title: Patient KQ 038

description:
Patient kq_038
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 032

status: Public on Apr 09 2013

type: genomic

city: shenyang

first: lu

last: yongping

address: huanggu strict puhe street

country: China

institute: key lab of liaoning province family planning research institution

description:
Patient kq_032
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.

hyb_protocol: To prepare Cy3 labeled single strand products, 10μL allele-specific extension products were added 10μL mix containing 1.33×SSC, 0.067% SSC, 0.033mg/ml salmon sperm DNA, and 50nM Cy3-labeled com-tag. The mix was denatured at 94°C for 10 min and cooled 5 min on ice. Hybridization was then performed using this hybridization solution in a hybridization chamber at 60°C for 2 hours. Hybridization was followed by two washes in 2×SSC/0.1%SDS (preheated to 50°C) for 5min, proceeded by washing in 0.2×SSC/0.1%SDS for 1 min, then rinsed in dH2O and dried by centrifugation 3 min at 500 r.p.m.

scan_protocol: Microarrays were scanned at 100-μm resolution, using GenePix 4000B scanner (Axon instruments, USA), the TIFF images were imported into GenePix 6.0 software (Axon Instruments, USA).

data_processing:
The sample data table contains the mean single value of the spot subtracted the mean single of background as the spot's single (F532 Mean - B532), used for AF (allele B/allele A + allele B) calculation.
For example, for mother kq_001,  The single of allele T= (27709+27469)/2=27589, The single of allele C= (22835+32770)/2=27802.5, thus, the AF of rs3771494=27589/27859+27802.5=0.498, which is between 0.4 and 0.6, so the genotype was heterozygote.For mother kq_002, the single of allele T=(27709+32380)/2=30044.5, the single of allele C=(305+545)/2=425. The AF of rs3771494=30044.5/30044.5+425=0.985, which was >0.6, so the genotype was T homozygote.

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Multiplex PCR was amplified with the Multiplex PCR Assay Kit (Takara) in 20μL [Multiplex PCR mix2 10μL, Multiplex PCR mix1 0.2μL, 0.2μM primers, 50ng DNA]. Thermocycling was performed with an initial 60 second denaturation at 94°C followed by 35 cycles of: 30 seconds at 94°C, 90 seconds at 57°C and 90 seconds at 72°C, and final extension at 72°C for 10 minutes. The PCR product was used as a template for Multiplex allele-specific primer extension. In order to remove excess dNTPs and primers, a mix was added into 10μL PCR product, containing 2 units of shrimp alkaline phosphatase (Takara) and 4 units EXO I(Takara) with incubation at 37°C for 30 min followed by 96°C for 10 min. 10μL of treated PCR products was added to 5μL ASPE mix containing 1×Thermopol reaction buffer, 80μM of each dATP, dGTP, dTTP (Takara), 40μM Cy3-dCTP (GE), 0.2 unit of a vent exo- DNA polymerase(New England Biolabs), 25nM allele-specific primers. The extension conditions were as follows: an initial 3min at 94°C, 35 cycles of 94°C for 30 second, 60°C for 30 second 72°C for 1 min, and final extension at 72°C for 5minutes.

extract_protocol: DNA was obtained from the blood samples using TIANamp Blood DNA kit (TianGen).

tag: sample group

value: unrelated patients

tag: clinical type

value: cleft lip, left

tag: tissue

value: blood


title: Patient KQ 033

description:
Patient kq_033
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 029

description:
Patient kq_029
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 031

description:
Patient kq_031
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 030

description:
Patient kq_030
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: GM02781B_1.5Gy_C5

type: RNA

city: Morrisville

first: Tong

last: Zhou

state: NC

address: 133 Southcenter Court, Suite 400

department: Clincial Genetics

country: USA

institute: Gentris Corperation

description: cell lines with same ATM genotype receiving the same treatment (Sham or IR) are biological replicates of one-another

hyb_protocol: The labeled cRNA from human lymphoblastoid cells was hybridized with the labeled global reference cRNA on an Agilent array in a hybridization oven at 60°C for 17 hr.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B US23502387 Images were quantified using Agilent Feature Extraction Software (version A.7.1.1).

data_processing: Each RNA sample was subjected to microarray analysis twice with C3/C5 dyes swap (C3 labeled test sample / C5 labeled reference, C5 labeled test sample /C3 labeled reference) in both Basal and IR study. The data from each array were normalized using EPIG method, which included array-based systematic variation normalization [Chou, J.W., Paules, R.S., and Bushel, P.R. (2005). Systematic variation normalization in microarray data to get gene expression comparison unbiased. J. Bioinform. Comput.Biol. 3, 225-241], profile-based C3/C5 dye-swap correction, and biological reference state alignment [Chou, J.W., Zhou, T., Kaufmann, W. K., Paules, R.S., and Bushel, P.R. (2007). Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes. BMC Bioinformatics 8, 427. doi:10.1186/1471-2105-8-427].

molecule: total RNA

source_name: AT carrier

label_protocol: 1 μg of sample RNA and global reference RNA  were converted to cDNA with reverse transcriptase and then amplified using T7 RNA polymerase while labeling with either cyanine 3 deoxyuridine triphosphate (Cy3-dUTP) or Cy5-dUTP. The quality of each labeled cRNA was evaluated using an Agilent 2100 bioanalyzer before hybridization; 750 ng of Cy3- and Cy5-labeled cRNA were used in the hybridization.

growth_protocol: Cells were cultured in RPMI supplemented with 15% FBS (Life Technologies).  All cell lines obtained from the NIGMS were maintained at 37oC in a humidified atmosphere of 5% CO2 and were routinely tested and shown to be free of mycoplasma contamination using a commercial assay

extract_protocol: Total RNA was isolated using Qiagen RNeasy kit (Qiagen Sciences). The quality of all RNA samples was confirmed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: cell line

tag: cell type

value: lymphoblastoid

tag: genotype

value: ATM+/-

source_name: Global reference RNA

tag: source

value: Stratagene


title: GM02781B_1.5Gy_C3


title: GM03188A_sham_C3


title: Brain - Low post-mortem interval - SM-2AXWE

city: Cambridge

first: Kristin

last: Ardlie

state: MA

address: 7 Cambridge Center

institute: The Broad Institute of MIT and Harvard

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing:
Probe level data were summarized using custom probeset definitions provided by the BrainArrray resource (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp). RMA normalization was using Ensembl gene definitions.
probe group file: HuGene11stv1_Hs_ENSG.cdf

label: biotin

source_name: Brain - Anterior cingulate cortex (BA24) - Low post-mortem interval

label_protocol: Affymetrix protocol

extract_protocol: Affymetrix protocol

tag: gender

value: Male

tag: age

value: 40-49 years

tag: rin

value: Brain

value: Not Available


title: Brain - Low post-mortem interval - SM-2AXW8

source_name: Brain - Amygdala - Low post-mortem interval

value: Brain - Amygdala


title: Brain - Low post-mortem interval - SM-2QU5D

source_name: Brain - Cerebellar Hemisphere - Low post-mortem interval

value: Brain - Cerebellar Hemisphere


title: Brain - Low post-mortem interval - SM-2AXV6

source_name: Brain - Substantia nigra - Low post-mortem interval

value: Brain - Substantia nigra


title: GM03188A_sham_C5


title: Patient KQ 040

description:
Patient kq_040
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Brain - Low post-mortem interval - SM-2AXVF

source_name: Brain - Hippocampus - Low post-mortem interval

value: Brain - Hippocampus


title: GM02781B_sham_C5


title: Brain - Low post-mortem interval - SM-2QU5B

source_name: Brain - Frontal Cortex (BA9) - Low post-mortem interval

value: Brain - Frontal Cortex (BA9)


title: GM02781B_sham_C3


title: Patient KQ 028

description:
Patient kq_028
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 027

description:
Patient kq_027
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Blood - Low post-mortem interval - SM-2D43F

source_name: Whole Blood - Low post-mortem interval

value: Blood

value: Whole Blood

value: 4-7 hours


title: Patient KQ 026

description:
Patient kq_026
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.

value: unrelated patients

value: cleft lip, left


title: Patient KQ 025

description:
Patient kq_025
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.

value: blood


title: Human Fetal Brain NPC in Serum 30d Replicate 3

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

hyb_protocol: Labeled cDNA was hybridized, washed and stained to separate Affymetrix GeneChip Human Gene 1.0 ST Arrays by sample according to the protocols described by Affymetrix (Affymetrix, Inc).  Per staining, streptavidin phycoerythrin solution was used (Molecular Probes, Carlsbad, CA) and enhanced by an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: The Affymetrix Gene Chip Scanner 3000 was used to scan each Affymetrix GeneChip Human Gene 1.0 ST Array.  After, gene probe intensities were generated using the Affymetrix AGCC software (Affymetrix, Inc).

data_processing: The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe intensities and generate 33,297 RMA normalized gene fragment expression values for each hybridized cRNA.

label: Biotin

source_name: Human fetal brain-derived multipotential CNS progenitor cells (NPCs)

label_protocol: 200 nanograms of total RNA per sample was used in conjunction with the Affymetrix recommended protocol for the GeneChip Human Gene 1.0 ST Array (Affymetrix, Inc).

growth_protocol: The isolation and culture of multipotential human central nervous system progenitor cells has been described previously (Messam et al., 2003). Briefly, cells were grown as two-dimensional attached cultures on poly-D-lysine (PDL) coated plasticware at 37°C in 5% CO2. Progenitor cells were grown in serum-free neurobasal medium supplemented with N2 components, neural survival factor, 2mM L-glutamine, 50 ug/mL gentamycin, recombinant basic fibroblast growth factor (25ng/ml bFGF; Peprotech), and recombinant epidermal growth factor (20ng/ml EGF; Peprotech). To induce differentiation, progenitor growth media was removed, cells were washed twice with 37°C phosphate buffered saline, and PDA media was added. PDAs were maintained in minimal essential medium (Cellgro) supplemented with 10% FBS, 2 mM L-glutamine and 50 mg/mL gentamycin. For differentiation experiments cells were plated 3-4 days prior to isolation of RNA/protein. All time points up to and including 3 days post-differentiation were plated 3 days prior to differentiation. Later time points were differentiated in flasks, and plated 3-4 days prior to isolation of RNA/protein. Cells were plated at a density of 2x105 cells per well in 6-well plates for RNA isolation and plated on PDL coated glass cover slips in 12-well plates at a density of 5x104 cells per well for immunofluorescence.

extract_protocol: RNA was extracted by sample using the Qiagen RNAeasy kit.  Post extreaction, RNA quality and quantity was ensured using the Bioanalyzer (Agilent, Inc) and NanoDrop (Thermo Scientific, Inc) respectively.

