title: 3 dpi, Infected Tassel, Rep 7 (Cy5)

city: Stanford

first: John

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

description: 9 dpi, Infected Tassel compared to 3 dpi, Infected Tassel

hyb_protocol: 750 ng of each labeled target cRNA were hybridized for 17 h at 60C.

scan_protocol: Slides were scanned on an Agilent G2565AA microarray scanner as indicated in the manual.  Images were processed with the Agilent Feature Extraction software (Version 9.5.1.1)

data_processing: After removal of spots flagged by Feature Extraction as below background or saturated or outliers, dye normalized values for each channel from Feature Extraction were normalized again to the median array intensity.  Average intensities were then calculated for probes with at least 3 of 4 good intensities.

organism:
Zea mays
Mycosarcoma maydis

label_protocol: Total RNA (500 ng) was amplified & labeled with Cy3 or Cy5 using Agilent Low RNA Input Fluorescent Linear Amplification Kit.

growth_protocol: Plants were grown in multiple plantings in a greenhouse equipped with lights providing 50% of summer noon solar fluence (16-h light/8-h dark) at Stanford CA; infected and dissected  greenhouse; tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA was extracted from 30 - 60 mg of frozen tissues with Qiagen RNeasy Mini kit, digested with DNase I, and cleaned up with RNeasy columns.

treatment_protocol: Needle infections of 8-day seedlings were performed  by injecting approximately 300 L of previously of U. maydis cell suspension into the base of the seedling.   Adult leaves and tassels were infected by injecting 300 L of U. maydis cell suspension with a 26G hypodermic needle through the whorl of leaves and into the tassel primordium (to allow infection of meristematic tissue) of maize plants approximately 35 days post-sowing.

tag: time

value: 3 dpi

tag: infection

value: infected

value: Tassel


title: 9 dpi, Mock-injected Adult leaf, Rep 3 (Cy5)

status: Public on Apr 01 2010

type: RNA

middle: F

state: CA

country: USA

description: 9 dpi, Infected Adult leaf compared to 9 dpi, Mock-injected Adult leaf

molecule: total RNA

value: 9 dpi

value: Mock-injected

tag: tissue

value: Adult leaf


title: 9 dpi, Infected Tassel, Rep 2 (Cy5)

description: 9 dpi, Mock-injected Tassel compared to 9 dpi, Infected Tassel


title: 9 dpi, Mock-injected Tassel, Rep 3 (Cy5)

description: 9 dpi, Infected Tassel compared to 9 dpi, Mock-injected Tassel


title: 3 dpi, Infected Tassel, Rep 3 (Cy5)

description: 3 dpi, Infected Adult leaf compared to 3 dpi, Infected Tassel


title: 1 dpi, Infected Seedling, Rep 4 (Cy5)

description: 3 dpi, Infected Seedling compared to 1 dpi, Infected Seedling

value: 1 dpi

value: Seedling


title: 3 dpi, Mock-injected Adult leaf, Rep 3 (Cy5)

description: 3 dpi, Infected Adult leaf compared to 3 dpi, Mock-injected Adult leaf


title: 1 dpi, Mock-injected Seedling, Rep 3 (Cy5)

description: 1 dpi, Infected Seedling compared to 1 dpi, Mock-injected Seedling


title: 9 dpi, Infected Tassel, Rep 4 (Cy5)

description: 3 dpi, Infected Tassel compared to 9 dpi, Infected Tassel


title: 3 dpi, Mock-injected Tassel, Rep 3 (Cy5)

description: 3 dpi, Infected Tassel compared to 3 dpi, Mock-injected Tassel


title: 3 dpi, Infected Seedling, Rep 3 (Cy5)

description: 3 dpi, Infected Adult leaf compared to 3 dpi, Infected Seedling


title: 3 dpi, Infected Seedling, Rep I (Cy5)

description: 3 dpi, Infected Tassel compared to 3 dpi, Infected Seedling


title: 9 dpi, Infected Adult leaf, Rep 4 (Cy5)

description: 3 dpi, Infected Adult leaf compared to 9 dpi, Infected Adult leaf


title: 9 dpi, Infected Adult leaf, Rep 2 (Cy5)

description: 9 dpi, Mock-injected Adult leaf compared to 9 dpi, Infected Adult leaf


title: 3 dpi, Infected Adult leaf, Rep 1 (Cy5)

description: 3 dpi, Infected Tassel compared to 3 dpi, Infected Adult leaf


title: 3 dpi, Infected Tassel, Rep 1 (Cy5)

description: 3 dpi, Infected Seedling compared to 3 dpi, Infected Tassel


title: 3 dpi, Infected Seedling, Rep 2 (Cy5)

description: 3 dpi, Mock-injected Seedling compared to 3 dpi, Infected Seedling


title: Differentiated primary culture of human airway epithelia, biological replicate 16

status: Public on Apr 15 2010

city: Iowa City

first: Bartley

middle: Joseph

last: Brown

state: IA

institute: The University of Iowa

description: Gene expression data from airway epithelia

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix HsAirway array. The arrays were washed and stained using the Affymetrix Model 450 Fluidics Station.

scan_protocol: The arrays were scanned using the Affymetrix Model 3000 scanner

data_processing: Raw data .cel files were imported into Partek Genomics Suite v 6.4 and normalized using the RMA algorithm.

label: Biotin

organism: Homo sapiens

source_name: Differentiated primary culture of human airway epithelia, air-liquid interface,trachea

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

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen)

tag: condition

value: In vitro

tag: surface

value: Air-liquid interface

tag: localization

value: Trachea

tag: sample date


title: 3 dpi, Infected Adult leaf, Rep 2 (Cy5)

description: 3 dpi, Mock-injected Adult leaf compared to 3 dpi, Infected Adult leaf


title: 3 dpi, Infected Tassel, Rep 2 (Cy5)

description: 3 dpi, Mock-injected Tassel compared to 3 dpi, Infected Tassel


title: 3 dpi, Infected Adult leaf, Rep 4 (Cy5)

description: 9 dpi, Infected Adult leaf compared to 3 dpi, Infected Adult leaf


title: 3 dpi, Infected Seedling, Rep 4 (Cy5)

description: 1 dpi, Infected Seedling compared to 3 dpi, Infected Seedling


title: 3 dpi, Mock-injected Seedling, Rep 3 (Cy5)

description: 3 dpi, Infected Seedling compared to 3 dpi, Mock-injected Seedling


title: 3 dpi, Infected Tassel, Rep 2 (Cy3)


title: 3 dpi, Infected Seedling, Rep 2 (Cy3)


title: 1 dpi, Infected Seedling, Rep 2 (Cy5)

description: 1 dpi, Mock-injected Seedling compared to 1 dpi, Infected Seedling


title: Differentiated primary culture of human airway epithelia, biological replicate 4

source_name: Differentiated primary culture of human airway epithelia, air-liquid interface,bronchus

value: Bronchus


title: 3 dpi, Infected Seedling, Rep 4 (Cy3)

description: 3 dpi, Infected Seedling compared to 3 dpi, Infected Adult leaf


title: 3 dpi, Infected Adult leaf, Rep 4 (Cy3)


title: 3 dpi, Infected Adult leaf, Rep 3 (Cy5)


title: 1 dpi, Infected Seedling, Rep 3 (Cy3)


title: 3 dpi, Infected Adult leaf, Rep 2 (Cy3)

description: 3 dpi, Infected Adult leaf compared to 3 dpi, Infected Tassel


title: 9 dpi, Infected Adult leaf, Rep 3 (Cy3)


title: 3 dpi, Infected Tassel, Rep 7 (Cy3)


title: 9 dpi, Infected Tassel, Rep 3 (Cy3)

description: 9 dpi, Infected Tassel compared to 3 dpi, Infected Tassel


title: 3 dpi, Infected Tassel, Rep 3 (Cy3)

description: 3 dpi, Infected Tassel compared to 9 dpi, Infected Tassel


title: 3 dpi, Infected Adult leaf, Rep 3 (Cy3)


title: 9 dpi, Mock-injected Adult leaf, Rep 1 (Cy3)


title: 3 dpi, Infected Seedling, Rep 3 (Cy3)

description: 3 dpi, Infected Seedling compared to 1 dpi, Infected Seedling


title: 3 dpi, Infected Tassel, Rep 1 (Cy3)

description: 3 dpi, Infected Tassel compared to 3 dpi, Mock-injected Tassel


title: 3 dpi, Mock-injected Seedling, Rep 1 (Cy3)


title: 3 dpi, Infected Seedling, Rep 1 (Cy3)


title: 3 dpi, Mock-injected Tassel, Rep 1 (Cy3)


title: 9 dpi, Infected Tassel, Rep 1 (Cy3)

description: 9 dpi, Infected Tassel compared to 9 dpi, Mock-injected Tassel


title: 9 dpi, Infected Adult leaf, Rep 1 (Cy3)

description: 9 dpi, Infected Adult leaf compared to 9 dpi, Mock-injected Adult leaf


title: 3 dpi, Infected Adult leaf, Rep 1 (Cy3)

description: 3 dpi, Infected Adult leaf compared to 3 dpi, Mock-injected Adult leaf


title: 3 dpi, Mock-injected Adult leaf, Rep 1 (Cy3)


title: 1 dpi, Infected Seedling, Rep 1 (Cy3)

description: 1 dpi, Infected Seedling compared to 1 dpi, Mock-injected Seedling


title: 9 dpi, Mock-injected Tassel, Rep 1 (Cy3)

description: 9 dpi, Mock-injected Tassel compared to 9 dpi, Infected Tassel


title: 1 dpi, Mock-injected Seedling, Rep 1 (Cy3)

description: culture-grown Ustilago maydis compared to 1 dpi, Infected Seedling

organism: Mycosarcoma maydis

tag: growth protocol

value: culture-grown


title: PTC1 with SDS and AFB1 rep3

city: Tukuba

first: Tadahiro

last: Suzuki

state: Ibaraki

address: kan-nondai 2-1-12

department: Applied Microbiology Division

country: Japan

institute: National Food Rsearch Institute

description:
S. cerevisiae PTC1 mutant strain grown in YPD with chemicals
Gene expression data from yeast

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: CEL file MAS5 normalized

label: biotin

organism: Saccharomyces cerevisiae

source_name: PTC1 with SDS and AFB1

label_protocol: Approximately 4 µg of total RNA was processed to produce biotinylated cRNA targets using Affymetrix One-Cycle Target prep protocol.

growth_protocol: Parental 4743 (BY4743; MATa/α his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 lys2Δ0) and that derivative ptc1 (PTC1 (YDL006w) knock-out strain) were grown in YPD medium at 25C for 2 days.

extract_protocol: Each sample of total RNA was extracted using FastRNA Pro Red kit (MP Biomedicals, US) according to the manufacturer’s instructions.

treatment_protocol: Both strains were grown in YPD medium including 0.01% SDS or 0.01% SDS with 25 ppm Aflatoxin B1.

tag: genetic background

tag: genotype

value: PTC1 KO


title: PTC1 with SDS and AFB1 rep2


title: FSL Hippocampus Cohort 2, biological rep6

city: Stevenage

first: Adam

last: Taylor

address: Medicine Research Center

country: United Kingdom

institute: GalxoSmithKline

description: Gene expression data from Hippocampus of Flinders Depression Sensitive line (FRL) rats

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data was analysed with Rosetta Resolver version 5.0

organism: Rattus norvegicus

source_name: Hippocampus from Flinders Depression Sensitive Line (FSL) rats

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

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

tag: strain

value: FSL

tag: brain region

value: Hippocampus

tag: cohort

value: Cohort 2


title: FSL Hippocampus Cohort 1, biological rep9

value: Cohort 1


title: FSL Hippocampus Cohort 2, biological rep3


title: FSL Hippocampus Cohort 2, biological rep2


title: FSL Hippocampus Cohort 2, biological rep4


title: FSL Hippocampus Cohort 2, biological rep5


title: FSL Hippocampus Cohort 2, biological rep8


title: FSL Hippocampus Cohort 2, biological rep7


title: FSL Hippocampus Cohort 1, biological rep4


title: FSL Hippocampus Cohort 2, biological rep1


title: FSL Hippocampus Cohort 1, biological rep3


title: FSL Hippocampus Cohort 1, biological rep6


title: FSL Hippocampus Cohort 1, biological rep5


title: FSL Hippocampus Cohort 1, biological rep7


title: PTC1 with SDS rep2

source_name: PTC1 with SDS

treatment_protocol: Both strains were grown in YPD medium including 0.01% SDS.


