title: saliva from normal control No.7 _no treatment_rep7

city: Guangzhou

first: Zijun

last: Xie

address: No.106,zhongshan 2nd round

institute: Guangdong General Hospital

description: microRNA expression profile of  saliva from healthy control No.7

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: 1)Using the mirVana PARIS kit (Ambion, USA),1.2ml of saliva was distributed equally to 2 microcentrifuge tubes.That is to say, each microcentrifuge tube contains 600μL of saliva.  2)200μL of 2x denaturing solution was added to each tube.  3) Add 0.8ml of  Acid-Phenol:Chloroform to each tube, and vortex for 30–60 sec to mix.  4) Centrifuge for 5 min at maximum speed (≥10,000×g) at room temp to separate the mixture into aqueous and organic phases. After centrifugation, the interphase should be compact; if it is not, repeat the centrifugation.  5) Carefully remove the aqueous (upper) phase without disturbing the lower phase or the interphase, and transfer it to a fresh tube.  6) Add 1.25 volumes 100% ethanol to the aqueous phase, and mix thoroughly.  7) For each sample, place a Filter Cartridge into one of the Collection Tubes. Pipet the lysate/ethanol mixture onto the Filter Cartridge. And apply the mixture in successive applications to the same filter. Centrifuge for ~30 sec or until the mixture has passed through the filter. Discard the flow-through, and repeat until all of the lysate/ethanol mixture is through the filter. Save the Collection Tube for the washing steps.  8) Wash the filter with 700 μLWash Solution 1.  9) Wash the filter twice with 500 μL Wash Solution 2/3.  10)RNA in the filter was eluted in 30μL of preheated nuclease-free water(95℃)

treatment_protocol: Subjects were asked to refrain from eating, drinking, smoking, and oral hygiene procedures for at least 2 hours before the collection. To stimulate glandular salivary flow, subjects received a  citric acid solution for application to the surface of the tongue with a cotton swab for 5 s every 30 s. The citric acid stimulation continued at 30-second intervals during the entire collection procedure. Up to 3 mL of saliva from each subject was collected in a 50-mL centrifuge tube. Saliva samples was centrifuged at 3,000 × g for 15 min at 4°C to spin down exfoliated cells, and the supernatant was transferred into microcentrifuge tubes followed by a second centrifugation at 12,000 × g for 10 min at 4°C to completely remove cellular components. Samples were stored at -80°C until use.

tag: disease state

value: normal control

tag: sample type

value: saliva supernatant

value: female

tag: age (year)


title: Astrocytoma 42

status: Public on Dec 15 2013

type: protein

city: Phoenix

first: Phillip

last: Stafford

state: AZ

address: 1001 S. McAllister

department: Center for Innovations in Medicine

country: USA

institute: Biodesign Institute

description: Alexa-647 conjugated goat anti-human secondary antibody

hyb_protocol: Antibodies were incubated with the peptide microarrays for 1 hour at room temperature according to Stafford et al. (Stafford, Halperin, Legutki, Magee, Galgiani, Johnston, "Physical characterization of the Immunosignaturing Effect", MCP 11(4), 2012).

scan_protocol: Scanning was done on an Agilent 'C' scanner at 10um resolution, high laser power, 70% PMT, autofocus ON, 638nm.

data_processing:
Median normalization per slide was done, and any negative values were adjusted to 0.01.
GeneSpring 7.3.1 was used to load and median-normalize raw gpr files.  Matrix of values were copied directly from GeneSpring as double-precision values.

label: direct-labeled anti-human IgG (Alexa 647)

molecule: protein

organism: Homo sapiens

source_name: Astrocytoma

label_protocol: Alexafluor 647-labeled goat anti-human IgG heavy-chain (Rockland antibodies) secondary antibody.

tag: cell type

value: Astrocytoma


title: Breast cancer - test10

source_name: Breast cancer (Stage IIIa, b site 1)

value: Breast cancer


title: saliva from normal control No.8 _no treatment_rep8

type: RNA

country: China

description: microRNA expression profile of  saliva from healthy control No.8

molecule: total RNA

tag: gender


title: saliva from normal control No.6 _no treatment_rep6

description: microRNA expression profile of  saliva from healthy control No.6

value: male


title: saliva from normal control No.4 _no treatment_rep4

description: microRNA expression profile of  saliva from healthy control No.4


title: Efaecalis_subdermalt0_rabbit4

type: mixed

city: Minneapolis

first: Kristi

middle: L

last: Frank

state: MN

address: 420 Delaware St SE, MMC196

department: Dept. of Microbiology

institute: University of Minnesota

hyb_protocol: Labeled cDNA was mixed with 0.5 μg labeled gDNA, dried down to ~10 μl in a speedvac, and mixed with ~40 μl of hybridization probe solution that contained a final concentration of 50% formamide, 5X SSC, 0.1 mg/ml salmon sperm DNA, and 0.1% SDS.  The probe was incubated at 95°C for 5 min and cooled at room temperature.  Hybridizations were performed at 42°C for 17-19 hours in a MAUI hybridization system (BioMicro Systems, Salt Lake City, UT) using the appropriate MAUI mixers.  Slides were then washed twice with 2X SSC, 0.5% SDS, once with 1X SSC, and once with 0.1X SSC before being dried by low-speed centrifugation for 10 min.

scan_protocol: Slides were scanned on a ScanArray 5000 scanner (Perkin Elmer, Waltham, MA).

data_processing: Scanned images were imported into BlueFuse version 3.6 or earlier (BlueGnome Ltd., Cambridge, UK) where spots were picked using Bayesian statistical modeling to extract the fluorescence intensities.  Data were then filtered based upon intensity, Bluefuse confidence, and spot size.  Due to a malfunction during slide printing, block 1 spots were unusable and were removed from the analysis at this step.  Replicate spots were fused by averaging the intensities of high quality spots.  The filtered raw values were exported for further analysis in Expressionist Analyst version 5.3.2 or earlier software (Genedata Inc., Basel, Switzerland).  The ratio of the cDNA intensity to the gDNA intensity for each fused spot was calculated and the data from all chips were quantile normalized, as previously described for analyzing gene expression in bacterial systems [9].  The fold change for each gene was calculated by dividing the cDNA/gDNA ratio obtained at either of the sampled time points (i.e., 2 or 8 hours post-inoculation) by the corresponding cDNA/gDNA ratio of the input inoculum (i.e., 0 hours) for each biological replicate.  Individual fold changes were then averaged to obtain the final average fold change.  Paired t-tests comparing the cDNA/gDNA ratio for each gene in each time point analysis (i.e., 0 versus 2 hours, 0 versus 8 hours) were performed.  Results were filtered for genes showing at least a 2-fold change in expression with a p-value of less than 0.05. For simplicity, data from only those spots known to represent genes in the genome of E. faecalis OG1RF were included in the final analysis. [9] Mehra S, Lian W, Jayapal KP, Charaniya SP, Sherman DH, et al. (2006) A framework to analyze multiple time series data: a case study with Streptomyces coelicolor. J Ind Microbiol Biotechnol 33: 159-172.

label: Alexa Fluor 647

organism: Enterococcus faecalis OG1RF

source_name: E. faecalis OG1RF cDNA, subdermal chamber, time 0

label_protocol: Total RNA (9 μl) was reverse transcribed and labeled with Alexa Fluor 647-aha-dUTP using the SuperScript Direct cDNA Labeling System (Invitrogen Corp.).   Labeled nucleic acids were purified with the QIAquick PCR purification kit (Qiagen Inc.) and eluted with two 30 μl volumes of 10 mM Tris-Cl, pH 8.5, that were pooled together.

