title: microRNA expression in Cntl (Sample A) vs LMP1 (Sample B) transduced Mutu E1dn Cl. 3 cells - prep 5

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

description: No additional comments

hyb_protocol: Hybridization is performed using a micro-circulation pump (Atactic Technologies).  The hybridization conditions are 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide, 34 °C, and overnight.

scan_protocol: Hybridization images are collected using a laser scanner (GenePix 4000B, Molecular Device).  Scan resolution is set at 10 µ and PTM is set between 350 to 700 V.

data_processing:
Data are analyzed by first subtracting the background and then normalization.  The background is determined using a regression-based background mapping method.  The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots.  Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data.
The VALUE column reports normalized log2 (LMP1/Control) ratios.

source_name: pEhyg (Cntl) transduced Mutu E1dn Cl.3 cells - RNA prep 5

label_protocol: Small RNAs (< 300 nt) are 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag is then ligated to the poly(A) tail for later fluorescent dye staining; two different tags are used for the two RNA samples in dual-sample experiments.

extract_protocol: Modified Trizol RNA prep

tag: Mutu E1dn Cl. 3 cells are an EBV negative derivative of the EBV positive Burkitt's lymphoma cell line, Mutu, in which EBV genomes were eradicated by transduction with dominant negative form of the EBV EBNA1 episomal replication factor.  Cells for this sample were transduced with the empty retroviral vector, pEhyg.

source_name: pEhyg-FLAG-LMP1 transduced Mutu E1dn Cl. 3 cells – RNA prep 5

tag: Mutu E1dn Cl. 3 cells are an EBV negative derivative of the EBV positive Burkitt's lymphoma cell line, Mutu, in which EBV genomes were eradicated by transduction with dominant negative form of the EBV EBNA1 episomal replication factor.  Cells for this sample were transduced with the empty retroviral vector, pEhyg-FLAG-LMP1.


title: Breast cancer cell antigen Grb10_immuno high vaccine_rep1

status: Public on Jan 09 2008

type: RNA

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

country: USA

institute: GenUs BioSystems, Inc.

hyb_protocol: Complete CodeLink protocol with Cy5-streptavidin staining

scan_protocol: Axon 4000B scanner, 10um resolution, TIFF image data extracted with CodeLink v.4.1 software.

data_processing: CodeLink v. 4.1 software used to extract raw data from TIFF image.  All data normalized to the median raw value of the array

label: Biotin-UTP

molecule: total RNA

organism: Mus musculus

source_name: Mouse fibroblasts, DNA transfected, immuno high vaccine

label_protocol: MessageAmp II (standard protocol)

extract_protocol: Ribopure (Ambion)

tag: Strain C3H/He, female, 8-12 weeks old, DNA transfected fibroblasts


title: microRNA expression in LMP1 (Sample A) vs Cntl (Sample B) transduced Mutu E1dn Cl. 3 cells - prep 4

description: No additional comments

organism: Homo sapiens

source_name: pEhyg-FLAG-LMP1 transduced Mutu E1dn Cl. 3 cells – RNA prep 4

source_name: pEhyg (Cntl) transduced Mutu E1dn Cl.3 cells - RNA prep 4


title: microRNA expression in LMP1 (Sample A) vs Cntl (Sample B) transduced Mutu E1dn Cl. 3 cells - prep 2

description: No additional comments

source_name: pEhyg-FLAG-LMP1 transduced Mutu E1dn Cl. 3 cells – RNA prep 2

source_name: pEhyg (Cntl) transduced Mutu E1dn Cl.3 cells - RNA prep 2


title: Breast cancer cell antigen Grb10_non-selected vaccine_rep2

source_name: Mouse fibroblasts, DNA transfected, non-selected vaccine


title: Breast cancer cell antigen Grb10_immuno low vaccine_rep2

source_name: Mouse fibroblasts, DNA transfected, immuno low vaccine


title: bovine_testis_4wk_rep2

status: Public on Jan 08 2008

city: Pullman

first: Derek

middle: J

last: McLean

state: WA

department: School of Molecular Biosciences

institute: Washington State University

description: Gene expression profile of bovine testis tissue at 4 weeks of age with the use of Affymetrix bovine GeneChip

label: biotin

organism: Bos taurus

source_name: bovine testis tissue 4 wk of age

tag: Angus bull calf testis tissue 4 weeks of age, replicate 2


title: microRNA expression in Cntl (Sample A) vs LMP1 (Sample B) transduced Mutu E1dn Cl. 3 cells - prep 1

description: No additional comments

source_name: pEhyg (Cntl) transduced Mutu E1dn Cl.3 cells - RNA prep 1

source_name: pEhyg-FLAG-LMP1 transduced Mutu E1dn Cl. 3 cells – RNA prep 1


title: Pinealectomised (PX):Control (CON) 3

city: Cambridge

first: Akhilesh

middle: Basi

last: Reddy

address: Hills Road

department: Institute of Metabolic Science

country: United Kingdom

institute: University of Cambridge

description: Biological replicate 3 of 3

hyb_protocol: After overnight hybridisation using established, standardized protocols for spotted cDNA arrays, the arrays were subjected to a series of washes (in SSC) at room temperature, then dried by centrifugation before scanning.

scan_protocol: Feature sizes, background and feature fluorescence (either Cy3/Cy5 channels) were calculated using the automated default parameters of Imagene 4.1 software (Biodiscovery).

data_processing: The mean fluorescence value for the pixels within the feature was calculated, and the raw data for each channel was then normalized by reference to the mean fluorescence of the total feature set for that channel. A ratio (Cy5/Cy3) ratio was then calculated.

organism: Mesocricetus auratus

source_name: control testes

label_protocol: Total RNA was transcribed into cDNA with incorporation of fluorescently-labelled (with Cy3 dye) dUTP by reverse transcription using SuperScript II (Invitrogen). Oligo-dT25, complementary to 3' poly(A) tails of mRNA, was used as the primer for this reaction. The template RNA was degraded by alkaline hydrolysis and the resulting Cy3-labelled single-stranded cDNA was cleaned using CentriSep columns (PE Biosystems) to remove enzymes and unincorporated primers/nucleotides before application to the spotted microarray for hybridization.

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

tag: Tissue

value: testes

source_name: pinealectomised testes


title: Breast cancer cell antigen Grb10_immuno low vaccine_rep1


title: bovine_testis_8wk_rep2

description: Gene expression profile of bovine testis tissue at 8 weeks of age with the use of Affymetrix bovine GeneChip

source_name: bovine testis tissue 8 wk of age, replicate 2

tag: Angus bull calf testis tissue 8 weeks of age, replicate 2


title: Pinealectomised (PX):Control (CON) 2

description: Biological replicate 2 of 3


title: Breast cancer cell antigen Grb10_non-selected vaccine_rep1


title: bovine_testis_8wk_rep1

source_name: bovine testis tissue 8 wk of age

tag: Angus bull calf testis tissue 8 weeks of age


title: H1650

city: Tokyo

first: Akihiko

last: Gemma

address: Bumkyo-ku

country: Japan

institute: Nippon Medical School

description: adenocarcinoma cell line

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: Human cancer cell line

label_protocol: Approximately 1µg of mRNA was processed to produce biotinylated cRNA targets.

extract_protocol: Standard Affymetrix protocol

tag: adenocarcinoma cell line


title: bovine_testis_4wk_rep1

tag: Angus bull calf testis tissue 4 weeks of age


title: LCD

description: adenocarcinoma cell line


title: DTT-treated cells_polysomal

status: Public on Jan 07 2008

type: other

city: Norwich

first: Colin

last: Hanfrey

state: Norfolk

address: Norwich Research Park

institute: Institute of Food Research

description: Polyribosomes following DTT or control treatment

hyb_protocol: Following fragmentation, 20 μg of cRNA were hybridized for 16 hr at 45oC on high-density oligonucleotide Yeast Genome S98 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray 3000 Scanner, according to the Affymetrix Manual II.

data_processing: The data were analysed with Affymetrix CGOS software. The average intensity of all probe seta was used for normalisation and scaled to 100 in the absolute analysis for each probe array.

molecule: other

organism: Saccharomyces cerevisiae

source_name: RNA purified from DTT-treated cells_polysomal fraction of polyribosomes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 μg total RNA (Affymetrix Manual II).

growth_protocol: S. cerevisiae strain BY4741 (MATa his3Δ1 leu2Δ0 met5Δ0 ura3Δ0) was grown in YEPD (2% w/v bacto-peptone, 2% w/v glucose, 1% w/v yeast extract) adjusted to pH 5.4, with 200rpm rotary aeration at 30oC.

