title: gat201 KO vs. wt in DMEM CHM7-251 flip


title: T7, sniSh, biological rep2

status: Public on Jul 15 2011

type: RNA

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

country: USA

institute: UCLA

description: L4-L5 rat DRGs after sciatic SNISh lesion

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Array data were preprocessed with the robust multichip analysis algorithm (RMA)

label: biotin

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Affymetrix protocol

growth_protocol: Eight- to 12-week-old Wistar rats were subjected to crush lesion

extract_protocol: Qiagen Rneasy

treatment_protocol: L4/L5 DRG were dissected from lesioned animals at the indicated time points

tag: time after lesion (days)

tag: lesion

value: sniSh

tag: strain

value: Wistar

tag: age

value: 8 to 12 weeks old


title: T21, sniSh, biological rep2


title: T40, sni, biological rep3

description: L4-L5 rat DRGs after sciatic SNI lesion

value: sni


title: T3, sniSh, biological rep2


title: T3, sniSh, biological rep1


title: am1-pramsE_prawtE-Rep4-Cy5-prawtE

city: Stanford

first: John

middle: F

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

description:
Cy5-145-4
am1-pra allele 1.0mm anthers - ms vs wt Rep 4

hyb_protocol: 825 ng of each labeled target cRNA were hybridized for 17 h at 65C

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

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

organism: Zea mays

label_protocol: Total RNA (1000 ng) was amplified & labeled with Cy3 or Cy5 using Agilent Low RNA Input Linear Amplification Kit.

growth_protocol: Plants were grown and dissected at the Stanford field; tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA was extracted from 30 - 60  of frozen anthers with Invitrogen Purelink RNA Mini kit with DNase I treatment.

tag: tissue

value: anther

tag: anther length (mm)

tag: allele

tag: wild-type vs male-sterile

value: wild-type


title: am1-pramsE_prawtE-Rep3-Cy5-pramsE

description:
Cy5-145-3
am1-pra allele 1.0mm anthers - ms vs wt Rep 3

value: male-sterile


title: HCT116low1

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: HCT116 ROS low replicate 1.

hyb_protocol: Microarray = Affymetrix GeneChip Human Genome U133 Plus 2.0; Affymetrix Hybridization Oven= 645; Affymetrix Fluidics Station= 450; Fluidics Protocol= EukGE-WS2.

scan_protocol: Affymetrix GeneChip Scanner= 3000-7G; Controller= GCOS.

data_processing: MAS5 algorithm as implemented by the call.exprs function of Bioconductor simpleaffy package version 2.22.0 using custom CDF file HGU133Plus2_Hs_ENSG (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12.1.0/ensg.asp), 2% trimmed mean set to 100.

organism: Homo sapiens

source_name: HCT116, ROS low

label_protocol: Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655).

growth_protocol: MCF7-BOS cells were a gift from Dr. Toshi Shioda. HCT116 cells were purchased from ATCC. MCF7-BOS cells were maintained in DMEM 10% FCS, 40 mM glutamine and Pen/Strep. HCT116 cells were maintained in McCoy’s 5α medium with 10% FCS and Pen/Strep.

extract_protocol: QIAGEN RNeasy protocol and reagents were used for extraction of total RNA.

treatment_protocol: For isolation of ROS low and ROS high cells, cancer cells were incubated for 30 min. with 2.5 μM DCFDA (Invitrogen), and then washed for one hour with PBS at 37°C before isolation on a BD FACSAria cell sorter.

tag: cell line

tag: cell type

value: colorectal carcinoma cells

tag: ros

value: low


title: untagged wild type sample replicate #2

type: genomic

city: San Francisco

first: Cheryl

last: Chun

institute: UC San Francisco

description: untagged wild type sample replicate #2 Median of Ratios (635/532)

hyb_protocol: see Nobile, C.J., Nett, J.E., Hernday, A.D., Homann, O.R., Deneault, J.S., Nantel, A., Andes, D.R., Johnson, A.D., and Mitchell, A.P. (2009). Biofilm matrix regulation by Candida albicans Zap1. PLoS Biol 7, e1000133.

data_processing: Median of Ratios (635/532) were further analyzed.  Analysis was performed by calculating the median of the top five probes in the 2kb flanking the start codon of each gene. The median value for the untagged strain was subtracted from the median value of the tagged strain, yielding the difference for the pair of untagged/tagged arrays. The calculation was repeated for a second duplicate pair of untagged/tagged arrays. The calculated differences were clustered using the software Cluster, and the cluster showing increased binding in both pairs was isolated for additional analysis.

molecule: genomic DNA

organism: Cryptococcus neoformans

source_name: untagged wild type sample replicate #2

label_protocol: generated DNA probes with incorporated aminoallyl-dUTP

growth_protocol: grown in DMEM, 37C, 5% CO2

extract_protocol: The cultures were fixed with 1% formaldehyde, followed by quenching with 125 mM glycine, then harvested by centrifugation and snap freezing. Samples were lyophilized, and chromatin immunoprecipitation performed as previously described (Nobile et al., 2009) with the following minor modifications: zirconia/silica beads (0.5 mm diameter) were used to lyse the cells via a Bead Beater-8, used for thirty minutes with frequent rests on ice. The chromatin in the cell pellet was sonicated for 1 hr in a Diagenode Bioruptor (settings: 4x15 min, 30 s on, 1 min off) at 4ºC. Immunoprecipitation was performed with an anti-FLAG antibody.

treatment_protocol: sonication settings: 4x15 min, 30 s on, 1 min off

value: wild type

tag: antibody

value: anti-FLAG

tag: antibody manufacturer

value: Sigma

tag: antibody catalog #

source_name: whole cell extract

tag: sample type

value: whole cell extract


title: T40, sni, biological rep2

description: L4-L5 rat DRGs after sciatic SNI lesion


title: T7, sniSh, biological rep1


title: HCT116low3

description: HCT116 ROS low replicate 3.


title: am1-489msE_489msF-Rep3-Cy5-489msF

description:
Cy5-145-1
am1-489 allele ms anthers - 1.0mm vs 1.5mm Rep 3


title: MCF7low3

description: MCF7 ROS low replicate 3.

source_name: MCF7, ROS low

value: breast adenocarcinoma cells


title: am1-489msE_489msF-Rep4-Cy5-489msE

description:
Cy5-145-2
am1-489 allele ms anthers - 1.0mm vs 1.5mm Rep 4


title: HCT116low2

description: HCT116 ROS low replicate 2.


title: am1-pramsF_prawtF-Rep3-Cy5-pramsF

description:
Cy5-146-1
am1-pra allele 1.5mm anthers - ms vs wt Rep 3


title: am1-pramsF_prawtF-Rep4-Cy5-prawtF

description:
Cy5-146-2
am1-pra allele 1.5mm anthers - ms vs wt Rep 4


title: MCF7low1

description: MCF7 ROS low replicate 1.


title: MCF7low2

description: MCF7 ROS low replicate 2.


title: T7, sniSh, biological rep3


title: am1-pramsF_prawtF-Rep2-Cy5-pramsF

description:
Cy5-144-4
am1-pra allele 1.5mm anthers - ms vs wt Rep 2


title: T40, sni, biological rep1

description: L4-L5 rat DRGs after sciatic SNI lesion


title: T21, sni, biological rep2

description: L4-L5 rat DRGs after sciatic SNI lesion


title: T21, sni, biological rep3

description: L4-L5 rat DRGs after sciatic SNI lesion


title: HCT116high3

description: HCT116 ROS high replicate 3.

source_name: HCT116, ROS high

value: high


title: T21, sni, biological rep1

description: L4-L5 rat DRGs after sciatic SNI lesion


title: T7, sni, biological rep2

description: L4-L5 rat DRGs after sciatic SNI lesion


title: T3, sni, biological rep3

description: L4-L5 rat DRGs after sciatic SNI lesion


title: T7, sni, biological rep3

description: L4-L5 rat DRGs after sciatic SNI lesion


title: T0,naïve, biological rep2

description: L4-L5 rat DRGs naïve

value: naïve


title: T7, sni, biological rep1

description: L4-L5 rat DRGs after sciatic SNI lesion


title: T3, sni, biological rep2

description: L4-L5 rat DRGs after sciatic SNI lesion


title: am1-489msE_489wtE-Rep4-Cy5-489wtE

description:
Cy5-144-2
am1-489 allele 1.0mm anthers - ms vs wt Rep 4


title: T0,naïve, biological rep3

description: L4-L5 rat DRGs naïve


title: HCT116high2

description: HCT116 ROS high replicate 2.


