to IC50 dose of o-xylene for 3 h, using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).

tag: treament

value: o-xylene

tag: treament dose

tag: treament time

value: 3 hr


title: Gene expression profiles of HL-60 cells exposed to toluene (IC50) [sample 3]

description: HL-60 cells were treated with 2.74 mM toluene for 3 h, and the RNA was subjected to microarray analysis.

tag: cell type

source_name: HL-60 cells treated with toluene (IC50) for 3 h

extract_protocol: Total RNA was extracted from the HL-60 cells treated to IC50 dose of toluene for 3 h, using the Trizol reagent (Invitrogen, USA) and purified using RNeasy mini kit (Qiagen, USA) according to the manufacturer's instructions. Genomic DNA was removed using RNase-free DNase set (Qiagen, USA) during RNA purification. RNA quality were assessed with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, USA) (260/280 nm ratios) and only samples with an A260/A280 ratio between 1.9 and 2.2 were considered for suitable use. The RNA quality was checked with the Experion automated electrophoresis station (Bio-Rad Laboratories, USA) (28S/18S ratio).

value: toluene


title: Gene expression profiles of HL-60 cells exposed to o-xylene (IC50) [sample 3]


title: Gene expression profiles of HL-60 cells exposed to toluene (IC50) [sample 2]


title: H hnRNP-siRNA versus control replicate 3

description:
HeLa transfection set biological replicate 2 of 2. Technical replicate 1 of 1. H hnRNP-siRNA versus control comparsion.
12456671H-2Cy5VsC-2Cy3_sat_comp.gpr

value: H hnRNP-interfering RNAi in pSuper


title: Gene expression profiles of HL-60 cells exposed to o-xylene (IC50) [sample 1]


title: Gene expression profiles of HL-60 cells exposed to toluene (IC50) [sample 1]


title: EBV transformed lymphoblastoid cell line (microRNA, Sample 75)

value: high grade