extract_protocol: Cells were spun down (6000rpm, 4mins, 4oC), and washed twice in 2.5 mL lysis buffer (20mM Tris-HCl pH 8.0, 140mM KCl, 1.5mM MgCl2, 0.5mM DTT, 1% v/v Triton X-100, 0.1mg/mL cycloheximide, 1mg/mL heparin). Following resuspension in 0.7 mL lysis buffer, cells were transferred to a chilled 15 mL corex tube, and 0.5 mL chilled glass beads (0.45-0.55mm) were added. Cells were vortexed 4 times for 20 secs each, with 90 secs on ice between. Cells were then spun (5000rpm, 5 mins, 4oC), and the supernatant was transferred to a chilled 1.5 mL tube, and spun again (9500rpm, 5 mins, 4oC). The supernatant was loaded onto an 11 mL 15-60% sucrose gradient, prepared in 20mM Tris-HCl pH 8.0, 140mM KCl, 5mM MgCl2, 0.5mM DTT, 0.1mg/mL cycloheximide, 0.5mg/mL heparin, in a 12 mL ultra-clear tube (Beckman). Sucrose gradients were spun at 35000rpm for 2.5 hours at 4oC. Using a programmable density gradient system (ISCO), 0.5 mL fractions were collected from the sucrose gradients into 1.5 mL tubes containing 1 mL of 6M guanidine HCl, mixed by inversion and immediately chilled on ice. Fractions were pooled into non-polysomal and polysomal samples according to OD254nm profiles. Non-polysomal and polysomal samples from 3 gradients were pooled together. Following addition of an equal volume of ethanol, pools were precipitated overnight at -20oC. RNA was spun down (10000rpm, 20 mins, 4oC), washed in 2 mL 70% ethanol, and resuspended in 400 μL TE buffer. RNA was re-precipitated by addition of 0.1 volume 3M Sodium acetate pH 5.2 and 2 volumes ethanol, at -20oC for 1 hour. RNA was spun down as before, washed in 1 mL 70% ethanol, and resuspended in 0.5 mL water. Any residual protein was removed by extraction with phenol:chloroform (1:1 v/v) and chloroform:IAA (24:1 v/v). An equal volume of 4M LiCL was added to the aqueous phase, and RNA was precipitated overnight at -20oC. RNA was spun down as before, washed in 1 mL 70% ethanol, resuspended in 400 μL water, and re-precipitated with 0.1 volume sodium acetate pH 5.2, 2 volumes ethanol. RNA was washed in 1 mL 70% ethanol, and resuspended in 20 μL water.

treatment_protocol: 100 mL cultures were grown to OD600nm 0.5, when DTT was added to a final concentration of 2mM (or an equivalent volume of water was added to control cultures), and flasks were returned to the incubator for a further 1 hour. Cyclohexomide was added to a final concentration of 0.1mg/mL, and flasks were cooled immediately on ice.

tag: strain BY4741


title: bovine_testis_2wk_rep2

description: Gene expression profile of bovine testis tissue at 2 weeks of age with the use of Affymetrix bovine GeneChip

source_name: bovine testis tissue 2 wk of age

tag: Angus bull calf testis tissue 2 weeks of age


title: bovine_testis_2wk_rep1

description: Gene expression profile of bovine testis at 2 wk of age. Series experiment with samples at 2, 4 and 8 weeks of age.  Two replicates at each age.

source_name: bull calf testis tissue, 2 weeks of age

extract_protocol: Trizol extraction

tag: Angus bull calf testis tissue, 2 weeks of age, replicate 1


title: Pinealectomised (PX):Control (CON) 1

description: Biological replicate 1 of 3


title: DTT-treated cells_sub-polysomal

source_name: RNA purified from DTT-treated cells_sub-polysomal fraction of polyribosomes


title: microRNA expression in Cntl (Sample A) vs LMP1 (Sample B) transduced Mutu E1dn Cl. 3 cells - prep 3

description: No additional comments

source_name: pEhyg (Cntl) transduced Mutu E1dn Cl.3 cells - RNA prep 3

source_name: pEhyg-FLAG-LMP1 transduced Mutu E1dn Cl. 3 cells – RNA prep 3


title: control cells_sub-polysomal

source_name: RNA purified from control cells_sub-polysomal fraction of polyribosomes


title: H1975

description: adenocarcinoma cell line


title: HUVEC control, biological rep1

status: Public on Jan 05 2008

city: Belmont

first: Katherine

last: Martin

state: MA

address: 61 Carleton Rd

institute: BioArray Consulting

description: Gene expression data from mock-infected HUVECs.

hyb_protocol: Standard protocol.

scan_protocol: Standard protocol.

data_processing: Signal values were calculated using robust multi-array analysis (RMA) (BioConductor), transformed using inverse nlog, and then imported into GeneSpring (Agilent) for chip normlaization to 50th percentile and gene normalization to the mean of controls (where available) for each cell type independently.

source_name: HUVECs, mock-infected control

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

growth_protocol: Blood samples were obtained from healthy volunteers. Monocytes and B cells were negatively selected from heparin-anti-coagulated blood using a rosetting antibody precipitation kit (StemCell) and maintained in RPMI 1640 medium supplemented with 10% FCS and antibiotics. Primary HUVECs were obtained from pooled umbilical cords (two to five donor pools per culture) and maintained in M199 supplemented with 10% FCS, 1 mM glutamine, endothelial cell growth stimulant, porcine intestinal heparin, and antibiotics. HUVEC cultures were split at a ratio of 1:3 or 1:4 for up to two passages.

extract_protocol: Total cellular RNA isolated using RNeasy kit (Qiagen).

treatment_protocol: DV (dengue 2 virus, New Guinea C) was cultured using the C6/36 insect cell line. HUVECs, monocytes and B cells were infected in vitro with DV. Cells were treated with uninfected C6/36 cell supernatant as a negative control (mock infection). Cells were collected for gene expression analysis at 48 h post-infection.

tag: Genotype

value: unknown

tag: Age


title: control cells_polysomal

source_name: RNA purified from control cells_polysomal fraction of polyribosomes


title: PBMCs-Healthy-H124_Healthy_B

status: Public on Jan 04 2008

city: Dallas

first: Ellen

last: Grishman

state: TX

address: 5323 Harry Hines Blvd

institute: UTSW Medical Center

description: Healthy patient.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 System.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: PBMCs from Healthy patient.

extract_protocol: RNeasy Mini

value: 16 yrs, when sample taken.

tag: Gender

value: F

tag: Ethnicity

value: (Ethnicity Not Reported)

tag: Race

value: White

tag: Illness

value: Healthy

tag: pH<7.30 at time of diagnosis


title: PBMCs-Healthy-INF447_Healthy_B

description: Healthy patient.

value: 24 mths, when sample taken.

value: M

value: (Race Not Reported)


title: PBMCs-Healthy-H125_Healthy_B

description: Healthy patient.


title: PBMCs-Healthy-H126_Healthy_B

description: Healthy patient.

value: 15 yrs, when sample taken.


title: PBMCs-Healthy-INF448_Healthy_B

description: Healthy patient.

value: Hispanic or Latino


title: HUVEC control, biological rep2


title: LCOK

description: adenocarcinoma cell line


title: PBMCs-Healthy-H98_Healthy_B

description: Healthy patient.


title: PBMCs-Healthy-INF408_Healthy_B

description: Healthy patient.

value: 2 yrs, when sample taken.

value: Not Hispanic or Latino


title: PBMCs-Healthy-H42_Healthy_B

description: Healthy patient.

value: 8 yrs, when sample taken.


title: PBMCs-Healthy-INF301_Healthy_B

description: Healthy patient.


title: ENCODE spikein competition, nonamplified sample, NimbleGen array 89840

type: genomic

city: Calgary

first: Mark

last: Bieda

state: AB

address: 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

description: all array processing by NimbleGen, Inc. See www.nimblegen.com for details

molecule: genomic DNA

source_name: DNA with spikein DNA; nonamplified. Source of DNA: Roche commercial DNA.

extract_protocol: artificial

tag: nonamplified DNA

source_name: DNA without spikeinDNA, nonamplified. Source of DNA: Roche commercial DNA.

extract_protocol: background DNA

tag: nonamplified


title: ENCODE spikein competition, nonamplified sample, NimbleGen array 89834

hyb_protocol: all array processing by NimbleGen, Inc. See www.nimblegen.com for details

source_name: DNA with spikein DNA, nonamplified. Source of DNA: Roche commercial DNA.

tag: nonamplified sample

tag: DNA with artificial spikein DNA

source_name: DNA without spikein DNA; nonamplified. Source of DNA: Roche commercial DNA.