value: PDA

tag: infection

value: JCV

tag: time


title: Human Fetal Brain NPC in Serum 30d Replicate 1


title: Brain - Low post-mortem interval - SM-2AXTV

source_name: Brain - Cortex - Low post-mortem interval

value: Female

value: 60-69 years

value: Brain - Cortex

value: 8-11 hours


title: Patient KQ 021

description:
Patient kq_021
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 019

description:
Patient kq_019
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 017

description:
Patient kq_017
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 022

description:
Patient kq_022
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 024

description:
Patient kq_024
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 023

description:
Patient kq_023
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 018

description:
Patient kq_018
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 016

description:
Patient kq_016
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Human Fetal Brain NPC in Serum 30d Replicate 2


title: Nerve - Low post-mortem interval - SM-2QU3I

source_name: Nerve - Tibial - Low post-mortem interval

value: Nerve

value: Nerve - Tibial


title: Patient KQ 015

description:
Patient kq_015
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 013

description:
Patient kq_013
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 012

description:
Patient kq_012
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 011

description:
Patient kq_011
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 014

description:
Patient kq_014
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 020

description:
Patient kq_020
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Human Fetal Brain NPC in Serum 7d Replicate 3


title: Human Fetal Brain NPC in Serum 7d Replicate 4


title: Brain - Low post-mortem interval - SM-2AXV3

source_name: Brain - Spinal cord (cervical c-1) - Low post-mortem interval

value: Brain

value: Brain - Spinal cord (cervical c-1)

value: Not Available


title: Brain - Low post-mortem interval - SM-2AXVN

source_name: Brain - Nucleus accumbens (basal ganglia) - Low post-mortem interval


title: Human Fetal Brain NPC in Serum 7d Replicate 2


title: Brain - Low post-mortem interval - SM-2AXTW

source_name: Brain - Cerebellum - Low post-mortem interval

value: Brain - Cerebellum


title: Patient KQ 010

description:
Patient kq_010
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Brain - Low post-mortem interval - SM-2AXVT

source_name: Brain - Caudate (basal ganglia) - Low post-mortem interval

value: Brain - Caudate (basal ganglia)


title: Human Fetal Brain NPC in Serum 7d Replicate 1


title: Brain - Low post-mortem interval - SM-2AXW1

value: Brain - Amygdala


title: Brain - Low post-mortem interval - SM-2AXVB

source_name: Brain - Hypothalamus - Low post-mortem interval

value: Brain - Hypothalamus


title: Human Fetal Brain NPC in Serum 1d Replicate 3


title: Human Fetal Brain NPC in Serum 1d Replicate 4


title: Brain - Low post-mortem interval - SM-2AXWC

value: Brain - Substantia nigra


title: Patient KQ 009

description:
Patient kq_009
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.

value: unrelated patients

value: cleft lip, left

value: blood


title: Patient KQ 008

description:
Patient kq_008
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 007

description:
Patient kq_007
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Human Fetal Brain NPC in Serum 1d Replicate 2

value: PDA

value: JCV


title: Human Fetal Brain NPC in Serum 1d Replicate 1


title: Patient KQ 005

description:
Patient kq_005
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 006

description:
Patient kq_006
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Brain - Low post-mortem interval - SM-2IZHU

value: Female

value: 60-69 years

value: Brain - Frontal Cortex (BA9)


title: Brain - Low post-mortem interval - SM-2IZHX

value: Brain - Cerebellar Hemisphere


title: Patient KQ 003

description:
Patient kq_003
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 004

description:
Patient kq_004
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 001

description:
Patient kq_001
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Patient KQ 002

description:
Patient kq_002
In this array, each tag of allele was spotted reduplicate. We take the mean single of the two spots as the single of allele.The AF was calculated by the formula: AF=allele B/allele A + allele B. While the AF values >0.6, genotypes were allele B homozygote; AF values <0.4, genotypes were allele A homozygote; AF values were between 0.4 and 0.6, genotypes were heterozygote.


title: Array#4;MSPC+ECFC in vivo (7,15,23 pool) vs Array#4;MSPC+ECFC in vitro (8,16,24 pool)

type: protein

city: Graz

first: Rokhsareh

last: Rohban

address: Stiftingtalstrasse 24

country: Austria

institute: Medical University Graz

description: comparison of signaling protein expression in MSPC+ECFC combination  plugs in vivo that leads in to vessel formation in later time point vs signaling protein expression in MSPC+ECFC plugs in vitro.

hyb_protocol: Washing steps were completed using manufacturer's protocols.

scan_protocol: A pair of 16-bit images from each array was captured with a Perkin-Elmer ScanArray Reader laser array scanner (Waltham, MA, USA). Signal quantification was carried out with ImaGene 8.0 from BioDiscovery (El Segundo, CA, USA) using pre-determined settings for spot partitioning as well as background correction according to the manufacturer's protocol

data_processing:
Z normalization for the data was used since it displays greater stability as a result of examining where each signal falls in the overall distribution of values within a given sample rather than adjusting all of the signals in a sample by a single common value . The z-ratio value was used to quantify the signal intensity.
Z scores were calculated by subtracting the overall average intensity of all spots within a sample from the raw intensity for each spot, and dividing it by the standard deviations (SD) of all of the measured intensities within each sample (Cheadle et al., 2003). Z-ratios were further calculated by taking the difference between the averages of the observed protein Z scores and dividing by the SD of all of the differences for that particular comparison.Calculated Z-ratios can be used in multiple comparisons without further reference to the individual conditional standard deviations by which they were derived. Z-ratio of equal to or more than ±1.2 was considered as a significantchange based on the core facility manufacturer’s instructions .

molecule: protein

source_name: Protein extraction from plugs containing MSPC+ECFC (N=3) harvested from in vivo system after 24h.

label_protocol: An amount of 50 µg of protein lysate from each sample was labeled with appropriate fluorescent dye followed by the non-specific fluorescent binding blockade. In order to load two samples in microarray fields side by side on the same array, an incubation chamber was mounted on to each microarray. Sample incubation and washing steps for removing unbound proteins was performed per manufacturer's protocol

growth_protocol: The MSPC and ECFC cells were isolated, purified and cultured for 7-10 days using alpha MEM and EGM-2 culture media enriched with  human pooled lysate (HPL) respectively.

extract_protocol: In order to detect signaling proteins, plugs containing a total number of 32x106 cells (to allow for recovery of an appropriate protein amount based on previous titration) were explanted one day (24h) after implantation. Explants were homogenized using 400 µL Triton X-100 lysis buffer containing proteinase- and phosphatase-inhibitors (Roche, IN, USA) followed by magNAlyser centrifugation (700xg, 20 sec.), sonification (5x10 sec. with 10 sec. cooling steps in between;Imlab, Boutersem, Belgium) and ultra-centrifugation (100,000xg,30 min;BeckmanCoulterGmbH, Vienna, Austria). Protein concentrations were determined by a Bradford assay (Bio-Rad, CA, USA) and optical density (OD) was measured with a Spectramax instrument (Molecular Devices, Sunnyvale, CA, USA). Protein lysates were subjected to the KinexTM antibody microarray as a customized service (Kinexus Bioinformatics Corp., Vancouver, Canada, www.kinexus.ca) comparing different cellular compositions for protein expression alterations.

treatment_protocol: Identical MSPC/ECFC pairs from healthy newborn humans, passage number 1 under normal condition without pretreatment

value: Umbilical Cord

value: Mesenchymal stem and progenitor cells and Endothelial Colony Forming Cells

source_name: Protein extraction from plugs containing MSPC+ECFC (N=3) from in vitro system after 24h.

growth_protocol: The MSPCs and ECFCs cells were isolated, purified and cultured for 7-10 days using alpha MEM and EGM-2 culture media enriched with human pooled lysate (HPL) respectively.

treatment_protocol: Identical MSPC/ECFC pairs from umbilical cord, healthy newborn humans, passage number 1 under normal condition (alpha MEM medium enriched with HPL, 7-10 days in 37°C incubator without pretreatment.


title: Array#3;MSPC+ECFC in vivo (5,13,21 pool) vs Array#3;Matrix only (6,14,22 pool)

description: comparison of signaling protein expression in MSPC+ECFC combination plugs in vivo that leads in to vessel formation in later time point vs control (Matrix only)

source_name: Protein extraction from plugs containing MSPC+ECFC (N=3) all harvested from in vivo system after 24h.

source_name: Protein extraction from plugs containing cell free Matrix (N=3), all harvested from in vivo system after 24h.

growth_protocol: No cell used in the chip2 of this microarray

treatment_protocol: Matrigel only. No cell input


title: Array#1;MSPC+ECFC in vivo (1,9,17 pool) vs Array#1;MSPC only in vivo (3,11,19 pool)

description: comparison of signaling protein expression in MSPC+ECFC combination plugs in vivo that leads in to vessel formation in later time point vs signaling protein expression in MSPC only plugs in vivo that leads in to bone formation in later time course.

source_name: Protein extraction from plugs containing MSPC only (N=3), all harvested from in vivo system after 24h.

growth_protocol: The MSPC cells were isolated, purified and cultured for 7-10 days using alpha MEM culture medium enriched with  human pooled lysate (HPL).

treatment_protocol: Cultured MSPCs from umbilical cord, healthy newborn humans, passage number 1 under normal condition (alpha MEM medium enriched with HPL, 7-10 days in 37°C incubator without pretreatment.

value: Mesenchymal stem and progenitor cells


title: Array#2;MSPC+ECFC in vivo (2,10,18 pool) vs Array#2;ECFC in vivo (4,12,20 pool)

description: comparison of signaling protein expression in MSPC+ECFC combination plugs in vivo that leads in to vessel formation in later time point vs signaling protein expression in ECFC only plugs in vivo.

source_name: Protein extraction from plugs containing ECFC only (N=3), all harvested from in vivo system after 24h.

growth_protocol: The ECFC cells were isolated, purified and cultured for 7-10 days using EGM-2 culture medium enriched with  human pooled lysate (HPL).

treatment_protocol: Cultured ECFCs from umbilical cord, healthy newborn humans, passage number 1 under normal condition (alpha MEM medium enriched with HPL, 7-10 days in 37°C incubator without pretreatment.