growth_protocol: A single colony of E. faecalis OG1RF was inoculated into 10-25 ml BH medium and incubated for approximately 15 hours, at which time a volume of the culture was diluted 1:5 into 25-50 ml of fresh BH medium and incubated for 2 more hours.  Bacteria were harvested by centrifugation for 15-20 min at 6000 rpm in a Beckman JA-17 rotor at 4°C.  Pelleted cells were resuspended to an optical density at 600 nm of ~1.3-1.6 in KPBS and 2 ml were used for each subdermal chamber infection.  2 ml volumes were removed from the subdermal chambers at 2, 4, 8, 24, and 96 hours post-inoculation.  ~0.1-0.2 ml aliquots of the initial inoculum and each aspirate were used for serial dilution and plating to quantitate the bacterial load at each time point.  Two ml of the initial inoculum, and the remainder of each aspirate (~1.8 ml), were immediately added to 4 ml of RNAprotect Bacteria Reagent (Qiagen Inc., Valencia, CA), vortexed, processed according to the manufacturer’s instructions, flash-frozen in a dry ice/ethanol bath, and stored at -80°C until RNA extraction.

extract_protocol:
RNA was prepared from subdermal aspirates as follows: frozen pellets were thawed, resuspended in 0.4 ml of RNase-free TE containing 50 mg/ml lysozyme and 1000 U/ml mutanolysin, homogenized using a hand-held motorized homogenizer with RNase-free pellet pestles (Fisher Scientific, Pittsburgh, PA), and incubated for 10 min at 37°C.  Each sample was then split in half and extracted in duplicate with the RNeasy Mini Kit (Qiagen Inc.) according to the manufacturer’s instructions with an added homogenization step using the QIAshredder (Qiagen Inc.) immediately after the addition of Buffer RLT.  RNA was eluted from each column with two 30 μl volumes of RNase-free water, and total RNA from duplicate extractions of each sample were pooled together.  RNA from uninfected serous fluid was extracted with TRIzol Reagent (Invitrogen Corp., Carlsbad, CA) as suggested by the manufacturer immediately following aspiration from the subdermal chamber.

Contaminating DNA was removed using a TURBO DNA-free kit (Ambion, Austin, TX) following the rigorous protocol as directed by the manufacturer.  RNA for microarray experiments was then ethanol precipitated in the presence of a glycogen carrier (Roche Applied Science, Indianapolis, IN) and resuspended in 10 μl RNase-free water; 1 μl was reserved for qPCR experiments.

tag: test

value: Enterococcus faecalis OG1RF, inoculum used to infect subdermal chambers

tag: time point

molecule: genomic DNA

source_name: E. faecalis OG1RF gDNA

label_protocol: Sheared gDNA, which was used as a reference in the microarray experiments, was labeled with Cy3-dUTP (GE Healthcare Life Sciences, Piscataway, NJ) using the BioPrime Array CGH Genomic Labeling Module kit (Invitrogen Corp.). Labeled nucleic acids were purified with the QIAquick PCR purification kit (Qiagen Inc.) and eluted with two 30 μl volumes of 10 mM Tris-Cl, pH 8.5, that were pooled together.

growth_protocol: gDNA was from a 50 ml culture of E. faecalis grown overnight in beef heart infusion at 37 degrees C.

extract_protocol: gDNA from a 50 ml culture of E. faecalis grown overnight was extracted using a Genomic-tip 500/G column (Qiagen, Inc.) as directed by the manufacturer.  Precipitated DNA was resuspended in 1.7 ml of 10 mM Tris-Cl, pH 8.5.  A 1.0 ml volume of gDNA was sheared by nebulization with nitrogen gas, essentially as previously described [9,10], at 25 psi for 4.5 min to obtain fragments of 0.8-1.5 kb.  Sheared DNA was ethanol precipitated, resuspended in 0.2 ml sterile water, and stored at -20°C until use in microarray experiments. [9] Mehra S, Lian W, Jayapal KP, Charaniya SP, Sherman DH, et al. (2006) A framework to analyze multiple time series data: a case study with Streptomyces coelicolor. J Ind Microbiol Biotechnol 33: 159-172. [10] Roe B, Crabtree J, Khan A (1996) DNA Isolation and Sequencing: Essential Techniques Series. New York: J. Wiley and Sons.

tag: reference

value: Enterococcus faecalis OG1RF genomic DNA (gDNA)


title: Breast cancer - test12

source_name: Breast cancer (Stage III site 1)


title: Efaecalis_subdermalt8_rabbit5

source_name: E. faecalis OG1RF cDNA, subdermal chamber, time 8

value: Enterococcus faecalis OG1RF, aspirate from subdermal chamber 8 hours post-infection


title: Efaecalis_subdermalt0_rabbit5


title: saliva from normal control No.5 _no treatment_rep5

description: microRNA expression profile of  saliva from healthy control No.5


title: Efaecalis_subdermalt2_rabbit5

source_name: E. faecalis OG1RF cDNA, subdermal chamber, time 2

value: Enterococcus faecalis OG1RF, aspirate from subdermal chamber 2 hours post-infection


title: Efaecalis_subdermalt8_rabbit4


title: Efaecalis_subdermalt8_rabbit2


title: Astrocytoma 41


title: Efaecalis_subdermalt2_rabbit4


title: Breast cancer - test9

source_name: Breast cancer (Stage III stite 1)


title: Breast cancer - test8

source_name: Breast cancer (Stage IIIa site 3)


title: Astrocytoma 40


title: saliva from normal control No.2 _no treatment_rep2

description: microRNA expression profile of  saliva from healthy control No.2


title: Astrocytoma 39


title: Efaecalis_subdermalt2_rabbit2


title: Breast cancer - test7


title: saliva from normal control No.3 _no treatment_rep3

description: microRNA expression profile of  saliva from healthy control No.3


title: saliva from normal control No.1 _no treatment_rep1

description: microRNA expression profile of  saliva from healthy control No.1


title: Efaecalis_subdermalt8_rabbit1


title: Efaecalis_subdermalt0_rabbit2


title: Breast cancer - test6


title: Astrocytoma 37


title: Breast cancer - test5

source_name: Breast cancer (Stage II site 2)


title: saliva from  resectable pancreatic cancer  patient No.8 _before treatment_rep7

description: microRNA expression profile of  saliva from resectable pancreatic cancer patient No.8

value: resectable pancreatic cancer


title: Astrocytoma 36


title: Breast cancer - test4


title: Efaecalis_subdermalt2_rabbit1


title: Breast cancer - test3

source_name: Breast cancer (Stage Iia site 2)


title: saliva from resectable pancreatic cancer  patient No.7 _before treatment_rep7

description: microRNA expression profile of  saliva from resectable pancreatic cancer patient No.7


title: Astrocytoma 35


title: Astrocytoma 34


title: Breast cancer - test2


title: Astrocytoma 33


title: Breast cancer - test1

source_name: Breast cancer (Stage IIIa site 1)


title: Brain cancer - test20

source_name: Brain cancer (Glioblastoma multiformae site 1)

value: Brain cancer


title: Astrocytoma 32


title: saliva from  resectable pancreatic cancer patient No.4 _before treatment_rep4

description: microRNA expression profile of  saliva from resectable pancreatic cancer patient No.4


title: Brain cancer - test18


title: Brain cancer - test19


title: saliva from  resectable pancreatic cancer  patient No.5 _before treatment_rep5

description: microRNA expression profile of  saliva from resectable pancreatic cancer patient No.5


title: Astrocytoma 30


title: saliva from  resectable pancreatic cancer  patient No.6 _before treatment_rep6

description: microRNA expression profile of  saliva from resectable pancreatic cancer patient No.6


title: saliva from  resectable pancreatic cancer patient No.3 _before treatment_rep3

description: microRNA expression profile of  saliva from resectable pancreatic cancer patient No.3