title: am1-489msF_489wtF-Rep4-Cy5-489wtF

description:
Cy5-144-3
am1-489 allele 1.5mm anthers - ms vs wt Rep 4


title: MCF7high3

description: MCF7 ROS high replicate 3.

source_name: MCF7, ROS high


title: am1-489msE_489wtE-Rep3-Cy5-489msE

description:
Cy5-144-1
am1-489 allele 1.0mm anthers - ms vs wt Rep 3


title: am1-489msE_pramsE-Rep2-Cy5-489msE

description:
Cy5-140-2
1.0mm ms anthers - am1-489 allele vs am1-pra allele Rep 2


title: MCF7high1

description: MCF7 ROS high replicate 1.


title: am1-489msF_pramsF-Rep2-Cy5-489msF

description:
Cy5-140-4
1.5mm ms anthers - am1-489 allele vs am1-pra allele Rep 2


title: am1-489msF_pramsF-Rep1-Cy5-pramsF

description:
Cy5-140-3
1.5mm ms anthers - am1-489 allele vs am1-pra allele Rep 1


title: am1-489msE_pramsE-Rep1-Cy5-pramsE

description:
Cy5-140-1
1.0mm ms anthers - am1-489 allele vs am1-pra allele Rep 1


title: MCF7high2

description: MCF7 ROS high replicate 2.


title: T3, sni, biological rep1

description: L4-L5 rat DRGs after sciatic SNI lesion


title: HCT116high1

description: HCT116 ROS high replicate 1.


title: 13969243 - Fir Ea-1 vs WS Ea-1

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

description: A meta-analysis ot the CATMA transcriptomic data has shown that an orphan gene of Arabidopsis: AT5E39460, recently remaned AT5G 44585, is highly responsive to biotic stresses. An homozygous mutant of this gene, named fireman has been produced and displays less cell death symptoms in comparison to the wild type in response to Erwinia amylovora infection. The purpose of this transcriptomic analysis is to understand which pathways are altered in this mutant versus the wild-type in response to this phytopathogenic bacteria.

hyb_protocol: WS Ea-1 Cy5 / Fir Ea-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: WS Ea-1

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: aerial - Soil Hygrometry 60% Temperature 19°C Light 8h

extract_protocol: WS Ea-1:30ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Erwinia infection - biotic stress - pathogen infection,erwinia amylovora:time 24hour . Strain 1430

tag: genotype/variation

value: wildtype

tag: cultivar

value: arabidopsis thaliana (wassilewskija)

tag: development stage (boyes et al. plant cell 2001)

tag: infection

value: Erwinia amylovora

source_name: Fir Ea-1

extract_protocol: Fir Ea-1:30ug. (Qiagen_RNeasy.pdf)

tag: genotype/varation

value: mutant (fireman)


title: T0,naïve, biological rep1

description: L4-L5 rat DRGs naïve

tag: time after lesion (days)

tag: lesion

tag: strain

value: Wistar

tag: age

value: 8 to 12 weeks old


title: T7, chSh, biological rep3

description: L4-L5 rat DRGs after sciatic ChSh lesion

value: chSh


title: T21, chSh, biological rep3


title: Day 4 differentiated

city: Kurashiki

first: Tsutomu

last: Nohno

address: 577 Matsushima

department: Molecular and Developmental Biology

country: Japan

institute: Kawasaki Medical School

description:
C2C12_D4
This Sample represents 3 replicates.

cDNA was used to amplify the gene of interest using specific primer combinations.

data_processing:
Data were evaluated by the ΔΔCt method against control cells cultured in proliferation medium (n = 4) using an on-line template (http://pcrdataanalysis.sabiosciences.com/pcr/arrayanalysis.php).
ΔCt values were calculated by subtracting average cycle threshold (Ct) values of housekeeping genes (glucuronidase, beta, Gusb; Heat shock protein 90 alpha (cytosolic), class B member 1, Hsp90ab1; glyceraldehyde-3-phosphate dehydrogenase, Gapdh; actin, beta, Actb; and hypoxanthine guanine phosphoribosyl transferase 1, Hprt1).

label: SYBR Green

organism: Mus musculus

source_name: myoblasts, day 4

label_protocol: RNA was reverse transcribed into cDNA (RT² First Strand Kit, SABiosciences), and the cDNA was used for quantitative PCR analysis. Expression in C2C12 cells was analyzed by quantitative Real-Time PCR using SABiosciences RT² SYBR Green Master Mixes. The PCR conditions were 95°C for 10 min followed by 40 cycles of 95°C for 15 sec and 60°C for 1 min. Analyses were performed on an ABI Real-Time PCR System 7500 (Applied Biosystems, Foster City, CA).

growth_protocol: C2C12 was cultured in Dulbecco’s modified Eagle’s medium (D-MEM) supplemented with 10% fetal bovine serum. Differentiation was induced by replacing the medium to D-MEM supplemented with 2% horse serum.

extract_protocol: Total RNA was extracted from C2C12 cells using ISOGEN (NIPPON GENE CO., Tokyo, Japan).

treatment_protocol: Myogenic differentiation was induced by serum starvation.

value: myoblasts

tag: days differentiated


title: T3, chSh, biological rep1


title: T40, ch, biological rep3

description: L4-L5 rat DRGs after sciatic CH lesion

value: ch


title: T21, chSh, biological rep2


title: T7, chSh, biological rep2


title: T40, ch, biological rep2

description: L4-L5 rat DRGs after sciatic CH lesion


title: Day 2 differentiated

description:
C2C12_D2
This Sample represents 3 replicates.

cDNA was used to amplify the gene of interest using specific primer combinations.

source_name: myoblasts, day 2

tag: cell line


title: T40, ch, biological rep1

description: L4-L5 rat DRGs after sciatic CH lesion


title: Day 0 control

description:
C2C12_D0
This Sample represents 4 replicates.

cDNA was used to amplify the gene of interest using specific primer combinations.

source_name: myoblasts, day 0

tag: cell type


title: T21, ch, biological rep3

description: L4-L5 rat DRGs after sciatic CH lesion


title: 13969242 - WS Ea-1 vs Fir Ea-1

hyb_protocol: Fir Ea-1 Cy5 / WS Ea-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969240 - Fir H2O-1 vs Fir Ea-1

hyb_protocol: Fir Ea-1 Cy5 / Fir H2O-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Fir H2O-1

extract_protocol: Fir H2O-1:30ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:H2O control for Erwinia - biotic stress - control,h2o:time 24hour .

value: H2O control


title: T7, chSh, biological rep1


title: T3, chSh, biological rep3


title: T7, ch, biological rep2

description: L4-L5 rat DRGs after sciatic CH lesion


title: 13969241 - Fir Ea-1 vs Fir H2O-1

hyb_protocol: Fir H2O-1 Cy5 / Fir Ea-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: T21, ch, biological rep1

description: L4-L5 rat DRGs after sciatic CH lesion


title: 13969236 - Fir H2O-1 vs WS H2O-1

hyb_protocol: WS H2O-1 Cy5 / Fir H2O-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WS H2O-1

extract_protocol: WS H2O-1:30ug. (Qiagen_RNeasy.pdf)


title: T3, chSh, biological rep2


title: T7, ch, biological rep3

description: L4-L5 rat DRGs after sciatic CH lesion


title: 13969233 - WS H2O-2 vs Fir H2O-2

hyb_protocol: Fir H2O-2 Cy5 / WS H2O-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Fir H2O-2

extract_protocol: Fir H2O-2:30ug. (Qiagen_RNeasy.pdf)

source_name: WS H2O-2

extract_protocol: WS H2O-2:30ug. (Qiagen_RNeasy.pdf)


title: 13969234 - Fir H2O-2 vs WS H2O-2

hyb_protocol: WS H2O-2 Cy5 / Fir H2O-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: wild-type Hexenal 2h rep3

city: Dübendorf

first: Beat

middle: B

last: Fischer

address: Ueberlandstr. 133

department: Department of Environmental Toxicology

country: Switzerland

institute: Eawag

hyb_protocol: Labeling, purification and hybridization was done according the ‘One-Color Microarray-Based Gene Expression Analysis’ system (Agilent Technologies) following the manufacturer's protocol.