value: Endothelial Colony Forming Cells


title: Brain - Low post-mortem interval - SM-2AXVA

value: Male

value: 50-59 years

value: Brain

value: Brain - Spinal cord (cervical c-1)

value: Not Available


title: Brain - Low post-mortem interval - SM-2AXVI

value: Brain - Hypothalamus


title: Human Fetal Brain NPC in Serum 1h Replicate 3


title: Brain - Low post-mortem interval - SM-2AXVZ

value: Brain - Caudate (basal ganglia)


title: Human Fetal Brain NPC in Serum 1h Replicate 1

value: PDA


title: Human Fetal Brain NPC 0h Replicate 4

description: Human Fetal Brain NPC 0h Replicate 4

value: NPC

value: JCV


title: Brain - Low post-mortem interval - SM-2AXVS

value: Brain - Nucleus accumbens (basal ganglia)


title: Brain - Low post-mortem interval - SM-2AXW6

source_name: Brain - Amygdala - Low post-mortem interval

value: Brain - Amygdala


title: Brain - Low post-mortem interval - SM-2AXWB

source_name: Brain - Anterior cingulate cortex (BA24) - Low post-mortem interval


title: Human Fetal Brain NPC 0h Replicate 2

description: Human Fetal Brain NPC 0h Replicate 2


title: Brain - Low post-mortem interval - SM-2AXV4

source_name: Brain - Substantia nigra - Low post-mortem interval

value: Brain - Substantia nigra


title: GM03189_1.5Gy_C5

description: cell lines with same ATM genotype receiving the same treatment (Sham or IR) are biological replicates of one-another

source_name: AT patient

value: lymphoblastoid

value: ATM-/-

source_name: Global reference RNA

value: Stratagene


title: GM03189_1.5Gy_C3


title: Brain - Low post-mortem interval - SM-2IZHM

source_name: Brain - Cerebellar Hemisphere - Low post-mortem interval

value: Brain - Cerebellar Hemisphere


title: Brain - Low post-mortem interval - SM-2AXVC

source_name: Brain - Hippocampus - Low post-mortem interval

value: Male

value: Brain - Hippocampus


title: Human Fetal Brain NPC 0h Replicate 3

description: Human Fetal Brain NPC 0h Replicate 3

source_name: Human fetal brain-derived multipotential CNS progenitor cells (NPCs)


title: Human Fetal Brain NPC in Serum 1h Replicate 2


title: Human Fetal Brain NPC 0h Replicate 1

description: Human Fetal Brain NPC 0h Replicate 1


title: KO_PMΦ_rep3

city: Münster

first: Niels-Arne

last: Münck

address: Roentgenstraße 21

department: Insitute of Immunology

country: Germany

institute: University of Münster

hyb_protocol: 5µg of fragmented cRNA was hybridized on a Affymetrix MoGene-1_0-st-v1. GeneChips were washed and stained in an Affymetrix Fluidics Station 450

scan_protocol: Scanning was performed on a GeneChip Scanner 3000 7G

data_processing: Data was processed with Affymetrix Expression Console 1.1 software using the RMA algorithm

organism: Mus musculus

source_name: Nfkbiz-/- peritonial macrophages

label_protocol: Probes were labeled using the GeneChip WT Terminal Labeling kit

growth_protocol: Female C57Bl/6 mice were euthanized by CO2 asphyxiation. For isolation of peritoneal macrophages (PMφ) the abdominal skin was removed, a catheter (24 GA) was inserted into the peritoneal cavity and 10 mL of ice-cold PBS were injected. After massage of the peritoneum, peritoneal fluids were aspirated, centrifuged at 500 g for 5 min, and yielded peritoneal cells (PMφ were resuspended in 0.5-1.5 mL Mφ medium containing DMEM, 10% FCS and MycoZapPlusCL antibiotics (Lonza). Next, cells were seeded in 96-well plates (100 µL of cells/ well) and cultivated at 37°C for 2 h

extract_protocol: RNA was extracted using RNeasy mini kit (Qiagen) according to the manufacturer's instructions. Single-strand cDNA was prepared using the Ambion WT Expression kit

treatment_protocol: Cells were treated with 1 µg/mL LPS for 4 h or left untreated

value: female

value: peritoneal macrophages

tag: strain

value: Nfkbiz-/-


title: Brain - Low post-mortem interval - SM-2IZHO

source_name: Brain - Frontal Cortex (BA9) - Low post-mortem interval

value: 50-59 years

value: Brain

value: Brain - Frontal Cortex (BA9)

value: Not Available


title: GM03189_sham_C3


title: KO_PMΦ_rep1


title: KO_PMΦ_rep2


title: GM09582_1.5Gy_C5


title: KO_PMΦ_4hLPS_rep3

source_name: Nfkbiz-/- peritonial macrophages incubated with 1µg/ml LPS for 4h


title: Blood - Low post-mortem interval - SM-2IZIU

source_name: Whole Blood - Low post-mortem interval

value: Blood

value: Whole Blood

value: 8-11 hours


title: KO_PMΦ_4hLPS_rep2


title: KO_PMΦ_4hLPS_rep1


title: GM03189_sham_C5


title: GM09582_sham_C5


title: GM09582_sham_C3


title: GM02782_1.5Gy_C5


title: Brain - Low post-mortem interval - SM-2QU3M

source_name: Brain - Hypothalamus - Low post-mortem interval

value: 60-69 years

value: Brain - Hypothalamus


title: WT_PMΦ_rep3

source_name: C57Bl/6 peritonial macrophages


title: GM02782_1.5Gy_C3

value: lymphoblastoid

value: ATM-/-


title: Brain - Low post-mortem interval - SM-2AXVL

source_name: Brain - Putamen (basal ganglia) - Low post-mortem interval

value: Brain - Putamen (basal ganglia)


title: GM02782_sham_C5

value: Stratagene


title: Brain - Low post-mortem interval - SM-2AXVQ

source_name: Brain - Nucleus accumbens (basal ganglia) - Low post-mortem interval

value: Male


title: GM13989_sham_C5


title: GM13989_1.5Gy_C3


title: Brain - Low post-mortem interval - SM-2AXVW

source_name: Brain - Caudate (basal ganglia) - Low post-mortem interval

value: Brain - Caudate (basal ganglia)


title: GM02782_sham_C3


title: GM13989_1.5Gy_C5


title: GM13873_sham_C5


title: WT_PMΦ_4hLPS_rep1

source_name: C57Bl/6 peritonial macrophages incubated with 1µg/ml LPS for 4h

value: female

value: peritoneal macrophages


title: GM03332_1.5Gy_C5


title: WT_PMΦ_4hLPS_rep3


title: GM03332_sham_C3


title: GM03332_sham_C5


title: Brain - Low post-mortem interval - SM-2AXWF

value: Brain - Substantia nigra


title: Brain - Low post-mortem interval - SM-2AXW9

source_name: Brain - Anterior cingulate cortex (BA24) - Low post-mortem interval

value: Brain


title: WT_PMΦ_4hLPS_rep2


title: WT_PMΦ_rep1


title: Brain - Low post-mortem interval - SM-2AXW4

source_name: Brain - Amygdala - Low post-mortem interval

value: Brain - Amygdala


title: GM13873_1.5Gy_C3

source_name: AT patient


title: GM03332_1.5Gy_C3

source_name: Global reference RNA


title: WT_PMΦ_rep2


title: GM13989_sham_C3


title: BALB/c intestine biological rep3

city: Montreal

first: Daniel

last: Leclerc

state: Quebec

address: 4060 Ste-Catherine West

department: Medical Genetics, Room 242

country: Canada

institute: Montreal Children's Hospital

description: Gene expression data from dissected duodenum tissue

hyb_protocol: Following fragmentation and labeling,  1.856ug of ssDNA were hybridized for 17 hrs at 45C on GeneChip® Mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with FlexArray using Affymetrix default analysis settings and APT as normalization method.

source_name: BALB/c mouse duodenum tissue

label_protocol: Labeled and fragmented ssDNAs were prepared according to the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay from 100ng of Total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay User guide P/N 701880 Rev. 5)

growth_protocol: After weaning, BALB/c Mthfr +/- mice and C57Bl/6 Mthfr +/- mice were fed with a control diet (CD, 2mg folate/kg) and a low folate diet (FD, 0.3mg folate/kg) for 1 year. Both diets contain succinylsulfanthiozole (1%) to prevent folate synthesis by intestine microbial biota.

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

treatment_protocol: Mice were sacrificed and intestines were removed to examine for tumour incidence under dissecting microscope. Normal intestines were frozen at -80 degree.

value: BALB/c

value: MTHFR+/-

value: duodenum

tag: treatment

value: low folate diet


title: Brain - Low post-mortem interval - SM-2IZHV

source_name: Brain - Cerebellar Hemisphere - Low post-mortem interval

value: 60-69 years

value: Brain - Cerebellar Hemisphere

value: Not Available


title: GM13873_1.5Gy_C5

value: lymphoblastoid

value: ATM-/-


title: Brain - Low post-mortem interval - SM-2AXV7

source_name: Brain - Hippocampus - Low post-mortem interval

value: Brain - Hippocampus


title: BALB/c intestine biological rep2


title: GM13873_sham_C3

value: Stratagene


title: Brain - Low post-mortem interval - SM-2IZHY

value: Male

value: Brain - Frontal Cortex (BA9)


title: BALB/c intestine biological rep4

value: female


title: GM03299_sham_C3

source_name: Non AT carrier

value: ATM+/+


title: GM03299_1.5Gy_C5


title: GM03299_sham_C5


title: GM03714_sham_C5


title: GM03299_1.5Gy_C3


title: AG15033_1.5Gy_C5


title: Heart - Low post-mortem interval - SM-2AXU8

source_name: Heart - Left Ventricle - Low post-mortem interval

value: 40-49 years

value: Heart

value: Heart - Left Ventricle

value: 4-7 hours


title: GM03714_sham_C3


title: Lung - Low post-mortem interval - SM-2AXU9

source_name: Lung - Low post-mortem interval

value: Lung


title: C57 intestine biological rep3

source_name: C57 mouse duodenum tissue

value: MTHFR+/-

value: duodenum

value: low folate diet


title: BALB/c intestine biological rep1

value: BALB/c


title: AG15033_1.5Gy_C3

value: lymphoblastoid


title: C57 intestine biological rep2


title: GM03714_1.5Gy_C3


title: AG15033_sham_C5


title: GM03714_1.5Gy_C5


title: Thyroid - Low post-mortem interval - SM-2AXU7

source_name: Thyroid - Low post-mortem interval

value: Thyroid


title: Blood Vessel - Low post-mortem interval - SM-2QU51

source_name: Artery - Tibial - Low post-mortem interval

value: Blood Vessel

value: Artery - Tibial


title: AG15014_1.5Gy_C3

value: Stratagene


title: Muscle - Low post-mortem interval - SM-2AXU6

source_name: Muscle - Skeletal - Low post-mortem interval

value: Male

value: Muscle

value: Muscle - Skeletal


title: Blood - Low post-mortem interval - SM-2AXUR

source_name: Whole Blood - Low post-mortem interval

value: 60-69 years

value: Blood

value: Whole Blood

value: 8-11 hours


title: AG15033_sham_C3

value: ATM+/+


title: GM13989_C5

description: cell lines with same ATM genotype are biological replicates of one-another

value: ATM-/-


title: C57 intestine biological rep4

value: MTHFR+/-

value: duodenum

value: female


title: C57 intestine biological rep1

value: low folate diet


title: Human Fetal Brain NPC in Serum 1h Replicate 4

source_name: Human fetal brain-derived multipotential CNS progenitor cells (NPCs)

value: PDA

value: JCV


title: Nerve - Low post-mortem interval - SM-2QU4B

source_name: Nerve - Tibial - Low post-mortem interval

value: 40-49 years

value: Nerve

value: Nerve - Tibial

value: 4-7 hours


title: AG15014_1.5Gy_C5

value: lymphoblastoid

value: Stratagene


title: GM13989_C3


title: GM13873_C5


title: AG15014_sham_C3


title: AG14832_1.5Gy_C3


title: AG14832_1.5Gy_C5


title: GM03332c_C3


title: AG14832_sham_C5


title: GM03332c_C5


title: AG15014_sham_C5


title: AG14778_sham_C3


title: Heart - Low post-mortem interval - SM-2AXUA

value: Female

value: 60-69 years

value: Heart

value: Heart - Left Ventricle


title: GM13873_C3

value: ATM-/-


title: AG14778_1.5Gy_C5

value: ATM+/+


title: AG14832_sham_C3


title: Lung - Low post-mortem interval - SM-2D43B

value: Lung


title: Brain - Low post-mortem interval - SM-2IZIT

source_name: Brain - Nucleus accumbens (basal ganglia) - Low post-mortem interval

value: Brain

value: Not Available


title: AG14778_sham_C5


title: GM03189D_C5


title: Brain - Low post-mortem interval - SM-2AXV9

source_name: Brain - Putamen (basal ganglia) - Low post-mortem interval

value: Brain - Putamen (basal ganglia)


title: GM09582_1.5Gy_C3

source_name: AT patient


title: AG14778_1.5Gy_C3

source_name: Global reference RNA


title: GM03189D_C3


title: GM09579_C5

source_name: AT carrier

value: ATM+/-


title: CXCR6 Lo biological rep.2

city: Toyama

first: yukihiro

last: furusawa

address: Kurokawa

country: Japan

institute: Toyama Prefectural University

description: Gene expression data from CXCR6 Lo T cells isolated from lamina proopria of CD45Rb hi transfer model