tag: background DNA


title: ENCODE spikein competition, nonamplified sample, NimbleGen array 96403

scan_protocol: all array processing by NimbleGen, Inc. See www.nimblegen.com for details

source_name: DNA with spikeinDNA, nonamplified. Source of DNA: Roche commercial DNA.

source_name: DNA without spikein DNA, nonamplified. Source of DNA: Roche commercial DNA.


title: PBMCs-Healthy-H176_Healthy_B

description: Healthy patient.

value: 14 yrs, when sample taken.


title: PBMCs-Healthy-H178_Healthy_B

description: Healthy patient.

value: 11 yrs, when sample taken.


title: PBMCs-Healthy-H122_Healthy_B

description: Healthy patient.


title: PBMCs-Type 2 Diabetes-T2D_7_New_B

source_name: PBMCs from Type 2 Diabetes patient and the timepoint at diagnosis.

value: 13 yrs, when sample taken.

value: Black or African American

value: Type 2 Diabetes

tag: Treatment

value: Insulin

value: No


title: PBMCs-Healthy-H149_Healthy_B

description: Healthy patient.

value: (Ethnicity Not Reported)


title: PBMCs-Type 2 Diabetes-T2D11_T2D_B

description: Type 2 Diabetes patient and the timepoint at diagnosis.

value: 12 yrs, when sample taken.


title: PBMCs-Type 2 Diabetes-T2D_3_New_B

value: F

value: White


title: PBMCs-Healthy-H148_Healthy_B

description: Healthy patient.

value: Healthy


title: ENCODE spikein competition, nonamplified sample, NimbleGen array 89832

data_processing: all array processing by NimbleGen, Inc. See www.nimblegen.com for details

source_name: DNA with artificial spike-in, non-amplified. Source of DNA: Roche commercial DNA.

tag: DNA with spikein DNA

source_name: DNA without spikein DNA; non-amplified. Source of DNA: Roche commercial DNA.


title: PBMCs-Type 2 Diabetes-T2D_1_New_B

value: 17 yrs, when sample taken.

value: M

value: (Race Not Reported)


title: ENCODE spikein competition, amplified Sample, NimbleGen array 92181

description: see www.nimblegen.com for array protocol information

source_name: DNA plus artificial spike-in DNA. Source of DNA: Roche commercial DNA.

label_protocol: Array processing by NimbleGen inc.

growth_protocol: not applicable

extract_protocol: artificial sample

treatment_protocol: amplification by "whole-genome amplification" method

tag: Amplified Spike-in sample

source_name: DNA without spikein (background DNA). Source of DNA: Roche commercial DNA.

label_protocol: all array processing by NimbleGen Inc. See NimbleGen website for details.

growth_protocol: not applicable; artificial sample

treatment_protocol: as channel 1

tag: DNA *without* spike-in DNA.


title: PBMCs-Type 2 Diabetes-T2D_6_New_B

value: Hispanic or Latino

value: Yes


title: PBMCs-Type 2 Diabetes-T2D_4_New_B

value: 15 yrs, when sample taken.

value: Not Hispanic or Latino


title: PBMCs-Type 2 Diabetes-T2D9_T2D_B


title: PBMCs-Healthy-H150_Healthy_B

description: Healthy patient.


title: PBMCs-Type 2 Diabetes-T2D_2_New_B

value: 9 yrs, when sample taken.


title: PBMCs-Healthy-H152_Healthy_B

description: Healthy patient.

value: 14 yrs, when sample taken.


title: PBMCs-Type 2 Diabetes-T2D_13_New_B

value: 13 yrs, when sample taken.

value: Black or African American

value: Type 2 Diabetes


title: PBMCs-Type 2 Diabetes-T2D_5_New_B

value: Asian

value: Insulin

value: No


title: PBMCs-Type 2 Diabetes-T2D_8_New_B

value: 11 yrs, when sample taken.

value: F


title: ENCODE spikein competition, amplified sample, rep 2of3, NimbleGen array 92303

hyb_protocol: see www.nimblegen.com for array protocol information

tag: artificial


title: PBMCs-Healthy-H166_Healthy_B

description: Healthy patient.

value: 16 yrs, when sample taken.

value: (Ethnicity Not Reported)

value: Healthy


title: PBMCs-Type 1 Diabetes-IDDM9_T1D_New_B

source_name: PBMCs from Type 1 Diabetes patient and the timepoint at diagnosis.

value: White

value: Type 1 Diabetes


title: PBMCs-Type 2 Diabetes-T2D_10_New_B

value: 17 yrs, when sample taken.

value: M

value: Hispanic or Latino


title: PBMCs-Type 1 Diabetes-IDDM8_T1D_New_B

description: Type 1 Diabetes patient and the timepoint at diagnosis.

value: 12 yrs, when sample taken.

value: Not Hispanic or Latino


title: PBMCs-Type 1 Diabetes-IDDM7_T1D_New_B

value: 4 yrs, when sample taken.

value: (Race Not Reported)


title: ENCODE spikein competition, amplified sample, NimbleGen array 96391

description:
see www.nimblegen.com for array protocol information
IMPORTANT: same DNA samples as used in other arrays in this series; these are technical array replicates


title: PBMCs-Type 1 Diabetes-IDDM61_T1D_New_B

value: 6 yrs, when sample taken.

value: Yes


title: PBMCs-Type 1 Diabetes-IDDM59_T1D_New_B

value: 7 yrs, when sample taken.

value: Insulin


title: PBMCs-Type 1 Diabetes-IDDM61_T1D_1MO_B

source_name: PBMCs from Type 1 Diabetes patient and the timepoint 1 month after diagnosis.

value: F


title: PBMCs-Type 1 Diabetes-IDDM56_T1D_New_B

value: No


title: PBMCs-Type 1 Diabetes-IDDM53_T1D_New_B

value: 13 yrs, when sample taken.


title: PBMCs-Type 1 Diabetes-IDDM6_T1D_New_B

value: 8 yrs, when sample taken.


title: PBMCs-Type 1 Diabetes-IDDM54_T1D_4MO_B

source_name: PBMCs from Type 1 Diabetes patient and the timepoint 4 months after diagnosis.


title: PBMCs-Type 1 Diabetes-IDDM56_T1D_4MO_B

description: Type 1 Diabetes patient and the timepoint 4 months after diagnosis.

value: White


title: PBMCs-Type 1 Diabetes-IDDM57_T1D_1MO_B

description: Type 1 Diabetes patient and the timepoint 1 month after diagnosis.

value: 5 yrs, when sample taken.

value: Type 1 Diabetes


title: PBMCs-Type 1 Diabetes-IDDM54_T1D_New_B


title: PBMCs-Type 1 Diabetes-IDDM59_T1D_1MO_B


title: PBMCs-Type 1 Diabetes-IDDM57_T1D_New_B


title: PBMCs-Type 1 Diabetes-IDDM61_T1D_4MO_B


title: PBMCs-Type 1 Diabetes-IDDM55_T1D_New_B


title: PBMCs-Type 1 Diabetes-IDDM52_T1D_New_B

value: M


title: PBMCs-Type 1 Diabetes-IDDM59_T1D_4MO_B

value: Hispanic or Latino


title: PBMCs-Type 1 Diabetes-IDDM56_T1D_1MO_B


title: PBMCs-Type 1 Diabetes-IDDM53_T1D_1MO_B

value: 14 yrs, when sample taken.


title: PBMCs-Type 1 Diabetes-IDDM57_T1D_4MO_B

value: Not Hispanic or Latino


title: PBMCs-Type 1 Diabetes-IDDM50_T1D_1MO_B

value: 12 yrs, when sample taken.


title: PBMCs-Type 1 Diabetes-IDDM50_T1D_New_B


title: PBMCs-Type 1 Diabetes-IDDM54_T1D_1MO_B

value: (Race Not Reported)


title: PBMCs-Type 1 Diabetes-IDDM50_T1D_4MO_B


title: PBMCs-Type 1 Diabetes-IDDM52_T1D_4MO_B


title: PBMCs-Type 1 Diabetes-IDDM48_T1D_New_B

value: (Ethnicity Not Reported)


title: PBMCs-Type 1 Diabetes-IDDM47_T1D_New_B

value: 6 yrs, when sample taken.

value: Other


title: PBMCs-Type 1 Diabetes-IDDM53_T1D_4MO_B

value: Insulin


title: PBMCs-Type 1 Diabetes-IDDM47_T1D_1MO_B


title: PBMCs-Type 1 Diabetes-IDDM46_T1D_1MO_B

value: 7 yrs, when sample taken.

value: F


title: PBMCs-Type 1 Diabetes-IDDM46_T1D_New_B

value: No


title: PBMCs-Type 1 Diabetes-IDDM45_T1D_4MO_B

value: 3 yrs, when sample taken.