title: PTC1 with SDS and AFB1 rep1


title: FSL Hippocampus Cohort 1, biological rep1


title: FRL Hippocampus Cohort 2, biological rep10

description: Gene expression data from Hippocampus of Flinders Depression Resistant line (FRL) rats

source_name: Hippocampus from Flinders Depression Resistent Line (FRL) rats

value: FRL


title: FRL Hippocampus Cohort 2, biological rep9


title: PTC1 with SDS rep1


title: FRL Hippocampus Cohort 2, biological rep5


title: FSL Hippocampus Cohort 1, biological rep2


title: FRL Hippocampus Cohort 2, biological rep8


title: FRL Hippocampus Cohort 2, biological rep7


title: FRL Hippocampus Cohort 2, biological rep6


title: FRL Hippocampus Cohort 2, biological rep4


title: FSL Hippocampus Cohort 1, biological rep8


title: Armigeres_pahangi_v_malayi_2-3d_rep3

city: Madison

first: Bruce

middle: M

last: Christensen

state: WI

address: 1656 Linden Drive

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

description: Analysis used mosquitoes exposed to B. malayi-infected bloodmeals at 2-3d PI as control samples for comparison with experimental samples taken at the same time.

hyb_protocol: Purified, dye-coupled cDNA was measured at 260 nm (Cy5 @ 650 nm and Cy3 @ 550 nm) to calculate yield.  Probes (10 pmol/dye/slide) were dried down using a speedvac, resuspended at room temperature in 45 μl Pronto!TM hybridization buffer, incubated at 95˚C for 5 minutes, and applied to the arrays.  Arrays were hybridized overnight at 42˚C and washed following manufacturer’s specifications.

scan_protocol: Microarrays were scanned with an Axon GenePix 4000B (Molecular Devices, Foster City, CA) scanner and software using a 10 μm pixel size.  Laser power was set at 100%, and the photomultiplier tube (PMT) was adjusted automatically to maximize the effective dynamic range and to minimize pixel saturation.  Spot, size, location, and quality were determined using GenePix Pro 6.1.

data_processing: Signal intensities were normalized using GeneSpring GX 7.3.1 software.  All slides were normalized using a global linear regression (Lowess) curve fit to the log-intensity vs. log-ratio plot, and 20% of the data were 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 ten, then ten was used instead.  All data were averaged for replicate spots upon a slide, and then further averaged across slides.  Minimum and maximum values were recorded and t-test p-values generated for all replicate sets.  Genes showing differential expression over controls were isolated using volcano plots at a 95% confidence interval over 2-fold values.  Tests were parametric, but all variances were considered equal.

organism: Armigeres subalbatus

source_name: whole mosquito 2-3d following exposure to a B. pahangi-infected bloodmeal

label_protocol: cDNA synthesis was done according to the Pronto!TM Plus Indirect Labeling System with modification (use of an anchored oligo(dT) primer) (TM261, Promega).  Priming with anchored oligo(dT) directed the start of synthesis from the 5’ end of the poly-A tail.  Twenty μg of total RNA were used as a template for the synthesis of amino allyl-modified cDNA.  Purified cDNA from each synthesis reaction was coupled to Cy3 or Cy5 according to manufacturers’ instructions.  The CyDye probes were purified using the ChipShotTM Membrane Clean-Up system (TM261, Promega).

extract_protocol: RNA was collected for all microarray analyses from whole female Ar. subalbatus. RNA was extracted from collected mosquitoes via the single-step acid guanidinium thiocynate-phenol-chloroform extraction method.  RNA then was purified using the Promega SV Total RNA Isolation System, which includes a DNase treatment step performed directly on the column membrane to reduce genomic DNA contamination.  RNA was eluted from the column, dried using a speedvac, re-suspended, and measured at 260 nm to determine RNA concentration of each sample.

value: whole body

tag: gender

value: female

tag: parasite infection

value: Brugia pahangi

tag: infection time

tag: parasite developmental stage

source_name: whole mosquito 2-3d following exposure to a B. malayi-infected bloodmeal

value: Brugia malayi

value: melanized microfilariae

tag: sample type

value: control


title: Armigeres_pahangi_v_malayi_2-3d_rep3_dyeswap


title: FRL Hippocampus Cohort 1, biological rep12


title: Armigeres_pahangi_v_malayi_2-3d_rep1_dyeswap


title: Armigeres_pahangi_v_malayi_2-3d_rep2_dyeswap


title: FRL Hippocampus Cohort 1, biological rep9


title: Armigeres_pahangi_v_malayi_2-3d_rep2


title: FRL Hippocampus Cohort 1, biological rep11


title: FRL Hippocampus Cohort 2, biological rep2


title: FRL Hippocampus Cohort 1, biological rep8


title: Armigeres_pahangi_v_malayi_24h_rep3

description: Analysis used mosquitoes exposed to B. malayi-infected bloodmeals at 24h PI as control samples for comparison with experimental samples taken at the same time.

source_name: whole mosquito 24h following exposure to a B. pahangi-infected bloodmeal

source_name: whole mosquito 24h following exposure to a B. malayi-infected bloodmeal


title: FRL Hippocampus Cohort 2, biological rep1


title: Armigeres_pahangi_v_malayi_2-3d_rep1


title: Armigeres_pahangi_v_malayi_24h_rep3_dyeswap


title: FRL Hippocampus Cohort 1, biological rep5


title: FRL Hippocampus Cohort 1, biological rep7


title: FSL Frontal Cortex Cohort 2, biological rep6

description: Gene expression data from Frontal Cortex of Flinders Depression Sensitive line (FSL) rats

source_name: Frontal cortex from Flinders Depression Sensitive Line (FRL) rats

value: Frontal Cortex


title: FRL Hippocampus Cohort 1, biological rep6


title: Armigeres_pahangi_v_malayi_24h_rep2b


title: FRL Hippocampus Cohort 1, biological rep4


title: FSL Frontal Cortex Cohort 2, biological rep8


title: FRL Hippocampus Cohort 1, biological rep10


title: FRL Hippocampus Cohort 1, biological rep3


title: FRL Hippocampus Cohort 1, biological rep1


title: Armigeres_pahangi_v_malayi_24h_rep1_dyeswap


title: Armigeres_pahangi_v_malayi_24h_rep2


title: FRL Hippocampus Cohort 1, biological rep2


title: FSL Frontal Cortex Cohort 2, biological rep7


title: FSL Frontal Cortex Cohort 2, biological rep5


title: FSL Frontal Cortex Cohort 2, biological rep4


title: Armigeres_pahangi_v_malayi_12h_rep3_dyeswap

description: Analysis used mosquitoes exposed to B. malayi-infected bloodmeals at 12h PI as control samples for comparison with experimental samples taken at the same time.

source_name: whole mosquito 12h following exposure to a B. pahangi-infected bloodmeal

value: microfilariae

source_name: whole mosquito 12h following exposure to a B. malayi-infected bloodmeal


title: PTC1 with SDS rep3


title: FSL Frontal Cortex Cohort 1, biological rep9


title: FSL Frontal Cortex Cohort 2, biological rep3


title: FSL Frontal Cortex Cohort 1, biological rep6


title: FSL Frontal Cortex Cohort 1, biological rep8


title: FSL Frontal Cortex Cohort 2, biological rep2


title: Armigeres_pahangi_v_malayi_12h_rep2_dyeswap


title: Armigeres_pahangi_v_malayi_12h_rep2


title: Armigeres_pahangi_v_malayi_24h_rep1


title: Armigeres_pahangi_v_malayi_12h_rep1_dyeswap


title: Armigeres_pahangi_v_malayi_12h_rep3


title: FSL Frontal Cortex Cohort 1, biological rep4


title: Armigeres_pahangi_v_malayi_12h_rep1


title: FSL Frontal Cortex Cohort 1, biological rep3


title: FSL Frontal Cortex Cohort 1, biological rep2


title: FSL Frontal Cortex Cohort 1, biological rep5


title: FRL Frontal Cortex Cohort 2, biological rep10

description: Gene expression data from Frontal Cortex of Flinders Depression Resistant line (FRL) rats

source_name: Frontal cortex from Flinders Depression Resistent Line (FRL) rats


title: FRL Hippocampus Cohort 2, biological rep3


title: FSL Frontal Cortex Cohort 1, biological rep7


title: FRL Frontal Cortex Cohort 2, biological rep9


title: FSL Frontal Cortex Cohort 1, biological rep1


title: FSL Frontal Cortex Cohort 2, biological rep1


title: FRL Frontal Cortex Cohort 2, biological rep8


title: FRL Frontal Cortex Cohort 2, biological rep4


title: Armigeres_pahangi_v_malayi_6h_rep3

description: Analysis used mosquitoes exposed to B. malayi-infected bloodmeals at 6h PI as control samples for comparison with experimental samples taken at the same time.

source_name: whole mosquito 6h following exposure to a B. pahangi-infected bloodmeal

source_name: whole mosquito 6h following exposure to a B. malayi-infected bloodmeal


title: Armigeres_pahangi_v_malayi_6h_rep3_dyeswap


title: FRL Frontal Cortex Cohort 2, biological rep6


title: Armigeres_pahangi_v_malayi_6h_rep2_dyeswap


title: Armigeres_pahangi_v_malayi_6h_rep2


title: FRL Frontal Cortex Cohort 2, biological rep3


title: FRL Frontal Cortex Cohort 2, biological rep7


title: FRL Frontal Cortex Cohort 2, biological rep2


title: FRL Frontal Cortex Cohort 1, biological rep12


title: Armigeres_pahangi_v_malayi_6h_rep1_dyeswap


title: FRL Frontal Cortex Cohort 2, biological rep5


title: FRL Frontal Cortex Cohort 1, biological rep11


title: FRL Frontal Cortex Cohort 1, biological rep7


title: FRL Frontal Cortex Cohort 2, biological rep1


title: FRL Frontal Cortex Cohort 1, biological rep5


title: Armigeres_pahangi_v_malayi_1h_rep3_dyeswap

description: Analysis used mosquitoes exposed to B. malayi-infected bloodmeals at 1h PI as control samples for comparison with experimental samples taken at the same time.

source_name: whole mosquito 1h following exposure to a B. pahangi-infected bloodmeal

source_name: whole mosquito 1h following exposure to a B. malayi-infected bloodmeal


title: FRL Frontal Cortex Cohort 1, biological rep9


title: FRL Frontal Cortex Cohort 1, biological rep8


title: Armigeres_pahangi_v_malayi_6h_rep1


title: Armigeres_pahangi_v_malayi_1h_rep2


title: Armigeres_pahangi_v_malayi_1h_rep1


title: Armigeres_pahangi_v_malayi_1h_rep1_dyeswap


title: Armigeres_pahangi_v_malayi_1h_rep3


title: Armigeres_pahangi_v_malayi_1h_rep2_dyeswap


title: FRL Frontal Cortex Cohort 1, biological rep3


title: FRL Frontal Cortex Cohort 1, biological rep10


title: Armigeres_pahangi_13-14d_rep3

description: Analysis used mosquitoes exposed to uninfected bloodmeals at 13-14d PI as control samples for comparison with experimental samples taken at the same time.

source_name: whole mosquito 13-14d following exposure to a B. pahangi-infected bloodmeal

source_name: whole mosquito 13-14d following exposure to an uninfected bloodmeal

value: uninfected

tag: time


title: Armigeres_pahangi_13-14d_rep2_dyeswap

tag: tissue


title: Armigeres_pahangi_13-14d_rep1


title: Armigeres_pahangi_13-14d_rep3_dyeswap


title: Armigeres_pahangi_8-9d_rep3

description: Analysis used mosquitoes exposed to uninfected bloodmeals at 8-9d PI as control samples for comparison with experimental samples taken at the same time.