title: Astrocytoma 29


title: Brain cancer - test17


title: Efaecalis_subdermalt0_rabbit1

growth_protocol: A single colony of E. faecalis OG1RF was inoculated into 10-25 ml beef heart dialysate medium and incubated for approximately 15 hours, at which time a volume of the culture was diluted 1:5 into 25-50 ml of fresh BH medium and incubated for 2 more hours.  Bacteria were harvested by centrifugation for 15-20 min at 6000 rpm in a Beckman JA-17 rotor at 4°C.  Pelleted cells were resuspended to an optical density at 600 nm of ~1.3-1.6 in KPBS and 2 ml were used for each subdermal chamber infection.  2 ml volumes were removed from the subdermal chambers at 2, 4, 8, 24, and 96 hours post-inoculation.  ~0.1-0.2 ml aliquots of the initial inoculum and each aspirate were used for serial dilution and plating to quantitate the bacterial load at each time point.  Two ml of the initial inoculum, and the remainder of each aspirate (~1.8 ml), were immediately added to 4 ml of RNAprotect Bacteria Reagent (Qiagen Inc., Valencia, CA), vortexed, processed according to the manufacturer’s instructions, flash-frozen in a dry ice/ethanol bath, and stored at -80°C until RNA extraction.

label_protocol: Sheared gDNA, which was used as a reference in the microarray experiments, was labeled with Cy3-dUTP (GE Healthcare Life Sciences, Piscataway, NJ) using the BioPrime Array CGH Genomic Labeling Module kit (Invitrogen Corp.).  Labeled nucleic acids were purified with the QIAquick PCR purification kit (Qiagen Inc.) and eluted with two 30 μl volumes of 10 mM Tris-Cl, pH 8.5, that were pooled together.


title: Astrocytoma 31


title: Astrocytoma 28


title: Brain cancer - test16


title: 1345-BP-88

city: Atlanta

first: Shuzhao

last: Li

state: GA

address: 954 Gatewood Rd NE

department: Emory Vaccine Center

institute: Emory University

hyb_protocol: Per Affymetrix protocol

scan_protocol: Per Affymetrix protocol

data_processing: Hybridization data of all samples passed quality control and expression data were normalized by RMA R package

label: biotin

label_protocol: Per Affymetrix protocol

extract_protocol: Total RNA was extracted from PBMC using Trizol (Invitrogen, 1 ml of Trizol to ~1.5 million cells) according to manufacture's recommendation.

treatment_protocol: Healthy adult volunteers  were randomized to be vaccinated subcutaneously with MPSV4 (Menomune®, n=13) or intramuscularly with MCV4 (MenactraTM, n=17) (Sanofi Pasteur, Swiftwater, PA), according to manufacture's recommendations.

tag: time

value: 0 days

tag: treatment

value: PBMC


title: Astrocytoma 27


title: Brain cancer - test15


title: 1345-BP-89

value: 3 days


title: saliva from resectable pancreatic cancer patient No.1 _before treatment_rep1

description: microRNA expression profile of  saliva from resectable pancreatic cancer patient No.1


title: Astrocytoma 26


title: Brain cancer - test14


title: Astrocytoma 25


title: 1345-BP-86


title: Brain cancer - test13


title: 1345-BP-87

value: 7 days


title: 1345-BP-84


title: 1345-BP-90


title: 1345-BP-82


title: saliva from  resectable pancreatic cancer patient No.2 _before treatment_rep2

description: microRNA expression profile of  saliva from resectable pancreatic cancer patient No.2


title: Astrocytoma 24


title: 1345-BP-85


title: Brain cancer - test12


title: Astrocytoma 23


title: Brain cancer - test11


title: M202(Sub1) 1d

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

institute: University of Nebraska

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: RMA normalization of raw data (CEL files)

organism: Oryza sativa

source_name: shoot tissue

label_protocol: Standard Affymetrix IVT protocol

growth_protocol: Rice seeds were germinated and cultured in soil until treatment.

extract_protocol: Trizol total RNA extraction protocol was used for these experiments

treatment_protocol: 18 day old seedlings were completely submerged in greenhouse conditions for either 1 day or 6 day before sampling shoot tissue for RNA.

tag: genotype

tag: development stage

value: 18 day old seedlings

tag: time submerged

tag: tissue

value: shoot


title: 1345-BP-83


title: 1345-BP-80


title: Astrocytoma 22


title: M202 6d


title: M202 1d


title: Brain cancer - test10


title: Astrocytoma 21


title: Brain cancer - test9


title: 1345-BP-79


title: 1345-BP-81


title: 1345-BP-78


title: Sample-4B-U133A Day+2

first: Yoga

last: Balagurunathan

address: 445 N. Fifth street

institute: TGEN

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 5 time points: day (-2), day (0), day (1), day (2) day (3), where day (0) designates a point of 100% confluence.This Sample-4B-U133A is Day+2

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The Cell files extracted from scanner was quantified in Affymetrix MAS5 methods implemented in Bioconductor for R (default analysis settings used)  and global scaling as normalization method.

label: biotin.

source_name: Human Keratinocytes  Differentiation.

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

growth_protocol: Primary foreskin keratinocytes were grown in serum free medium and allowed to reach confluence in order to induce differentiation.

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

treatment_protocol: Confluence-induced differentiation.

value: Primary human neonatal foreskin keratinocytes

value: Day+2 of point of confluence


title: Astrocytoma 20

description: Alexa-647 conjugated goat anti-human secondary antibody

value: Astrocytoma


title: Sample-3B-U133A Day+1

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 5 time points: day (-2), day (0), day (1), day (2) day (3), where day (0) designates a point of 100% confluence.This Sample-3B-U133A is Day+1.

value: Day+1 of point of confluence


title: Brain cancer - test8


title: M202(Sub1) 6d


title: Sample-5B-U133A Day+3

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 5 time points: day (-2), day (0), day (1), day (2) day (3), where day (0) designates a point of 100% confluence.This Sample-5B-U133A is Day+3.

value: Day+3 of point of confluence


title: Astrocytoma 38


title: Brain cancer - test7


title: Astrocytoma 19


title: 1345-BP-76


title: Astrocytoma 18


title: Brain cancer - test6


title: 1345-BP-75


title: Astrocytoma 17


title: Sample-2B-U133A Day0

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 5 time points: day (-2), day (0), day (1), day (2) day (3), where day (0) designates a point of 100% confluence.This Sample-2B-U133A is Day0.

value: Day0 of point of confluence


title: Brain cancer - test4


title: Astrocytoma 15


title: Brain cancer - test5


title: Sample-1B-U133A Day-2

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 5 time points: day (-2), day (0), day (1), day (2) day (3), where day (0) designates a point of 100% confluence..This Sample-1B-U133A is Day-2.

value: Day-2 of point of confluence


title: 1345-BP-74


title: Brain cancer - test3


title: Astrocytoma 14


title: Brain cancer - test2


title: Sample-Pit201 Day+5

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 8 time points: day (-3)day,(-2)day, (-1)day,day (0), day (1), day (2) day (3),day(5), where day (0) designates a point of 100% confluence..This Sample-Pit201 is Day+5.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

value: Day+5 of point of confluence


title: 1345-BP-72


title: Astrocytoma 16


title: Astrocytoma 13


title: 1345-BP-71


title: Brain cancer - test1


title: Sample-Pit198 Day+1

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 8 time points: day (-3)day,(-2)day, (-1)day,day (0), day (1), day (2) day (3),day(5), where day (0) designates a point of 100% confluence..This Sample-Pit198 is Day+1.


title: Sample-Pit200 Day+3

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 8 time points: day (-3)day,(-2)day, (-1)day,day (0), day (1), day (2) day (3),day(5), where day (0) designates a point of 100% confluence..This Sample-Pit200 is Day+3.