scan_protocol: Hybridized slides were scanned with the Agilent DNA Microarray scanner and quantified using the Agilent Feature Extraction software following the manufacturer's protocol.

data_processing: Data analyses were performed with the R/Bioconductor software provided by the Functional Genomics Center Zürich using the log2 values of the 50 percentile -normalized and background-processed median signals. Significant differences of average signal intensities between conditions was determined by one-way analysis of variance (ANOVA) followed by Tukey’s pairwise comparison. Induction was calculated as log2 of the ratio between the sample and the untreated wild-type condition using only genes with a threshold signal value of 10.

organism: Chlamydomonas reinhardtii

source_name: wild-type Hexenal 2h

growth_protocol: Cultures were grown mixotrophically in a Tris-acetate phosphate (TAP) medium at 25°C and 100 μmol photons m-2 s-1 photosynthetically active radiation (PAR) on a rotary shaker (120 rpm).

extract_protocol: Samples were harvested by centrifugation (3000g, 5 min) and total RNA was isolated with the RNeasy Mini Kit (Qiagen) as described by the manufacturer’s protocol with the following modifications. Cells were sonicated two times 5 s in the RLT buffer on ice to break cells, and DNA was digested on column using the RNase-Free DNase Set (Qiagen). After purification, RNA was quantified with a NanoDrop2000 (Thermo Fisher Scientific) and quality was assessed on a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: 20 ml of cultures grown to a cell density of 2×10^6 cells ml-1 were transferred into a 100 ml Erlenmayer flask, exposed either to DBMIB (2 µM), 2(E)-Hexenal (0.3 mM), neutral red (NR, 3 µM), tert-butylhydroperoxide (tBOOH, 100 µM) or no chemical and incubated for 2 h at 25°C and 100 μmol photons m-2 s-1 PAR before RNA was isolated.

value: 4A+ is a wild-type C. reinhardtii strains in the 137c background

tag: genotype

value: wild type 4A+

tag: genetic background

tag: treatment

value: Hexenal


title: wild-type Hexenal 2h rep1

label_protocol: Labeling, purification and hybridization was done according the ‘One-Color Microarray-Based Gene Expression Analysis’ system (Agilent Technologies) following the manufacturer's protocol.


title: 13969235 - WS H2O-1 vs Fir H2O-1

hyb_protocol: Fir H2O-1 Cy5 / WS H2O-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: T7, ch, biological rep1

description: L4-L5 rat DRGs after sciatic CH lesion


title: wild-type Hexenal 2h rep2


title: T3, ch, biological rep3

description: L4-L5 rat DRGs after sciatic CH lesion


title: 13969232 - Fir Ea-2 vs Fir H2O-2

hyb_protocol: Fir H2O-2 Cy5 / Fir Ea-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Fir Ea-2

extract_protocol: Fir Ea-2:30ug. (Qiagen_RNeasy.pdf)


title: T3, ch, biological rep2

description: L4-L5 rat DRGs after sciatic CH lesion


title: T3, ch, biological rep1

description: L4-L5 rat DRGs after sciatic CH lesion


title: T40, cci, biological rep2

description: L4-L5 rat DRGs after sciatic CCI lesion

value: cci


title: T40, cci, biological rep3

description: L4-L5 rat DRGs after sciatic CCI lesion


title: T21, cci, biological rep3

description: L4-L5 rat DRGs after sciatic CCI lesion


title: T40, cci, biological rep1

description: L4-L5 rat DRGs after sciatic CCI lesion


title: T21, cci, biological rep1

description: L4-L5 rat DRGs after sciatic CCI lesion


title: T21, cci, biological rep2

description: L4-L5 rat DRGs after sciatic CCI lesion


title: wild-type DBMIB 2h rep3

source_name: wild-type DBMIB 2h

value: DBMIB


title: 13969231 - Fir H2O-2 vs Fir Ea-2

hyb_protocol: Fir Ea-2 Cy5 / Fir H2O-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: T7, cci, biological rep1

description: L4-L5 rat DRGs after sciatic CCI lesion


title: T3, cci, biological rep2

description: L4-L5 rat DRGs after sciatic CCI lesion


title: T7, cci, biological rep3

description: L4-L5 rat DRGs after sciatic CCI lesion


title: T3, cci, biological rep3

description: L4-L5 rat DRGs after sciatic CCI lesion


title: wild-type DBMIB 2h rep2


title: wild-type tBOOH 2h rep3

source_name: wild-type tBOOH 2h

value: tBOOH


title: T3, cci, biological rep1

description: L4-L5 rat DRGs after sciatic CCI lesion


title: 13969239 - WS Ea-1 vs WS H2O-1

hyb_protocol: WS H2O-1 Cy5 / WS Ea-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969228 - WS Ea-2 vs Fir Ea-2

hyb_protocol: Fir Ea-2 Cy5 / WS Ea-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WS Ea-2

extract_protocol: WS Ea-2:30ug. (Qiagen_RNeasy.pdf)


title: 13969229 - Fir Ea-2 vs WS Ea-2

hyb_protocol: WS Ea-2 Cy5 / Fir Ea-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: wild-type tBOOH 2h rep1


title: 13969238 - WS H2O-1 vs WS Ea-1

hyb_protocol: WS Ea-1 Cy5 / WS H2O-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969227 - WS Ea-2 vs WS H2O-2

hyb_protocol: WS H2O-2 Cy5 / WS Ea-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: wild-type tBOOH 2h rep2


title: wild-type NR 2h rep3

source_name: wild-type NR 2h

value: NR


title: T7, cci, biological rep2

description: L4-L5 rat DRGs after sciatic CCI lesion

hyb_protocol: Affymetrix protocol


title: wild-type NR 2h rep2


title: 13969226 - WS H2O-2 vs WS Ea-2

hyb_protocol: WS Ea-2 Cy5 / WS H2O-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: wildtype


title: Akt1 wild type 2

city: Providence

first: Mary

middle: L.

last: Hixon

state: RI

address: GE505 70 Ship Street

institute: Brown University

hyb_protocol: 10 ucg of  c RNA were hybridized for 17 hours at 45 degrees Celsius, 60rpm, FS450_0007

scan_protocol: Gene chips were scanned using the  Affymetrix  7G3000 scanner

data_processing: RMA expression value derived from Partek software

source_name: mammary gland

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

growth_protocol: animals were housed in Brown University's accredited animal care facility

extract_protocol: RNA trizol

tag: gender

value: PND70 female


title: Akt1-deficient 1


title: Akt1-deficient 2


title: sor1 control rep3

source_name: sor1 untreated

treatment_protocol: 20 ml of cultures grown to a cell density of 2×106 cells ml-1 were transferred into a 100 ml Erlenmayer flask and incubated for 2 h at 25°C and 100 μmol photons m-2 s-1 PAR before RNA was isolated.

tag: sample type

value: sor1 is a singlet oxygen resistant mutant derived from the 4A+ wild-type strain with a single nucleotide polymorphism in a gene coding for a putative bZIP transcription factor.

value: sor1 mutant


title: sor1 control rep2


title: Akt1 wild type 3


title: Akt1 wild type 1


title: Wildtype_HSC_Rep4

city: Ann Arbor

first: Shenghui

last: He

state: Michigan

address: 210 Washtenaw Avenue, 5258 LSI

department: Life Science institute

institute: University of Michigan

description:
Gene expresion data from hematopoietic stem cells isolated from 8-week old wild type control mice after 5 days of Doxycycline treatment
WT_HSC4.CEL

hyb_protocol: 2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.

scan_protocol: The chips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: Data was analyzed using the limma, oligo and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: hematopoietic stem cells from 8-week old wild type control mice after 5 days of Doxycycline administration

label_protocol: cDNA was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN).