source_name: whole mosquito 8-9d following exposure to a B. pahangi-infected bloodmeal

source_name: whole mosquito 8-9d following exposure to an uninfected bloodmeal


title: Armigeres_pahangi_8-9d_rep3_dyeswap


title: FRL Frontal Cortex Cohort 1, biological rep6


title: Armigeres_pahangi_13-14d_rep2


title: Armigeres_pahangi_8-9d_rep2


title: Armigeres_pahangi_13-14d_rep1_dyeswap


title: Armigeres_pahangi_8-9d_rep2_dyeswap


title: Armigeres_pahangi_8-9d_rep1


title: Armigeres_pahangi_5-6d_rep3

description: Analysis used mosquitoes exposed to uninfected bloodmeals at 5-6d PI as control samples for comparison with experimental samples taken at the same time.

source_name: whole mosquito 5-6d following exposure to a B. pahangi-infected bloodmeal

source_name: whole mosquito 5-6d following exposure to an uninfected bloodmeal


title: FRL Frontal Cortex Cohort 1, biological rep2


title: FRL Frontal Cortex Cohort 1, biological rep1


title: Armigeres_pahangi_5-6d_rep2_dyeswap


title: Armigeres_pahangi_2-3d_rep2

description: Analysis used mosquitoes exposed to uninfected bloodmeals at 2-3d PI as control samples for comparison with experimental samples taken at the same time.

source_name: whole mosquito 2-3d following exposure to a B. pahangi-infected bloodmeal

source_name: whole mosquito 2-3d following exposure to an uninfected bloodmeal


title: Armigeres_pahangi_5-6d_rep1


title: FRL Frontal Cortex Cohort 1, biological rep4


title: Armigeres_pahangi_8-9d_rep1_dyeswap


title: Armigeres_pahangi_24h_rep3

description: Analysis used mosquitoes exposed to uninfected bloodmeals at 24h PI as control samples for comparison with experimental samples taken at the same time.

source_name: whole mosquito 24h following exposure to a B. pahangi-infected bloodmeal

source_name: whole mosquito 24h following exposure to an uninfected bloodmeal


title: Armigeres_pahangi_2-3d_rep1


title: Armigeres_pahangi_2-3d_rep3_dyeswap


title: Armigeres_pahangi_24h_rep3_dyeswap


title: Armigeres_pahangi_5-6d_rep2


title: Armigeres_pahangi_5-6d_rep1_dyeswap


title: Armigeres_pahangi_2-3d_rep3


title: Armigeres_pahangi_5-6d_rep3_dyeswap


title: Armigeres_pahangi_24h_rep1


title: Armigeres_pahangi_2-3d_rep1_dyeswap


title: Armigeres_pahangi_24h_rep2_dyeswap


title: Armigeres_pahangi_12h_rep3

description: Analysis used mosquitoes exposed to uninfected bloodmeals at 12h PI as control samples for comparison with experimental samples taken at the same time.

source_name: whole mosquito 12h following exposure to a B. pahangi-infected bloodmeal

source_name: whole mosquito 12h following exposure to an uninfected bloodmeal


title: Armigeres_pahangi_12h_rep1_dyeswap


title: Armigeres_pahangi_12h_rep2


title: Armigeres_pahangi_2-3d_rep2_dyeswap


title: Armigeres_pahangi_12h_rep1


title: Armigeres_pahangi_12h_rep3_dyeswap


title: Armigeres_pahangi_6h_rep1_dyeswap

description: Analysis used mosquitoes exposed to uninfected bloodmeals at 6h PI as control samples for comparison with experimental samples taken at the same time.

source_name: whole mosquito 6h following exposure to an uninfected bloodmeal


title: Armigeres_pahangi_3h_rep3_dyeswap

description: Analysis used mosquitoes exposed to uninfected bloodmeals at 3h PI as control samples for comparison with experimental samples taken at the same time.

source_name: whole mosquito 3h following exposure to a B. pahangi-infected bloodmeal

source_name: whole mosquito 3h following exposure to an uninfected bloodmeal


title: Armigeres_pahangi_12h_rep2_dyeswap


title: Armigeres_pahangi_3h_rep3


title: Armigeres_pahangi_6h_rep2

source_name: whole mosquito 6h following exposure to a B. pahangi-infected bloodmeal


title: Armigeres_pahangi_3h_rep1_dyeswap


title: Armigeres_pahangi_6h_rep3


title: Armigeres_pahangi_24h_rep2


title: Armigeres_pahangi_3h_rep2_dyeswap


title: Armigeres_pahangi_6h_rep2_dyeswap


title: Armigeres_pahangi_3h_rep2


title: Armigeres_pahangi_6h_rep3_dyeswap


title: Armigeres_pahangi_1h_rep3_dyeswap

description: Analysis used mosquitoes exposed to uninfected bloodmeals at 1h PI as control samples for comparison with experimental samples taken at the same time.

source_name: whole mosquito 1h following exposure to a B. pahangi-infected bloodmeal

source_name: whole mosquito 1h following exposure to an uninfected bloodmeal


title: Armigeres_pahangi_6h_rep1


title: Armigeres_pahangi_1h_rep2_dyeswap


title: Armigeres_pahangi_3h_rep1


title: Armigeres_pahangi_1h_rep1_dyeswap


title: Armigeres_pahangi_1h_rep2


title: Armigeres_pahangi_1h_rep3


title: 36 h infected vs. uninfected

status: Public on Mar 31 2010

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description: 36hrs post infection of Neuro2 cells

hyb_protocol: 750ng of each Cyanine-3 and Cyanine-5 labeled cRNA were combined with 50μl of 10x Blocking agent. The volume is made upto 240 ul using Nuclease free water. 10μl of 25x Fragmentation buffer (Agilent) were added and incubated at 60°C for 30 minutes in dark. The fragmented cRNA were mixed with 250μl of 2x Hybridization Buffer (Agilent). About 490μl of the resulting mixture was applied to the 22k Gene Expression Microarray (Agilent Technologies), and hybridized at 65°C for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer-I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer-II at 37ºC. Slides were finally rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Scanned on an Agilent G2505B scanner and Images were quantified using Agilent Feature Extraction Software (version  9.5.1.1)

data_processing: Normalization of the data was done using Per spot per chip intensity dependant lowess normalization. Further quality control of normalized data was done using correlation based condition tree to eliminate bad experiments. One fold and above differentially regulated genes were filtered from the data. Ontology based biological analysis was done using Gene Ontology browser in GeneSpring Gx. Further, pathways that were significantly regulated was done using bio script library in GeneSpring Gx

organism: Mus musculus

source_name: Mouse Neuroblastoma Cells

label_protocol: Low RNA Input Linear Amplification Kit (Agilent, Santa Clara, CA) was used for labeling. Briefly, both first and second strand cDNA were synthesized by incubating 500ng of total RNA with 1.2μl of oligo dT-T7 Promoter Primer in nuclease-free water at 65ºC for 10 min followed by incubation with 4.0μl of 5× First strand buffer, 2μl of 0.1M DTT, 1 μl of 10mM dNTP mix, 1μl of 200 U/μl MMLV RT, and 0.5μl of 40U/μl RNaseOUT, at 40ºC for 2 hour. Immediately following cDNA synthesis, the reaction mixture was incubated with 2.4 μl of 10 mM Cyanine-3 CTP or 2.4 μl of 10 mM Cyanine-5 CTP (Perkin-Elmer, Boston, MA), 20μl of 4X Transcription buffer, 8 μl of NTP mixture, 6 μl of 0.1M DTT, 0.5 μl of RNaseOUT, 0.6μl of Inorganic pyrophosphatase, 0.8 μl of T7 RNA polymerase, and 15.3μl of nuclease-free water at 40 ºC for 2 hour. Qiagen’s RNeasy mini spin columns were used for purifying amplified aRNA samples. The quantity and specific activity of cRNA was determined by using NanoDrop ND-1000 UV-VIS Spectrophotometer version3.2.1. Samples with specific activity >8 were used for hybridization.

growth_protocol: Neuro2a cells were grown in DMEM (Sigma) and infected with 1 m.o.i. of Japanese encephalitis virus

extract_protocol: Total cellular RNA was extracted using RNEasy protect kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Neuro2a cells were infected with 1m.o.i. of JE virus and at time intervals of 24hrs, 36hrs and 48hrs post infection the total cellular RNA were extracted

tag: time point

value: 36 hrs

tag: infection

value: Japanese encephalitis virus

tag: cell lilne

tag: tag


title: Armigeres_pahangi_24h_rep1_dyeswap


title: Armigeres_pahangi_1h_rep1


title: 24 h infected vs. uninfected

description: 24hrs post infection of Neuro2a cells

value: 24 hrs


title: 48 h infected vs. uninfected

description: 48hrs post infection of Neduro2a cells

value: 48 hrs


title: Low iron replicate 3

status: Public on Mar 22 2010

city: Clayton

first: Miranda

last: Lo

address: Wellington Road

country: Australia

institute: Monash University

description: Biological replicate 3 of 3. Comparison of transcription patterns in wild-type grown under low iron versus growth under normal iron conditions in EMJH.

hyb_protocol: The microarray was prehybridized for 45 min at 50°C using a solution containing formamide-based hybridization buffer (vial 7 from the 3DNA Array 900MPX kit) and 1 mg/ml sheared herring sperm DNA according to the recommendations of the manufacturer.  Hybridization with the cDNA hybridization mix was performed at 50°C and the 3DNA hybridization mix at 50°C for 4 h was performed following 3DNA Array 900MPX detection kit (Genisphere) protocol. The vial 7 buffer was used in both hybridization mixes. Slides were washed in ultrapure water and dried by centrifugation at 1,000 xg for 3 min prior to scanning.

scan_protocol: Scanned on GMS model 418 microarray scanner (Genetic Microsystems). The spot intensities were quantitated with ImaGene version 5.1 (Biodiscovery) and poor spots were flagged for elimination from analysis.

data_processing: The web-based program Bioarray Software Environment (BASE) was used for data analysis.  Spot-specific median signals were corrected for local background by subtracting spot-specific median background intensities. Spots with very low intensities (<250) were omitted and each array was then normalized independently using loess per print-tip group (74) followed by normalization between replicate arrays such that they all had the same median absolute deviation. The P values associated with moderated t test, which borrows information from all other genes to obtain better estimates of the variances, were calculated using empirical Bayes. Differentially expressed genes were considered to be statistically significant if an absolute relative ratio was greater than 2-fold with a P value of less than 0.05.

organism: Leptospira interrogans

source_name: Wild-type grown under low iron (EMJH + 40 µM 2,2-dipyridyl)

label_protocol: Labeled cDNA probes were synthesized from 2 µg of total RNA using random primers contained in the 3DNA Array 900MPX Expression Array Detection kit (Genisphere) according to the manufacturer’s instructions.

growth_protocol: L. interrogans serovar Manilae wild-type strain or la1857 mutant strain (M776) were grown in EMJH broth medium (with or without 40 µM 2,2-dipyridyl) at 30°C under aerobic conditions. Kanamycin (50ug/ml) was added to the medium of the mutant strain. Leptospires were grown to exponential phase at an approximate density of 2.5 x 10^8 - 6.5 x 10^8 cells/ml before harvesting.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) following the manufacturer's instructions and then treated with Turbo DNA-free kit (Ambion) as per the manufacturer's instructions. RNA was further puriﬁed using QIAGEN RNeasy mini-columns with on-column DNase treatment according to the manufacturer’s protocol.

treatment_protocol: To study the effects of iron limitation, triplicate 25 ml cultures of parent and la1857 mutant were grown to mid-log phase (4 × 10^8 – 6 × 10^8 cells/ml), then bacteria were pelleted (4,000 × g, 15 min, RT), washed in 10 ml of EMJH base (Difco) and resuspended in 1 ml EMJH base. The culture was then transferred to 100 ml EMJH medium with or without preincubation with 40 µM 2,2’-dipyridyl (Sigma) and grown to 2.5 × 10^8 – 6.5 × 10^8 cells/mlbefore harvesting for RNA isolation.The 100 ml cultures were divided equally between 2 tubes and harvested by centrifugation at 6,000 xg for 10 min at room temperature then resuspended in 1 ml Trizol reagent (Invitrogen).