title: Sample-Pit197 Day0

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 8 time points: day (-3)day,(-2)day, (-1)day,day (0), day (1), day (2) day (3),day(5), where day (0) designates a point of 100% confluence..This Sample-Pit197 is Day0.


title: 1345-BP-73


title: 1345-BP-69


title: Sample-Pit199 Day+2

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 8 time points: day (-3)day,(-2)day, (-1)day,day (0), day (1), day (2) day (3),day(5), where day (0) designates a point of 100% confluence..This Sample-Pit199 is Day+2.


title: Astrocytoma 12


title: 1345-BP-70


title: Astrocytoma 11


title: 1345-BP-68


title: 1345-BP-67


title: Sample-Pit194 Day-3

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 8 time points: day (-3)day,(-2)day, (-1)day,day (0), day (1), day (2) day (3),day(5), where day (0) designates a point of 100% confluence..This Sample-Pit194 is Day-3.

value: Day-3 of point of confluence


title: Astrocytoma 10


title: Astrocytoma 9


title: Sample-Pit195 Day-2

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 8 time points: day (-3)day,(-2)day, (-1)day,day (0), day (1), day (2) day (3),day(5), where day (0) designates a point of 100% confluence..This Sample-Pit195 is Day-2.


title: 1345-BP-66


title: Astrocytoma 8


title: round sperm cells, biological rep2

city: Beijing

first: Wei

address: Beichen West Road

department: State key lab of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description: Gene expression data from round sperm cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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: Rattus norvegicus

source_name: round sperm cells

growth_protocol: Rat androgenetic haploid ES cells and normal diploid ES cells were cultured in N2B27-2i medium and were routinely passaged every 2-3 days at a ratio of 1:3-1:4

extract_protocol: Trizol extraction of total RNA was performed using Trizol reagent (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Rat androgenetic haploid ES cells and normal diploid ES cells were dissociated with 0.25% trypsin with 2% chicken serum for 3-4 mins

tag: rat strain

value: DA (Dark Agouti) inbred

value: freshly isolated cells

value: round sperm cells


title: Astrocytoma 7


title: round sperm cells, biological rep3


title: 1345-BP-65

value: PBMC


title: 1345-BP-64

value: 0 days


title: 1345-BP-63

value: 7 days


title: Sample-Pit196 Day-1

description: Gene expression data from primary human keratinocyte subjected confluence-induced differentiation over 8 time points: day (-3)day,(-2)day, (-1)day,day (0), day (1), day (2) day (3),day(5), where day (0) designates a point of 100% confluence..This Sample-Pit196 is Day-1.

value: Day-1 of point of confluence


title: 1345-BP-62

value: 3 days


title: diploid ES cell line DA5-3, biological rep3

description: Gene expression data from cell line DA5-3

source_name: diploid ES cell line DA5-3

value: culture cell line DA5-3

value: diploid embryonic stem cells


title: 1345-BP-61


title: DCs-NDV infected-8h-2

city: NEW YORK

first: Boris

middle: Michael

last: Hartmann

state: NY

address: One Gustave L Levy Place

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: According to standard Affymetrix protocol.

data_processing: Raw data was processed with the Partek Pro software using the RMA Background Correction, with an adjustment of GC content as pre-background adjustment.

source_name: DCs infected with NDV for 8 hours

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

growth_protocol: Human peripheral blood mononuclear cells were isolated from buffy coats by Ficoll density gradient centrifugation (Histopaque, Sigma Aldrich) at 1450 r.p.m. and CD14+ monocytes were immunomagnetically purified by using a MACS CD14 isolation kit (Miltenyi Biotech). Monocytes were then differentiated into naïve DCs by 5–6 day incubation at 37°C and 5% CO2 in DC growth media, which contains RPMI Medium 1640 (Invitrogen/Gibco) supplemented with 10% fetal calf serum (Hyclone), 2 mM of l-glutamine, 100 U/ml penicillin and 100 g/ml streptomycin (Pen/Strep) (Invitrogen), 500 U/ml hGM-CSF (Preprotech) and 1000 U/ml hIL-4 (Preprotech).

extract_protocol: RNA was extracted with the RNeasy plus kit (Qiagen) following the manufacturer’s protocol.

treatment_protocol: Antiviral activated dendritic cells (AVDCs) were generated by employing a trans-well system. The trans-well system consists of an upper and a lower chamber separated by a 0.4 μm PET membrane (Millipore) that allows diffusion of cytokines and chemokines through the membrane but avoids the interaction of the cells in both chambers. To generate the AVDCs, naïve DCs were infected as described above. After the 40 minutes incubation, the cells were washed with PBS, and cultured in the trans-well system. Infected and non-infected DCs were allocated in the upper and lower chamber respectively. Two independent wells were set-up with infected or naïve non-infected DCs as positive and negative controls. The cultures were incubated at 37ºC in 5% CO2 for 18 hours.

value: monocyte derived dendritic cellc (DCs)


title: Astrocytoma 5

source_name: Astrocytoma

value: Astrocytoma


title: round sperm cells, biological rep1


title: diploid ES cell line DA5-3, biological rep1


title: DCs-NDV infected-8h-3

scan_protocol: According to standard Affymetrix protocol.


title: diploid ES cell line DA5-3, biological rep2


title: Astrocytoma 4


title: DCs-naïve-3

source_name: Naïve DCs


title: Astrocytoma 6


title: 1345-BP-60


title: RahES cell line RAH-2, biological rep3

description: Gene expression data from cell line RAH-2

source_name: RahES cell line RAH-2

value: culture cell line RAH-2

value: androgenetic embryonic stem cells (RahES)


title: DCs-NDV infected-8h-1


title: Astrocytoma 1


title: DCs-naïve-1


title: recurrent Breast cancer 61

source_name: recurrent Breast cancer

value: recurrent Breast cancer


title: RahES cell line RAH-2, biological rep2


title: 1345-BP-59


title: RahES cell line RAH-6, biological rep2

description: Gene expression data from cell line RAH-6

source_name: RahES cell line RAH-6

value: culture cell line RAH-6


title: 1345-BP-57


title: recurrent Breast cancer 60

description: Alexa-647 conjugated goat anti-human secondary antibody


title: 1345-BP-58


title: DCs-NDV supernatant-8h-2

source_name: DCs were exposed to supernatants from NDV infected DCs for 8 hours.