growth_protocol: 10,000 unclutured CD150+CD48-Lineage-Sca1+cKit+ hematopoietic stem cells from Sox17-transgenic ((tetO)7CMVSox17-IRES-NucEGFP;B6.Cg-Gt(ROSA)26Sortm1(rtTA*M2)Jae/J double transgenic) and littermate control mice bone marrow were double-sorted into Trizol (Invitroen)

extract_protocol: Total RNA was extracted using Trizol with 25 µg/ml linear acrylamide (Ambion). The extracted RNA (10 µl volume) was treated with 2 Units of RNase-free recombinant DNase I (Ambion) for 15 min at 25˚C, followed by 15 min at 37˚C to remove any contaminating genomic DNA. The DNA-free RNA samples were purified using the RNA Clean & Concentrator™-5 from Zymo Research and eluted in 10 µl of nuclease-free water. Purified RNA was reverse transcribed and amplified using the WT-Ovation™ Pico RNA Amplification system (NuGEN Technologies) following the manufacturer’s instructions. Sense strand cDNA was generated using WT-Ovation™ Exon Module (NuGEN).

treatment_protocol: Eight-week old Sox17 trangenic mice and littermate control mice were treated with 2mg/ml Doxycycline in drinking water for 5 days prior to isolation of HSCs

value: CD150+CD48-Lineage-Sca1+ckit+ bone marrow hematopoietic stem cells

tag: genotype/variation

value: wild type

value: 8 weeks

value: 2mg/ml Doxycycline in drinking water, 5 days


title: Wildtype_HSC_Rep1

description:
Gene expresion data from hematopoietic stem cells isolated from 8-week old wild type control mice after 5 days of Doxycycline treatment
WT_HSC1.CEL


title: Sox17_transgenic_HSC_Rep5

description:
Gene expresion data from hematopoietic stem cells isolated from 8-week old Sox17-transgenic mice after 5 days of Doxycycline treatment
Sox17TG_HSC5.CEL

source_name: Hematopoietic stem cells from 8-week old Sox17-transgenic mice after 5 days of Doxycycline administration

value: Sox17-transgenic ((tetO)7CMVSox17-IRES-NucEGFP;B6.Cg-Gt(ROSA)26Sortm1(rtTA*M2)Jae/J double transgenic)


title: Wildtype_HSC_Rep5

description:
Gene expresion data from hematopoietic stem cells isolated from 8-week old wild type control mice after 5 days of Doxycycline treatment
WT_HSC5.CEL


title: wild-type control rep2

source_name: 4A+ untreated


title: Wildtype_HSC_Rep2

description:
Gene expresion data from hematopoietic stem cells isolated from 8-week old wild type control mice after 5 days of Doxycycline treatment
WT_HSC2.CEL


title: wild-type DBMIB 2h rep1


title: Wildtype_HSC_Rep3

description:
Gene expresion data from hematopoietic stem cells isolated from 8-week old wild type control mice after 5 days of Doxycycline treatment
WT_HSC3.CEL


title: Akt1-deficient 3


title: wild-type control rep3


title: Darr Site(+) with a vector expressing ArrH18A compared to wild-type M. smegmatis Site(+)

city: St Louis

first: Christina

middle: Leigh

last: Stallings

state: Mo

address: 660 South Euclid Avenue, Box 8230

department: Molecular Microbiology

institute: Washington University School of Medicine

description: 3 biological replicates of each strain for each experiment.

hyb_protocol: Labeled cDNA was mixed to 500ul of Ambion SlideHyb#3 hybridization buffer (cat# AM8863). Hybridization mix was spin at 15,000xg for 5 min, denatured at 98C for 2 min and kept at 70C until loading onto the slide. Hybridization was performed in the Agilent hybridization chambers and oven for 18hrs, at 50C, rotation setting at 7.  At the end of hybridization, slides were disassembled in 0.2xSSC/0.1%SDS, washed for 15 min at RT in 0.2xSSC/0.1%SDS, then 15min at RT in 0.1xSSC and dried by centrifugation at 1000rpm for 3 min.

scan_protocol: Arrays were scanned using an Axon 4200AL scanner (Axon Instruments Inc) using the “autoscanning” function.

data_processing:
Images were analyzed using GenePix Pro 6.0 (Axon Instruments Inc) for background subtraction, quantile normalization and processing. Partek software was used for analysis
average normalized Cy5/Cy3 log ratio of replicates. pValue for replicates also shown in the supplementary file on the Series record.

organism: Mycolicibacterium smegmatis

source_name: mgm3062 (Darr, expressing ArrH18A)

label_protocol: 10 ug of RNA was reversed transcribed with Stratagene Fairplay kit and the cDNA was coupled to either Cy5 or Cy3 dyes

growth_protocol: Mycobacterium smegmatis strains were grown in LB media to an OD600 of 0.7. Samples were collected for RNA extraction.

extract_protocol: Total RNA was extracted using Trizol and bead beating

value: mgm3062 (Darr, expressing ArrH18A)


title: Sox17_transgenic_HSC_Rep2

description:
Gene expresion data from hematopoietic stem cells isolated from 8-week old Sox17-transgenic mice after 5 days of Doxycycline treatment
Sox17TG_HSC2.CEL


title: Sox17_transgenic_HSC_Rep4

description:
Gene expresion data from hematopoietic stem cells isolated from 8-week old Sox17-transgenic mice after 5 days of Doxycycline treatment
Sox17TG_HSC4.CEL


title: wild-type NR 2h rep1

value: 4A+ is a wild-type C. reinhardtii strains in the 137c background


title: Sox17-expressing_CD48+LSK_Rep3

description:
Gene expresion data from Sox17-expressing CD48+LSK hematopoietic progenitors isolated from primary recipients that were reconsituted with MSCV-Sox17 retrovirus infected adult bone marrow cells 12-weeks earlier
Sox17_CD48+LSK3.CEL

source_name: Sox17-expressing CD48+LSK hematopoietic progenitors isolated from primary recipients that were reconstituted with MSCV-Sox17 retrovirus infected adult bone marrow cells 12 weeks earlier

growth_protocol: 3 independent replicates of uncultured 10,000 E16.5 fetal liver HSCs, 10,000 fetal liver CD48+LSK cells, 10,000 adult bone marrow HSCs, 10,000 adult bone marrow CD48+LSK cells and 10,000 Sox17-expressing CD48+LSK cells isolated from primary recipients 12 weeks after transplantation of MSCV-Sox17-infected bone marrow cellswere double-sorted into Trizol (Invitroen)

treatment_protocol: The isolated hematopoietic stem/progenitor cells were processed without treatment.

value: CD48+Lineage-Sca1+ckit+  bone marrow hematopoietic progenitors

tag: developmental stage

value: Adult

value: MSCV-Sox17 retrovirus infected


title: Sox17-expressing_CD48+LSK_Rep2

description:
Gene expresion data from Sox17-expressing CD48+LSK hematopoietic progenitors isolated from primary recipients that were reconsituted with MSCV-Sox17 retrovirus infected adult bone marrow cells 12-weeks earlier
Sox17_CD48+LSK2.CEL


title: Sox17_transgenic_HSC_Rep1

description:
Gene expresion data from hematopoietic stem cells isolated from 8-week old Sox17-transgenic mice after 5 days of Doxycycline treatment
Sox17TG_HSC1.CEL


title: Sox17-expressing_CD48+LSK_Rep1

description:
Gene expresion data from Sox17-expressing CD48+LSK hematopoietic progenitors isolated from primary recipients that were reconsituted with MSCV-Sox17 retrovirus infected adult bone marrow cells 12-weeks earlier
Sox17_CD48+LSK1.CEL


title: 8-week_ bone marrow_CD48+LSK_Rep2

description:
Gene expresion data from CD48+LSK hematopoietic progenitors isolated from 8-week old mouse bone marrow
Adult_CD48+LSK2.CEL

source_name: CD48+LSK hematopoietic progenitors from 8-week old wild type mouse bone marrow

value: CD48+Lineage-Sca1+ckit+ bone marrow hematopoietic progenitors

value: untreated


title: Darr Site(+) with an empty vector compared to wild-type M. smegmatis Site(+)

source_name: mgm3060 (Darr, vector control)

value: mgm3060 (Darr, vector control)


title: T21, chSh, biological rep1

description: L4-L5 rat DRGs after sciatic ChSh lesion

extract_protocol: Qiagen Rneasy

value: chSh

value: Wistar

value: 8 to 12 weeks old


title: 8-week_ bone marrow_HSC_Rep3

description:
Gene expresion data from HSCs isolated from 8-week old mouse bone marrow
Adult_HSC3.CEL

source_name: HSC from 8-week old wild type mouse bone marrow

value: CD150+CD48-Lineage-Sca1+ckit+ bone marrow HSCs


title: 8-week_ bone marrow_CD48+LSK_Rep3

description:
Gene expresion data from CD48+LSK hematopoietic progenitors isolated from 8-week old mouse bone marrow
Adult_CD48+LSK3.CEL


title: 8-week_ bone marrow_CD48+LSK_Rep1

description:
Gene expresion data from CD48+LSK hematopoietic progenitors isolated from 8-week old mouse bone marrow
Adult_CD48+LSK1.CEL


title: Darr Site(+) with a vector expressing Arr D83A compared to wild-type M. smegmatis Site(+)

source_name: mgm3064 (Darr, expressing D83A)

value: mgm3064 (Darr, expressing D83A)


title: sor1 control rep1

value: sor1 is a singlet oxygen resistant mutant derived from the 4A+ wild-type strain with a single nucleotide polymorphism in a gene coding for a putative bZIP transcription factor.