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: CXCR6 Lo T cells isolated from colonic lamina propria

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using 3'-IVT Express Kit

extract_protocol: QIAGEN Rneasy Micro according to manuacture's instruction

value: CD3+CD4+CXCR6 Lo

tag: background mouse strain

value: BALB/c


title: CXCR6 Lo biological rep.1


title: CXCR6 Hi biological rep.2

description: Gene expression data from CXCR6 Hi T cells isolated from lamina proopria of CD45Rb hi transfer model

source_name: CXCR6 Hi T cells isolated from colonic lamina propria

value: CD3+CD4+CXCR6 Hi


title: CXCR6 Hi biological rep.1


title: GM09579_C3


title: CD45Rb Hi

description: Gene expression data from CD45Rb Hi T cells isolated from lamina proopria of healthy mice

source_name: CD45Rb hi Naive T cells isolated from spleen

value: CD3+CD4+CD45Rb Hi


title: Brain - Low post-mortem interval - SM-2AXVM

source_name: Brain - Caudate (basal ganglia) - Low post-mortem interval

value: Brain - Caudate (basal ganglia)


title: liver exposed to progesterone (P4T), biological replication 4

city: São Paulo

first: Carla

middle: A

last: Piccinato

state: SP

address: Rua Albert Einstein, 627- 2SS Bloco A

department: Instituto de Ensino e Pesquisa Albert Einstein

country: Brazil

institute: Hospital Albert Einstein

description: Gene expression data from bovine liver of ovariectomized cows with progesterone exposure for 14 days.

hyb_protocol: The fragmented and biotinylated aRNA were hybridized to the BovineGeneChip expression arrays for 16 h at 45°C. The arrays were processed using the Affymetrix Fluidics 450 Station. A complex was then formed on features that had hybridized with the biotinylated aRNA by incubating with streptavidin, R-phycoerythrin as well as antistreptavidin antibodies that had been biotinylated.

scan_protocol: The image was captured using an Affymetrix GC3000 scanner. Arrays were scanned using the Affymetrix GCOS 1.4 software. Fluorescent signals corresponding to hybridization intensities were analyzed with the Affymetrix Microarray Suite (MAS) 5.0 algorithm using with default analysis settings.

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

organism: Bos taurus

source_name: bovine liver exposed to 14 days of intradermal progesterone

label_protocol: Biotinylated cRNA were prepared with Message Amp II Biotin Enhanced kit (Ambion)  from 2ug of mRNA. Affymetrix poly-A RNA control kit was also spiked to offer another level of qulity control.

extract_protocol: After grinding liver tissue, 20mg of the fine powder was lysed with 400 ul of lysis buffer and was sheared by passing the homogenate through a 25-guage needle. Messenger RNA was isolated from the liver samples using Magnetight oligo (dT) magnetic beads. The mRNA was eluted by heating 10ul of elution buffer and the isolated mRNA was stored at -70C.

treatment_protocol: no hormonal exposure (controls), intradermal ear implant that releases estradiol (E2T); vaginal device that delivers progesterone (P4 T); both ear implant and vaginal device (E2P4T).

value: liver

tag: Sex

value: female

tag: breed

value: Holstein cows

tag: physiologycal status

value: dry (non-lactating) ovariectomized cows


title: Brain - Low post-mortem interval - SM-2AXVY

source_name: Brain - Anterior cingulate cortex (BA24) - Low post-mortem interval

value: Female

value: 60-69 years


title: Skin - Low post-mortem interval - SM-2AXU5

source_name: Skin - Sun Exposed (Lower leg) - Low post-mortem interval

value: Male

value: 40-49 years

value: Skin

value: Skin - Sun Exposed (Lower leg)

value: 4-7 hours


title: liver exposed to progesterone (P4T), biological replication 6


title: liver exposed to progesterone (P4T), biological replication 5


title: GM03334_C3

value: lymphoblastoid

value: ATM+/-

value: Stratagene


title: liver exposed to progesterone (P4T), biological replication 2


title: GM03334_C5


title: Brain - Low post-mortem interval - SM-2AXW5

source_name: Brain - Substantia nigra - Low post-mortem interval

value: Brain

value: Brain - Substantia nigra

value: Not Available


title: liver exposed to progesterone (P4T), biological replication 3

value: liver


title: GM03188A_C3


title: Brain - Low post-mortem interval - SM-2AXV2

source_name: Brain - Hypothalamus - Low post-mortem interval

value: Brain - Hypothalamus


title: Brain - Low post-mortem interval - SM-2AXWA

source_name: Brain - Hippocampus - Low post-mortem interval

value: Brain - Hippocampus


title: Brain - Low post-mortem interval - SM-2IZHP

source_name: Brain - Cerebellar Hemisphere - Low post-mortem interval

value: Brain - Cerebellar Hemisphere


title: liver exposed to estradiol and progesterone (E2P4T), biological replication 7

description: Gene expression data from bovine liver of ovariectomized cows with estradiol and progesterone exposure for 14 days.

source_name: bovine liver exposed to 14 days of intradermal estradiol and progesterone

value: female

value: Holstein cows

value: dry (non-lactating) ovariectomized cows


title: liver exposed to progesterone (P4T), biological replication 7


title: liver exposed to progesterone (P4T), biological replication 1


title: liver exposed to estradiol and progesterone (E2P4T), biological replication 6


title: Brain - Low post-mortem interval - SM-2QU53

source_name: Brain - Cortex - Low post-mortem interval

value: Female

value: 60-69 years

value: Brain - Cortex

value: 8-11 hours


title: GM02781B_C5

value: lymphoblastoid


title: Brain - Low post-mortem interval - SM-2IZHQ

source_name: Brain - Frontal Cortex (BA9) - Low post-mortem interval

value: Brain - Frontal Cortex (BA9)


title: liver exposed to estradiol and progesterone (E2P4T), biological replication 5


title: GM03188A_C5

value: ATM+/-

value: Stratagene


title: GM02781B_C3


title: Brain - Low post-mortem interval - SM-2D43A

source_name: Brain - Cerebellum - Low post-mortem interval

value: Male

value: Brain

value: Brain - Cerebellum

value: 20-23 hours


title: AG15033_C5

source_name: Non AT carrier

value: ATM+/+

source_name: Global reference RNA


title: AG15033_C3


title: In_vitro_rep_3

city: Yokohama

first: Pamela

last: Gan

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN Plant Sciences

institute: RIKEN

description: Gene expression of C. orbiculare mycelia in vitro

hyb_protocol: 600 ng of linearly amplified cRNA (specific activity >10 pmol Cy3/ug) was fragmented according to the Low Input Quick Amp Labeling Kit (Agilent) manufacturer's instructions. Fragmented cRNA was hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately using an air gun.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Profile AgilentG3_GX_1Color).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.  Only control and fungal features which did not hybridize to plant only controls were used for normalization.

organism: Colletotrichum orbiculare

source_name: In vitro grown hyphae replicate 3

label_protocol: Cyanine-3 labelled cRNA was prepared from total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: In vitro hyphae were cultured in potato dextrose at 24 °C. Conidia were harvested from 7 day old mycelia.

extract_protocol: Samples were ground in liquid nitrogen or a chilled ShakeMaster (BMS bio medical sciences).  Total RNA was extracted using the QIAgen Rneasy Plant mini kit according to the manufacturer's instructions including the on-column DNase digestion step.

treatment_protocol: For infections, a suspension of 2.5x10E6 Colletotrichum orbiculare conidia/mL was brushed on the abaxial side of a fully expanded Nicotiana benthamiana leaf using a soft brush. At 24 hours after inoculation (hpi) and 3 days post inoculation (dpi), the abaxial epidermis was peeled with forceps.  At 7 dpi, regions showing necrotic lesions were excised.

tag: organism

value: Colletotrichum orbiculare

value: Hyphae


title: liver exposed to estradiol and progesterone (E2P4T), biological replication 3

tag: tissue

value: liver

value: female

value: Holstein cows


title: AG15014_C5

tag: cell line


title: liver exposed to estradiol and progesterone (E2P4T), biological replication 2

value: dry (non-lactating) ovariectomized cows


title: Brain - Low post-mortem interval - SM-2D43D

value: 60-69 years

value: Brain - Cortex


title: Lung - Low post-mortem interval - SM-2AXU3

source_name: Lung - Low post-mortem interval

value: Lung


title: AG15014_C3

tag: cell type

value: lymphoblastoid


title: In_vitro_rep_2

source_name: In vitro grown hyphae replicate 2


title: In_vitro_rep_1

source_name: In vitro grown hyphae replicate 1


title: Brain - Low post-mortem interval - SM-2AXVR

source_name: Brain - Amygdala - Low post-mortem interval

value: Female

value: Brain - Amygdala

value: Not Available


title: Blood Vessel - Low post-mortem interval - SM-2QU2Q

source_name: Artery - Tibial - Low post-mortem interval

value: Male

value: Blood Vessel

value: Artery - Tibial


title: AG14832_C5

tag: genotype

value: ATM+/+

value: Stratagene


title: AG14832_C3

tag: source


title: liver exposed to estradiol (E2T), biological replication 7

description: Gene expression data from bovine liver of ovariectomized cows with estradiol exposure for 14 days.