title: RahES cell line RAH-2, biological rep1


title: Astrocytoma 2


title: recurrent Breast cancer 59


title: DCs-naïve-2


title: RahES cell line RAH-6, biological rep1


title: RahES cell line RAH-6, biological rep3


title: DCs-IFNβ-8h-2

source_name: DCs were exposed to IFNβ for 8 hours


title: recurrent Breast cancer 58


title: DCs-IFNβ-8h-1


title: recurrent Breast cancer 57


title: CTX.d8.DTR+.AREG#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

organism: Mus musculus

source_name: Muscle

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: age

value: 8 Weeks Old

tag: genetic background

tag: genetic variation

tag: source prep

value: TA muscle flash-frozen in liquid nitrogen, then homogenized in Trizol

value: skeletal muscle

value: diphtheria toxin + amphireguline


title: 1345-BP-53

value: PBMC


title: 1345-BP-52

value: 0 days


title: recurrent Breast cancer 56


title: 1345-BP-77


title: 1345-BP-56


title: DCs-NDV supernatant-8h-1


title: 1345-BP-54

value: 7 days


title: CTX.d8.DTR+.PBS#1

value: diphtheria toxin + PBS


title: 1345-BP-51


title: CTX.d8.DTR+.PBS#3


title: recurrent Breast cancer 55


title: CTX.d8.DTR+.AREG#2


title: recurrent Breast cancer 54


title: CTX.d8.DTR+.PBS#2


title: recurrent Breast cancer 53


title: recurrent Breast cancer 52


title: CTX.d4.DTR-.PBS#3


title: recurrent Breast cancer 51


title: recurrent Breast cancer 49


title: recurrent Breast cancer 50


title: 1345-BP-50

value: 3 days


title: CTX.d8.DTR+.AREG#1


title: 1345-BP-47


title: CTX.d4.DTR-.PBS#2


title: recurrent Breast cancer 48


title: 1345-BP-44


title: 1345-BP-48


title: CTX.d4.DTR-.AREG#1


title: CTX.d4.DTR-.AREG#3


title: recurrent Breast cancer 47


title: 1345-BP-49


title: 1345-BP-43


title: 1345-BP-46


title: 1345-BP-40


title: TR.4dINJ.Sp#1

hyb_protocol: Affymetrix WT Sense Target Labeling Kit

source_name: Spleen

tag: exclusion markers

value: CD8a, CD11b, CD11c, CD49b, CD19, Ter119, DAPI

tag: phenotype markers

value: TCRb+ CD4+ GFP+

tag: separation method

value: MoFlo Sorter

tag: Sex

value: Male

value: Skeletal muscle injured with cardiotoxin 4 days before cell isolation. Collagenase digestion-Percoll- sorting in Moflo

value: Tregs

value: injured with cardiotoxin

value: 4 d


title: 1345-BP-41

tag: cell type


title: recurrent Breast cancer 46

value: recurrent Breast cancer


title: recurrent Breast cancer 45


title: 1345-BP-42


title: TR.4dINJ.Sp#3

value: 8 Weeks Old


title: 1345-BP-45


title: TR.4dINJ.Sp#2


title: recurrent Breast cancer 43


title: TR.4dINJ.Mu#3


title: recurrent Breast cancer 42


title: CTX.d4.DTR-.AREG#2

value: TA muscle flash-frozen in liquid nitrogen, then homogenized in Trizol

value: skeletal muscle


title: 1345-BP-39

value: PBMC


title: recurrent Breast cancer 40


title: recurrent Breast cancer 39


title: recurrent Breast cancer 44


title: TR.4dINJ.Mu#2


title: 1345-BP-38


title: TR.2wkINJ.Sp#3

value: Skeletal muscle injured with cardiotoxin 14 days before cell isolation. Collagenase digestion-Percoll- sorting in Moflo


title: TR.4dINJ.Mu#1


title: 1345-BP-36

value: 7 days


title: 1345-BP-34

value: 0 days


title: recurrent Breast cancer 38


title: TR.2wkINJ.Sp#2


title: TR.2wkINJ.Mu#3


title: 1345-BP-37


title: recurrent Breast cancer 41


title: recurrent Breast cancer 37


title: recurrent Breast cancer 36


title: recurrent Breast cancer 35


title: TR.2wkINJ.Mu#1


title: recurrent Breast cancer 33


title: 1345-BP-33


title: recurrent Breast cancer 32


title: TR.2wkINJ.Mu#2


title: TC.4dINJ.Sp#3

value: TCRb+ CD4+ GFP-

value: Tconvs


title: TR.2wkINJ.Sp#1

value: CD8a, CD11b, CD11c, CD49b, CD19, Ter119, DAPI

value: TCRb+ CD4+ GFP+


title: 1345-BP-31


title: Astrocytoma 3

value: Astrocytoma


title: TC.2wkINJ.Sp#3

value: MoFlo Sorter

value: Male


title: TC.4dINJ.Mu#2

value: Skeletal muscle injured with cardiotoxin 4 days before cell isolation. Collagenase digestion-Percoll- sorting in Moflo

value: injured with cardiotoxin


title: 1345-BP-35

value: 3 days


title: 1345-BP-30


title: TC.4dINJ.Sp#2

value: 8 Weeks Old

value: 4 d


title: TC.4dINJ.Sp#1


title: recurrent Breast cancer 34

value: recurrent Breast cancer


title: TC.4dINJ.Mu#3


title: 1345-BP-55

value: PBMC


title: recurrent Breast cancer 30


title: 1345-BP-29


title: recurrent Breast cancer 31


title: TC.2wkINJ.Sp#2

value: Skeletal muscle injured with cardiotoxin 14 days before cell isolation. Collagenase digestion-Percoll- sorting in Moflo


title: recurrent Breast cancer 29


title: 1345-BP-26


title: TC.4dINJ.Mu#1


title: recurrent Breast cancer 28


title: 1345-BP-32


title: recurrent Breast cancer 27


title: 1345-BP-28


title: 1345-BP-27

value: 7 days


title: 1345-BP-24


title: 1345-BP-22

value: 0 days


title: recurrent Breast cancer 24


title: TC.2wkINJ.Mu#3

value: TCRb+ CD4+ GFP-


title: 1345-BP-23


title: TC.2wkINJ.Mu#1

value: Tconvs


title: recurrent Breast cancer 22


title: MDX.PC61.B#3

value: 6 Weeks Old

value: mdx

value: Muscle flash-frozen in liquid nitrogen, then homogenized in Trizol

value: skeletal muscle

value: anti-CD25 mAb


title: 1345-BP-20


title: MDX.PC61.B#2

value: Male


title: TC.2wkINJ.Sp#1

value: CD8a, CD11b, CD11c, CD49b, CD19, Ter119, DAPI

value: MoFlo Sorter

value: injured with cardiotoxin


title: 1345-BP-21


title: recurrent Breast cancer 23


title: recurrent Breast cancer 26


title: 1345-BP-25


title: TC.2wkINJ.Mu#2

value: 8 Weeks Old


title: CTX.d4.DTR-.PBS#1

value: TA muscle flash-frozen in liquid nitrogen, then homogenized in Trizol

value: diphtheria toxin + PBS


title: 1345-BP-17

value: 3 days

value: PBMC


title: 1345-BP-18

value: 7 days


title: 1345-BP-15


title: recurrent Breast cancer 20

value: recurrent Breast cancer


title: MDX.IGG.B#3

value: rat IgG


title: 1345-BP-19

value: 0 days


title: recurrent Breast cancer 18


title: recurrent Breast cancer 21


title: recurrent Breast cancer 17


title: 1345-BP-14


title: MDX.IGG.B#2

value: 6 Weeks Old

value: mdx


title: 1345-BP-16


title: recurrent Breast cancer 16


title: MDX.PC61.B#1

value: Muscle flash-frozen in liquid nitrogen, then homogenized in Trizol

value: skeletal muscle


title: recurrent Breast cancer 15


title: DTR-.xINJ.d8.TA#3

value: Male

value: Skeletal muscle injured with cardiotoxin 8 days before cell isolation. TA muscle flash-frozen in liquid nitrogen, then homogenized in Trizol


title: recurrent Breast cancer 14


title: DTR-.xINJ.d8.TA#2


title: DTR-.xINJ.d8.TA#1


title: DTR-.xINJ.d4.TA#3

value: Skeletal muscle injured with cardiotoxin 4 days before cell isolation. TA muscle flash-frozen in liquid nitrogen, then homogenized in Trizol


title: recurrent Breast cancer 12


title: recurrent Breast cancer 11


title: 1345-BP-12


title: DTR-.xINJ.d4.TA#1

value: injured with cardiotoxin


title: 1345-BP-9


title: 1345-BP-11


title: MDX.IGG.B#1


title: DTR-.CTx.d8.TA#3

value: 8 Weeks Old


title: recurrent Breast cancer 10


title: 1345-BP-10


title: 1345-BP-8


title: recurrent Breast cancer 13


title: recurrent Breast cancer 9


title: 1345-BP-7


title: DTR-.CTx.d8.TA#1


title: recurrent Breast cancer 8


title: 1345-BP-5


title: recurrent Breast cancer 7


title: recurrent Breast cancer 6


title: DTR-.CTx.d8.TA#2


title: recurrent Breast cancer 5


title: 1345-BP-91


title: DTR-.CTx.d4.TA#1


title: 1345-BP-3


title: DTR+.xINJ.d8.TA#2


title: DTR+.xINJ.d8.TA#1


title: 1345-BP-2


title: 1345-BP-1


title: recurrent Breast cancer 3


title: recurrent Breast cancer 4


title: DTR-.CTx.d4.TA#3


title: T73

type: genomic

city: Valencia

first: Clara

last: Ibáñez

address: Avenue Agustín Escardino, 7

country: Spain

institute: Institute of Agrochemistry and Food Technology

description: Duplicate arrays and Cy5-dCTP and Cy3-dCTP dye-swap assays.