value: sor1 mutant


title: 8-week_ bone marrow_HSC_Rep2

description:
Gene expresion data from HSCs isolated from 8-week old mouse bone marrow
Adult_HSC2.CEL


title: Stationary phase cultures induced to express I-SceI for 15 minutes (T=15, +ATc)

description:
Replicate 1, 2, and 3 combined and averaged
ATc added for 15 minutes, Biological replicates 1, 2 and 3

data_processing:
Images were analyzed using GenePix Pro 6.0 (Axon Instruments Inc) for background subtraction, lowess normalization and processing. GeneSpring software (v. 7.3.1) was used for analysis
VALUE = average normalized Cy5(mgm182)/Cy3(mgm181) log ratio of replicates. pValue for replicates also shown.

label_protocol: 10 ug of RNA was reversed transcribed with Stratagene Fairplay kit and the cDNA was coupled to either Cy5 (mgm182) or Cy3 (mgm181) dyes

growth_protocol: Mycobacterium smegmatis strains mgm182 (site(+)) and mgm181 (site(-)) were grown to an OD600 of 0.7 (log) or >2.0 (stationary). Samples were collected for the T=0 timepoint and then a final concentration of 50ng/ml of ATc was added. 15 minutes and 45 minutes later samples were collected (T=15 and T=45, respectively).


title: 8-week_ bone marrow_HSC_Rep1

description:
Gene expresion data from HSCs isolated from 8-week old mouse bone marrow
Adult_HSC1.CEL


title: Darr Site(+) with a vector expressing WT Arr compared to wild-type M. smegmatis Site(+)

source_name: mgm3061 (Darr, expressing WT Arr)

value: mgm3061 (Darr, expressing WT Arr)


title: E16.5_fetal liver_HSC_Rep2

description:
Gene expresion data from HSCs isolated from E16.5 wild type mouse fetal liver.
Fetal_HSC2.CEL

source_name: HSC from E16.5 wild type mouse fetal liver

value: CD150+CD48-Lineage-Sca1+ckit+ fetal liver HSCs

value: Fetal


title: Stationary cultures control without induction of I-SceI expression (T=0, -Atc)

description:
Replicate 1, 2, and 3 combined and averaged
No ATc added, Biological replicates 1, 2 and 3


title: E16.5_fetal liver_HSC_Rep1

description:
Gene expresion data from HSCs isolated from E16.5 wild type mouse fetal liver.
Fetal_HSC1.CEL


title: Log phase cultures induced to express I-SceI for 45 minutes (T=45, +ATc)

description:
Replicate 1, 2, and 3 combined and averaged
ATc added for 45 minutes, Biological replicates 1, 2 and 3


title: Δmbs2 exp2

city: Seoul

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

description: Ctr vs Δmbs2_exp2

hyb_protocol: Microarray Hybridization and Washing.  A C. neoformans serotype D 70-mer microarray slide containing 7,936 probes (Duke University) was pre-hybridized at 42°C in 60 ml of pre-hybridization buffer (42.4 ml sterile distilled water, 2 ml 30% BSA (Sigma), 600 µl 10% SDS, 15 ml 20x SSC (Saline-Sodium Citrate, 3 M NaCl, 0.3 M Na-citrate, pH 7.0)), washed with distilled water and isopropanol, and dried by brief centrifugation (110g, 2 min).  The Cy3- and Cy5-labeled cDNA samples were combined, concentrated through a Microcon30 filter, and vacuum-dried.  The dried cDNA samples were resuspended with 24 µl of 1x hybridization buffer (250 µl 50% formamide, 125 µl 20x SSC, 5 µl 10% SDS, 120 µl dH2O, total 500 µl), added with 1 µl polyA tail DNA (Sigma), further incubated at 100°C for 3 min and allowed to cool for 5 min at room temperature.  The microarray slides were aligned into the hybridization chamber (DieTech), removed of any dust, and covered by Lifterslips (Erie Scientific).  The Cy3/Cy5-labeled cDNA samples were applied in between Lifterslips and slides.  To prevent slides from drying, 10 µl of 3x SSC buffer was applied onto the slides, which were subsequently incubated for 16 hr at 42°C.  After incubation, the microarray slides were washed with three different washing buffers (wash buffer 1 (10 ml 20x SSC, 600 µl 10% SDS, 189.4 ml dH2O, preheated at 42°C), wash buffer 2 (3.5 ml 20x SSC, 346.5 ml dH2O), wash buffer 3 (0.88 ml 20x SSC, 349.12 ml dH2O)) for 2, 5, and 5 min, respectively, on an orbital shaker.  Three independent DNA microarrays with 3 independent biological replicates were performed

scan_protocol: After hybridization and washing, the microarray slides were scanned with a GenePix 4000B scanner (Axon Instrument) and the signals were analyzed with GenePix Pro (Ver. 4.0) and gal file (http://genome.wustl.edu/activity/ma/cneoformans).

data_processing: Since total RNAs isolated from serotype A C. neoformans strains were hybridized on the microarray slides printed with the serotype D 70-mer oligonucleotide sequences, the serotype A gene sequences were mapped to those of the serotype D using BLASTN.  C. neoformans H99 gene sequences that were updated at 24 November 2008 were downloaded from Broad institute (http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans).  The serotype D C. neoformans JEC21 gene sequences that were updated 27 April 2005 were downloaded from JCVI (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/c_neoformans/).  The functional category of each C. neoformans H99 gene was assigned using the NCBI KOG database (http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi).  Using the serotype A gene sequence, each S. cerevisiae gene name or ID listed in the supplementary Tables was identified by blastp search (e-value cut-off: e-6). For hierarchical and statistical analysis, data transported from GenePix software were analyzed with GeneSpring (Agilent) by employing LOWESS normalization, reliable gene filtering, clustering (standard correlation and average linkage) and zero-transformation, and ANOVA analysis (P<0.01), and Microsoft Excel software (Microsoft).

organism: Cryptococcus neoformans H99

source_name: Δmbs2 _exp2

label_protocol: For cDNA synthesis, the total RNA concentration was adjusted to 1 µg/µl with DEPC-treated water, and 15 µl of the total RNA (15 µg) was added to 1 µl of 5 µg/µl oligo dT (5’-TTTTTTTTTTTTTTTTTTTTV-3’)/pdN6 (Amersham, 1:1 mixture of 10 µg/µl, respectively), incubated at 70°C for 10 min, and place on ice for 10 min.  Then 15 µl of cDNA synthesis mixture (3 µl 0.1 M DTT, 0.5 µl RNasin (Promega), 0.6 µl aa-dUTP (5-(3-aminoallyl)-2’-deoxyuridine 5’-triphosphate)/dNTPs (a mixture of 6 µl dTTP (100 mM), 4 µl aa-dUTP (100 mM), 10 µl dATP (100 mM), 10 µl dCTP (100 mM), 10 µl dGTP (100 mM)), 1.5 µl AffinityScript reverse transcriptase (Stratagene), 3 µl AffinityScript buffer, 7 µl water) was added and incubated at 42°C for 2 hrs.  Then 10 µl of 1 N NaOH and 10 µl of 0.5 M EDTA (pH 8.0) were added and incubated at 65°C for 15 min.  After incubation, 25 µl of 1 M HEPES buffer (pH 8.0) and 450 µl of DEPE-treated water were added, and the whole mixture was concentrated through a Microcon30 filter (Millipore) and vacuum-dried for 1 hr. For Cy3 and Cy5 (Amersham) labeling of the prepared cDNA, Cy3 and Cy5 were dissolved in 10 µl DMSO and 1.25 µl of each dye was aliquoted into separate tubes.  The cDNAs prepared as described above were added to 9 µl of 0.05 M Na-bicarbonate (pH 8.0) and incubate at room temperature for 15 min.  The cDNAs prepared from pooled reference RNAs were mixed with Cy3 as a control and the cDNAs prepared from each test RNA (each experimental condition) were mixed with Cy5.  For a dye-swap experiment, control and test RNAs were labeled oppositely.  Each mixture was further incubated at room temperature for 1 hr in the dark and purified by QIAquick PCR purification kit (QIAGEN).