tag: serovar

value: Manilae

source_name: Wild-type grown under normal iron conditions


title: la1857 mutant replicate 1

description: Biological replicate 1 of 3. Comparison of transcription patterns in la1857 mutant versus wild-type both growth under normal iron conditions in EMJH.

source_name: la1857 mutant grown under normal iron conditions


title: la1857 mutant replicate 3

description: Biological replicate 3 of 3. Comparison of transcription patterns in la1857 mutant versus wild-type both growth under normal iron conditions in EMJH.


title: la1857 mutant replicate 2

description: Biological replicate 2 of 3. Comparison of transcription patterns in la1857 mutant versus wild-type both growth under normal iron conditions in EMJH.


title: Low iron replicate 2

description: Biological replicate 2 of 3. Comparison of transcription patterns in wild-type grown under low iron versus growth under normal iron conditions in EMJH.


title: Low iron replicate 1

description: Biological replicate 1 of 3. Comparison of transcription patterns in wild-type grown under low iron versus growth under normal iron conditions in EMJH.


title: GMP sample 2

status: Public on Mar 15 2010

city: Boston

first: Amit

last: Sinha

state: MA

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: purified Lineage-  Sca1- CD117+ CD34+ CD16/32+ cells form 8 week old female mice

hyb_protocol: 3.75 micrograms of biotinylated material was hybridized according to the standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol

data_processing: RMA background correction and quantile normalization done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/) which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al Biostatistics (2003).

label_protocol: 10 to 50 nanograms of total RNA was amplified and processed to produce biotinylated cDNA targets using two round of in vitro RNA synthesis

extract_protocol: Trizol extraction following manufacturer's protocol.

tag: genetic background

tag: cell type

value: GMP


title: LSEC_0h_16

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from liver sinusoidal endothelial cells freshly isolated without culturing step

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 3.2, from SAS. Gene expression profiling was performed using arrays of rat 230_2 -type from Affymetrix. A Custom CDF Version 12 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: Liver sinusoidal endothelial cells freshly isolated without culturing step

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA extraction was carried out with a RNeasy RNA-extraction Kit (Qiagen) according to the manufacturers protocols

value: Liver


title: Knock Down_replicate3

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

description: Knock Down_replicate3

hyb_protocol: Chips hybridized according to Manufacturer's protocol

scan_protocol: GS3000, according to Manufacturer's protocol

data_processing: MAS5, data corrected to 1500 Baseline

source_name: mutant HEK293 cell line with knocked out expression of MOF

label_protocol: Chips labeled with biotin according to Manufacturer's protocol

growth_protocol: Standard cell culture gowth media Dulbecco's MEM with 10% FBS & 1% Penn/Strept was used

extract_protocol: Total RNA was isolated from cells using RNeasy Kit (QIAGEN Inc. Valencia, CA, USA)

treatment_protocol: Overexpression & knockdowns were done using standard transfection protocols following to manufacturers' recommendations

tag: cell line

value: hMOF knock-down


title: LMEC_0h_21

description: Gene expression data from lung microvascular endothelial cells freshly isolated without culturing step

source_name: Lung microvascular endothelial cells freshly isolated without culturing step

value: Lung


title: LMEC_0h_19


title: GMP sample 1


title: Wild type_replicate3

description: Wild type_replicate3

source_name: wild type HEK293 cell line

value: wild type


title: LMEC_0h_22


title: LGMP derived from MLL-AF9 transduced GMP_sample 2

description: Purified Lineage- Sca1- CD117+ CD16/32high CD34-/low from mouse sucumbed to AML

source_name: Lin(CD3e; CD4, CD8a, CD19, CD45R, CD127; Gr1, TER119)- Sca1- CD117+ CD34+/low CD16/32high


title: LGMP derived from MLL-AF9 transduced GMP_sample 1


title: CMP sample 3

description: purified Lineage-  Sca1- CD117+ CD34+/low CD16/32-low cells form 8 week old female mice

value: CMP


title: Knock Down_replicate1

description: Knock Down_replicate1


title: Over Expression_replicate3

description: Over Expression_replicate3

source_name: mutant HEK293 cell line overexpressing MOF

value: hMOF over-expressed


title: LSEC_0h_15


title: Over Expression_replicate2

description: Over Expression_replicate2


title: HSC sample 3

description: purified Lineage-  CD117+ Sca1+ cells form 8 week old female mice

value: HSC


title: LMEC_0h_20


title: CMP sample 1


title: LMEC_0h_18


title: HSC sample 2


title: Knock Down_replicate2

description: Knock Down_replicate2


title: Wild type_replicate2

description: Wild type_replicate2


title: LGMP derived from MLL-AF9 transduced GMP_sample 3


title: LSEC_0h_17


title: GMP sample 3


title: HSC sample 1


title: Wild type_replicate1

description: Wild type_replicate1


title: CMP sample 2


title: Over Expression replicate1

description: Over Expression replicate1


title: LSEC_0h_14


title: LSEC_42h_3

description: Gene expression data from liver sinusoidal endothelial cells after 42h in culture

source_name: Liver sinusoidal endothelial cells after 42h in culture


title: LSEC_0h_13


title: LSEC_42h_1


title: LSEC_2h_5

description: Gene expression data from liver sinusoidal endothelial cells after 2h in culture

source_name: Liver sinusoidal endothelial cells after 2h in culture


title: LSEC_42h_2


title: LSEC_2h_6


title: LSEC_2h_4


title: LSEC_42h_12


title: thymus replicate1

status: Public on Mar 08 2010

city: Wageningen

first: Haisheng

last: Nie

address: Marijkeweg 40

country: Netherlands

institute: Wageningen University

description: biological replicate 1 of 5, normal thymus tissue

hyb_protocol: 1 ug of labeled cRAN was used to hybridize on the chicken 20k oligo array overnight on a GeneTAC hybridization station (Genomic Solutions)

scan_protocol: Scanned on an Agilent DNA microarray scanner. Images were quantified using GenePix Pro 5.0 (Axon).

data_processing: median values of both foreground and background intensities were used, raw data were further analyzed using R package limma, background was corrected using normexp+offset(50), printtip loess normalized within array, Rquantile normalized among arrays.

organism: Gallus gallus

source_name: common reference

label_protocol: RNA was amplified using MessageAmp II aRNA kit (Ambion), cRNA was further used for chemical coupling with ULS-Cy3/Cy5 (ULS aRNA labeling kit, Kreatech, Amsterdam, the Netherlands).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, followed by a subsequent sample clean-up using Rneasy Mini Kit (Qiagene).

tag: strain

value: Lohmann Brown

tag: sample

value: pooled common reference from individual tissues

tag: age

value: 10 wk

source_name: thymus

value: thymus


title: thymus replicate5

description: biological replicate 5 of 5, normal thymus tissue


title: thymus replicate4

description: biological replicate 4 of 5, normal thymus tissue


title: lung replicate5

description: biological replicate 5 of 5, normal lung tissue

source_name: lung

value: lung


title: spleen replicate5

description: biological replicate 5 of 5, normal spleen tissue

source_name: spleen

value: spleen


title: liver replicate2

description: biological replicate 2 of 5, normal liver tissue

source_name: liver

value: liver


title: spleen replicate3

description: biological replicate 3 of 5, normal spleen tissue


title: spleen replicate1

description: biological replicate 1 of 5, normal spleen tissue


title: thymus replicate3

description: biological replicate 3 of 5, normal thymus tissue


title: thymus replicate2

description: biological replicate 2 of 5, normal thymus tissue


title: spleen replicate4

description: biological replicate 4 of 5, normal spleen tissue


title: liver replicate3

description: biological replicate 3 of 5, normal liver tissue


title: lung replicate1

description: biological replicate 1 of 5, normal lung tissue


title: lung replicate2

description: biological replicate 2 of 5, normal lung tissue


title: lung replicate4

description: biological replicate 4 of 5, normal lung tissue


title: liver replicate4

description: biological replicate 4 of 5, normal liver tissue


title: liver replicate1

description: biological replicate 1 of 5, normal liver tissue


title: LSEC_2h_7

description: Gene expression data from liver sinusoidal endothelial cells after 2h in culture


title: jejunum replicate3

description: biological replicate 3 of 5, normal jejunum tissue

source_name: jejunum

value: jejunum


title: kidney replicate5

description: biological replicate 5 of 5, normal kidney tissue

source_name: kidney

value: kidney


title: jejunum replicate2

description: biological replicate 2 of 5, normal jejunum tissue


title: kidney replicate2

description: biological replicate 2 of 5, normal kidney tissue


title: jejunum replicate4

description: biological replicate 4 of 5, normal jejunum tissue


title: bursa replicate5

description: biological replicate 5 of 5, normal bursa tissue

source_name: bursa

value: bursa


title: bursa replicate4

description: biological replicate 4 of 5, normal bursa tissue


title: jejunum replicate5

description: biological replicate 5 of 5, normal jejunum tissue


title: kidney replicate3

description: biological replicate 3 of 5, normal kidney tissue


title: kidney replicate1

description: biological replicate 1 of 5, normal kidney tissue


title: bursa replicate3

description: biological replicate 3 of 5, normal bursa tissue


title: jejunum replicate1

description: biological replicate 1 of 5, normal jejunum tissue


title: bursa replicate2

description: biological replicate 2 of 5, normal bursa tissue


title: spleen replicate2

description: biological replicate 2 of 5, normal spleen tissue


title: bursa replicate1

description: biological replicate 1 of 5, normal bursa tissue


title: brain replicate2

description: biological replicate 2 of 5, normal brain tissue

source_name: brain

value: brain


title: brain replicate1

description: biological replicate 1 of 5, normal brain tissue


title: brain replicate4

description: biological replicate 4 of 5, normal brain tissue


title: brain replicate5

description: biological replicate 5 of 5, normal brain tissue


title: lung replicate3

description: biological replicate 3 of 5, normal lung tissue


title: Female CM

status: Public on Mar 04 2010

type: genomic

city: Ferrara

first: Matteo

last: Bovolenta

address: 74, Fossato di Mortara

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

hyb_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol v5.0

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.1). Scanned on an Agilent G2565AA scanner.

data_processing: CGH analytics software (v3.5)

molecule: genomic DNA

source_name: DNA from blood

extract_protocol: Nucleon™ BACC Genomic DNA Extraction Kit (GE Healthcare)

tag: gender

value: Female

value: blood

tag: phenotype

value: Multiple Sclerosis

source_name: Promega Female reference DNA


title: Male GE

label_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol v5.0

value: Male

source_name: Promega Male reference DNA


title: Female CF


title: Female MC


title: Male FR


title: Female VF


title: Male MU


title: Male RM


title: Male DD


title: Female LS


title: Female PB


title: Male CC


title: Female HH


title: class S, rep90

status: Public on Mar 01 2010

city: Vancouver

first: Christian

last: Steidl

state: BC

address: 675 West 10th Avenue

department: Pathology

country: Canada

institute: BC Cancer Agency

hyb_protocol: 11µg of labeled cRNA were hybridized on the array overnight. The arrays were washed and stained using Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Bioconductor (R), and normalized and summaried using the rma function in the affy package.  The quality control thresholds used were present call rates >20% and normalized unscaled standard errors <1.05 (NUSE).  Batch-normalization was performed using ComBat.

source_name: Vancouver sample

label_protocol: 1-8 µg of extracted RNA were used to prepared biotinylated cRNA in a one-cycle reaction following routine protocols including reverse transcription and labeling in-vitro transcription reactions.

extract_protocol: Total RNA was extracted from multiple (10-20x) 20µm freshly cut tissue sections after mechanical homogenization using Allprep RNA extraction kits.