value: Yes


title: PBMCs-Type 1 Diabetes-IDDM48_T1D_1MO_B

value: 13 yrs, when sample taken.

value: White


title: PBMCs-Type 1 Diabetes-IDDM45_T1D_1MO_B

value: M

value: Type 1 Diabetes


title: PBMCs-Type 1 Diabetes-IDDM5_T1D_New_B

value: 9 yrs, when sample taken.


title: PBMCs-Type 1 Diabetes-IDDM42_T1D_New_B

value: 10 yrs, when sample taken.

value: Hispanic or Latino


title: PBMCs-Type 1 Diabetes-IDDM47_T1D_4MO_B


title: PBMCs-Type 1 Diabetes-IDDM43_T1D_New_B

value: 15 yrs, when sample taken.

value: Not Hispanic or Latino


title: PBMCs-Type 1 Diabetes-IDDM42_T1D_4MO_B

value: 11 yrs, when sample taken.

value: (Race Not Reported)


title: PBMCs-Type 1 Diabetes-IDDM46_T1D_4MO_B

value: Insulin


title: PBMCs-Type 1 Diabetes-IDDM42_T1D_1MO_B


title: PBMCs-Type 1 Diabetes-IDDM43_T1D_1MO_B


title: PBMCs-Type 1 Diabetes-IDDM45_T1D_New_B


title: PBMCs-Type 1 Diabetes-IDDM43_T1D_4MO_B


title: PBMCs-Type 1 Diabetes-IDDM39_T1D_New_B


title: DNAmeth_MethylatedDNA_532_LS replicate2

city: New Haven

first: Hang

last: He

state: CT

address: 165 Prospect St

department: MCDB

institute: Yale University

description: Enriched for methylated DNA at all sequenced contexts

hyb_protocol: Microarray slides were incubated in prehybridization buffer (5X SSC, 0.1% SDS, 1% BSA) for 30min - 1hour at 42 ºC and washed with water. Slides were then hybridized with Cy3 or Cy5- labeled DNA targets in hybridization buffer (5X SSC, 0.1% SDS, 0.5 mg/ml salmon sperm DNA, 0.5 mg/ml BSA) for 16-20 hours at 50 ºC. After hybridization, slides were washed sequentially with 2X SSC / 0.1% SDS, 0.2X SSC /0.1% SDS and 0.2X SSC for 10 min at room temperature.

scan_protocol: The dried slides were scanned with a GenePix 4200A scanner (Axon).

data_processing: Gene chip data files were processed using quantile normalization.

organism: Oryza sativa

source_name: light shoot

label_protocol: About 2.0 µg recovered methylated DNA or sonicated total genomic DNA (< 500 bp) were labeled with Cy3 or Cy5 using the BioPrime Array CGH Genomic Labeling System (Invitrogen) and used for microarray hybridization.

extract_protocol: Methylated DNA was isolated using a McrBC digestion method adapted from restriction enzyme that cleaves between two [A/G] C sites separated by 40-3000 bp, only when the C residue in  [A/G] C motif is methylated.


title: PBMCs-Type 1 Diabetes-IDDM41_T1D_4MO_B

value: 14 yrs, when sample taken.

value: Black or African American


title: PBMCs-Type 1 Diabetes-IDDM39_T1D_4MO_B

value: 12 yrs, when sample taken.

value: No


title: PBMCs-Type 1 Diabetes-IDDM4_T1D_New_B

value: F

value: Selected More than One Race

value: Yes


title: PBMCs-Type 1 Diabetes-IDDM41_T1D_1MO_B


title: PBMCs-Type 1 Diabetes-IDDM39_T1D_1MO_B

value: M

value: White


title: PBMCs-Type 1 Diabetes-IDDM41_T1D_New_B

value: Type 1 Diabetes


title: PBMCs-Type 1 Diabetes-IDDM38_T1D_New_B

value: 7 yrs, when sample taken.


title: IMR90 from the ES(IMR90)-5 sample

type: mixed

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

description: Total RNA from iPS clone was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations.

hyb_protocol: Hybridizations were performed in 3.6X SSC buffer with 35% formamide and 0.07% SDS at 42% C overnight.

scan_protocol: Arrays were washed, dried and scanned with the GenePix 4000B Scanner

data_processing: Gene Expression data was extracted using NimbleScan Software v2.3

source_name: Genomic DNA extracted from H1 Human Embryonic Stem Cells

label_protocol: Sonicated genomic DNA was primed with random octamers and labeled using Klenow in the present of 5-(3-aminoallyl)-dUTP

extract_protocol: Phenol/Chloroform Extraction

tag: DNA was extracted from h1 ES cells

source_name: IMR90 from the ES(IMR90)-5 sample

label_protocol: Total RNA was enriched for the polyA fraction using Oligotex mRNA Mini Kit (Qiagen). Enriched mRNA (250 ng) was primed using random hexamers and reversed transcribed using Superscript III (Invitrogen) in the presence of 5-(3-aminoallyl)-dUTP (Ambion).

extract_protocol: Qiagen on column kit

tag: Total RNA from IMR90 cells were extracted


title: DNAmeth_Genomic_635_LS replicate1

description: Depleted for methylated DNA at all sequenced contexts


title: DNAmeth_Genomic_635_LS replicate2

tag: Depleted for methylated DNA at all sequenced contexts


title: PBMCs-Type 1 Diabetes-IDDM34_T1D_4MO_B

tag: Age

tag: Gender

tag: Ethnicity


title: PBMCs-Type 1 Diabetes-IDDM34_T1D_1MO_B

tag: Race

tag: Illness

tag: pH<7.30 at time of diagnosis


title: PBMCs-Type 1 Diabetes-IDDM34_T1D_New_B


title: DNAmeth_MethylatedDNA_532_LS replicate1

tag: Enriched for methylated DNA at all sequenced contexts


title: PBMCs-Type 1 Diabetes-IDDM32_T1D_4MO_B


title: PBMCs-Type 1 Diabetes-IDDM37_T1D_New_B

value: 9 yrs, when sample taken.


title: PBMCs-Type 1 Diabetes-IDDM27_T1D_1MO_B


title: PBMCs-Type 1 Diabetes-IDDM30_T1D_New_B


title: DNAmeth_Genomic_635_CC replicate2

source_name: Cultured cell


title: DNAmeth_MethylatedDNA_532_CC replicate1


title: PBMCs-Type 1 Diabetes-IDDM32_T1D_1MO_B


title: PBMCs-Type 1 Diabetes-IDDM30_T1D_4MO_B


title: PBMCs-Type 1 Diabetes-IDDM25_T1D_New_B

value: 15 yrs, when sample taken.


title: PBMCs-Type 1 Diabetes-IDDM30_T1D_1MO_B

value: Not Hispanic or Latino


title: DNAmeth_Genomic_635_CC replicate1


title: DNAmeth_MethylatedDNA_532_CC replicate2


title: PBMCs-Type 1 Diabetes-IDDM3_T1D_New_B


title: PBMCs-Type 1 Diabetes-IDDM27_T1D_4MO_B

value: 8 yrs, when sample taken.


title: PBMCs-Type 1 Diabetes-IDDM27_T1D_New_B


title: PBMCs-Type 1 Diabetes-IDDM24_T1D_New_B

value: 2 yrs, when sample taken.


title: HL60-RG cell

city: Shanghai

first: Luan

last: Yang

address: 555 Zu Chong Zhi Road , Zhang Jiang Hi-Tech Park, Pudong,

country: China

institute: Shanghai Institute of Materia Medica , Chinese Academy of Sciences

hyb_protocol: according to the standard GeneChip Mapping 10K (V2.0) Xba Assay protocol (Affymetrix Inc., Santa Clara, CA).Hybridized arrays were processed with an Affymetrix Fluidics Station 450.

scan_protocol: fluorescence signals were detected using the Affymetrix GeneChip Scanner 3000.

data_processing: Alleles (AA, AB, or BB) at each SNP were called using the algorithm of Affymetrix software package GDAS. The generated CEL. file and TXT. file were imported into a dChip software for copy number analysis. Regional LOH was identified whenever an uninterrupted contiguous stretch of >50 homozygous (AA or BB) genotypes was encountered, with the segments of DNA greater than ~15Mb.

source_name: cell line

extract_protocol: cell were cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum and kanaMYCin (50 µg/ml). The cultures were incubated at 37 °C in a 5% CO2 atmosphere with 100% humidity

tag: HL60 cell line，derived from the human acute promyelotic leukemia, can be induced to differentiate to morphologically and functionally mature granulocyutes.HL60-RG is the sub-line of the HL60, was isolated after a long-term continuous culture of HL60, having faster growth rate with doubling time around 20hr, about half the HL60’s.