growth_protocol: The wild-type H99 strain mbs1 (YSB488) and mbs2 (YSB538)mutant strains were grown in 50 ml YPD medium at 30°C for 16 h. Then 2.5 ml of the overnight culture was inoculated into 50 ml of fresh YPD medium and further incubated for 4 h at 30°C  to an optical density at 600 nm (OD600 =1.0)

extract_protocol: For total RNA isolation, the lyophilized cell pellets were added to 3 ml volume of sterile 3 mm glass bead (SIGMUND LINDER), homogenized by shaking, added to 4 ml of TRizol reagent (Tri reagent, Molecular Research Center), and allowed to incubate at room temperature for 5 min.  Then 800 µl of chloroform was added, incubated for 3 min at room temperature, transferred to 15 ml round-bottom tubes (SPL), and centrifuged by 10,000 rpm at 4°C for 15 min (Sorvall SS-34 rotor).  Two milliliters of the supernatant was transferred to a new round-bottom tube, 2 ml isopropanol was added, inverted several times, and allowed to incubate for 10 min at room temperature.  Then the mixture was re-centrifuged at 10,000 rpm at 4°C for 10 min, and the pellet was washed with 4 ml of 75% ethanol diluted with diethylpyrocarbonate (DEPC)-treated water and centrifuged at 8,000 rpm at 4°C for 5 min.  The pellet was dried and resuspended with 500 µl DEPC-treated water.  Concentration and purity of total RNA samples were calculated by measuring OD260nm and gel-electrophoresis, respectively.  For control total RNA, all total RNAs prepared from WT, mbs1 and mbs2 mutant cells grown in conditions described above were pooled (pooled reference RNAs).

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

source_name: pooled total RNA from all strain all treatment


title: Stationary cultures induced to express I-SceI for 45 minutes (T=45, +ATc)


title: Δmbs2 exp3

description: Ctr vs Δmbs2_exp3

source_name: Δmbs2 _exp3

value: pooled total RNA from all strain all treatment


title: PestF_1hr26vs1hr37_14004130_MDS.mev.refIsIB.out

status: Public on Jul 14 2011

city: Rockville

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95 C degree  prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

data_processing:
Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).
VALUE = log2(QUERY/REF), i.e., the base 2 logarithm of the ratio of QUERY_INTEGRATED_INTENSITY over REF_INTEGRATED_INTENSITY where REF refers to channel 2 (grown at 26 C) and QUERY refers to channel 1 (grown at 37 C).

organism: Yersinia pestis

source_name: Total RNA extracted after 1 hour at 37 degrees

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

growth_protocol: Grown in custom media and samples collected at 1 hour post temperature shift.

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manufacturer.

value: PestoidesF

source_name: Total RNA extracted after 1 hour at 26 degrees

growth_protocol: Grown in custom media and samples collected after 1 hour at 26 degrees


title: PBIB15_8hr26vs8hr37_14004101_MDS.mev.refIsIB.out

source_name: Total RNA extracted after 8 hours at 37 degrees

growth_protocol: Grown in custom media and samples collected at 8 hours post temperature shift.

source_name: Total RNA extracted after 8 hours at 26 degrees

growth_protocol: Grown in custom media and samples collected after 8 hours at 26 degrees


title: PestF_4hr26vs4hr37_14004134_MDS.mev.refIsIB.out

source_name: Total RNA extracted after 4 hours at 37 degrees

growth_protocol: Grown in custom media and samples collected at 4 hours post temperature shift.

source_name: Total RNA extracted after 4 hours at 26 degrees

growth_protocol: Grown in custom media and samples collected after 4 hours at 26 degrees


title: PestF_8hr26vs8hr37_14004103_MDS.mev.refIsIB.out


title: PestF_2hr26vs2hr37_14004132_MDS.mev.refIsIB.out

source_name: Total RNA extracted after 2 hours at 37 degrees

growth_protocol: Grown in custom media and samples collected at 2 hours post temperature shift.

source_name: Total RNA extracted after 2 hours at 26 degrees

growth_protocol: Grown in custom media and samples collected after 2 hours at 26 degrees


title: PBIB15_2hr26vs2hr37_14004099_MDS.mev.refIsIB.out


title: PBIB15_1hr26vs1hr37_14004095_MDS.mev.refIsIB.out


title: Δmbs2 exp1

description: Ctr vs Δmbs2_exp1

source_name: Δmbs2 _exp1


title: wild-type control rep1

source_name: 4A+ untreated

value: 4A+ is a wild-type C. reinhardtii strains in the 137c background

value: wild type 4A+


title: E16.5_fetal liver_HSC_Rep3

description:
Gene expresion data from HSCs isolated from E16.5 wild type mouse fetal liver.
Fetal_HSC3.CEL


title: COW5_8hr26vs8hr37_14004104_MDS.mev.refIsIB.out


title: Log phase cultures without induction of I-SceI expression (T=0, -Atc)


title: PBIB15_4hr26vs4hr37_14004100_MDS.mev.refIsIB.out


title: COW5_2hr26vs2hr37_14004107_MDS.mev.refIsIB.out


title: Sox17_transgenic_HSC_Rep3

description:
Gene expresion data from hematopoietic stem cells isolated from 8-week old Sox17-transgenic mice after 5 days of Doxycycline treatment
Sox17TG_HSC3.CEL

source_name: Hematopoietic stem cells from 8-week old Sox17-transgenic mice after 5 days of Doxycycline administration

value: CD150+CD48-Lineage-Sca1+ckit+ bone marrow hematopoietic stem cells

value: Sox17-transgenic ((tetO)7CMVSox17-IRES-NucEGFP;B6.Cg-Gt(ROSA)26Sortm1(rtTA*M2)Jae/J double transgenic)

value: 8 weeks

value: 2mg/ml Doxycycline in drinking water, 5 days


title: COW5_4hr26vs4hr37_14004106_MDS.mev.refIsIB.out


title: PestF_2hr37vs2hr26_14004131_MDS.mev.refIsIA.out

growth_protocol: Grown in custom media and samples collected after 2 hour at 26 degrees


title: PestF_4hr37vs4hr26_14004133_MDS.mev.refIsIA.out

growth_protocol: Grown in custom media and samples collected after 4 hour at 26 degrees


title: PestF_8hr37vs8hr26_14004135_MDS.mev.refIsIA.out

growth_protocol: Grown in custom media and samples collected after 8 hour at 26 degrees


title: COW5_1hr26vs1hr37_14004108_MDS.mev.refIsIB.out


title: PestF_1hr37vs1hr26_14004129_MDS.mev.refIsIA.out


title: COW5_4hr37vs4hr26_14004110_MDS.mev.refIsIA.out


title: COW5_8hr37vs8hr26_14004109_MDS.mev.refIsIA.out


title: COW5_1hr37vs1hr26_14004113_MDS.mev.refIsIA.out

growth_protocol: Grown in custom media and samples collected at 1, post temperature shift.


title: 3T3-L1-PPARg agonist GW347845-1

city: Cambridge

first: Julian

last: Griffin

address: Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol. Illumina Infinium Gene Expression BeadArrays (Illumina Inc, San Diego, CA) were used to perform transcriptomics. A mouse WG6 array platform was used with 45281 probes.