hyb_protocol: The mixture of the required Cy3- and Cy5-labelled samples was adjusted to 60 μl with hybridization solution (50% formamide, 5X SSC, 0,1% SDS, 100 μg/ml salmon sperm DNA and water), incubated for 1 minute at 95 ºC and centrifuged at 13000 X g for 1 min. The supernatants were applied to microarrays and the hybridizations were allowed to proceed overnight at 65°C.

scan_protocol: Arrays were scanned using an Axon GenePix 4100A scanner and GenePix Pro 6.0 software.

data_processing: Using Acuity 4.0 software (Molecular Devices Corp., Union City, CA, USA), manually flagged bad spots were eliminated and the local background was subtracted before averaging the replicate features on the array. Log2 intensity ratios (M values) were then Median normalized to correct for differences in genomic DNA labelling efficiency between samples. The relative hybridization signal of each ORF was derived from the average of the two dye-swap hybridizations performed for each strain. The normalized log2 ratio (M value) was considered as a measure of the relative abundance of each ORF relatively to that of the reference strain S288C. Deviations from the 1:1 hybridization ratio were taken as indicative of changes in DNA copy number. Given that the variability usually observed between S. cerevisiae genomes (either within laboratory strains or natural isolates) is much lower than this estimate (Adams et al. 1992, Carreto et al. 2008), we interpreted statistically significant variations in hybridization signal as ORF deletions or duplications. Data imported from Acuity was manipulated and clustered, using established algorithms implemented in the software program Genesis. Average linkage clustering with centered correlation was used to generate visual representations of clusters.

organism: Saccharomyces cerevisiae

label_protocol: Approximately 2 μg of these DNAs were labelled with fluorescently-tagged nucleotides (Amersham, Piscataway, NJ, USA), either Cy3-dCTP for the reference strain and Cy5 dCTP for the studied strains or vice-versa, using Exo-Klenow Fragment and random primer Mix (Bioprime Array CGH Kit, Invitrogen). Dye-swap hybridizations were performed for each strain. After labeling, the reactions were heat inactivated, the experimental (Cy5- or Cy3-labeled) and reference (Cy3- or Cy5-labeled) DNAs were mixed and purified away from unincorporated label using the MinElute PCR Purification Kit (QIAGEN). The degree of labeling was determined by measuring the absorbance at 260 nm and at 550 nm for Cy3- labeled DNA or at 260 nm and 650 nm for Cy5-labeled DNA. Samples with a base/dye ratio between 40 and 80 for both Cy3 and Cy5 were routinely obtained.

growth_protocol: Yeast strains were cultivated in 5ml YPD (1% yeast extract, 2% peptone, 2% glucose) at 28 ºC for 24 hours.

extract_protocol: DNA was isolated according to standard procedures (Querol et al., 1992). After isolation, the DNAs were digested with HinfI (Takara Bio Inc., Japan) and purified with the High Pure PCR Product Purification Kit (Roche Molecular Biochemicals, Mannheim, Germany).

tag: strain

tag: source

value: Traditional wine strain

tag: sample type

value: reference strain


title: DTR-.xINJ.d4.TA#2

tag: treatment

tag: time


title: 1345-BP-6


title: DTR-.CTx.d4.TA#2


title: recurrent Breast cancer 1


title: recurrent Breast cancer 19


title: Kyokai

source_name: Kyokai, YPD, 24h

value: kyokai

value: Sake strain (Japón)


title: PE35M

source_name: PE35M, YPD, 24h

value: Masato strain


title: GB-FlorC

source_name: GB-FlorC, YPD, 24h

value: GB-FlorC

value: Jerez wine


title: Temohaya-26

source_name: Temohaya, YPD, 24h

value: Temohaya

value: Traditional agave fermentation


title: DTR+.xINJ.d4.TA#2


title: recurrent Breast cancer 2

value: recurrent Breast cancer


title: DTR+.CTx.d8.TA#2


title: DTR+.CTx.d8.TA#3


title: DTR+.d0.TA#1

value: TA muscle flash-frozen in liquid nitrogen, then homogenized in Trizol

value: control


title: 10131

value: Centaurea alba (Spain)


title: DTR+.CTx.d4.TA#3

value: Male

value: skeletal muscle


title: DTR+.CTx.d8.TA#1

value: Skeletal muscle injured with cardiotoxin 8 days before cell isolation. TA muscle flash-frozen in liquid nitrogen, then homogenized in Trizol

value: injured with cardiotoxin


title: RCAP_(40/2)Ace/Glu_1

status: Public on Dec 14 2013

city: Ankara

first: Nilufer

last: Erkal

address: Üniversiteler Mahallesi

country: Turkey

institute: Mİddle East Technical University

hyb_protocol: Labeled samples were hybridized with Rhodobacter capsulatus TR_RCH2a520699F array (Affymetrix) at 50°C  for 17 hours, washed and stained at GeneChip Fluidics Station 450 at the METU Central Laboratory, Molecular Biology and Biotechnology R&D Center.

scan_protocol: Arrays were scanned using GeneChip® Scanner 3000 which was operated by GCOS according to instructions of the manufacturer (Affymetrix).

data_processing: CHP files from the scanned arrays were generated by GCOS and analyzed by using GeneSpring GX 11 software (Agilent Technologies, Santa Clara, CA).

organism: Rhodobacter capsulatus

source_name: Bacterial cell

label_protocol: The fragmented cDNA was biotinylated with the GeneChip DNA Labeling Reagent (Affymetrix).

growth_protocol: 1.5x109 bacterial cells grown on different nitrogen sources and different concentrations of acetate were collected via centrifugation.

extract_protocol: Total RNA isolation was performed by using Trizol Reagent (Invitrogen) according to manufacturar’s manual.

treatment_protocol: The cell pellets were frozen in liquid nitrogen and stored at -80°C until RNA isolation.

value: 40mM acetate with 2 mM glutamate


title: RCAP_(80/2)Ace/Glu_3

value: 80mM acetate with 2 mM glutamate


title: RCAP_(40/2)Ace/NH4Cl_1

value: 40mM acetate with 5mM ammonium chloride


title: RCAP_(40/2)Ace/Glu_2


title: RCAP_(40/2)Ace/NH4Cl_2


title: RCAP_(40/2)Ace/Glu_4


title: RCAP_(40/2)Ace/Glu_3


title: RCAP_(80/2)Ace/Glu_1


title: RCAP_(80/2)Ace/Glu_2


title: DTR+.CTx.d4.TA#2

value: 8 Weeks Old

value: Skeletal muscle injured with cardiotoxin 4 days before cell isolation. TA muscle flash-frozen in liquid nitrogen, then homogenized in Trizol


title: MCL cells_dual PI3K/mTOR inhibitor treated_biological rep2

city: BARCELONA

first: DOLORS

last: COLOMER

address: VILLARROEL 170

institute: IDIBAPS-HOSPITAL CLINIC

description: Gene expression data from primary MCL cells treated with a dual PI3K/mTOR inhibitor

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the Gene Titan instrument.