title: PBMCs-Type 1 Diabetes-IDDM32_T1D_New_B

value: Insulin


title: PBMCs-Type 1 Diabetes-IDDM22_T1D_New_B


title: H3K4Me3_Genomic_635_CC replicate3

description: Enriched for genomic DNA at all sequenced contexts

label_protocol: 2.0 µg amplified ChIP or Input DNA was labeled with Cy3 or Cy5 using the BioPrime Array CGH Genomic Labeling System (Invitrogen) and used for microarray hybridization.

extract_protocol: Chromatin from light-grown shoots and cultured cells was immunoprecipitated with antibodies against H3K4Me2 (Upstate), H3K4Me3 (Abcam) (Nagaki et al., 2004) as described in Gendrel et al, 2005. ChIP (enriched) and iInput (whole cell extract) DNA samples were amplified using a random amplification procedure as described (Lippman et al., 2005).


title: 1xMIC novobiocin for 30min, biological rep3

status: Public on Jun 01 2008

city: Schwabenheim

first: Elena

last: Melnikow

address: Zur Propstei

department: Drug Discovery

country: Germany

institute: Intervet Innovation GmbH

description: Gene expression data from Pasteurella multocida treated with 1xMIC novobiocin for 30min

hyb_protocol: Following fragmentation, 2.5 ug of cDNA were hybridized for 16 hr at 45°C on a custom-made GeneChip Genome Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner.

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

organism: Pasteurella multocida

source_name: P. multocida treated with 1xmic novobiocin for 30 min

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

growth_protocol: P. multocida was cultured in 40 ml BHI medium for 3h at 37°C by 200 rpm.

extract_protocol: Extraction of total RNA was performed usind RNAeasy Midi Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: 1xMIC of each antibiotic was added to the P. multocida culture for 10 min and 30 min at an optical density of approximately 0.5. The bacteria were harvested by centifugation for 5 min at 5000 rpm at 4 °C.

tag: Strain

value: 1xmic novobiocin for 30 min


title: PBMCs-Type 1 Diabetes-IDDM20_T1D_New_B

tag: Treatment


title: PBMCs-Type 1 Diabetes-IDDM19_T1D_New_B

value: 3 yrs, when sample taken.


title: PBMCs-Type 1 Diabetes-IDDM23_T1D_New_B

value: 6 yrs, when sample taken.


title: PBMCs-Type 1 Diabetes-IDDM16_T1D_New_B

value: 17 yrs, when sample taken.

value: Hispanic or Latino

value: (Race Not Reported)

value: No


title: PBMCs-Type 1 Diabetes-IDDM18_T1D_New_B

value: 13 yrs, when sample taken.

value: F


title: PBMCs-Type 1 Diabetes-IDDM15_T1D_New_B

value: White

value: Type 1 Diabetes

value: Yes


title: Myeloid_NUP98NSD1 immortalized_in SCF_clone 1

city: La Jolla

middle: Philip

last: Kamps

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

hyb_protocol: Standard Affymetrix protocols were followed

data_processing:
dchip1.3 used in publication analysis

NOTE: CEL files and dChip1.3 data were requested by GEO but not provided.

source_name: Primary marrow progenitor immortalized by NUP98NSD1

growth_protocol: Derived in medium supplemented with Stem Cell Factor, no GM-CSF

extract_protocol: Qiagen RNeasy Midi for Cytoplasm of Cells. Utilizing denaturation by guanidine isothiocyanate.

tag: Balb/c mouse


title: H3K4Me3_Genomic_635_LS replicate2

tag: Enriched for genomic DNA at all sequenced contexts


title: PBMCs-Type 1 Diabetes-IDDM17_T1D_New_B

value: 5 yrs, when sample taken.


title: Myeloid_NUP98NSD1 immortalized_in SCF_clone 3

scan_protocol: Standard Affymetrix protocols were followed


title: H3K4Me3_Genomic_635_CC replicate2


title: H3K4Me3_MethylatedDNA_532_CC replicate3

description: Enriched for ChIP at all sequenced contexts


title: PBMCs-Type 1 Diabetes-IDDM14_T1D_New_B

value: 10 yrs, when sample taken.

value: M

value: Not Hispanic or Latino


title: Myeloid_MLL-ENL immortalized_in SCF

description: Myeloid_MLL-ENL immortalized_in SCF

source_name: Primary marrow progenitor immortalized by MLL-ENL

label_protocol: Standard Affymetrix protocols were followed


title: H3K4Me3_Genomic_635_CC replicate1


title: Myeloid_HoxA9+Meis1 immortalized_in SCF_clone 3

source_name: Primary marrow progenitor immortalized by coexpression of HoxA9 + Meis1


title: H3K4Me3_MethylatedDNA_532_CC replicate1

tag: Enriched for ChIP at all sequenced contexts


title: Myeloid_NUP98NSD1 immortalized_in SCF_clone 2


title: H3K4Me3_Genomic_635_LS replicate3


title: H3K4Me3_Genomic_635_LS replicate1


title: H3K4Me3_MethylatedDNA_532_LS replicate2


title: PBMCs-Type 1 Diabetes-IDDM11_T1D_New_B

value: Insulin


title: H3K4Me2_Genomic_635_CC replicate2


title: H3K4Me2_Genomic_635_CC replicate3


title: H3K4Me3_MethylatedDNA_532_LS replicate3


title: H3K4Me3_MethylatedDNA_532_CC replicate2


title: H3K4Me3_MethylatedDNA_532_LS replicate1


title: Myeloid_HoxA9+Meis1 immortalized_in SCF_clone 2


title: H3K4Me2_Genomic_635_LS replicate3


title: PBMCs-Healthy-HIDDM4_Healthy_B

description: Healthy patient.

source_name: PBMCs from Healthy patient.

value: 14 yrs, when sample taken.

value: Healthy


title: H3K4Me2_Genomic_635_CC replicate1


title: PBMCs-Healthy-H48_Healthy_B

description: Healthy patient.

value: 12 yrs, when sample taken.

value: (Ethnicity Not Reported)


title: PBMCs-Healthy-H37_Healthy_B

description: Healthy patient.

value: 9 yrs, when sample taken.


title: EBV positive Burkitt's lymphoma cell line Akata, control vs miR-146a infection pair 2 - Dye Swap

description: Dual color scanning

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray  processing protocol using the Agilent Gene Expression Hybridization Kit  (Agilent  Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA  were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome  Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% Nlauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated  0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing  step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using  Agilent’s DNA microarray scanner (Agilent Technologies).

data_processing:
The Agilent Feature Extraction Software (FES) was used to read out and process the  microarray image files. The software determines feature intensities and ratios (including  background subtraction and normalization), rejects outliers and calculates statistical  confidences (p-values). For determination of differential gene expression FES derived output  data files were further analyzed using the Rosetta Resolver  gene expression data analysis  system (Rosetta Biosoftware).
VALUE = LogRatio (base 10) - log(miR-146a/control) per feature (processed signals used)

source_name: Akata LMP1 (pEhyg- miR-146a) infection 2

label_protocol: For the linear T7-based amplification step, 1 μg of each total RNA sample was used as  starting material. To produce Cy3- and Cy5-labeled cRNA, the RNA samples were amplified  and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following  the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured  with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: Qiagen total RNA purification kit - Standard conditions

tag: Akata cells were then infected with a retrovirus encoding miR-146a (pEhyg-miR-146a). This sample represents infection 2 of two separate infections with pEhyg-miR-146a.

source_name: Akata control (pEhyg) infection 2

extract_protocol: Qiagen total RNA purification kit - standard conditions

tag: Akata cells were then infected with a control retrovirus (pEhyg-).  This sample represents infection 2 of two separate infections with pEhyg.


title: H3K4Me2_Genomic_635_LS replicate2


title: NDSF stimulated chondrocytes rep 2

city: Berlin

first: Thomas

last: Häupl

address: Charitéplatz 1

department: Rheumatology

institute: Charité

description: human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 2, NDSF stimulated

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol.