data_processing:
The R package lumi was used with the detection p-value threshold set to 0.01. Probes were required to be successfully detected (p-value<0.01 in Lumi) in at least one sample to pass the selection. The data was transformed using variance stabilization and then normalised using quantile normalisation. Gene expression was compared using the R package limma with a 5% confidence interval.
Data were normalized in two batches: cont v gamm AND cont v delt. Therefore, there are two sets of normalized data for the controls (both derived from the same raw data).

source_name: 3T3-L1 Adipocytes, PPARg agonist GW347845 treated

label_protocol: Standard Illumina labeling protocol

growth_protocol: 3T3-L1 preadipocytes were grown in T75 flasks and maintained in Dulbecco’s modified Eagles media (DMEM) (high glucose 4.5 g/l; Sigma-aldrich) supplemented with 10% (v/v) new born calf serum (Sigma-Aldrich), 50 units/ml penicillin, and 50 µg/ml streptomycin (Sigma-Aldrich) in a humidified 5% CO2 incubator at 37ºC. At 2 days post-confluence cells were induced to differentiate with DMEM supplemented with 10% v/v fetal bovine serum (FBS) (Invitrogen), 1 uM dexamethasone (Sigma-Aldrich), 0.5 mM isobutylmethylxanthine (Sigma-Aldrich), 100 nM insulin (Sigma-Aldrich), 50 units/ml penicillin, and 50 µg/ml streptomycin. The cells were maintained in this media for 72h as this was found to improve the reproducibility of differentiation between flasks. After 72 h the media was replaced with DMEM supplemented with 10% FBS, 100 nM insulin, 50 units/ml penicillin, and 50 µg/ml streptomycin. The media was subsequently changed for DMEM supplemented with 10% FBS, 50 units/ml penicillin, and 50 µg/ml streptomycin every 48 h. (Roberts et al 2009b)

extract_protocol: Cells were collected by removing the media and washing each T75 flask with 10 ml of PBS. Cells were then washed with 1.5 ml trypsin-EDTA solution (5 BAEE units trypsin/ml, 1.8 µg EDTA/ml; Sigma-Aldrich) for 2 min at 37ºC to remove the cells from the surface of the flask. 8.5 ml DMEM supplemented with 10% (v/v) new born calf serum, 50 units/ml penicillin, and 50 µg/ml streptomycin was added to each flask. The DMEM containing the cells was transferred to a falcon tube and centrifuged at 200 g for 2 min to pellet the cells. The remaining media was removed and the cells washed with physiological saline (0.9% NaCl) solution. RNA from 3T3-L1 adipocytes was extracted using RNeasy (Qiagen GmbH, Hilden, Germany). Approximately 5mg of cells was used per sample for RNA isolation. Procedures were carried out according to the manufacturer’s instructions. Extracted RNA was quantified and its purity assessed using a Nanodrop ND-1000 Spectrometer (Nanodrop Technologies Inc., Wilmington, USA) to measure the absorbance at 260 nm and the A260/A280 ratio, respectively.

treatment_protocol: At day 11 post induction the media on the cells was replaced with DMEM supplemented with 10% FBS, 100 nM insulin, 50 units/ml penicillin, and 50 µg/ml streptomycin containing DMSO (control; n=6), GW610742 PPARd selective agonist (n=6 1uM) or GW347845 PPARg selective agonist (n=6 100uM) for 2 days prior to cell collection and RNA extraction.

value: 3T3-L1 Adipocytes


title: 3T3-L1-PPARg agonist GW347845-2

description: replicate 2


title: 3T3-L1-PPARg agonist GW347845-6

description: replicate 6


title: COW5_2hr37vs2hr26_14004112_MDS.mev.refIsIA.out


title: 3T3-L1-PPARg agonist GW347845-4

description: replicate 4


title: PBIB15_2hr37vs2hr26_14004125_MDS.mev.refIsIA.out

source_name: Total RNA extracted after 2 hours 37 degrees

source_name: Total RNA extracted after 2 hours 26 degrees


title: 3T3-L1-DMSO Control-6 (gamma normalized)

description: replicate 6

source_name: 3T3-L1 Adipocytes, Control DMSO treated


title: 3T3-L1-PPARg agonist GW347845-5

description: replicate 5


title: 3T3-L1-DMSO Control-2 (gamma normalized)

description: replicate 2


title: 3T3-L1-DMSO Control-1 (gamma normalized)

description: replicate 1


title: 3T3-L1-PPARd agonist GW610742-6

description: replicate 6

source_name: 3T3-L1 Adipocytes, PPARd agonist GW610742 treated


title: PBIB15_8hr37vs8hr26_14004127_MDS.mev.refIsIA.out


title: 3T3-L1-DMSO Control-5 (gamma normalized)

description: replicate 5


title: 3T3-L1-PPARd agonist GW610742-4

description: replicate 4


title: 3T3-L1-DMSO Control-3 (gamma normalized)

description: replicate 3


title: PBIB15_1hr37vs1hr26_14004102_MDS.mev.refIsIA.out


title: 3T3-L1-PPARd agonist GW610742-3

description: replicate 3


title: 3T3-L1-DMSO Control-4 (gamma normalized)

description: replicate 4


title: 3T3-L1-PPARd agonist GW610742-5

description: replicate 5


title: 3T3-L1-PPARd agonist GW610742-2

description: replicate 2


title: 3T3-L1-PPARd agonist GW610742-1

description: replicate 1


title: PBIB15_4hr37vs4hr26_14004126_MDS.mev.refIsIA.out


title: 3T3-L1-DMSO Control-4 (delta normalized)

description: replicate 4


title: 3T3-L1-PPARg agonist GW347845-3

description: replicate 3


title: 3T3-L1-DMSO Control-6 (delta normalized)

description: replicate 6


title: 3T3-L1-DMSO Control-5 (delta normalized)

description: replicate 5


title: 3T3-L1-DMSO Control-1 (delta normalized)

description: replicate 1


title: 3T3-L1-DMSO Control-2 (delta normalized)

description: replicate 2


title: Donor: 351; Visit Number: 31; Visit Type: FOLLOW UP

first: Andrew

last: Hill

address: 300 Technology Square

department: Research Business Technology

institute: Pfizer

description: Donor: 351;Visit Number:31;Visit Type:FOLLOW UP

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: Affymetrix MAS 5.0 algorithm

label_protocol: Affymetrix in-vitro labeling protocol

extract_protocol: RNA was extracted from human PBMCs

tag: history of acid reflux  0=no  1=yes

value: not reported

tag: fasting status

value: YES

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

tag: initial processing lab

value: ICON-F

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

value: Moderate Persistent

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

value: W

tag: days since quiet visit

tag: visit number

tag: country

value: USA

tag: fev1 predicted

tag: leukotriene receptor antagonist use  0=no  1=yes

value: PBMC


title: Donor: 761; Visit Number: 20; Visit Type: QUIET

description: Donor: 761;Visit Number:20;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

value: ICON-D

value: Severe Persistent

value: GBR

tag: cell type


title: 3T3-L1-DMSO Control-3 (delta normalized)

description: replicate 3

tag: cell line


title: Donor: 404; Visit Number: 31; Visit Type: FOLLOW UP

description: Donor: 404;Visit Number:31;Visit Type:FOLLOW UP

value: NO

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

value: B

tag: days since quiet visit

tag: visit number

tag: country

tag: fev1 predicted

tag: leukotriene receptor antagonist use  0=no  1=yes


title: Donor: 804; Visit Number: 30; Visit Type: EXACERBATION

description: Donor: 804;Visit Number:30;Visit Type:EXACERBATION

tag: history of acid reflux  0=no  1=yes

tag: fasting status

value: NON-FASTING

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

value: Non-Atopic

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

value: DeCODE

value: ISL

tag: cell type


title: Donor: 848; Visit Number: 31; Visit Type: EXACERBATION

description: Donor: 848;Visit Number:31;Visit Type:EXACERBATION

value: Atopic

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

tag: fev1 predicted


title: Donor: 452; Visit Number: 31; Visit Type: FOLLOW UP

description: Donor: 452;Visit Number:31;Visit Type:FOLLOW UP

tag: history of acid reflux  0=no  1=yes

value: not reported

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

tag: leukotriene receptor antagonist use  0=no  1=yes


title: Donor: 711; Visit Number: 40; Visit Type: QUIET

description: Donor: 711;Visit Number:40;Visit Type:QUIET

value: YES

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

tag: cell type


title: Donor: 401; Visit Number: 30; Visit Type: QUIET

description: Donor: 401;Visit Number:30;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