source_name: bovine liver exposed to 14 days of intradermal estradiol


title: Heart - Low post-mortem interval - SM-2AXU2

source_name: Heart - Left Ventricle - Low post-mortem interval

tag: gender

value: Heart

value: Heart - Left Ventricle

value: 20-23 hours


title: liver exposed to estradiol (E2T), biological replication 6

value: liver

value: female

value: Holstein cows


title: liver exposed to estradiol and progesterone (E2P4T), biological replication 1

value: dry (non-lactating) ovariectomized cows


title: 7_dpi_C_orb_N_benth_rep_2

description: Gene expression of C. orbiculare at 7 dpi on N. benthamiana

source_name: Colletotrichum orbiculare-infected Nicotiana benthamiana leaf, infected for 7 dpi, replicate 2

value: Colletotrichum orbiculare and N. benthamiana

value: Infected leaf


title: 7_dpi_C_orb_N_benth_rep_3

source_name: Colletotrichum orbiculare-infected Nicotiana benthamiana leaf, infected for 7 dpi, replicate 3


title: 7_dpi_C_orb_N_benth_rep_1

source_name: Colletotrichum orbiculare-infected Nicotiana benthamiana leaf, infected for 7 dpi, replicate 1


title: Muscle - Low post-mortem interval - SM-2QU34

source_name: Muscle - Skeletal - Low post-mortem interval

tag: age

value: 60-69 years

value: Muscle

value: Muscle - Skeletal

value: 16-19 hours


title: AG14778_C5

value: lymphoblastoid


title: Thyroid - Low post-mortem interval - SM-2AXU4

source_name: Thyroid - Low post-mortem interval

value: Male

tag: rin

value: Thyroid


title: liver exposed to estradiol (E2T), biological replication 4


title: liver exposed to estradiol (E2T), biological replication 3


title: AG14778_C3

value: ATM+/+

value: Stratagene


title: Brain - Low post-mortem interval - SM-2AXVD

source_name: Brain - Hypothalamus - Low post-mortem interval

value: Brain

value: Brain - Hypothalamus

value: Not Available


title: Brain - Low post-mortem interval - SM-2AXV5

source_name: Brain - Putamen (basal ganglia) - Low post-mortem interval

value: Brain - Putamen (basal ganglia)


title: liver exposed to estradiol (E2T), biological replication 5

value: liver

value: female

value: Holstein cows


title: 3_dpi_C_orb_N_benth_rep_3

description: Gene expression of C. orbiculare at 3 dpi on N. benthamiana

source_name: Colletotrichum orbiculare-infected Nicotiana benthamiana leaf epidermal peels, infected for 3 dpi, replicate 3

value: Colletotrichum orbiculare and N. benthamiana

value: Infected leaf epidermal peel


title: liver exposed to estradiol (E2T), biological replication 2

value: dry (non-lactating) ovariectomized cows


title: Brain - Low post-mortem interval - SM-2AXWD

source_name: Brain - Nucleus accumbens (basal ganglia) - Low post-mortem interval

value: 60-69 years


title: 3_dpi_C_orb_N_benth_rep_2

source_name: Colletotrichum orbiculare-infected Nicotiana benthamiana leaf epidermal peels, infected for 3 dpi, replicate 2


title: Caco-2 with B. breve, biological rep2

city: Paris

first: Thierry

last: Pedron

address: 28 rue du Docteur Roux

department: Biologie cellulaire et Infection

country: France

institute: Pasteur Institute

description: gene expression data

hyb_protocol: 12.5 microgramms of fragmented cRNA were hybridized to an HG-U133A and the chips were washed and stained with streptavidin-phycoerythrin using a fluidics station.

scan_protocol: The arrays were scanned at 570 nm with a resolution of 3 mm/pixel using a GeneArray scanner from Agilent Technologies.

data_processing: Preprocessing by Robust Multichip Average (RMA) was applied to process individual probe values (perfect match) and to generate summary values for each probe set (transcript). The dChip software was used for comparative analysis and for hierarchical clustering with Euclidean distance and average as a linkage method

source_name: Caco-2 cells cultured with B. breve

label_protocol: cDNA were synthetized using Superscript Choice system, Biotin-labeled-cRNA was synthetized with the Enzo BioArrayHigh Yield RNA transcript labeling kit.

growth_protocol: overnight cultures of Caco-cells co-cultured with or without bacteria

extract_protocol: Rneasy mini kit (Qiagen)

treatment_protocol: Before extraction, cells were whashed twice  with cold PBS

tag: cells

tag: cultured with

value: Bifidobacterium breve


title: Brain - Low post-mortem interval - SM-2AXW7

source_name: Brain - Caudate (basal ganglia) - Low post-mortem interval

value: Brain - Caudate (basal ganglia)


title: Caco-2 with B. breve, biological rep3

description: gene expression data


title: 3_dpi_C_orb_N_benth_rep_1

source_name: Colletotrichum orbiculare-infected Nicotiana benthamiana leaf epidermal peels, infected for 3 dpi, replicate 1

tag: time


title: Caco-2 with L. casei, biological rep3

description: gene expression data

source_name: Caco-2 cells cultured with L. casei

value: Lactobacillus casei


title: liver exposed to estradiol and progesterone (E2P4T), biological replication 4

source_name: bovine liver exposed to 14 days of intradermal estradiol and progesterone


title: Caco-2 with B. breve, biological rep1

description: gene expression data


title: Brain - Low post-mortem interval - SM-2AXVU

source_name: Brain - Anterior cingulate cortex (BA24) - Low post-mortem interval

value: Male


title: 24_hpi_C_orb_N_benth_rep_1

description: Gene expression of C. orbiculare at 24 hpi on N. benthamiana

source_name: Colletotrichum orbiculare-infected N. benthamiana leaf epidermal peels, infected for 24 hpi, replicate 1


title: liver control, biological replication 7

description: Gene expression data from bovine liver of ovariectomized cows with no exposure of steroid hormones for 14 days.

source_name: bovine liver exposed to no hormone treatments


title: liver control, biological replication 6


title: liver exposed to estradiol (E2T), biological replication 1

source_name: bovine liver exposed to 14 days of intradermal estradiol


title: 24_hpi_C_orb_N_benth_rep_2

source_name: Colletotrichum orbiculare-infected Nicotiana benthamiana leaf epidermal peels, infected for 24 hpi, replicate 2


title: 24_hpi_C_orb_N_benth_rep_3

source_name: Colletotrichum orbiculare-infected Nicotiana benthamiana leaf epidermal peels, infected for 24 hpi, replicate 3


title: Conidia_rep_3

description: Gene expression of C. orbiculare ungerminated conidia

source_name: Conidia replicate 3

value: Colletotrichum orbiculare

value: Conidia


title: Brain - Low post-mortem interval - SM-2IZK7

source_name: Brain - Substantia nigra - Low post-mortem interval

value: Brain

value: Brain - Substantia nigra


title: Caco-2 with L. casei, biological rep2

description: gene expression data


title: liver control, biological replication 5


title: liver control, biological replication 4


title: Caco-2 with L. casei, biological rep1

description: gene expression data


title: Brain - Low post-mortem interval - SM-2AXW2

source_name: Brain - Amygdala - Low post-mortem interval

value: Brain - Amygdala

value: Not Available


title: Caco-2 alone, biological rep3

description: gene expression data

source_name: Caco-2 cells alone


title: liver control, biological replication 3

value: liver


title: Conidia_rep_1

source_name: Conidia replicate 1


title: Conidia_rep_2

source_name: Conidia replicate 2


title: Caco-2 alone, biological rep2

description: gene expression data


title: Blood - Low post-mortem interval - SM-2D43E

source_name: Whole Blood - Low post-mortem interval

value: Blood

value: Whole Blood

value: 16-19 hours


title: Brain - Low post-mortem interval - SM-2IZJW

source_name: Brain - Frontal Cortex (BA9) - Low post-mortem interval

value: Brain - Frontal Cortex (BA9)


title: Brain - Low post-mortem interval - SM-2AXVJ

source_name: Brain - Hippocampus - Low post-mortem interval

value: Brain - Hippocampus


title: liver control, biological replication 2

value: female

value: Holstein cows

value: dry (non-lactating) ovariectomized cows


title: Caco-2 alone, biological rep1

description: gene expression data


title: liver control, biological replication 1


title: Bcrp-_Brain_11

status: Public on Apr 08 2013

city: Indianapolis

first: Keith

middle: M

last: Goldstein

state: IN

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly & Co.

description: Male SAGE Bcrp knockout Sprague-Dawley rats 8-11 weeks old

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Affymetrix standard procedures.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 30007G using GeneChip Operating Software to generate raw and averaged image files (.DAT and .CEL).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 1500.

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared using a modified MessageAmp procedure (Life Technologies, Inc.) from 1 ug total RNA.

extract_protocol: RNA was isolated using Qiagen RNeasy columns according to the manufacturer's protocol

treatment_protocol: SAGE knockout of Mdr1a, Mrp2, Bcrp (www.sageresearchmodels.com)

tag: strain

value: Sprague Dawley

value: male

tag: genotype/variation

value: Bcrp Knockout


title: Bcrp-_Brain_12


title: Bcrp-_Brain_10


title: Brain - Low post-mortem interval - SM-2IZJZ

source_name: Brain - Cerebellar Hemisphere - Low post-mortem interval

value: Male

value: 60-69 years

value: Brain - Cerebellar Hemisphere


title: Bcrp-_Jejunum_11

value: Jejunum


title: Bcrp-_Duodenum_12

value: Duodenum


title: Bcrp-_Ileum_11

value: Ileum


title: Bcrp-_Jejunum_12


title: Bcrp-_Duodenum_11


title: Bcrp-_Kidney_cortex_11

value: Kidney cortex


title: Bcrp-_Kidney_cortex_10


title: Bcrp-_Kidney_cortex_12


title: Bcrp-_Jejunum_9


title: Bcrp-_Ileum_9


title: Bcrp-_Jejunum_10


title: Bcrp-_Ileum_12


title: Bcrp-_Duodenum_10


title: Bcrp-_Ileum_10


title: Bcrp-_Brain_9

value: Brain


title: Bcrp-_Kidney_cortex_9


title: Bcrp-_Liver_10

value: Liver


title: Bcrp-_Kidney_medulla_9

value: Kidney medulla


title: Bcrp-_Kidney_medulla_12


title: Bcrp-_Liver_11


title: Bcrp-_Duodenum_9


title: Bcrp-_Kidney_medulla_11


title: Bcrp-_Kidney_medulla_10


title: Bcrp-_Liver_9


title: Bcrp-_Liver_12


title: Mdr1a-_Brain_6

description: Male SAGE Mdr1a knockout Sprague-Dawley rats 8-11 weeks old

value: Mdr1a knockout


title: Mdr1a-_Brain_7


title: Mdr1a-_Duodenum_5


title: Mdr1a-_Kidney_cortex_7


title: BE(2)-C ATRA_5uM + VPA_1mM 72hr, rep. 2

city: Boston

first: Kimberly

last: Stegmaier

address: Harvard Medical School

department: Department of Pediatric Oncology

institute: Dana-Farber Cancer Institute and Children’s Hospital Boston

description: BE(2)-C cells treated with 5uM ATRA + 1mM valproic acid (VPA) for 72 hours, rep. 2

hyb_protocol: Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.

scan_protocol: Scans were performed on Affymetrix scanners.

data_processing: Raw expression values were normalized using Robust Multiarray Averaging (RMA) in Bioconductor.

label_protocol: First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.

growth_protocol: Neuroblastoma cell line BE(2)-C was maintained in DMEM (Cellgro, Manassas, VA, USA) supplemented with 10% fetal bovine serum (Sigma-Aldrich, St. Louis, MO, USA) and 1% penicillin-streptomycin with glutamine (Cellgro).

extract_protocol: RNA was extracted using the RNeasy kit and on column digestion of DNA (Qiagen).

treatment_protocol: BE(2)-C cells were treated in triplicate with either vehicle (DMSO), 5 μM all-trans retinoic acid (ATRA), 1 mM valproic acid (VPA), or 5 μM ATRA + 1 mM VPA for 6, 24, or 72 hours.

tag: treatment

value: 5uM ATRA + 1mM valproic acid (VPA)

tag: treatment duration (hours)


title: Mdr1a-_Jejunum_5


title: Mdr1a-_Liver_5


title: Mdr1a-_Duodenum_8


title: Mdr1a-_Ileum_7


title: Mdr1a-_Kidney_medulla_5


title: BE(2)-C ATRA_5uM + VPA_1mM 72hr, rep. 3

description: BE(2)-C cells treated with 5uM ATRA + 1mM valproic acid (VPA) for 72 hours, rep. 3


title: 1-KO

city: New York

first: Hongxia

last: Ren

state: NY

address: 1150 St Nicholas Ave, Rm237

department: Medicine

institute: Columbia University

hyb_protocol: Hybridization was performed by Columbia University microarray core facility. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was performed by Columbia University microarray core facility. GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: RMA by software Partek

source_name: FoxO1 KO

label_protocol: Labeled cRNA were prepared according to the standard Nugen protocol.

growth_protocol: All animal studies were approved by the Columbia Animal Care and Use Committee.