data_processing:
Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software version 1.1 (AGCC) (Affymetrix).
Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm of the BioConductor Affy Package.

source_name: Primary MCL cells treated with a dual PI3K/mTOR inhibitor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA

growth_protocol: MCL cells were incubated in complete RPMI medium plus 10%FBS at 37ºC 5%CO2

extract_protocol: Total RNA was extracted, using the Trizol  reagent

treatment_protocol: Treatment with a mTOR inhibitor, a pan-PI3K inhibitor and a dual PI3K/mTOR inhibitor for 8 hours

value: Primary MCL cells

tag: disease state

value: mantle cell lymphoma

value: treated with a dual PI3K/mTOR inhibitor


title: MCL cells_pan-PI3K inhibitor treated_biological rep2

description: Gene expression data from primary MCL cells treated with a pan-PI3K inhibitor

source_name: Primary MCL cells treated with a pan-PI3K inhibitor

value: treated with a pan-PI3K inhibitor


title: MCL cells_mTOR inhibitor treated_biological rep2

description: Gene expression data from primary MCL cells treated with a mTOR inhibitor

source_name: Primary MCL cells treated with a mTOR inhibitor

value: treated with a mTOR inhibitor


title: MCL cells_dual PI3K/mTOR inhibitor treated_biological rep1


title: MCL cells_mTOR inhibitor treated_biological rep1


title: MCL cells_untreated_ biological rep1

description: Gene expression data from untreated primary MCL cells

source_name: Primary MCL cells untreated

value: untreated


title: Pineal_Light_CT22

city: Tel Aviv

first: Shahar

last: Alon

address: Tel Aviv University

department: Department of Neurobiology, The George S. Wise Faculty of Life Sciences

country: Israel

institute: Tel Aviv University

hyb_protocol: The target cRNA generated from each sample was fragmented and 15 micogram of the fragmented cRNA was added to the hybridization cocktail which includes in addition to the fragmented target, probe array controls (pre-mixed biotin-labeled bioB, bioC, bioD and cre, in staggered concentrations, ready to be added directly to the hybridization cocktail. These controls facilitate monitoring of the hybridization process for troubleshooting), BSA, and herring sperm DNA. It was then hybridized to the probe array during a 16-hour incubation at 45 deg (C). The array was then washed and stained on the Affymetrix fluidic station (using Streptavidin-Phycoerythrin which binds to the biotinylated UTP and CTP incorporated previously in the hybridized cRNA).

scan_protocol: The stained array was scanned on the Affymetrix scanner (450).

data_processing: The GCOS (Gene Operating System) generates the numerical data from the scanned intensities using the MAS 5 software (MicroArray suite 5.0; Affymetrix).

organism: Danio rerio

source_name: pineal glands at CT22, after light exposure

label_protocol: Double-strand cDNA was generated from 10-100 ng of mRNA by using a T7-linked oligo(dT) primer (Affymetrix). After second-strand synthesis, in vitro transcription was performed with MEGAscript® T7 Kit (Ambion, Inc.). The cRNA (600ng) was then used for second cycle first-strand cDNA (Affymetrix) by using a T7-linked oligo(dT) primer (Affymetrix). After 2nd cycle - second-strand synthesis, in vitro transcription was again performed; this time biotinylated UTP and CTP (Affymetrix) were incorporated in the cRNA, resulting in approximately 1800-fold amplification of labeled RNA.

growth_protocol: Adult zebrafish were raised in a light- and temperature-controlled recirculation water system under a 12-h light/12-h dark cycle at 28 °C and fed twice a day.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy, Qiagen).

treatment_protocol: Fish were transferred to constant darkness (DD) at the end of the day prior to the experiment. Fish were exposed to a 1-hr light pulse (light intensity of 12 W/m2) prior to sampling (light treatment) or kept under constant darkness for control (dark treatment). The tissues were collected from light- and dark-treated fish at 6 time points with 4-hr intervals throughout one daily cycle, corresponding to CT2, 6, 10, 14, 18 and 22. Fish were anesthetized in 1.5 mM Tricane (Sigma) and sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. 12 pineal glands were collected and pooled at each time point.

value: light exposure

tag: time point

tag: tissue

value: pineal gland

tag: gender

value: males and females

value: adult (0.5-1.5 years old)

value: Tg(aanat2:EGFP)Y8 transgenic zebrafish


title: Pineal_Light_CT10

source_name: pineal glands at CT10, after light exposure

tag: age


title: MCL cells_pan-PI3K inhibitor treated_biological rep1


title: Pineal_Light_CT14

source_name: pineal glands at CT14, after light exposure


title: Pineal_Light_CT2

source_name: pineal glands at CT2, after light exposure


title: recurrent Breast cancer 25

source_name: recurrent Breast cancer

value: recurrent Breast cancer


title: Pineal_Light_CT18

source_name: pineal glands at CT18, after light exposure


title: Pineal_Dark_CT22

source_name: pineal glands at CT22, constant darkness

value: constant darkness


title: Pineal_Light_CT6

source_name: pineal glands at CT6, after light exposure


title: HUVEC_1

city: Buffalo

first: Thomas

middle: R

last: Cimato

state: New York

address: Clinical and Translational Research Center

department: Medicine/Cardiovascular Medicine

institute: SUNY at Buffalo School of Medicine and Biomedical Sciences

hyb_protocol: Cy3-labeled cRNA (1.65 µg) was hybridized per individual 44K array on Human (G4112F) whole-genome microarrays for 17 hours at 65C

scan_protocol: Slides were scanned using the Agilent Scan Control 7.0 software and data extracted with Feature Extraction 9.1 software.

data_processing: Data processing was perfomred in R/Bioconductor using the Agi4x44PreProcess library. Background correction was performed using the 'half' algorithm, quantile normalization using raw mean signal ('MeanSignal') and median local background ('BGMedianSignal') measures, respectively. Probe filtration was performed using filter.probes using recommended settings. Probe summarization using 'summarize.probe'. The expression matrix was then assembled into an expression set object (Bioconductor 'biobase').

source_name: HUVECs

label_protocol: Cy3-CTP labeled cRNA was produced from 200 ng of total RNA using the Agilent Low RNA Input Liner Amplification kit.

growth_protocol: WiCell H14 hESCs were differentiated as follows: Briefly, cells were passaged from MEF feeders (hESCs) using collagenase IV, or from Matrigel coated dishes (hiPSCs) using dispase. Stem cell colonies were gently triturated into small aggregates of cells in the presence of the Rho-associated kinase (ROCK) inhibitor Y-27632 (10µM, Sigma) and plated at a density of 5000 cells/cm2 on ultra-low attachment six well cluster culture dishes (Corning) in Neurobasal/DMEM-F12 medium supplemented with 10ng/mL of BMP4, bFGF, and VEGF-A (R&D Systems, Minneapolis, MN) for five days and immunostained for NRP1 and CD34.      Cells were dissociated to single cell suspension using 0.05% Trypsin-EDTA (Invitrogen) and resuspended in DMEM/F12 medium containing HEPES (Invitrogen) supplemented with 10% fetal bovine serum. Cells were stained with conjugated antibodies at a 1:10 dilution for one hour at 4degC prior to cell sorting on a BD FACS Aria. Matched fluorescence minus-one controls were used to set appropriate gates following forward and side-scatter based gating and doublet discrimination to exclude dead cells and debris respectively. Antibodies for cell sorting were NRP-1 APC (clone AD5-17F6, Miltenyi Biotec, Auburn CA), CD34-FITC (clone 581, BD Biosciences), mouse IgG-FITC (BD Biosciences), and mouse IgG1-APC (Miltenyi Biotec). Immediately following cell sorting, RNA was extracted from NRP1+CD34+ and NRP1+CD34- sorted cells using TRIzol (Invitrogen). RNA was also extracted from WiCell H14 hESCs and HUVECs (passage 3) for controls in microarray analysis.