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

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database SiPaGene (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA).

source_name: NDSF stimulated chondrocytes

label_protocol: 2.5µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix).

growth_protocol: Human chondrocytes obtained from lateral condyle of femur bones of 6 donors post mortem were amplified by cultivation in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, subsequently 3D cultured in alginate beads for 14 days in presence of 170µM L-ascorbic acid 2-phosphate and finally stimulated with conditioned medium of RASF and NDSF, respectively, or remaining unstimulated as control.

extract_protocol: Prior to RNA extraction, alginate beads were solubilized on ice in 55mM sodium citrate, 30mM EDTA and 150mM NaCl and cells were centrifuged at 800g for 5min (4°C). Total RNA isolation was proceeded according to the manufacturer’s protocol. Additionally, a proteinase K and DNase I digestion were performed.   Isolation of total RNA was done for the six different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes  were pooled, yielding two different experimental groups of NDSF and RASF stimulated chondrocytes and of unstimulated chondrocytes, respectively.

treatment_protocol: Human chondrocytes were isolated by enzymatic digestion (1 U collagenase P, 333 U collagenase II and 33 U hyaluronidase), passage 2 chondrocytes were encapsulated in alginate beads (20 Mio cells/ml in 1,5% (w/v) alginate) and stimulated with conditioned medium of RASF and NDSF.

tag: human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with supernatant of NDSF cultured in the same medium


title: Myeloid_HoxA9+Meis1 immortalized_in SCF_clone 1


title: Myeloid_HoxA9 immortalized_in SCF_clone 3

source_name: Primary marrow progenitor immortalized by HoxA9


title: PBMCs-Healthy-HIDDM2_Healthy_B

description: Healthy patient.

value: Hispanic or Latino

value: Selected More than One Race


title: unstimulated chondrocytes rep 1

description: human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 1, unstimulated

source_name: unstimulated chondrocytes

tag: human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with medium control


title: unstimulated chondrocytes rep 2

description: human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 2, unstimulated


title: Myeloid_HoxA9 immortalized_in SCF_clone 2


title: H3K4Me2_Genomic_635_LS replicate1


title: NDSF stimulated chondrocytes rep 1

description: human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 1, NDSF stimulated


title: PBMCs-Type 1 Diabetes-IDDM1_T1D_New_B

source_name: PBMCs from Type 1 Diabetes patient and the timepoint at diagnosis.

tag: Age


title: EBV positive Burkitt's lymphoma cell line Akata, control vs miR-146a infection pair 1 - Dye Swap

description: Dual color scanning

source_name: Akata LMP1 (pEhyg- miR-146a) infection 1

tag: Akata cells were then infected with a retrovirus encoding miR-146a (pEhyg-miR-146a). This sample represents infection 1 of two separate infections with pEhyg-miR-146a.

source_name: Akata control (pEhyg) infection 1

tag: Akata cells were then infected with a control retrovirus (pEhyg-).  This sample represents infection 1 of two separate infections with pEhyg.


title: RASF stimulated chondrocytes rep 2

description: human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 2, RASF stimulated

source_name: RASF stimulated chondrocytes

tag: human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with supernatant of RASF cultured in the same medium


title: PBMCs-Healthy-H28_Healthy_B

description: Healthy patient.

value: 13 yrs, when sample taken.

tag: Gender

tag: Ethnicity

tag: Race

value: (Race Not Reported)

tag: Illness


title: Myeloid_HoxA9 immortalized_in SCF_clone 1


title: PBMCs-Healthy-H171_Healthy_B

description: Healthy patient.

value: 13 yrs  when sample taken.

value: Black or African American

tag: pH<7.30 at time of diagnosis


title: EBV positive Burkitt's lymphoma cell line Akata, control  vs miR-146a infection pair 2

description: Dual color scanning

source_name: Akata LMP1 (pEhyg- FLAG-miR-146a) infection 2


title: H3K4Me2_MethylatedDNA_532_CC replicate2

source_name: Cultured cell


title: H3K4Me2_MethylatedDNA_532_CC replicate3


title: H3K4Me2_MethylatedDNA_532_CC replicate1


title: PBMCs-Healthy-H133_Healthy_B

description: Healthy patient.

value: 6 yrs, when sample taken.

value: F

value: White


title: H3K4Me2_MethylatedDNA_532_LS replicate2

source_name: light shoot


title: H3K4Me2_MethylatedDNA_532_LS replicate3


title: EBV positive Burkitt's lymphoma cell line Akata, control  vs miR-146a infection pair 1

description: Dual color scanning


title: Halobacterium non-natively expressed and C-terminally 6-His tagged TFBg. Array 7667

status: Public on Jan 03 2008

city: Seattle

first: Marc

last: Facciotti

address: 1441 North 34th Street

institute: Institute for Systems Biology

description: Non-native expression of c-terminally 6x-his tagged tfbG expressed form the pMTFCHIS vector versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-49

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing: AnalyzerDG software for spotfinding.  see http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details

label: Alexa 532

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium NRC-1, non-native expression of transcription factor tfbG.

growth_protocol: Non-native expression of c-terminally 6HIS-tagged tfbG grown to late-stationary phase in standard growth media.

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

tag: Non-native expression of c-terminally 6x-his tagged tfbG expressed form the pMTFCHIS vector.

label: Alexa 647

source_name: Halobacterium standard reference sample

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1 reference sample.

tag: Halobacterium NRC-1 grown in standard growth media


title: H3K4Me2_MethylatedDNA_532_LS replicate1


title: Halobacterium non-natively expressed and C-terminally 6-His tagged TFBg. Array 7719

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-50


title: Halobacterium general transcription factor knockout (tfbD). Array 7297

description: Knockout of general transcription factor tfbD grown in standard media versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-48

source_name: Halobacterium NRC-1, knockout of transcription factortfbD

growth_protocol: Knockout of general transcription factor tfbD grown in standard growth media to an OD600 of 0.610.

tag: Knockout of general transcription factor tfbD grown in standard media.


title: RASF stimulated chondrocytes rep 1

description: human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 1, RASF stimulated


title: Halobacterium general transcription factor knockout (tbpC). Array 7254

description: Knockout of general transcription factor tbpC grown in standard media versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-37

source_name: Halobacterium NRC-1, knockout of transcription factortbpC

growth_protocol: Knockout of general transcription factor tbpC grown in standard growth media to an OD600 of 0.719.

tag: Knockout of general transcription factor tbpC grown in standard media.


title: Halobacterium general transcription factor knockout (tfbA). Array 7256

description: Knockout of general transcription factor tfbA grown in standard media versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-41

source_name: Halobacterium NRC-1, knockout of transcription factortfbA

growth_protocol: Knockout of general transcription factor tfbA grown in standard growth media to an OD600 of 0.626.

tag: Knockout of general transcription factor tfbA grown in standard media.


title: Halobacterium general transcription factor knockout (tfbC). Array 7296

description: Knockout of general transcription factor tfbC grown in standard media versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-46

source_name: Halobacterium NRC-1, knockout of transcription factortfbC

growth_protocol: Knockout of general transcription factor tfbC grown in standard growth media to an OD600 of 0.685.

tag: Knockout of general transcription factor tfbC grown in standard media.


title: Halobacterium general transcription factor knockout (tfbC). Array 7258

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-45


title: Halobacterium general transcription factor knockout (tfbA). Array 7294

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-42


title: Halobacterium general transcription factor knockout (tfbB). Array 7295

description: Knockout of general transcription factor tfbB grown in standard media versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-44

source_name: Halobacterium NRC-1, knockout of transcription factortfbB

growth_protocol: Knockout of general transcription factor tfbB grown in standard growth media to an OD600 of 0.707.

tag: Knockout of general transcription factor tfbB grown in standard media.


title: Halobacterium general transcription factor knockout (tbpD). Array 7255

description: Knockout of general transcription factor tbpD grown in standard media versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-39

source_name: Halobacterium NRC-1, knockout of transcription factortbpD

growth_protocol: Knockout of general transcription factor tbpD grown in standard growth media to an OD600 of 0.708.

tag: Knockout of general transcription factor tbpD grown in standard media.


title: Halobacterium oxygen and light perturbation in gap deletion strain. Array 7660

description: Halobacterium NRC-1 ura3 and gap gene knockouts in low oxygen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-232

source_name: Halobacterium NRC-1 ura3 and gap gene knockouts.

growth_protocol: Halobacterium NRC-1 ura3 and gap gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in light.

tag: Halobacterium NRC-1 ura3 and gap gene knockouts in low oxygen and in light.


title: Halobacterium general transcription factor knockout (tbpD). Array 7293

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-40


title: Halobacterium oxygen and light perturbation in gap deletion strain. Array 7485

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-231


title: Halobacterium general transcription factor knockout (tfbD). Array 7259

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-47


title: Halobacterium general transcription factor knockout (tfbB). Array 7257

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-43


title: Halobacterium general transcription factor knockout (tbpA). Array 7253

description: Knockout of general transcription factor tbpA grown in standard media versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

source_name: Halobacterium NRC-1, knockout of transcription factortbpA

growth_protocol: Knockout of general transcription factor tbpA grown in standard growth media to an OD600 of 0.586.

tag: Knockout of general transcription factor tbpA grown in standard media.


title: Halobacterium general transcription factor knockout (tbpA). Array 7291

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-36


title: Halobacterium oxygen and light perturbation in gap deletion strain. Array 7657

description: Halobacterium NRC-1 ura3 and gap gene knockouts in high oxgen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-230

growth_protocol: Halobacterium NRC-1 ura3 and gap gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and gap gene knockouts in high oxgen and in dark.