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

treatment_protocol: Mice were maintained in a pathogen-free facility, with 4–5 animals  per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food  and water ad libitum. Age and sex matched littermate cohorts were used for all the  experiments to account for potential strain differences.

value: Hypothalamic neurons expressing Agouti-related peptide

value: FoxO1 KO

tag: genetic background

value: mixed


title: 2-HET

source_name: FoxO1 heterozygous KO

value: FoxO1 heterozygous KO


title: Mdr1a-_Duodenum_7

value: Sprague Dawley

value: male


title: Mdr1a-_Jejunum_7


title: Mdr1a-_Duodenum_6


title: Mdr1a-_Ileum_6


title: Mdr1a-_Kidney_medulla_8


title: Mdr1a-_Jejunum_6


title: Mdr1a-_Jejunum_8


title: Mdr1a-_Kidney_cortex_5


title: Mdr1a-_Kidney_cortex_6


title: Mdr1a-_Ileum_8


title: Mdr1a-_Kidney_medulla_6


title: Mdr1a-_Kidney_medulla_7


title: Mdr1a-_Kidney_cortex_8


title: Mdr1a-_Liver_6


title: Mdr1a-_Brain_8


title: Mrp2-_Brain_13

description: Male SAGE Mrp2 knockout Sprague-Dawley rats 8-11 weeks old

value: Mrp2 knockout


title: Mdr1a-_Brain_5


title: Mdr1a-_Ileum_5


title: Mdr1a-_Liver_7


title: BE(2)-C ATRA_5uM 72hr, rep. 1

description: BE(2)-C cells treated with 5uM ATRA for 72 hours, rep. 1

value: 5uM ATRA


title: Mrp2-_Duodenum_13


title: Mrp2-_Duodenum_15


title: BE(2)-C ATRA_5uM 72hr, rep. 2

description: BE(2)-C cells treated with 5uM ATRA for 72 hours, rep. 2


title: BE(2)-C ATRA_5uM + VPA_1mM 72hr, rep. 1

description: BE(2)-C cells treated with 5uM ATRA + 1mM valproic acid (VPA) for 72 hours, rep. 1


title: Mrp2-_Brain_14


title: Mrp2-_Duodenum_16


title: BE(2)-C DMSO 72hr, rep. 1

description: BE(2)-C cells treated with vehicle (DMSO) for 72 hours, rep. 1

value: DMSO


title: Mdr1a-_Liver_8


title: BE(2)-C VPA_1mM 72hr, rep. 2

description: BE(2)-C cells treated with 1mM valproic acid (VPA) for 72 hours, rep. 2

value: 1mM valproic acid (VPA)


title: BE(2)-C ATRA_5uM 72hr, rep. 3

description: BE(2)-C cells treated with 5uM ATRA for 72 hours, rep. 3


title: BE(2)-C VPA_1mM 72hr, rep. 1

description: BE(2)-C cells treated with 1mM valproic acid (VPA) for 72 hours, rep. 1


title: Mrp2-_Ileum_13

value: Ileum


title: Mrp2-_Duodenum_14

value: Duodenum


title: BE(2)-C VPA_1mM 72hr, rep. 3

description: BE(2)-C cells treated with 1mM valproic acid (VPA) for 72 hours, rep. 3


title: Mrp2-_Ileum_14


title: BE(2)-C DMSO 72hr, rep. 2

description: BE(2)-C cells treated with vehicle (DMSO) for 72 hours, rep. 2


title: BE(2)-C ATRA_5uM + VPA_1mM 24hr, rep. 2

description: BE(2)-C cells treated with 5uM ATRA + 1mM valproic acid (VPA) for 24 hours, rep. 2


title: Mrp2-_Ileum_16


title: Mrp2-_Brain_16

value: Brain


title: BE(2)-C ATRA_5uM + VPA_1mM 24hr, rep. 1

description: BE(2)-C cells treated with 5uM ATRA + 1mM valproic acid (VPA) for 24 hours, rep. 1


title: Mrp2-_Brain_15


title: BE(2)-C ATRA_5uM + VPA_1mM 24hr, rep. 3

description: BE(2)-C cells treated with 5uM ATRA + 1mM valproic acid (VPA) for 24 hours, rep. 3


title: BE(2)-C ATRA_5uM 24hr, rep. 3

description: BE(2)-C cells treated with 5uM ATRA for 24 hours, rep. 3


title: Mrp2-_Jejunum_15

value: Jejunum


title: Mrp2-_Ileum_15


title: Mrp2-_Jejunum_14


title: BE(2)-C ATRA_5uM 24hr, rep. 2

description: BE(2)-C cells treated with 5uM ATRA for 24 hours, rep. 2


title: Patient 42 ATA-20

city: Bucheon-si

first: Seung-Woo

last: Shin

state: Gyeonggi-do

address: 1174 Jung-dong, Wonmi-gu

department: Genome research Center for Allergy and Respiratory Diseases

country: South Korea

institute: Soon Chun Hyang University hospital

hyb_protocol: The purified cDNA was resuspended in 100 uL of hybridization solution containing 5% SSC, 0.1% SDS, 30% formamide, 20 ug of Human Cot-1 DNA, 20 ug of poly A RNA, and 20 ug of Yeast tRNA (Invitrogen). The hybridization mixtures were heated at 100C for 2 to 3 min and directly pipetted onto microarrays. The arrays were hybridized at 42C for 12 to 16 h in a humidified hybridization chamber (Genomictree, Korea). The hybridized microarrays were washed with 2% SSC/0.1% SDS for 5 min, 0.1% SSC/0.1% SDS for 10 min, and 0.1% SSC for 2 min twice. The washed microarrays were immediately dried using a microarray centrifuge (Genomictree, Korea).

scan_protocol: Axon 4000B scanner (Molecular Devices, CA, USA). The signals and the background fluorescence intensities were calculated for each probe by averaging the intensities of every pixel inside the probe spot region using GenePix Pro 4.0 software (Molecular Devices). Spots of poor quality or indistinguishable signal level from the background were excluded.

data_processing: To analyze differentially expressed genes between ATA and AERD samples, the Cross gene error model for replicates was activated. Gene expression data was normalized in two ways: LOWESS and per gene normalization.  In per gene normalization, the data from a given gene was normalized to the median expression level of the gene across all samples.

source_name: Patient 42 ATA-20_PBMC

label_protocol: Briefly, each 50 ug of total RNA was mixed with 2 ug of oligo-24N (dT) (GenoTech, Korea) in 15.4 uL of RNase free water and incubated at 65C for 10 min. After incubation, the single-stranded cDNA was synthesized in the presence of Cy3-dUTP or Cy5-dUTP (1 mM each, NEN Life Science Products, Boston, USA) at 42C for 2 h. Total RNA from test samples and common reference RNA pooled from 10 normal samples were labeled with Cy5 and Cy3, respectively. Both Cy3- and Cy5-labeled cDNA were purified using PCR purification kit (Qiagen) as recommended by the manufacturer.

extract_protocol: Total RNA was isolated from PBMC using a modified guanidinium thiocyanate–phenol–chloroform extraction method.

tag: condition

value: ATA

tag: onset of asthma (age)

tag: wbc

tag: blood eosinophil percentage

tag: % fall

tag: Sex

value: F

tag: birthday

tag: smoke

value: NS

tag: height

tag: weight

tag: bmi

tag: fvc%

source_name: common reference RNA

tag: common reference

value: RNA pooled from 10 normal samples


title: Mrp2-_Kidney_cortex_13

tag: strain

tag: gender

tag: genotype/variation

tag: age

tag: tissue

value: Kidney cortex


title: BE(2)-C VPA_1mM 24hr, rep. 3

description: BE(2)-C cells treated with 1mM valproic acid (VPA) for 24 hours, rep. 3

tag: cell line

tag: treatment

tag: treatment duration (hours)


title: BE(2)-C ATRA_5uM 24hr, rep. 1

description: BE(2)-C cells treated with 5uM ATRA for 24 hours, rep. 1


title: Patient 41 ATA-19

source_name: Patient 41 ATA-19_PBMC

tag: condition

tag: onset of asthma (age)

tag: wbc

tag: blood eosinophil percentage

tag: % fall

value: M


title: BE(2)-C VPA_1mM 24hr, rep. 2

description: BE(2)-C cells treated with 1mM valproic acid (VPA) for 24 hours, rep. 2


title: Patient 40 ATA-18

source_name: Patient 40 ATA-18_PBMC

tag: Sex

tag: birthday

tag: smoke

tag: height

tag: weight


title: BE(2)-C DMSO 24hr, rep. 2

description: BE(2)-C cells treated with vehicle (DMSO) for 24 hours, rep. 2


title: Mrp2-_Jejunum_13

description: Male SAGE Mrp2 knockout Sprague-Dawley rats 8-11 weeks old

tag: strain

tag: gender


title: Mrp2-_Jejunum_16

tag: genotype/variation

tag: age


title: BE(2)-C DMSO 24hr, rep. 3

description: BE(2)-C cells treated with vehicle (DMSO) for 24 hours, rep. 3

tag: cell line


title: Patient 37 ATA-14

source_name: Patient 37 ATA-14_PBMC

value: es

tag: bmi

tag: fvc%

tag: common reference


title: Patient 38 ATA-16

source_name: Patient 38 ATA-16_PBMC

tag: condition

tag: onset of asthma (age)


title: Mrp2-_Kidney_cortex_16

value: Sprague Dawley

tag: tissue


title: Mrp2-_Kidney_cortex_15

value: male


title: BE(2)-C ATRA_5uM 6hr, rep. 3

description: BE(2)-C cells treated with 5uM ATRA for 6 hours, rep. 3

tag: treatment

tag: treatment duration (hours)