tag: tissue type

value: lymphoma

tag: disease status

value: chronic Hodgkin lymphoma

tag: relapse type

tag: age (years)

tag: sex

value: F

tag: disease stage

tag: albumin level

tag: hemoglobin level

tag: lymphocyte percentage

tag: white blood count

tag: international prognostic score (ips)


title: class S, rep91

value: M


title: class S, rep89


title: Female PF

tag: tissue


title: class S, rep88


title: class S, rep85


title: class S, rep87


title: class S, rep86


title: class S, rep83


title: brain replicate3

description: biological replicate 3 of 5, normal brain tissue

tag: strain

value: Lohmann Brown

value: pooled common reference from individual tissues

value: 10 wk


title: class S, rep84


title: class S, rep81


title: class S, rep82


title: class S, rep77


title: class S, rep74


title: class S, rep80


title: class S, rep78


title: liver replicate5

description: biological replicate 5 of 5, normal liver tissue

tag: sample


title: class S, rep72


title: class S, rep76


title: class S, rep79


title: class S, rep75


title: class S, rep69


title: class S, rep73


title: class S, rep61


title: class S, rep66


title: class S, rep67


title: class S, rep71


title: class S, rep62


title: class S, rep64


title: class S, rep63


title: kidney replicate4

description: biological replicate 4 of 5, normal kidney tissue

tag: age


title: class S, rep59


title: class S, rep65


title: class S, rep58


title: class S, rep70


title: class S, rep60


title: class S, rep56


title: class S, rep68


title: class S, rep55


title: class S, rep53


title: class S, rep52


title: class S, rep57


title: class S, rep54


title: class S, rep51


title: Male BL

tag: gender


title: class S, rep45


title: class S, rep50


title: class S, rep44


title: class S, rep92


title: class S, rep41


title: class S, rep47


title: class S, rep49


title: class S, rep38


title: class S, rep46


title: class S, rep37


title: class S, rep40


title: class S, rep33

value: f


title: class S, rep42


title: class S, rep30


title: class S, rep32


title: class S, rep48


title: class S, rep31


title: class S, rep36


title: class S, rep39


title: class S, rep34


title: class S, rep35


title: class S, rep43


title: class S, rep24


title: class S, rep29


title: class S, rep27


title: class S, rep26


title: class S, rep28


title: class S, rep25


title: class S, rep19


title: class S, rep21


title: class S, rep22


title: class S, rep16


title: class S, rep20


title: class S, rep17


title: class S, rep18


title: class S, rep15


title: class S, rep12


title: class S, rep10

source_name: Nebraska sample


title: class S, rep9


title: class S, rep11


title: class S, rep4


title: class S, rep8


title: class S, rep6


title: class S, rep14


title: class S, rep13


title: class S, rep2


title: class S, rep3


title: class S, rep7


title: class S, rep5


title: class S, rep1


title: class F, rep38

value: REFRACTORY


title: class F, rep37


title: class F, rep34


title: class F, rep30

value: LATE


title: class F, rep35


title: class F, rep31


title: class F, rep27


title: class F, rep32


title: class F, rep28


title: class F, rep25


title: class F, rep33


title: class F, rep26


title: class F, rep24


title: class F, rep29


title: class F, rep20


title: class F, rep11


title: class F, rep22

value: EARLY


title: class F, rep36


title: class F, rep17


title: class F, rep19


title: class F, rep13


title: class F, rep18


title: class F, rep16


title: class F, rep10


title: class F, rep5


title: class F, rep9


title: class F, rep12


title: class F, rep8


title: class F, rep23


title: class S, rep23


title: class F, rep14


title: class F, rep21


title: class F, rep7


title: class F, rep15


title: class F, rep4


title: class F, rep6


title: class F, rep2


title: class F, rep3


title: null Placenta_Saline_rep3

city: St. John's

first: Christopher

middle: S

last: Kovacs

state: Newfoundland

address: Health Sciences Centre, 300 Prince Philip Drive

department: Faculty of Medicine - Endocrinology

institute: Memorial University of Newfoundland

description: Fetuses were treated in utero with saline, 90 min prior to harvesting the placenta.

hyb_protocol: Following fragmentation and labeling, 5.5 ug of cRNA were hybridized on the GeneChip Mouse Gene 1.0 ST Array. GeneChips were then washed and stained according to the FS450_007 fluidics protocol. The Affymetrix GeneChip Hybridization, Wash, and Staining Kit was utilized, and protocols were carried out as per the users manual.

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

data_processing: The data were normalized with RMA algorithm implemented in bioconductor (www.bioconductor.org). Probesets without gene names/gene assignments were removed from further analyses.

source_name: Placenta harvested from Pth-null fetuses injected in utero with saline

label_protocol: Biotinylated cRNA were prepared from 200 ng of total RNA. This was preformed using the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay, and was carried out as per the user manual.

growth_protocol: Adult mice were given water and a standard chow (1% calcium) ad lib. Female heterozygous-deleted mice were subjected to timed matings with heterozygous-deleted stud males, allowing placenta to be consistently harvested on ED 18.5.

extract_protocol: Total RNA was extracted using the RNeasy Midi Kit (Quiagen). Extraction was performed as per the product insert.

treatment_protocol: Pregnant dams were anesthetized, a pelvic incision was made, and fetuses were given an intraabdominal injection of 1 nmol of PTH (1-84) in 2µl of saline or 2 µl of saline. 90 minutes later placenta were collected, snap-frozen in liquid nitrogen, and stored at – 70 °C for subsequent RNA extraction.

value: Placenta

tag: genotype

value: Pth-null

tag: embryonic day

value: female

tag: treatment

value: saline


title: null Placenta_PTH_rep3

description: Fetuses were treated in utero with PTH (1-84), 90 min prior to harvesting the placenta.

source_name: Placenta harvested from Pth-null fetuses injected in utero with PTH (1-84)

value: parathyroid hormone (1-84)


title: WT Placenta_PTH_rep3

source_name: Placenta harvested from WT fetuses injected in utero with PTH (1-84)

value: WT


title: WT Placenta_Saline_rep1

source_name: Placenta harvested from WT fetuses injected in utero with saline


title: class F, rep1

tag: tissue type

value: lymphoma

tag: disease status

tag: relapse type


title: WT Placenta_Saline_rep2


title: WT Placenta_Saline_rep3


title: null Placenta_PTH_rep1


title: null Placenta_Saline_rep1


title: null Placenta_Saline_rep2


title: WT Placenta_PTH_rep1


title: EHEC WT DMEM

city: Dallas

first: Vanessa

last: Sperandio

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Cells grown to O.D.600 1.0 in DMEM

hyb_protocol: The RNA processing, labelling hybridization, and slide-scanning were preformed as described in the Affymetrix Gene Expression Technical Manual (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

data_processing: The output scan from each single replicate array was obtained using GCOS v 1.4 according to the manufacturer's instructions.  The resulting data were compared to determine features whose expression was increased or decreased in response to inactivation of the qseD gene.

organism: Escherichia coli

source_name: EHEC DMEM O.D.600 1.0

growth_protocol: EHEC 8624 and its QseD mutant BH68, and K-12 and its QseD mutant were inoculated into LB and DMEM at 1:100 from an LB OVN and grown to and O.D. 600 of 1.0.

extract_protocol: 10 mls of Bacterial strains were pelleted and resuspended in 1.0 mL Trizol. RNA was extracted using RiboPure Bacteria RNA isolation kit (Ambion) according to the manufacturer’s guidelines.

value: EHEC

tag: genotype/variation

tag: growth protocol

value: DMEM


title: K-12 WT LB

description: Cells grown to O.D.600 1.0 in LB

scan_protocol: The RNA processing, labelling hybridization, and slide-scanning were preformed as described in the Affymetrix Gene Expression Technical Manual (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

organism: Escherichia coli K-12

value: LB


title: K-12 QseD Mutant LB

description: Cells grown to O.D.600 1.0 in LB

source_name: K-12 QseD mutant LB O.D.600 1.0

label_protocol: The RNA processing, labelling hybridization, and slide-scanning were preformed as described in the Affymetrix Gene Expression Technical Manual (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

value: QseD Mutant


title: null Placenta_PTH_rep2


title: K-12 WT DMEM

description: Cells grown to O.D.600 1.0 in DMEM


title: EHEC QseD Mutant DMEM

description: Cells grown to O.D.600 1.0 in DMEM

source_name: EHEC QseD mutant DMEM O.D.600 1.0


title: K-12 QseD Mutant DMEM

description: Cells grown to O.D.600 1.0 in DMEM

source_name: K-12 QseD mutant DMEM  O.D.600 1.0


title: WT Placenta_PTH_rep2


title: ALL9_34D_diagnosis

city: Nijmegen

first: Roland

middle: P.

last: Kuiper

address: Geert Grooteplein 10

department: Human Genetics

institute: Radboud University Nijmegen Medical Centre

description: primary ALL diagnosis sample

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix) using an Affymetrix scanner 3000.

data_processing: copy number detection using CNAG2.0 software (http://www.genome.umin.jp/)

source_name: Bone marrow

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3, Affymetrix).

extract_protocol: QiaAmp purification kit (Qiagen)

value: male

value: Bone marrow

tag: disease state

value: primary ALL diagnosis sample


title: ALL9_32R_second relapse

description: ALL relapse sample

value: ALL relapse sample


title: ALL9_28D_diagnosis

description: primary ALL diagnosis sample


title: ALL8_30D_diagnosis

description: primary ALL diagnosis sample

source_name: Peripheral blood

value: Peripheral blood


title: ALL8_31D_diagnosis

description: primary ALL diagnosis sample


title: ALL8_33D_diagnosis

description: primary ALL diagnosis sample


title: ALL8_30R_relapse

description: ALL relapse sample


title: ALL9_28R_second relapse

description: ALL relapse sample


title: ALL9_32R_first relapse

description: ALL relapse sample


title: ALL9_26D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_34F_complete remission

description: complete remission sample

value: complete remission sample


title: ALL8_29D_diagnosis

description: primary ALL diagnosis sample


title: ALL8_31R_relapse

description: ALL relapse sample


title: ALL9_26R_relapse

description: ALL relapse sample


title: ALL9_24F_complete remission

description: complete remission sample


title: ALL8_29R_relapse

description: ALL relapse sample


title: ALL9_27D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_28F_complete remission

description: complete remission sample


title: ALL9_25R_relapse

description: ALL relapse sample


title: ALL9_34R_relapse

description: ALL relapse sample


title: ALL9_26F_complete remission

description: complete remission sample


title: ALL9_28R_first relapse

description: ALL relapse sample


title: ALL9_23R_relapse

description: ALL relapse sample


title: ALL9_27R_relapse

description: ALL relapse sample


title: ALL9_24D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_24R_relapse

description: ALL relapse sample


title: ALL9_23D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_22D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_23F_complete remission

description: complete remission sample


title: ALL9_21R_first relapse

description: ALL relapse sample


title: ALL9_22R_relapse

description: ALL relapse sample


title: ALL9_20R_second relapse

description: ALL relapse sample


title: ALL9_20R_first relapse

description: ALL relapse sample


title: ALL9_21D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_21F_complete remission

description: complete remission sample


title: ALL8_17R_relapse

description: ALL relapse sample


title: ALL8_19D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_21R_second relapse

description: ALL relapse sample


title: ALL8_17D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_14R_second relapse

description: ALL relapse sample


title: ALL9_32D_diagnosis

description: primary ALL diagnosis sample


title: ALL7_16R_relapse

description: ALL relapse sample


title: ALL9_20F_complete remission

description: complete remission sample


title: ALL8_18R_relapse

description: ALL relapse sample


title: ALL7_16D_diagnosis

description: primary ALL diagnosis sample


title: ALL8_19R_relapse

description: ALL relapse sample


title: ALL9_14R_first relapse

description: ALL relapse sample


title: ALL8_18D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_15D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_20D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_15F_complete remission

description: complete remission sample


title: ALL9_14D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_15R_relapse

description: ALL relapse sample


title: ALL9_25D_diagnosis

description: primary ALL diagnosis sample


title: ALL8_13D_diagnosis

description: primary ALL diagnosis sample


title: ALL8_13R_relapse

description: ALL relapse sample


title: ALL9_25F_complete remission

description: complete remission sample


title: ALL9_12R_relapse

description: ALL relapse sample


title: TQ MF CGH replicate 4

city: College Park

first: Gerald

last: Wilkinson

state: MD

address: Bldg 144, 4094 Campus Dr

department: Biology

institute: University of Maryland

description: Biological replicate 4 of 4

hyb_protocol: Agilent array-based CGH protocol with hybridization for 24 h at 65oC

scan_protocol: Scanned using an Agilent G2539A microarray scanner Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used. Features were excluded from further analysis if the majority of pixels were saturated or the median pixel intensity was less than two times the background. Intensity scores were normalized using the linear normalization methodology. Data included in the Matrix table differ from the LogRatio column in the Agilent Feature Extraction Files in that each sample has been normalized. The order of data manipulation was 1) probes normalized by agilent software, 2) median probe value for each ORF calculated, 3) median value of logratio(F/M) centralized so peak above 0

organism: Teleopsis quinqueguttata

source_name: Total DNA from four flies, labeled with Cyanine-5 (red).