title: Halobacterium oxygen and light perturbation in gap deletion strain. Array 7661

description: Halobacterium NRC-1 ura3 and gap gene knockouts in low oxygen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-234

growth_protocol: Halobacterium NRC-1 ura3 and gap gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and gap gene knockouts in low oxygen and in dark.


title: Halobacterium oxygen and light perturbation in gap deletion strain. Array 7487

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-233


title: Halobacterium general transcription factor knockout (tbpC). Array 7132

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-38


title: Halobacterium oxygen and light perturbation in gap deletion strain. Array 7483

description: Halobacterium NRC-1 ura3 and gap gene knockouts in high oxgen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-227

growth_protocol: Halobacterium NRC-1 ura3 and gap gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in light.

tag: Halobacterium NRC-1 ura3 and gap gene knockouts in high oxgen and in light.


title: Halobacterium oxygen and light perturbation in vng19h deletion strain. Array 7654

description: Halobacterium NRC-1 ura3 and vng19h gene knockouts in low oxygen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-224

source_name: Halobacterium NRC-1 ura3 and vng19h gene knockouts.

growth_protocol: Halobacterium NRC-1 ura3 and vng19h gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in light.

tag: Halobacterium NRC-1 ura3 and vng19h gene knockouts in low oxygen and in light.


title: Halobacterium oxygen and light perturbation in vng19h deletion strain. Array 7655

description: Halobacterium NRC-1 ura3 and vng19h gene knockouts in low oxygen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-226

growth_protocol: Halobacterium NRC-1 ura3 and vng19h gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and vng19h gene knockouts in low oxygen and in dark.


title: Halobacterium oxygen and light perturbation in vng19h deletion strain. Array 7482

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-225


title: Halobacterium oxygen and light perturbation in vng19h deletion strain. Array 7481

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-223


title: Halobacterium oxygen and light perturbation in gap deletion strain. Array 7656

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-228


title: Halobacterium oxygen and light perturbation in vng19h deletion strain. Array 7480

description: Halobacterium NRC-1 ura3 and vng19h gene knockouts in high oxgen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-221

growth_protocol: Halobacterium NRC-1 ura3 and vng19h gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and vng19h gene knockouts in high oxgen and in dark.


title: Halobacterium oxygen and light perturbation in vng19h deletion strain. Array 7652

description: Halobacterium NRC-1 ura3 and vng19h gene knockouts in high oxgen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-220

growth_protocol: Halobacterium NRC-1 ura3 and vng19h gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in light.

tag: Halobacterium NRC-1 ura3 and vng19h gene knockouts in high oxgen and in light.


title: Halobacterium oxygen and light perturbation in vng19h deletion strain. Array 7653

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-222


title: Halobacterium oxygen and light perturbation in sop2 deletion strain. Array 7650

description: Halobacterium NRC-1 ura3 and sop2 gene knockouts in low oxygen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-216

source_name: Halobacterium NRC-1 ura3 and sop2 gene knockouts.

growth_protocol: Halobacterium NRC-1 ura3 and sop2 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in light.

tag: Halobacterium NRC-1 ura3 and sop2 gene knockouts in low oxygen and in light.


title: Halobacterium oxygen and light perturbation in vng19h deletion strain. Array 7479

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-219

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1 reference sample.

tag: Halobacterium NRC-1 grown in standard growth media


title: Halobacterium oxygen and light perturbation in sop2 deletion strain. Array 7651

description: Halobacterium NRC-1 ura3 and sop2 gene knockouts in low oxygen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-218

growth_protocol: Halobacterium NRC-1 ura3 and sop2 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and sop2 gene knockouts in low oxygen and in dark.


title: Halobacterium oxygen and light perturbation in sop2 deletion strain. Array 7478

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-217


title: Halobacterium oxygen and light perturbation in sop2 deletion strain. Array 7476

description: Halobacterium NRC-1 ura3 and sop2 gene knockouts in high oxgen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-213

growth_protocol: Halobacterium NRC-1 ura3 and sop2 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and sop2 gene knockouts in high oxgen and in dark.


title: Halobacterium oxygen and light perturbation in sop2 deletion strain. Array 7649

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-214


title: Halobacterium oxygen and light perturbation in sop2 deletion strain. Array 7477

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-215


title: Halobacterium oxygen and light perturbation in sop2 deletion strain. Array 7648

description: Halobacterium NRC-1 ura3 and sop2 gene knockouts in high oxgen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-212

growth_protocol: Halobacterium NRC-1 ura3 and sop2 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in light.

tag: Halobacterium NRC-1 ura3 and sop2 gene knockouts in high oxgen and in light.


title: Halobacterium oxygen and light perturbation in sop2 deletion strain. Array 7475

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-211


title: Halobacterium oxygen and light perturbation in kinA2 deletion strain. Array 7647

description: Halobacterium NRC-1 ura3 and kinA2 gene knockouts in low oxygen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-210

source_name: Halobacterium NRC-1 ura3 and kinA2 gene knockouts.

growth_protocol: Halobacterium NRC-1 ura3 and kinA2 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and kinA2 gene knockouts in low oxygen and in dark.


title: Halobacterium oxygen and light perturbation in gap deletion strain. Array 7484

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-229


title: Halobacterium oxygen and light perturbation in kinA2 deletion strain. Array 7474

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-209


title: Halobacterium oxygen and light perturbation in kinA2 deletion strain. Array 7471

description: Halobacterium NRC-1 ura3 and kinA2 gene knockouts in high oxgen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-203

growth_protocol: Halobacterium NRC-1 ura3 and kinA2 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in light.

tag: Halobacterium NRC-1 ura3 and kinA2 gene knockouts in high oxgen and in light.


title: Halobacterium oxygen and light perturbation in kinA2 deletion strain. Array 7473

description: Halobacterium NRC-1 ura3 and kinA2 gene knockouts in low oxygen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-207

growth_protocol: Halobacterium NRC-1 ura3 and kinA2 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in light.

tag: Halobacterium NRC-1 ura3 and kinA2 gene knockouts in low oxygen and in light.


title: Halobacterium oxygen and light perturbation in kinA2 deletion strain. Array 7646

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-208


title: Halobacterium oxygen and light perturbation in kinA2 deletion strain. Array 7644

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-204


title: Halobacterium oxygen and light perturbation in kinA2 deletion strain. Array 7472

description: Halobacterium NRC-1 ura3 and kinA2 gene knockouts in high oxgen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-205

growth_protocol: Halobacterium NRC-1 ura3 and kinA2 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and kinA2 gene knockouts in high oxgen and in dark.


title: Halobacterium oxygen and light perturbation in kinA2 deletion strain. Array 7645

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-206


title: Halobacterium oxygen and light perturbation in zim deletion strain. Array 7081

description: Halobacterium NRC-1 ura3 and zim gene knockouts in low oxygen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-202

source_name: Halobacterium NRC-1 ura3 and zim gene knockouts.

growth_protocol: Halobacterium NRC-1 ura3 and zim gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and zim gene knockouts in low oxygen and in dark.


title: Halobacterium oxygen and light perturbation in zim deletion strain. Array 7070

description: Halobacterium NRC-1 ura3 and zim gene knockouts in low oxygen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-200

growth_protocol: Halobacterium NRC-1 ura3 and zim gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in light.

tag: Halobacterium NRC-1 ura3 and zim gene knockouts in low oxygen and in light.


title: Halobacterium oxygen and light perturbation in zim deletion strain. Array 7071

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-201


title: Halobacterium oxygen and light perturbation in zim deletion strain. Array 7066

description: Halobacterium NRC-1 ura3 and zim gene knockouts in high oxgen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-196

growth_protocol: Halobacterium NRC-1 ura3 and zim gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in light.

tag: Halobacterium NRC-1 ura3 and zim gene knockouts in high oxgen and in light.


title: Halobacterium oxygen and light perturbation in zim deletion strain. Array 7068

description: Halobacterium NRC-1 ura3 and zim gene knockouts in high oxgen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-198

growth_protocol: Halobacterium NRC-1 ura3 and zim gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and zim gene knockouts in high oxgen and in dark.


title: Halobacterium oxygen and light perturbation in zim deletion strain. Array 7069

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-199


title: Halobacterium oxygen and light perturbation in zim deletion strain. Array 7067

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-197


title: Halobacterium oxygen and light perturbation in vng2334c deletion strain. Array 7051

description: Halobacterium NRC-1 ura3 and vng2334c gene knockouts in high oxgen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-189

source_name: Halobacterium NRC-1 ura3 and vng2334c gene knockouts.