title: Patient 39 ATA-17

source_name: Patient 39 ATA-17_PBMC

tag: wbc

tag: blood eosinophil percentage

tag: % fall

tag: Sex

tag: birthday


title: Mrp2-_Kidney_cortex_14

tag: strain

tag: gender

value: Mrp2 knockout


title: BE(2)-C ATRA_5uM + VPA_1mM 6hr, rep. 2

description: BE(2)-C cells treated with 5uM ATRA + 1mM valproic acid (VPA) for 6 hours, rep. 2

value: 5uM ATRA + 1mM valproic acid (VPA)


title: BE(2)-C ATRA_5uM + VPA_1mM 6hr, rep. 3

description: BE(2)-C cells treated with 5uM ATRA + 1mM valproic acid (VPA) for 6 hours, rep. 3


title: Patient 36 ATA-13

source_name: Patient 36 ATA-13_PBMC

tag: age

tag: smoke

tag: height

tag: weight


title: BE(2)-C VPA_1mM 24hr, rep. 1

description: BE(2)-C cells treated with 1mM valproic acid (VPA) for 24 hours, rep. 1

tag: cell line


title: BE(2)-C VPA_1mM 6hr, rep. 3

description: BE(2)-C cells treated with 1mM valproic acid (VPA) for 6 hours, rep. 3


title: BE(2)-C DMSO 24hr, rep. 1

description: BE(2)-C cells treated with vehicle (DMSO) for 24 hours, rep. 1

value: DMSO


title: BE(2)-C ATRA_5uM + VPA_1mM 6hr, rep. 1

description: BE(2)-C cells treated with 5uM ATRA + 1mM valproic acid (VPA) for 6 hours, rep. 1


title: BE(2)-C ATRA_5uM 6hr, rep. 2

description: BE(2)-C cells treated with 5uM ATRA for 6 hours, rep. 2

value: 5uM ATRA


title: Mrp2-_Kidney_medulla_13

tag: genotype/variation

value: Kidney medulla


title: BE(2)-C ATRA_5uM 6hr, rep. 1

description: BE(2)-C cells treated with 5uM ATRA for 6 hours, rep. 1


title: Mrp2-_Kidney_medulla_14


title: Mrp2-_Kidney_medulla_15


title: Patient 35 ATA-12

source_name: Patient 35 ATA-12_PBMC

tag: condition

tag: onset of asthma (age)

value: ES

tag: bmi

tag: fvc%

tag: common reference


title: Patient 33 ATA-10

source_name: Patient 33 ATA-10_PBMC

tag: wbc

tag: blood eosinophil percentage


title: BE(2)-C DMSO 6hr, rep. 3

description: BE(2)-C cells treated with vehicle (DMSO) for 6 hours, rep. 3

tag: treatment

tag: treatment duration (hours)


title: BE(2)-C DMSO 6hr, rep. 2

description: BE(2)-C cells treated with vehicle (DMSO) for 6 hours, rep. 2


title: Patient 32 ATA-09

source_name: Patient 32 ATA-09_PBMC

tag: % fall

tag: Sex

tag: birthday

value: SM


title: Patient 29 ATA-06

source_name: Patient 29 ATA-06_PBMC

tag: age

tag: smoke


title: Patient 31 ATA-08

source_name: Patient 31 ATA-08_PBMC

tag: height

tag: weight


title: BE(2)-C VPA_1mM 6hr, rep. 2

description: BE(2)-C cells treated with 1mM valproic acid (VPA) for 6 hours, rep. 2

tag: cell line

value: 1mM valproic acid (VPA)


title: Patient 30 ATA-07

source_name: Patient 30 ATA-07_PBMC

tag: condition

value: ATA


title: BE(2)-C DMSO 6hr, rep. 1

description: BE(2)-C cells treated with vehicle (DMSO) for 6 hours, rep. 1


title: Patient 34 ATA-11

source_name: Patient 34 ATA-11_PBMC

tag: onset of asthma (age)

value: F


title: Subcutaneous adipose tissue of barrow, biological rep1

city: Beijing

first: Yuchang

last: Yao

address: College of Animal Science and Technology, China Agricultural University, 2 Yuanmingyuan Xilu, Haidian District

institute: China Agricultural University

description: Gene expression data from subcutaneous adipose tissue of barrow at 175 d of age

hyb_protocol: Following fragmentation, the cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained with SAPE at an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

organism: Sus scrofa

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

growth_protocol: All pigs were managed under normal husbandry conditions and were allowed ad libitum access to feed and water until slaughter

extract_protocol: Total RNA from adipose tissues was isolated by the Qiagen RNeasy Lipid Tissue Mini Kit, according to the manufacturer’s standard instructions

treatment_protocol: Fifteen pairs of full sibs, a total of 30 male piglets produced from the crossing of Pietrain sire and Landrace dam, were selected at 7 d of age. At 7 d of age, both testicles of one piglet in each pair were removed by surgical castration under anesthesia, and the other remained intact. All pigs were weaned at 30 d of age. At 175 d of age, all pigs were killed by electric stunning and exsanguinations. The middle layer of backfat of the 6th rib was removed immediately after slaughter and frozen in liquid nitrogen until RNA isolation.

tag: tissue

value: subcutaneous adipose tissue

tag: gender

tag: breed

value: hybrid of Pietrain and Landrace


title: Wild-type_Brain_1

description: Male wild-type Sprague-Dawley rats 8-11 weeks old

tag: strain

tag: genotype/variation

value: Wild-type

value: Brain


title: Subcutaneous adipose tissue of boar, biological rep2

department: College of Animal Science and Technology

description: Gene expression data from subcutaneous adipose tissue of boar at 175 d of age


title: Mrp2-_Liver_15

description: Male SAGE Mrp2 knockout Sprague-Dawley rats 8-11 weeks old

value: Liver


title: Subcutaneous adipose tissue of barrow, biological rep2

source_name: subcutaneous adipose tissue of barrow at 175 d of age


title: Subcutaneous adipose tissue of barrow, biological rep3


title: Subcutaneous adipose tissue of boar, biological rep1

source_name: subcutaneous adipose tissue of boar at 175 d of age


title: Wild-type_Brain_4

value: Sprague Dawley


title: Patient 27 ATA-04

source_name: Patient 27 ATA-04_PBMC

tag: wbc

tag: blood eosinophil percentage

value: M

tag: bmi

tag: fvc%

tag: common reference

value: RNA pooled from 10 normal samples


title: Mrp2-_Liver_13

value: male

value: Mrp2 knockout

tag: age


title: BE(2)-C VPA_1mM 6hr, rep. 1

description: BE(2)-C cells treated with 1mM valproic acid (VPA) for 6 hours, rep. 1

tag: treatment

tag: treatment duration (hours)


title: Subcutaneous adipose tissue of boar, biological rep3


title: Mrp2-_Kidney_medulla_16


title: Wild-type_Brain_2


title: Mrp2-_Liver_16


title: Patient 28 ATA-05

source_name: Patient 28 ATA-05_PBMC

tag: % fall

tag: Sex

tag: birthday

tag: smoke

value: NS

tag: height

tag: weight

source_name: common reference RNA


title: Mrp2-_Liver_14

tag: gender

tag: tissue


title: Wild-type_Brain_3

tag: strain

tag: genotype/variation


title: lung_immunotherapy_and_chemotherapy_rep3

city: Ribeirao Preto

first: Rodrigo

middle: Ferracine

last: Rodrigues

address: Avenida bandeirantes 3900

institute: University of Sao Paulo

description: Gene expression data from lung of mice infected with M. tuberculosis and treated with DNAhsp65 immunotherapy and isoniazid and rifampicin drugs

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array for 16 hr at 45°C and 60 rpm in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Gene expression levels were normalized using the GC-RMA algorithm and flags were computed using MAS5. Quality assessment of the chips has been performed with affyQCReport R package. The “P50” probe list has been used for comparison according to flagged (A= absent; P = present) measurement in the chips. The “P50” list has been created filtering probes flagged as “Present” for at least two of the three chips of each group.

source_name: Lung from Infected mice that received DNAhsp65 immunotherapy and isoniazid and rifampicin chemotherapy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Affymetrix User Manual GeneChip 3’ IVT Express Kit).

value: Balb/c

value: female

value: lung

tag: initial age (infection day)

value: eight weeks old

tag: infection (microorganism)

value: 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv

tag: infection (route)

value: intra-tracheal

tag: final age at death

value: approximately 18 weeks old

tag: death day

value: ten days after the end of therapy


title: Patient 25 ATA-02

source_name: Patient 25 ATA-02_PBMC

tag: condition

value: ATA

tag: onset of asthma (age)

tag: wbc

tag: blood eosinophil percentage

value: F

tag: age

tag: bmi

tag: fvc%

tag: common reference


title: Wild-type_Duodenum_3

tag: gender

value: Wild-type

value: Duodenum


title: Wild-type_Duodenum_2

value: Sprague Dawley

tag: tissue


title: Patient 24 AIA-R06

source_name: Patient 24 AIA-R06_PBMC

value: AERD

tag: drug response

value: Resp

tag: response rate

tag: % fall

tag: Sex

tag: birthday

tag: smoke

tag: height

tag: weight

value: nd

value: RNA pooled from 10 normal samples


title: lung_chemotherapy_rep3

description: Gene expression data from lung of mice infected with M. tuberculosis and treated with isoniazid and rifampicin drugs

source_name: Lung from Infected mice that received isoniazid and rifampicin chemotherapy

tag: strain

value: Balb/c

tag: initial age (infection day)

tag: infection (microorganism)

tag: infection (route)

tag: final age at death

tag: death day


title: lung_immunotherapy_and_chemotherapy_rep2

value: female


title: lung_immunotherapy_rep3

description: Gene expression data from lung of mice infected with M. tuberculosis and treated with DNAhsp65 immunotherapy

source_name: Lung from Infected mice that received DNAhsp65 immunotherapy

value: lung


title: Patient 22 AIA-R02

source_name: Patient 22 AIA-R02_PBMC

tag: condition

tag: onset of asthma (age)

tag: wbc

tag: blood eosinophil percentage

tag: age

value: NS

tag: bmi

tag: fvc%

tag: common reference


title: lung_immunotherapy_and_chemotherapy_rep1

tag: gender

tag: tissue

value: eight weeks old

value: 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv


title: Wild-type_Duodenum_4

value: male

tag: genotype/variation


title: lung_chemotherapy_rep1

tag: strain

value: intra-tracheal

value: approximately 18 weeks old

value: ten days after the end of therapy


title: lung_immunotherapy_rep2

tag: initial age (infection day)


title: Patient 23 AIA-R03

source_name: Patient 23 AIA-R03_PBMC

tag: drug response

value: Non-R

tag: response rate

tag: % fall

tag: Sex

value: F

tag: birthday

tag: smoke

tag: height

tag: weight


title: Patient 20 AIA-NR9

source_name: Patient 20 AIA-NR9_PBMC

tag: condition

tag: onset of asthma (age)

tag: wbc

tag: blood eosinophil percentage

value: M

tag: age

value: SM


title: Wild-type_Ileum_2

value: Sprague Dawley

tag: gender

value: Wild-type

tag: tissue

value: Ileum


title: Patient 21 AIA-R01

source_name: Patient 21 AIA-R01_PBMC

value: AERD

value: Resp

tag: bmi

tag: fvc%

tag: common reference

value: RNA pooled from 10 normal samples


title: lung_immunotherapy_rep1

tag: strain

value: Balb/c

value: female

value: lung

tag: initial age (infection day)

tag: infection (microorganism)

tag: infection (route)

tag: final age at death

tag: death day


title: lung_not_treated_rep1

description: Gene expression data from lung of mice infected with M. tuberculosis and not treated

source_name: Lung from Infected mice not treated

value: eight weeks old

value: 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv


title: Patient 19 AIA-NR7

source_name: Patient 19 AIA-NR7_PBMC

tag: drug response

tag: response rate

tag: % fall

tag: Sex

tag: birthday

tag: smoke

value: NS

tag: height

tag: weight


title: Colony 4-4 (cy5) - Colony 5-3 (cy3)

city: Miami

first: Anthony

middle: John

last: Bellantuono

state: FL

department: Biological Sciences

institute: Florida International University

hyb_protocol: Static hybridizations were performed using formamide-based hybribization buffer (Genisphere).  Prehybridization used 1 μg Human Cot-1 DNA for 90 minutes. Hybridization with cDNA was performed for 14 hours at 47°C. Arrays were washed in 65°C 2x SSC/0.2% SDS for 15 minutes, 2x SSC at room temperature for 15 minutes, and 0.2x SSC at room temperature for 15 minutes. Dye capture with Array 900 3DNA capture reagents (Genisphere) was performed at 50°C for 4 hours, followed by washing. Arrays were dipped in DyeSaver II (Genisphere).