label_protocol: Each DNA sample was fractionated by restriction digestion with AluI and RsaI for 2 h at 37oC.  3 µg of each sample was then labeled with either Cy-3 or Cy-5

growth_protocol: Each sample consisted of 4 or 5 male or female adult flies that were taken from population cages maintained at the University of Maryland, College Park, derived from flies originally collected from SE Asia

extract_protocol: Genomic DNA was extracted from macerated fly bodies with Qiagen DNeasy kits using the insect sample protocol

tag: sex

value: adult

value: whole fly

tag: population

value: Gombak

source_name: Total DNA from four flies, labeled with Cyanine-3 (green).


title: TQ MF CGH replicate 3

description: Biological replicate 3 of 4

value: female


title: ALL9_12D_diagnosis

description: primary ALL diagnosis sample


title: TQ MF CGH replicate 2

description: Biological replicate 2 of 4


title: ALL8_05F_complete remission

description: complete remission sample


title: ALL9_09R_relapse

description: ALL relapse sample


title: ALL9_02F_complete remission

description: complete remission sample


title: TQ MF CGH replicate 1

description: Biological replicate 1 of 4


title: ALL9_04R_relapse

description: ALL relapse sample


title: ALL7_11D_diagnosis

description: primary ALL diagnosis sample


title: ALL8_10R_relapse

description: ALL relapse sample


title: ALL8_10D_diagnosis

description: primary ALL diagnosis sample


title: ALL7_11R_relapse

description: ALL relapse sample


title: TT MF CGH replicate 4

description: Biological replicate 4 of 4

organism: Teleopsis thaii

value: Chiang Mai


title: ALL8_08D_diagnosis

description: primary ALL diagnosis sample


title: ALL8_05R_relapse

description: ALL relapse sample


title: TT MF CGH replicate 3

description: Biological replicate 3 of 4


title: ALL8_07R_relapse

description: ALL relapse sample


title: TT MF CGH replicate 1

description: Biological replicate 1 of 4


title: TT MF CGH replicate 2

description: Biological replicate 2 of 4


title: ALL8_07D_diagnosis

description: primary ALL diagnosis sample


title: ALL8_06D_diagnosis

description: primary ALL diagnosis sample


title: TW MF CGH replicate 4

description: Biological replicate 4 of 4

organism: Teleopsis whitei


title: TW MF CGH replicate 2

description: Biological replicate 2 of 4


title: ALL8_06R_relapse

description: ALL relapse sample


title: TW MF CGH replicate 3

description: Biological replicate 3 of 4


title: ALL8_09F_complete remission

description: complete remission sample


title: TW MF CGH replicate 1

description: Biological replicate 1 of 4


title: TD MF CGH replicate 4

description: Biological replicate 4 of 4

organism: Teleopsis dalmanni


title: TD MF CGH replicate 3

description: Biological replicate 3 of 4


title: ALL8_05D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_02D_diagnosis

description: primary ALL diagnosis sample


title: ALL9_04D_diagnosis

description: primary ALL diagnosis sample


title: TD MF CGH replicate 1

description: Biological replicate 1 of 4


title: ALL8_09D_diagnosis

description: primary ALL diagnosis sample


title: ALL8_03D_diagnosis

description: primary ALL diagnosis sample


title: ALL8_06F_complete remission

description: complete remission sample


title: TD MF CGH replicate 2

description: Biological replicate 2 of 4


title: ALL8_01D_diagnosis

description: primary ALL diagnosis sample


title: dd_stat_4

city: Houston

first: Samuel

last: Shelburne

address: 1515 Holcombe Blvd

department: Infectious Diseases

institute: MD Anderson Cancer Center

hyb_protocol: per affymetrix protocol

scan_protocol: per affymetrix protocol

data_processing: data were normalized to overall chip signal intensity

organism: Streptococcus sp. 'group A'

source_name: covR ccpA grown to stationary phase in THY

label_protocol: per affymetrix protocol

extract_protocol: RNA was extracted using a qiagen RNeasy kit

value: covR ccpA mutant

tag: sample type


title: total eye RNA WT control versus Prpf31-MO injected larvae replicate 6

city: Singapore

first: Jan

last: Brocher

address: 14 Science Drive 4, Block S1A, Level 6

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

description: V4BP9_SLIDE86_CY3_NIC_CY5_PRP31_6_8UG_27052008.gpr

hyb_protocol: The respective pairs of Cy5- and Cy3-labeled cDNAs were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization on a single array at 42°C for 16 h in a hybridization chamber (MAUI, USA).

scan_protocol: Scanned on a Axon 4000B slide scanner with GenePix Pro 4.0

data_processing:
The Analysis was done by the Bioinformatics department of the Genome Institute Singapore (GIS)
The intensity values were normalized (lowess normalization)as described in the following reference: Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30, e15.
Statistical analysis was done using SAM version 3.0 (http://www-stat.stanford.edu/~tibs/SAM/) Genes with a fold-change higher than +1.5 (numerator(r): 0.584962501) or lower than -1.5 (numerator(r): -0.584962501) were considered as differentially expressed. The significance threshold was set by a q-value(%) of < 5%.

organism: Danio rerio

source_name: wildtype control

label_protocol: 8µg of total RNA per sample (control or morphant) were reverse transcribed using SuperScript II RT (Invitrogen), OligodT (20mer), 0.1 M DTT, RNaseOUT ribonuclease inhibitor, and 20X low-dT/aa-dUTP mix (Sigma-Aldrich, USA) for 1h at 42°C, followed by coupling with mono-functional NHS-ester Cy3 and Cy5 dyes (Amersham, USA), respectively.

growth_protocol: control and morphant zebrafish were incubated at 28-30°C

extract_protocol: At stage matched 3dpf larvae, eyes were manually disected, kept in RNAlater until total RNA was extracted using the Qiagen RNeasy Kit according to the manufacturers instructions

treatment_protocol: Prpf31 morpholino was injected into 1- and 2-cell stage embryos at a concentration of 2.5µg/µl

tag: genome/variation

value: wildtype control

tag: tissue

value: eye

tag: developmental stage


title: ALL9_02R_relapse

description: ALL relapse sample


title: total eye RNA WT control versus Prpf31-MO injected larvae replicate 5

description: V4BP9_SLIDE85_CY3_NIC_CY5_PRP31_5_8UG_27052008.gpr


title: ALL8_03R_relapse

description: ALL relapse sample


title: ALL8_08R_relapse

description: ALL relapse sample


title: dd_stat_1

value: covR ccpA grown to stationary phase in THY


title: dd_stat_3


title: dd_stat_2


title: covR_stat_4

source_name: covR grown to stationary phase in THY

value: covR mutant

value: covR grown to stationary phase in THY


title: total eye RNA WT control versus Prpf31-MO injected larvae replicate 3

description: V4BP9_SLIDE83_CY3_NIC_CY5_PRP31_3_8UG_27052008.gpr


title: covR_stat_3


title: total eye RNA WT control versus Prpf31-MO injected larvae replicate 4

description: V4BP9_SLIDE84_CY3_NIC_CY5_PRP31_4_8UG_27052008_s3.gpr


title: ALL8_01R_relapse

description: ALL relapse sample


title: MGAS2221__stat_4

source_name: MGAS2221 grown to stationary phase in THY

value: wild type


title: ccpA_stat_2

source_name: ccpA grown to stationary phase in THY

value: ccpA mutant

value: ccpA grown to stationary phase in THY


title: ccpA_stat_4


title: MGAS2221__stat_3

value: MGAS2221 grown to stationary phase in THY


title: ccpA_stat_1


title: covR_stat_2


title: ccpA_stat_3


title: covR_stat_1


title: total eye RNA WT control versus Prpf31-MO injected larvae replicate 2

description: V4BP9_SLIDE82_CY3_NIC_CY5_PRP31_2_8UG_27052008.gpr


title: MGAS2221__stat_2


title: dd_mid-exp_3

source_name: covR ccpA grown to mid-exponential phase in THY


title: dd_mid-exp_4

value: covR ccpA grown to mid-exponential phase in THY


title: MGAS2221__stat_1


title: dd_mid-exp_2


title: covR_mid-exp_4

source_name: covR grown in THY to mid-exponential phase


title: covR_mid-exp_1

source_name: covR grown to mid-exponential phase in THY


title: ccpA_mid-exp_4

source_name: ccpA grown to mid-exponential phase in THY


title: dd_mid-exp_1


title: covR_mid-exp_3

value: covR grown to mid-exponential phase in THY


title: ccpA_mid-exp_1

source_name: ccpA grown to mid-exponential phase

value: ccpA grown to mid-exponential phase in THY


title: ccpA_mid-exp_2

source_name: ccpA grown in mid-exponential phase in THY


title: ccpA_mid-exp_3

value: ccpA grown in mid-exponential phase in THY


title: MGAS2221_mid-exp_4

source_name: MGAS2221 grown to mid-exponential phase in THY

value: MGAS2221 grown in mid-exponential phase in THY


title: MGAS2221_mid-exp_3

value: MGAS2221 grown to mid-exponential phase in THY


title: covR_mid-exp_2


title: MGAS2221_mid-exp_2

source_name: MGAS2221 grown to mid-exponential phase


title: MGAS2221_mid-exp_1


title: total eye RNA WT control versus Prpf31-MO injected larvae replicate 1

description: V4BP9_SLIDE81_CY3_NIC_CY5_PRP31_1_8UG_27052008_s2.gpr


title: High-white count B-cell 3

city: atlanta

first: leon

last: bernal

state: GA

address: 1365 clifton road, bulding C

department: Hematolog and medical oncology

institute: Emory University

description: Bone marrow sample with > 80% blast

hyb_protocol: Performed by Agilent Technolies

scan_protocol: Agilent 2100 bioanalyser and Agilent MR-2 DNA microarray scaners(Agilent Technolies, Santa Clara, CA)

data_processing: R program/ Bioconductor -Agi4x44PreProcess. Normalization performed by Quantile normalization. R scripts and parameters provided as Series supplementary files.

source_name: Bone Marrow

label_protocol: standard Agilent protocol

extract_protocol: Qiagen Rneasy mini kit(Cat. 74104)

value: bone marrow


title: Low-white count B-cell 4

description: Bone marrow sample with > 80% blast


title: High-white count B-cell 4

description: Bone marrow sample with > 80% blast


title: Low-white count B-cell 3

description: Bone marrow sample with > 80% blast


title: High-white count B-cell 2

description: Bone marrow sample with > 80% blast


title: Low-white count B-cell 2

description: Bone marrow sample with > 80% blast


title: Peripheral blood RNA from sample 229

status: Public on Feb 28 2010

city: Groningen

first: Lude

last: Franke

state: Groningen

department: Genetics

institute: University Medical Centre Groningen

description: Gene expression from whole peripheral blood from unrelated Dutch or UK individuals.

hyb_protocol: Complementary RNA was hybridized to Illumina HumanRef H8-v2.0 Whole Genome BeadChips

scan_protocol: Illumina BeadArray Reader, data was handled through Illumina BeadStudio Gene Expression module v3

data_processing: Quantile-quantile normalized log2 transformed expression intensity. Subsequently, per sample the intensities have been centered to zero and subsequently scaled such that each individual has a standard deviation of 1 in probe

source_name: Total RNA from peripheral blood RNA.

label_protocol: 2.5 ml of peripheral blood was collected into a PAXgene tube (Becton Dickinson, UK, 762165). PAXgene vials were chosen to prevent density gradient centrifugation, immortalization or in vitro cell culture artifacts changing mRNA profiles. PAXgene tubes were mixed gently and incubated at room temperature for two hours. After collection, tubes were frozen at -20 degrees Celsius for at least 24 hours followed by storage at -80 degrees Celsius. RNA was isolated using the PAXgene Blood RNA isolation kit (Qiagen, UK, 762174). RNA was quantified using the Nanodrop (Nanodrop Technologies, USA). Total RNA integrity was analyzed using an Agilent Bioanalyzer (Agilent Technologies, USA).