value: ICON-F

tag: fev1 predicted


title: Donor: 819; Visit Number: 20; Visit Type: QUIET

description: Donor: 819;Visit Number:20;Visit Type:QUIET

value: FASTING

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

value: Moderate Persistent

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

tag: leukotriene receptor antagonist use  0=no  1=yes


title: Donor: 454; Visit Number: 51; Visit Type: EXACERBATION

description: Donor: 454;Visit Number:51;Visit Type:EXACERBATION

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

value: W

value: USA

tag: cell type


title: Donor: 558; Visit Number: 51; Visit Type: FOLLOW UP

description: Donor: 558;Visit Number:51;Visit Type:FOLLOW UP

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

tag: fev1 predicted

value: PBMC


title: Donor: 848; Visit Number: 30; Visit Type: QUIET

description: Donor: 848;Visit Number:30;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

tag: leukotriene receptor antagonist use  0=no  1=yes


title: Donor: 683; Visit Number: 20; Visit Type: QUIET

description: Donor: 683;Visit Number:20;Visit Type:QUIET

tag: initial processing lab

value: ICON-D

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

value: Severe Persistent

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

value: IRL

tag: cell type


title: Donor: 409; Visit Number: 20; Visit Type: QUIET

description: Donor: 409;Visit Number:20;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

tag: fev1 predicted


title: Donor: 824; Visit Number: 30; Visit Type: EXACERBATION

description: Donor: 824;Visit Number:30;Visit Type:EXACERBATION

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

tag: leukotriene receptor antagonist use  0=no  1=yes


title: Donor: 59; Visit Number: 50; Visit Type: QUIET

description: Donor: 59;Visit Number:50;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

value: AARI

value: AUS

tag: cell type


title: Donor: 755; Visit Number: 20; Visit Type: QUIET

description: Donor: 755;Visit Number:20;Visit Type:QUIET

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

value: GBR

tag: fev1 predicted


title: Donor: 821; Visit Number: 31; Visit Type: FOLLOW UP

description: Donor: 821;Visit Number:31;Visit Type:FOLLOW UP

tag: history of acid reflux  0=no  1=yes

tag: fasting status

value: NON-FASTING

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

value: DeCODE

tag: leukotriene receptor antagonist use  0=no  1=yes


title: Donor: 775; Visit Number: 60; Visit Type: EXACERBATION

description: Donor: 775;Visit Number:60;Visit Type:EXACERBATION

value: Atopic

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

tag: cell type


title: Donor: 774; Visit Number: 31; Visit Type: EXACERBATION

description: Donor: 774;Visit Number:31;Visit Type:EXACERBATION

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

value: not reported

tag: fev1 predicted


title: Donor: 454; Visit Number: 50; Visit Type: QUIET

description: Donor: 454;Visit Number:50;Visit Type:QUIET

value: NO

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

tag: leukotriene receptor antagonist use  0=no  1=yes


title: Donor: 806; Visit Number: 60; Visit Type: QUIET

description: Donor: 806;Visit Number:60;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

value: ISL

tag: cell type


title: Donor: 158; Visit Number: 20; Visit Type: QUIET

description: Donor: 158;Visit Number:20;Visit Type:QUIET

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

tag: fev1 predicted


title: Donor: 118; Visit Number: 40; Visit Type: QUIET

description: Donor: 118;Visit Number:40;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

value: FASTING

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

tag: leukotriene receptor antagonist use  0=no  1=yes


title: Donor: 351; Visit Number: 50; Visit Type: QUIET

description: Donor: 351;Visit Number:50;Visit Type:QUIET

value: YES

tag: initial processing lab

value: ICON-F

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

value: Moderate Persistent

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

tag: cell type


title: Donor: 406; Visit Number: 20; Visit Type: QUIET

description: Donor: 406;Visit Number:20;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

value: B

value: USA

tag: fev1 predicted

value: PBMC


title: Donor: 452; Visit Number: 41; Visit Type: QUIET

description: Donor: 452;Visit Number:41;Visit Type:QUIET

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

value: Severe Persistent

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

value: W

tag: days since quiet visit

tag: visit number

tag: country

tag: leukotriene receptor antagonist use  0=no  1=yes


title: Donor: 454; Visit Number: 20; Visit Type: QUIET

description: Donor: 454;Visit Number:20;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

tag: cell type


title: Donor: 118; Visit Number: 60; Visit Type: EXACERBATION

description: Donor: 118;Visit Number:60;Visit Type:EXACERBATION

tag: initial processing lab

value: AARI

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

value: AUS

tag: fev1 predicted


title: Donor: 752; Visit Number: 40; Visit Type: QUIET

description: Donor: 752;Visit Number:40;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

value: ICON-D

value: GBR

tag: leukotriene receptor antagonist use  0=no  1=yes


title: Donor: 419; Visit Number: 40; Visit Type: EXACERBATION

description: Donor: 419;Visit Number:40;Visit Type:EXACERBATION

value: Atopic

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

tag: cell type


title: Donor: 651; Visit Number: 20; Visit Type: QUIET

description: Donor: 651;Visit Number:20;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

value: not reported

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

value: IRL

tag: fev1 predicted


title: Donor: 109; Visit Number: 51; Visit Type: FOLLOW UP

description: Donor: 109;Visit Number:51;Visit Type:FOLLOW UP

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

tag: leukotriene receptor antagonist use  0=no  1=yes


title: Donor: 102; Visit Number: 40; Visit Type: EXACERBATION

description: Donor: 102;Visit Number:40;Visit Type:EXACERBATION

tag: history of acid reflux  0=no  1=yes

tag: fasting status

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

tag: cell type


title: Donor: 701; Visit Number: 50; Visit Type: QUIET

description: Donor: 701;Visit Number:50;Visit Type:QUIET

value: NO

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

tag: fev1 predicted


title: Donor: 109; Visit Number: 30; Visit Type: QUIET

description: Donor: 109;Visit Number:30;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

value: FASTING

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

tag: leukotriene receptor antagonist use  0=no  1=yes


title: Donor: 819; Visit Number: 51; Visit Type: EXACERBATION

description: Donor: 819;Visit Number:51;Visit Type:EXACERBATION

value: Non-Atopic

tag: initial processing lab

value: DeCODE

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

value: ISL

tag: cell type


title: Donor: 264; Visit Number: 20; Visit Type: QUIET

description: Donor: 264;Visit Number:20;Visit Type:QUIET

tag: history of acid reflux  0=no  1=yes

tag: fasting status

value: YES

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

value: ICON-F

tag: fev1 predicted


title: Donor: 654; Visit Number: 60; Visit Type: QUIET

description: Donor: 654;Visit Number:60;Visit Type:QUIET

tag: initial processing lab

tag: ige level

tag: any inhaled cs use  0=no  1=yes

tag: any intranasal cs use  0=no  1=yes

tag: rna extract srckey

tag: lims src id

tag: baseline severity  nih guideline

value: Moderate Persistent

tag: exacerbation visit subgroup  based on k-means clustering

tag: any systemic cs use  0=no  1=yes

tag: sa key

tag: race

tag: days since quiet visit

tag: visit number

tag: country

tag: leukotriene receptor antagonist use  0=no  1=yes

value: PBMC


title: Donor: 832; Visit Number: 32; Visit Type: FOLLOW UP

description: Donor: 832;Visit Number:32;Visit Type:FOLLOW UP

tag: history of acid reflux  0=no  1=yes

tag: fasting status

value: NON-FASTING

tag: bactin-gapdh 5' 3' ratio

tag: rn source key current

tag: sample collection date

tag: any relevant respiratory infections  0=no  1=yes

tag: atopy status

tag: days from visit to sample collection

tag: software analysis key current

tag: bmi

tag: lims hyb id

tag: maximum steroid exposure  4=systemic  3=inhaled  2=intranasal  1

tag: cel file path

tag: ratio of monocytes to lymphocytes  whole blood

value: W

tag: cell type