scan_protocol: Scanning was performed on a GenePix Personal 4100A (Axon Instruments) microarray scanner using GenePix Pro 4.1.

data_processing: Following gridding and quality control using GenePix Pro 4.1 (Axon Instruments), background-subtracted mean intensity values were log- and lowess-transformed using R/Maanova version 1.18 (Wu and Churchill 2008). A fixed-effect ANOVA model was fit to the normalized data. Empirical-Bayes Fs statistic was used to test for differentially expressed genes at each sampling time. P-values for each clone were calculated from 500 permutations of residual shuffling. False discovery rate adjustments were implemented using jsFDR (Storey 2002, J Roy Stat Soc B), using an adjusted p-value threshold of less than 0.05.

organism: Acropora millepora

source_name: Colony 4, within-colony biological replicate 4

label_protocol: cDNA probe synthesis was performed from 2.5 μg high-quality total RNA using Superscript II Reverse Transcriptase (Invitrogen) and the 3DNA Array 350 kit (Genisphere) according to the manufacturer’s guidelines. Two primers were used, which consisted of a Cy3 and Cy5 specific capture sequence and a poly-T tail. In order to make each sample specific for Cy3 and Cy5, each sample was reverse transcribed separately using only one primer.

extract_protocol: Coral fragments were immediately frozen in liquid nitrogen upon sampling. Frozen coral fragments were homogenized in Trizol Reagent (Invitrogen). Trizol RNA extraction protocol was followed as per manufacturer’s protocol through phase separation, after which  the aqueous phase was recovered, mixed with an equal volume of absolute ethanol, and processed with an RNeasy Mini kit (QIAGEN). RNA integrity was assessed with the use of a Bioanalyzer (Agilent); only high integrity RNA was used for cDNA synthesis and subsequent hybridization.

tag: genotype/variation

value: intron 4-500 haplotype 2

source_name: Colony 5, within-colony biological replicate 3


title: Colony 4-2 (cy5) - Colony 5-2 (cy3)

source_name: Colony 4, within-colony biological replicate 2

source_name: Colony 5, within-colony biological replicate 2


title: Wild-type_Ileum_3

tag: gender

value: male

tag: age

tag: tissue


title: Colony 4 (cy5) - Colony 1 (cy3)

source_name: Colony 4

source_name: Colony 1

value: intron 4-500 haplotype 1


title: Patient 18 AIA-NR5

source_name: Patient 18 AIA-NR5_PBMC

tag: condition

tag: onset of asthma (age)

tag: wbc

tag: blood eosinophil percentage

value: Non-R

value: M

tag: bmi

tag: fvc%

source_name: common reference RNA

tag: common reference


title: Patient 17 AIA-NR4

source_name: Patient 17 AIA-NR4_PBMC

tag: drug response

tag: response rate

tag: % fall

value: F

value: SM

value: nd


title: lung_not_treated_rep2

tag: strain

tag: initial age (infection day)

tag: infection (microorganism)

tag: infection (route)

value: intra-tracheal

tag: final age at death

value: approximately 18 weeks old

tag: death day

value: ten days after the end of therapy


title: Colony 6-4 (cy5) - Colony 4-4 (cy3)

source_name: Colony 6, within-colony biological replicate 4

tag: genotype/variation


title: Wild-type_Jejunum_3

value: Sprague Dawley

tag: gender

value: Wild-type

tag: age

tag: tissue

value: Jejunum


title: Patient 15 AIA-NR2

source_name: Patient 15 AIA-NR2_PBMC

tag: condition

value: AERD

tag: onset of asthma (age)

tag: wbc

tag: blood eosinophil percentage

tag: Sex

tag: birthday

tag: smoke

tag: height

tag: weight

value: RNA pooled from 10 normal samples


title: Patient 16 AIA-NR3

source_name: Patient 16 AIA-NR3_PBMC

tag: drug response

tag: response rate

tag: % fall

value: NS

tag: bmi

tag: fvc%

tag: common reference


title: Colony 5-1 (cy5) - Colony 6-1 (cy3)

source_name: Colony 5, within-colony biological replicate 1

tag: genotype/variation

value: intron 4-500 haplotype 2

source_name: Colony 6, within-colony biological replicate 1


title: Colony 5 (cy5) - Colony 2 (cy3)

source_name: Colony 5

source_name: Colony 2


title: lung_chemotherapy_rep2

source_name: Lung from Infected mice that received isoniazid and rifampicin chemotherapy

tag: strain

value: Balb/c

tag: gender

value: female

tag: tissue

value: lung

tag: initial age (infection day)

value: eight weeks old

tag: infection (microorganism)

value: 1.0 x 10e5 colony-forming units of Mycobacterium tuberculosis H37Rv

tag: infection (route)

tag: final age at death

tag: death day


title: Wild-type_Ileum_4

value: male

tag: age

value: Ileum


title: Patient 26 ATA-03

source_name: Patient 26 ATA-03_PBMC

tag: condition

value: ATA

tag: onset of asthma (age)

tag: wbc

tag: blood eosinophil percentage

tag: Sex

value: M

tag: birthday

tag: smoke

tag: height

tag: weight


title: lung_not_treated_rep3

source_name: Lung from Infected mice not treated

tag: strain

tag: gender

value: intra-tracheal

value: approximately 18 weeks old

value: ten days after the end of therapy


title: Colony 5-2 (cy5) - Colony 6-2 (cy3)

tag: genotype/variation

source_name: Colony 6, within-colony biological replicate 2


title: Colony 5-3 (cy5) - Colony 6-4 (cy3)

source_name: Colony 5, within-colony biological replicate 3


title: Wild-type_Jejunum_1

value: Sprague Dawley

value: Wild-type

tag: tissue

value: Jejunum


title: Wild-type_Jejunum_4


title: Wild-type_Kidney_cortex_1

value: Kidney cortex


title: Wild-type_Jejunum_2


title: Patient 14 AIA-NR1

source_name: Patient 14 AIA-NR1_PBMC

value: AERD

tag: drug response

value: Non-R

tag: response rate

tag: % fall

value: F

value: NS

tag: bmi

tag: fvc%

tag: common reference

value: RNA pooled from 10 normal samples


title: Colony 6-2 (cy5) - Colony 4-2 (cy3)

value: intron 4-500 haplotype 2

source_name: Colony 4, within-colony biological replicate 2


title: Patient 13 AIA-I10

source_name: Patient 13 AIA-I10_PBMC

tag: condition

tag: onset of asthma (age)

tag: wbc

tag: age


title: Colony 6 (cy5) - Colony 3 (cy3)

source_name: Colony 6

source_name: Colony 3

value: intron 4-500 haplotype 1


title: Colony 3-2 (cy5) - Colony 1-2 (cy3)

source_name: Colony 3, within-colony biological replicate 2

source_name: Colony 1, within-colony biological replicate 2


title: Colony 3-4 (cy5) - Colony 1-3 (cy3)

source_name: Colony 3, within-colony biological replicate 4

source_name: Colony 1, within-colony biological replicate 3


title: Wild-type_Ileum_1

value: male

value: Ileum


title: Patient 12 AIA-I09

source_name: Patient 12 AIA-I09_PBMC

tag: blood eosinophil percentage

tag: Sex

value: M

tag: birthday

tag: smoke

value: es

source_name: common reference RNA


title: Colony 3-1 (cy5) - Colony 1-1 (cy3)

source_name: Colony 3, within-colony biological replicate 1

source_name: Colony 1, within-colony biological replicate 1


title: Colony 2-4 (cy5) - Colony 3-4 (cy3)

source_name: Colony 2, within-colony biological replicate 4


title: Wild-type_Kidney_cortex_2

tag: strain

tag: gender


title: Colony 2-3 (cy5) - Colony 3-2 (cy3)

source_name: Colony 2, within-colony biological replicate 3

tag: genotype/variation


title: Patient 10 AIA-I07

source_name: Patient 10 AIA-I07_PBMC

tag: drug response

tag: height

tag: weight


title: Patient 11 AIA-I08

source_name: Patient 11 AIA-I08_PBMC

value: Resp

tag: response rate

tag: % fall

value: ES

tag: bmi


title: Colony 3 (cy5) - Colony 6 (cy3)


title: Wild-type_Kidney_medulla_1

value: Sprague Dawley

tag: tissue

value: Kidney medulla


title: Patient 9 AIA-I06

source_name: Patient 9 AIA-I06_PBMC

tag: condition

tag: onset of asthma (age)

tag: fvc%

tag: common reference


title: Colony 1-2 (cy5) - Colony 2-3 (cy3)


title: Colony 2 (cy5) - Colony 5 (cy3)

source_name: Colony 2

source_name: Colony 5


title: Patient 8 AIA-I04

source_name: Patient 8 AIA-I04_PBMC

tag: wbc

tag: blood eosinophil percentage

tag: Sex

tag: age


title: Colony 1-3 (cy5) - Colony 2-4 (cy3)


title: Colony 2-2 (cy5) - Colony 3-1 (cy3)

source_name: Colony 2, within-colony biological replicate 2


title: Patient 7 AIA-I02

source_name: Patient 7 AIA-I02_PBMC

tag: birthday

tag: smoke


title: Wild-type_Kidney_cortex_3

tag: strain

tag: gender

tag: genotype/variation

value: Wild-type


title: Wild-type_Kidney_medulla_3


title: Wild-type_Kidney_medulla_4


title: Wild-type_Kidney_cortex_4

value: Kidney cortex


title: Wild-type_Liver_1

value: Liver


title: Wild-type_Kidney_medulla_2


title: Patient 6 AIA-I01

source_name: Patient 6 AIA-I01_PBMC

value: AERD

tag: height

tag: weight