extract_protocol: PAXgene Blood RNA isolation kit protocol (Qiagen, UK, 762174)

value: Peripheral blood


title: High-white count B-cell 5

description: Bone marrow sample with > 80% blast


title: Peripheral blood RNA from sample 227


title: Low-white count B-cell 1

description: Bone marrow sample with > 80% blast


title: Low-white count B-cell 5

description: Bone marrow sample with > 80% blast


title: Peripheral blood RNA from sample 228


title: High-white count B-cell 1

description: Bone marrow sample with > 80% blast


title: Peripheral blood RNA from sample 207


title: Peripheral blood RNA from sample 213


title: Peripheral blood RNA from sample 211


title: Peripheral blood RNA from sample 219


title: Peripheral blood RNA from sample 225


title: Peripheral blood RNA from sample 216


title: Peripheral blood RNA from sample 222


title: Peripheral blood RNA from sample 210


title: Peripheral blood RNA from sample 223


title: Peripheral blood RNA from sample 221


title: Peripheral blood RNA from sample 209


title: Peripheral blood RNA from sample 204


title: Peripheral blood RNA from sample 226


title: Peripheral blood RNA from sample 203


title: Peripheral blood RNA from sample 214


title: Peripheral blood RNA from sample 220


title: Peripheral blood RNA from sample 208


title: Peripheral blood RNA from sample 224


title: Peripheral blood RNA from sample 201


title: Peripheral blood RNA from sample 212


title: Peripheral blood RNA from sample 202


title: Peripheral blood RNA from sample 217


title: Peripheral blood RNA from sample 218


title: Peripheral blood RNA from sample 215


title: Peripheral blood RNA from sample 205


title: Peripheral blood RNA from sample 206


title: Peripheral blood RNA from sample 199


title: Peripheral blood RNA from sample 200


title: Peripheral blood RNA from sample 198


title: Peripheral blood RNA from sample 196


title: Peripheral blood RNA from sample 193


title: Peripheral blood RNA from sample 192


title: Peripheral blood RNA from sample 197


title: Peripheral blood RNA from sample 172


title: Peripheral blood RNA from sample 175


title: Peripheral blood RNA from sample 195


title: Peripheral blood RNA from sample 187


title: Peripheral blood RNA from sample 191


title: Peripheral blood RNA from sample 180


title: Peripheral blood RNA from sample 183


title: Peripheral blood RNA from sample 189


title: Peripheral blood RNA from sample 181


title: Peripheral blood RNA from sample 170


title: Peripheral blood RNA from sample 176


title: Peripheral blood RNA from sample 171


title: Peripheral blood RNA from sample 182


title: Peripheral blood RNA from sample 188


title: Peripheral blood RNA from sample 190


title: Peripheral blood RNA from sample 169


title: Peripheral blood RNA from sample 186


title: Peripheral blood RNA from sample 178


title: Peripheral blood RNA from sample 184


title: Peripheral blood RNA from sample 185


title: Peripheral blood RNA from sample 177


title: Peripheral blood RNA from sample 179


title: Peripheral blood RNA from sample 174


title: Peripheral blood RNA from sample 173


title: Peripheral blood RNA from sample 167


title: Peripheral blood RNA from sample 168


title: Peripheral blood RNA from sample 166


title: Peripheral blood RNA from sample 163


title: Peripheral blood RNA from sample 162


title: Peripheral blood RNA from sample 156


title: Peripheral blood RNA from sample 154


title: Peripheral blood RNA from sample 148


title: Peripheral blood RNA from sample 150


title: Peripheral blood RNA from sample 164


title: Peripheral blood RNA from sample 151


title: Peripheral blood RNA from sample 157


title: Peripheral blood RNA from sample 144


title: Peripheral blood RNA from sample 145


title: Peripheral blood RNA from sample 160


title: Peripheral blood RNA from sample 158


title: Peripheral blood RNA from sample 165


title: Peripheral blood RNA from sample 147


title: Peripheral blood RNA from sample 159


title: Peripheral blood RNA from sample 152


title: Peripheral blood RNA from sample 146


title: Peripheral blood RNA from sample 139


title: Peripheral blood RNA from sample 141


title: Peripheral blood RNA from sample 153


title: Peripheral blood RNA from sample 140


title: Peripheral blood RNA from sample 161


title: Peripheral blood RNA from sample 142


title: Peripheral blood RNA from sample 155


title: Peripheral blood RNA from sample 143


title: Peripheral blood RNA from sample 149


title: Peripheral blood RNA from sample 138


title: Peripheral blood RNA from sample 137


title: Peripheral blood RNA from sample 131


title: Peripheral blood RNA from sample 135


title: Peripheral blood RNA from sample 125


title: Peripheral blood RNA from sample 129


title: Peripheral blood RNA from sample 123


title: Peripheral blood RNA from sample 132


title: Peripheral blood RNA from sample 117


title: Peripheral blood RNA from sample 128


title: Peripheral blood RNA from sample 134


title: Peripheral blood RNA from sample 122


title: Peripheral blood RNA from sample 119


title: Peripheral blood RNA from sample 194


title: Peripheral blood RNA from sample 120


title: Peripheral blood RNA from sample 116


title: Peripheral blood RNA from sample 126


title: Peripheral blood RNA from sample 136


title: Peripheral blood RNA from sample 113


title: Peripheral blood RNA from sample 130


title: Peripheral blood RNA from sample 114


title: Peripheral blood RNA from sample 124


title: Peripheral blood RNA from sample 118


title: Peripheral blood RNA from sample 133


title: Peripheral blood RNA from sample 127


title: Peripheral blood RNA from sample 111


title: Peripheral blood RNA from sample 115


title: Peripheral blood RNA from sample 112


title: Peripheral blood RNA from sample 121


title: Peripheral blood RNA from sample 110


title: Peripheral blood RNA from sample 109


title: Peripheral blood RNA from sample 105


title: Peripheral blood RNA from sample 106


title: Peripheral blood RNA from sample 104


title: Peripheral blood RNA from sample 100


title: Peripheral blood RNA from sample 99


title: Peripheral blood RNA from sample 103


title: Peripheral blood RNA from sample 90


title: Peripheral blood RNA from sample 97


title: Peripheral blood RNA from sample 91


title: Peripheral blood RNA from sample 98


title: Peripheral blood RNA from sample 107


title: Peripheral blood RNA from sample 96


title: Peripheral blood RNA from sample 93


title: Peripheral blood RNA from sample 92


title: Peripheral blood RNA from sample 101


title: Peripheral blood RNA from sample 102


title: Peripheral blood RNA from sample 94


title: Peripheral blood RNA from sample 85


title: Peripheral blood RNA from sample 82


title: Peripheral blood RNA from sample 86


title: Peripheral blood RNA from sample 88


title: Peripheral blood RNA from sample 84


title: Peripheral blood RNA from sample 108


title: Peripheral blood RNA from sample 87


title: Peripheral blood RNA from sample 81


title: Peripheral blood RNA from sample 95


title: Peripheral blood RNA from sample 80


title: Peripheral blood RNA from sample 89


title: Peripheral blood RNA from sample 79


title: Peripheral blood RNA from sample 83


title: Peripheral blood RNA from sample 78


title: Peripheral blood RNA from sample 76


title: Peripheral blood RNA from sample 74


title: Peripheral blood RNA from sample 72


title: Peripheral blood RNA from sample 75


title: Peripheral blood RNA from sample 68


title: Peripheral blood RNA from sample 73


title: Peripheral blood RNA from sample 71


title: Peripheral blood RNA from sample 67


title: Peripheral blood RNA from sample 69


title: Peripheral blood RNA from sample 60


title: Peripheral blood RNA from sample 56


title: Peripheral blood RNA from sample 70


title: Peripheral blood RNA from sample 66


title: Peripheral blood RNA from sample 59


title: Peripheral blood RNA from sample 54


title: Peripheral blood RNA from sample 62


title: Peripheral blood RNA from sample 55


title: Peripheral blood RNA from sample 50


title: Peripheral blood RNA from sample 77


title: Peripheral blood RNA from sample 51


title: Peripheral blood RNA from sample 61


title: Peripheral blood RNA from sample 57


title: Peripheral blood RNA from sample 63


title: Peripheral blood RNA from sample 64


title: Peripheral blood RNA from sample 58


title: Peripheral blood RNA from sample 65


title: Peripheral blood RNA from sample 53


title: Peripheral blood RNA from sample 52


title: Peripheral blood RNA from sample 47


title: Peripheral blood RNA from sample 46


title: Peripheral blood RNA from sample 45


title: Peripheral blood RNA from sample 48


title: Peripheral blood RNA from sample 49


title: Peripheral blood RNA from sample 39


title: Peripheral blood RNA from sample 44


title: Peripheral blood RNA from sample 31


title: Peripheral blood RNA from sample 38


title: Peripheral blood RNA from sample 42


title: Peripheral blood RNA from sample 23


title: Peripheral blood RNA from sample 25


title: Peripheral blood RNA from sample 36


title: Peripheral blood RNA from sample 28


title: Peripheral blood RNA from sample 30


title: Peripheral blood RNA from sample 24


title: Peripheral blood RNA from sample 40


title: Peripheral blood RNA from sample 27


title: Peripheral blood RNA from sample 19


title: Peripheral blood RNA from sample 41


title: Peripheral blood RNA from sample 26


title: Peripheral blood RNA from sample 32


title: Peripheral blood RNA from sample 20


title: Peripheral blood RNA from sample 34


title: Peripheral blood RNA from sample 29


title: Peripheral blood RNA from sample 17


title: Peripheral blood RNA from sample 21


title: Peripheral blood RNA from sample 43


title: Peripheral blood RNA from sample 37


title: Peripheral blood RNA from sample 18


title: Peripheral blood RNA from sample 16


title: Peripheral blood RNA from sample 33


title: Peripheral blood RNA from sample 35


title: Peripheral blood RNA from sample 15


title: Peripheral blood RNA from sample 14


title: Peripheral blood RNA from sample 12


title: Peripheral blood RNA from sample 8


title: Peripheral blood RNA from sample 10


title: Peripheral blood RNA from sample 6


title: Peripheral blood RNA from sample 9


title: Peripheral blood RNA from sample 11


title: Peripheral blood RNA from sample 3


title: Peripheral blood RNA from Dutch sample 1237

description: Gene expression from whole peripheral blood from unrelated Dutch individuals

hyb_protocol: Complementary RNA was hybridized to Illumina HumanHT12 v3.0 Whole Genome BeadChips

data_processing:
Quantile-quantile normalized log2 transformed expression intensity. Subsequently, per sample the intensities have been centered to zero and subsequently scaled such that each individual has a standard deviation of 1 in probe.