growth_protocol: Halobacterium NRC-1 ura3 and vng2334c gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and vng2334c gene knockouts in high oxgen and in dark.


title: Halobacterium oxygen and light perturbation in vng2334c deletion strain. Array 7054

description: Halobacterium NRC-1 ura3 and vng2334c gene knockouts in low oxygen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-192

growth_protocol: Halobacterium NRC-1 ura3 and vng2334c gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in light.

tag: Halobacterium NRC-1 ura3 and vng2334c gene knockouts in low oxygen and in light.


title: Halobacterium oxygen and light perturbation in vng2334c deletion strain. Array 7056

description: Halobacterium NRC-1 ura3 and vng2334c gene knockouts in low oxygen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-194

growth_protocol: Halobacterium NRC-1 ura3 and vng2334c gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and vng2334c gene knockouts in low oxygen and in dark.


title: Halobacterium oxygen and light perturbation in htr2 deletion strain. Array 6609

description: Halobacterium NRC-1 ura3 and htr2 gene knockouts in high oxgen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-171

source_name: Halobacterium NRC-1 ura3 and htr2 gene knockouts.

growth_protocol: Halobacterium NRC-1 ura3 and htr2 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in light.

tag: Halobacterium NRC-1 ura3 and htr2 gene knockouts in high oxgen and in light.


title: Halobacterium oxygen and light perturbation in vng1296c deletion strain. Array 7011

description: Halobacterium NRC-1 ura3 and vng1296c gene knockouts in high oxgen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-181

source_name: Halobacterium NRC-1 ura3 and vng1296c gene knockouts.

growth_protocol: Halobacterium NRC-1 ura3 and vng1296c gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and vng1296c gene knockouts in high oxgen and in dark.


title: Halobacterium oxygen and light perturbation in vng1296c deletion strain. Array 7047

description: Halobacterium NRC-1 ura3 and vng1296c gene knockouts in low oxygen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-185

growth_protocol: Halobacterium NRC-1 ura3 and vng1296c gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and vng1296c gene knockouts in low oxygen and in dark.

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1 reference sample.

tag: Halobacterium NRC-1 grown in standard growth media


title: Halobacterium oxygen and light perturbation in vng1296c deletion strain. Array 7045

description: Halobacterium NRC-1 ura3 and vng1296c gene knockouts in low oxygen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-183

growth_protocol: Halobacterium NRC-1 ura3 and vng1296c gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in light.

tag: Halobacterium NRC-1 ura3 and vng1296c gene knockouts in low oxygen and in light.


title: Halobacterium oxygen and light perturbation in zim deletion strain. Array 7065

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-195


title: Halobacterium oxygen and light perturbation in vng2334c deletion strain. Array 7055

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-193


title: Halobacterium oxygen and light perturbation in htr2 deletion strain. Array 6615

description: Halobacterium NRC-1 ura3 and htr2 gene knockouts in low oxygen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-177

growth_protocol: Halobacterium NRC-1 ura3 and htr2 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and htr2 gene knockouts in low oxygen and in dark.


title: Halobacterium oxygen and light perturbation in htr2 deletion strain. Array 6613

description: Halobacterium NRC-1 ura3 and htr2 gene knockouts in low oxygen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-175

growth_protocol: Halobacterium NRC-1 ura3 and htr2 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in light.

tag: Halobacterium NRC-1 ura3 and htr2 gene knockouts in low oxygen and in light.


title: Halobacterium oxygen and light perturbation in vng2334c deletion strain. Array 7049

description: Halobacterium NRC-1 ura3 and vng2334c gene knockouts in high oxgen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-187

growth_protocol: Halobacterium NRC-1 ura3 and vng2334c gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in light.

tag: Halobacterium NRC-1 ura3 and vng2334c gene knockouts in high oxgen and in light.


title: Halobacterium oxygen and light perturbation in htr2 deletion strain. Array 6611

description: Halobacterium NRC-1 ura3 and htr2 gene knockouts in high oxgen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-173

growth_protocol: Halobacterium NRC-1 ura3 and htr2 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and htr2 gene knockouts in high oxgen and in dark.


title: Halobacterium oxygen and light perturbation in vng1296c deletion strain. Array 7009

description: Halobacterium NRC-1 ura3 and vng1296c gene knockouts in high oxgen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-179

growth_protocol: Halobacterium NRC-1 ura3 and vng1296c gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in light.

tag: Halobacterium NRC-1 ura3 and vng1296c gene knockouts in high oxgen and in light.


title: Halobacterium oxygen and light perturbation in vng2334c deletion strain. Array 7053

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-191


title: Halobacterium oxygen and light perturbation in vng2334c deletion strain. Array 7052

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-190


title: Halobacterium oxygen and light perturbation in htr2 deletion strain. Array 6612

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-174


title: Halobacterium oxygen and light perturbation in htr2 deletion strain. Array 6614

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-176


title: Halobacterium oxygen and light perturbation in vng1296c deletion strain. Array 7010

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-180


title: Halobacterium oxygen and light perturbation in vng1296c deletion strain. Array 7046

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-184


title: Halobacterium oxygen and light perturbation in vng1296c deletion strain. Array 7044

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-182


title: Halobacterium oxygen and light perturbation in vng2334c deletion strain. Array 7050

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-188


title: Halobacterium oxygen and light perturbation in htr2 deletion strain. Array 6616

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-178


title: Halobacterium oxygen and light perturbation in vng1296c deletion strain. Array 7048

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-186


title: Halobacterium oxygen and light perturbation in htr2 deletion strain. Array 6610

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-172


title: Halobacterium oxygen and light perturbation in phoR deletion strain. Array 6021

description: Halobacterium NRC-1 ura3 and phoR gene knockouts in high oxgen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-169

source_name: Halobacterium NRC-1 ura3 and phoR gene knockouts.

growth_protocol: Halobacterium NRC-1 ura3 and phoR gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and phoR gene knockouts in high oxgen and in dark.


title: Halobacterium oxygen and light perturbation in phoR deletion strain. Array 6022

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-170

source_name: Halobacterium standard reference sample


title: Halobacterium oxygen and light perturbation in phoR deletion strain. Array 6017

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-165


title: Halobacterium oxygen and light perturbation in phoR deletion strain. Array 6019

description: Halobacterium NRC-1 ura3 and phoR gene knockouts in high oxgen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-167

growth_protocol: Halobacterium NRC-1 ura3 and phoR gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in light.

tag: Halobacterium NRC-1 ura3 and phoR gene knockouts in high oxgen and in light.


title: Halobacterium oxygen and light perturbation in wild-type cells. Array 6011

description: Halobacterium NRC-1  in low oxygen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-159

source_name: Halobacterium NRC-1

growth_protocol: Halobacterium NRC-1 grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in light.

tag: Halobacterium NRC-1  in low oxygen and in light.


title: Halobacterium oxygen and light perturbation in phoR deletion strain. Array 6015

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-163


title: Halobacterium oxygen and light perturbation in phoR deletion strain. Array 6018

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-166


title: Halobacterium oxygen and light perturbation in wild-type cells. Array 6013

description: Halobacterium NRC-1  in low oxygen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-161

growth_protocol: Halobacterium NRC-1 grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in dark (painted flask).

tag: Halobacterium NRC-1  in low oxygen and in dark.


title: Halobacterium oxygen and light perturbation in htr8 deletion strain. Array 6006

description: Halobacterium NRC-1 ura3 and htr8 gene knockouts in low oxygen and in dark versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-154

source_name: Halobacterium NRC-1 ura3 and htr8 gene knockouts.

growth_protocol: Halobacterium NRC-1 ura3 and htr8 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in dark (painted flask).

tag: Halobacterium NRC-1 ura3 and htr8 gene knockouts in low oxygen and in dark.


title: Halobacterium oxygen and light perturbation in htr8 deletion strain. Array 6003

description: Halobacterium NRC-1 ura3 and htr8 gene knockouts in low oxygen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-151

growth_protocol: Halobacterium NRC-1 ura3 and htr8 gene knockouts grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in low oxygen (shaking at 100RPM in stoppered flask) and in light.

tag: Halobacterium NRC-1 ura3 and htr8 gene knockouts in low oxygen and in light.


title: Halobacterium oxygen and light perturbation in wild-type cells. Array 6007

description: Halobacterium NRC-1  in high oxgen and in light versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-155

growth_protocol: Halobacterium NRC-1 grown in rich media (CM) to mid-log phase (50mL culture in 125mL flask) in high oxgen (shaking at 210RPM)  and in light.

tag: Halobacterium NRC-1  in high oxgen and in light.


title: Halobacterium oxygen and light perturbation in phoR deletion strain. Array 6020

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-168