RAW intensity is provided in the supplementary file on the Sample record (below).

source_name: Total RNA from peripheral blood


title: Peripheral blood RNA from sample 22


title: Peripheral blood RNA from Dutch sample 1239


title: Peripheral blood RNA from sample 2


title: Peripheral blood RNA from Dutch sample 1240


title: Peripheral blood RNA from sample 5


title: Peripheral blood RNA from Dutch sample 1238


title: Peripheral blood RNA from Dutch sample 1235


title: Peripheral blood RNA from sample 13


title: Peripheral blood RNA from sample 7


title: Peripheral blood RNA from Dutch sample 1236


title: Peripheral blood RNA from sample 1


title: Peripheral blood RNA from sample 4


title: Peripheral blood RNA from Dutch sample 1233


title: Peripheral blood RNA from Dutch sample 1231


title: Peripheral blood RNA from Dutch sample 1232


title: Peripheral blood RNA from Dutch sample 1234


title: Peripheral blood RNA from Dutch sample 1224


title: Peripheral blood RNA from Dutch sample 1223


title: Peripheral blood RNA from Dutch sample 1230


title: Peripheral blood RNA from Dutch sample 1229


title: Peripheral blood RNA from Dutch sample 1215


title: Peripheral blood RNA from Dutch sample 1228


title: Peripheral blood RNA from Dutch sample 1227


title: Peripheral blood RNA from Dutch sample 1212


title: Peripheral blood RNA from Dutch sample 1226


title: Peripheral blood RNA from Dutch sample 1217


title: Peripheral blood RNA from Dutch sample 1216


title: Peripheral blood RNA from Dutch sample 1210


title: Peripheral blood RNA from Dutch sample 1219


title: Peripheral blood RNA from Dutch sample 1225


title: Peripheral blood RNA from Dutch sample 1220


title: Peripheral blood RNA from Dutch sample 1218


title: Peripheral blood RNA from Dutch sample 1214


title: Peripheral blood RNA from Dutch sample 1209


title: Peripheral blood RNA from Dutch sample 1221


title: Peripheral blood RNA from Dutch sample 1211


title: Peripheral blood RNA from Dutch sample 1213


title: Peripheral blood RNA from Dutch sample 1222


title: Peripheral blood RNA from Dutch sample 1207


title: Peripheral blood RNA from Dutch sample 1206


title: Peripheral blood RNA from Dutch sample 1203


title: Peripheral blood RNA from Dutch sample 1204


title: Peripheral blood RNA from Dutch sample 1198


title: Peripheral blood RNA from Dutch sample 1208


title: Peripheral blood RNA from Dutch sample 1205


title: Peripheral blood RNA from Dutch sample 1195


title: Peripheral blood RNA from Dutch sample 1201


title: Peripheral blood RNA from Dutch sample 1192


title: Peripheral blood RNA from Dutch sample 1190


title: Peripheral blood RNA from Dutch sample 1200


title: Peripheral blood RNA from Dutch sample 1202


title: Peripheral blood RNA from Dutch sample 1187


title: Peripheral blood RNA from Dutch sample 1193


title: Peripheral blood RNA from Dutch sample 1181


title: Peripheral blood RNA from Dutch sample 1194


title: Peripheral blood RNA from Dutch sample 1184


title: Peripheral blood RNA from Dutch sample 1180


title: Peripheral blood RNA from Dutch sample 1199


title: Peripheral blood RNA from Dutch sample 1197


title: Peripheral blood RNA from Dutch sample 1182


title: Peripheral blood RNA from Dutch sample 1185


title: Peripheral blood RNA from Dutch sample 1191


title: Peripheral blood RNA from Dutch sample 1196


title: Peripheral blood RNA from Dutch sample 1183


title: Peripheral blood RNA from Dutch sample 1179


title: Peripheral blood RNA from Dutch sample 1188


title: Peripheral blood RNA from Dutch sample 1177


title: Peripheral blood RNA from Dutch sample 1189


title: Peripheral blood RNA from Dutch sample 1186


title: Peripheral blood RNA from Dutch sample 1178


title: Peripheral blood RNA from Dutch sample 1176


title: Peripheral blood RNA from Dutch sample 1175


title: Peripheral blood RNA from Dutch sample 1166


title: Peripheral blood RNA from Dutch sample 1164


title: Peripheral blood RNA from Dutch sample 1163


title: Peripheral blood RNA from Dutch sample 1174


title: Peripheral blood RNA from Dutch sample 1168


title: Peripheral blood RNA from Dutch sample 1167


title: Peripheral blood RNA from Dutch sample 1165


title: Peripheral blood RNA from Dutch sample 1171


title: Peripheral blood RNA from Dutch sample 1169


title: Peripheral blood RNA from Dutch sample 1173


title: Peripheral blood RNA from Dutch sample 1161


title: Peripheral blood RNA from Dutch sample 1162


title: Peripheral blood RNA from Dutch sample 1172


title: Peripheral blood RNA from Dutch sample 1155


title: Peripheral blood RNA from Dutch sample 1157


title: Peripheral blood RNA from Dutch sample 1156


title: Peripheral blood RNA from Dutch sample 1158


title: Peripheral blood RNA from Dutch sample 1160


title: Peripheral blood RNA from Dutch sample 1148


title: Peripheral blood RNA from Dutch sample 1149


title: Peripheral blood RNA from Dutch sample 1153


title: Peripheral blood RNA from Dutch sample 1170


title: Peripheral blood RNA from Dutch sample 1146


title: Peripheral blood RNA from Dutch sample 1147


title: Peripheral blood RNA from Dutch sample 1154


title: Peripheral blood RNA from Dutch sample 1152


title: Peripheral blood RNA from Dutch sample 1151


title: Peripheral blood RNA from Dutch sample 1145


title: Peripheral blood RNA from Dutch sample 1150


title: Peripheral blood RNA from Dutch sample 1159


title: Peripheral blood RNA from Dutch sample 1143


title: Peripheral blood RNA from Dutch sample 1142


title: Peripheral blood RNA from Dutch sample 1144


title: Peripheral blood RNA from Dutch sample 1137


title: Peripheral blood RNA from Dutch sample 1135


title: Peripheral blood RNA from Dutch sample 1133


title: Peripheral blood RNA from Dutch sample 1139


title: Peripheral blood RNA from Dutch sample 1134


title: Peripheral blood RNA from Dutch sample 1130


title: Peripheral blood RNA from Dutch sample 1141


title: Peripheral blood RNA from Dutch sample 1140


title: Peripheral blood RNA from Dutch sample 1132


title: Peripheral blood RNA from Dutch sample 1136


title: Peripheral blood RNA from Dutch sample 1129


title: Peripheral blood RNA from Dutch sample 1125


title: Peripheral blood RNA from Dutch sample 1126


title: Peripheral blood RNA from Dutch sample 1124


title: Peripheral blood RNA from Dutch sample 1128


title: Peripheral blood RNA from Dutch sample 1122


title: Peripheral blood RNA from Dutch sample 1118


title: Peripheral blood RNA from Dutch sample 1127


title: Peripheral blood RNA from Dutch sample 1121


title: Peripheral blood RNA from Dutch sample 1119


title: Peripheral blood RNA from Dutch sample 1116


title: Peripheral blood RNA from Dutch sample 1117


title: Peripheral blood RNA from Dutch sample 1114


title: Peripheral blood RNA from Dutch sample 1115


title: Peripheral blood RNA from Dutch sample 1106


title: Peripheral blood RNA from Dutch sample 1104


title: Peripheral blood RNA from Dutch sample 1120


title: Peripheral blood RNA from Dutch sample 1110


title: Peripheral blood RNA from Dutch sample 1105


title: Peripheral blood RNA from Dutch sample 1113


title: Peripheral blood RNA from Dutch sample 1103


title: Peripheral blood RNA from Dutch sample 1109


title: Peripheral blood RNA from Dutch sample 1107


title: Peripheral blood RNA from Dutch sample 1123


title: Peripheral blood RNA from Dutch sample 1108


title: Peripheral blood RNA from Dutch sample 1111


title: Peripheral blood RNA from Dutch sample 1102


title: Peripheral blood RNA from Dutch sample 1112


title: Peripheral blood RNA from Dutch sample 1100


title: Peripheral blood RNA from Dutch sample 1101


title: Peripheral blood RNA from Dutch sample 1098


title: Peripheral blood RNA from Dutch sample 1097


title: Peripheral blood RNA from Dutch sample 1092


title: Peripheral blood RNA from Dutch sample 1095


title: Peripheral blood RNA from Dutch sample 1138


title: Peripheral blood RNA from Dutch sample 1099


title: Peripheral blood RNA from Dutch sample 1093


title: Peripheral blood RNA from Dutch sample 1094


title: Peripheral blood RNA from Dutch sample 1090


title: Peripheral blood RNA from Dutch sample 1091


title: Peripheral blood RNA from Dutch sample 1088


title: Peripheral blood RNA from Dutch sample 1089


title: Peripheral blood RNA from Dutch sample 1085


title: Peripheral blood RNA from Dutch sample 1075


title: Peripheral blood RNA from Dutch sample 1078


title: Peripheral blood RNA from Dutch sample 1084


title: Peripheral blood RNA from Dutch sample 1081


title: Peripheral blood RNA from Dutch sample 1087


title: Peripheral blood RNA from Dutch sample 1074


title: Peripheral blood RNA from Dutch sample 1076


title: Peripheral blood RNA from Dutch sample 1086


title: Peripheral blood RNA from Dutch sample 1073


title: Peripheral blood RNA from Dutch sample 1083


title: Peripheral blood RNA from Dutch sample 1082


title: Peripheral blood RNA from Dutch sample 1077


title: Peripheral blood RNA from Dutch sample 1072


title: Peripheral blood RNA from Dutch sample 1070


title: Peripheral blood RNA from Dutch sample 1080


title: Peripheral blood RNA from Dutch sample 1079


title: Peripheral blood RNA from Dutch sample 1131


title: Peripheral blood RNA from Dutch sample 1068


title: Peripheral blood RNA from Dutch sample 1067


title: Peripheral blood RNA from Dutch sample 1071


title: Peripheral blood RNA from Dutch sample 1066


title: Peripheral blood RNA from Dutch sample 1064


title: Peripheral blood RNA from Dutch sample 1069


title: Peripheral blood RNA from Dutch sample 1065


title: Peripheral blood RNA from Dutch sample 1061


title: Peripheral blood RNA from Dutch sample 1060


title: Peripheral blood RNA from Dutch sample 1062


title: Peripheral blood RNA from Dutch sample 1053


title: Peripheral blood RNA from Dutch sample 1058


title: Peripheral blood RNA from Dutch sample 1054


title: Peripheral blood RNA from Dutch sample 1055


title: Peripheral blood RNA from Dutch sample 1057


title: Peripheral blood RNA from Dutch sample 1052


title: Peripheral blood RNA from Dutch sample 1056


title: Peripheral blood RNA from Dutch sample 1059


title: Peripheral blood RNA from Dutch sample 1047


title: Peripheral blood RNA from Dutch sample 1048


title: Peripheral blood RNA from Dutch sample 1051


title: Peripheral blood RNA from Dutch sample 1050


title: Peripheral blood RNA from Dutch sample 1043


title: Peripheral blood RNA from Dutch sample 1045


title: Peripheral blood RNA from Dutch sample 1096


title: Peripheral blood RNA from Dutch sample 1036


title: Peripheral blood RNA from Dutch sample 1046


title: Peripheral blood RNA from Dutch sample 1038


title: Peripheral blood RNA from Dutch sample 1035


title: Peripheral blood RNA from Dutch sample 1044


title: Peripheral blood RNA from Dutch sample 1033


title: Peripheral blood RNA from Dutch sample 1042


title: Peripheral blood RNA from Dutch sample 1040


title: Peripheral blood RNA from Dutch sample 1034


title: Peripheral blood RNA from Dutch sample 1037


title: Peripheral blood RNA from Dutch sample 1041


title: Peripheral blood RNA from Dutch sample 1039


title: Peripheral blood RNA from Dutch sample 1032


title: Peripheral blood RNA from Dutch sample 1030


title: Peripheral blood RNA from Dutch sample 1026


title: Peripheral blood RNA from Dutch sample 1049


title: Peripheral blood RNA from Dutch sample 1028


title: Peripheral blood RNA from Dutch sample 1024


title: Peripheral blood RNA from Dutch sample 1019


title: Peripheral blood RNA from Dutch sample 1023


title: Peripheral blood RNA from Dutch sample 1025


title: Peripheral blood RNA from Dutch sample 1020


title: Peripheral blood RNA from Dutch sample 1031


title: Peripheral blood RNA from Dutch sample 1018


title: Peripheral blood RNA from Dutch sample 1016


title: Peripheral blood RNA from Dutch sample 1015


title: Peripheral blood RNA from Dutch sample 1029


title: Peripheral blood RNA from Dutch sample 1021


title: Peripheral blood RNA from Dutch sample 1022


title: Peripheral blood RNA from Dutch sample 1007


title: Peripheral blood RNA from Dutch sample 1017


title: Peripheral blood RNA from Dutch sample 1008


title: Peripheral blood RNA from Dutch sample 1027


title: Peripheral blood RNA from Dutch sample 1009


title: Peripheral blood RNA from Dutch sample 1010


title: Peripheral blood RNA from Dutch sample 1011


title: Peripheral blood RNA from Dutch sample 1014


title: Peripheral blood RNA from Dutch sample 1013


title: Peripheral blood RNA from Dutch sample 1063