extract_protocol: Trizol (Invitrogen)

tag: cell

value: HUVECs


title: Pineal_Dark_CT18

source_name: pineal glands at CT18, constant darkness


title: Pineal_Dark_CT10

source_name: pineal glands at CT10, constant darkness


title: Pineal_Dark_CT14

source_name: pineal glands at CT14, constant darkness


title: NRP1posCD34neg_2

source_name: human hES cell derived

value: NRP1+CD34- cells


title: 1345-BP-92

value: 0 days

value: PBMC


title: Pineal_Dark_CT6

source_name: pineal glands at CT6, constant darkness


title: NRP1posCD34neg_3


title: MCL cells_untreated_ biological rep2

value: Primary MCL cells


title: NRP1posCD34neg_1


title: Pineal_Dark_CT2

source_name: pineal glands at CT2, constant darkness


title: NRP1posCD34pos_2

value: NRP1+CD34+ cells


title: NRP1posCD34pos_1


title: hES_1

value: hES cells (undifferentiated)


title: Patient 17 visit 2

city: Oklahoma City

first: Bart

state: OK

institute: OMRF

description: total RNA

hyb_protocol: cRNA was hybridized overnight to Illumina Human WG-6_v3 Expression BeadChips. Microarrays were washed to high stringency and following the manufacturer's directions and labeled with streptavidin -Cy3.

scan_protocol: Microarrays were scanned using an Illumina BeadArray Reader

data_processing: Raw signal intensities and detection p-values were obtained from the scanner using Illumina BeadStudio software. JMP Genomics v 3.2 software was used to quantile normalize and log (base 2) transform the data for the matrix normalized results.

source_name: PBMC

label_protocol: 250 ng of total RNA from each sample was labeled using the Illumina Total Prep RNA Amplification Kit following manufacturer's directions (Ambion).

extract_protocol: Total RNA was extracted from Trizol reagent according to the manufacturer's directions (Invitrogen). RNA was further purified using RNeasy MinElute Cleanup kit (QIAGEN, Valencia, CA) including a DNA digest according to the manufacturer's instructions.

treatment_protocol: Whole blood was drawn into 10-ml citrated CPT tubes (Becton Dickinson). Peripheral blood mononuclear cells (PBMC) were separated from granulocytes and red blood cells by density-gradient centrifugation and then were collected and placed immediately in TRIzol® reagent.

tag: flare status

value: flare


title: Patient 16 visit 1

description: total RNA

value: no flare


title: Competition VII: t24 colony T vs Ref

city: Lausanne

first: Yannick

last: Wurm

address: Biophore

department: Ecology and Evolution

country: Switzerland

institute: University of Lausanne

description: Competition VII. lost

hyb_protocol: Hybridization buffer (3x SSC, 0.18% SDS, 200 ng/μl yeast tRNA, 200 ng/µl polyA DNA; final concentration) was added to samples; samples were denatured, applied to microarrays, and hybridized overnight at 64°C. After hybridization, slides were washed sequential.

scan_protocol: Scanner: Agilent Technologies microarray scanner. Image quantification GenePix 5.1

data_processing: In brief, median signal and background levels for each probe were extracted from scanned microarray images using Axon Genepix software. Subsequently, the 18,444 Solenopsis invicta cDNA spots yielding a single PCR band (Wang et al. 2007) and passing visual and automated inspection were used for normalization and quality control. The limma 2.16 package (Smyth 2004) in Bioconductor (The R Development Core Team 2007; Gentleman et al. 2004) was used for normexp background correction, print-tip loess normalization within arrays, and aquantile normalization between arrays. Afterwards (but not visible here on GEO), the arrayQualityMetrics package (Kauffmann et al. 2009) and custom R scripts were used for quality control.  All statistical analyses were performed in R 2.9.0 (The R Development Core Team 2007).

organism: Solenopsis invicta

source_name: lost

label_protocol: Total RNA was amplified using the Ambion Message Amp II kit. Amplified RNA plus Alien spike control RNAs (Stratagene) were labeled using the indirect aa-dUTP labeling method. Reverse transcription primers: random 9mers.

growth_protocol: Monogyne S. invicta fire ant colonies, each containing at least 50 winged virgin queens and between 5,000 and 10,000 workers, were collected from a single population in Athens and Lexington, GA, USA in June 2006. There is genetic variability between colonies, however it is moderate because only few queens founded the North American S. invicta population when they were introduced from South America in the 1930s (Ross et al., 1993; Ross and Shoemaker, 2008). All colonies were returned to the laboratory and reared for one month under standard conditions (Jouvenaz et al., 1977). Queen- and male-destined brood were identified by their large size and removed weekly to ensure that only field-reared queens be used in for our experiment. Indeed, laboratory-reared queens do not normally grow to the same sizes as field-reared queens and rarely shed wings or initiate reproductive development after orphaning

extract_protocol: Our aim was to identify molecular markers that are likely to be responsible for post-orphaning differences in the likelihood of becoming a replacement queen (winners vs. losers) and that affect speed of wing shedding in virgin queens (faster vs. slower). However, by the time a queen can be assigned to these phenotype categories, the molecular changes responsible for that phenotype may have passed, and in case of losers, the queen is dead. Thus, we followed an indirect approach which consisted in comparing sisters of winning and losing queens on one hand, and sisters of faster and slower queens on the other hand. For this, examined gene expression using microarrays in orphaned virgin queens 24 hours after orphaning as follows. From the foraging area of each of the sixteen queen donor colonies that were used for competitions, we haphazardly collected five virgin queens for which we simulated orphaning by transferring them into individual colony fractions made up of 2g of mixed workers and brood in 10cm diameter petri dishes. Twenty-four hours after simulated orphaning, all queens were individually flash-frozen with liquid nitrogen in tubes containing 1g of 1.4mm Zirconium Silicate beads (QuackenBush). Samples werethen stabilized until RNA isolation by the addition of 900μl of Trizol reagent (Invitrogen), followed by homogenization with a FastPrep instrument (MP Biomedicals) and storage at -80°C. Using the Trizol protocol, total RNA was isolated from all individuals. RNA was pooled from 5 individuals per queen donor colony and treated with DNA-free (Ambion). Subsequently, impurities were filtered away with MicroCon-30 spin columns (Millipore), and RNA quality was assessed on a 1% agarose gel prior to linear amplification using the MessageAmp II kit (Ambion). Amplified mRNA samples from the 16 donor colonies were labeled with Cy3 and hybridized against Cy5-labeled “common reference” RNA to microarrays made from 22,560 independent fire ant cDNA spots, and scanned as previously described (Wang et al. 2008). For all procedures, precautions including randomization of sample order were taken to avoid introducing unwanted biases.

treatment_protocol: We determined the speed at which virgin queens shed their wings after orphaning, ranked the colonies by speed from fastest to slowest and subsequently conducted eight competitions between additional queens from eight pairs of of faster and slower colonies. For this we haphazardly collected 10 queens from the foraging area of a faster colony as well as from the paired slower colony. We immediately transferred these 20 queens into one of the queenless receiving colonies. This was repeated for each of the eight pairs of queen donor colonies. After 21 days, all surviving queens were collected. Their heads and thoraces were transferred to 1.5ml tubes for genotyping (below); their abdomens were dissected to compare reproductive status between surviving queens within each competition. We qualitatively compared ovarian development between surviving queens within each competition and designated the queen or queens with the strongest ovarian development as the winning queen or queens. In several competitions, two or more queens had similarly strongly developed ovaries. In one competition, no surviving queens could be found. We used microsatellite genotyping to identify which queen donor colonies the surviving queens originated from. In all but one competition in which the two winning queens did not originate from the same queen donor colony and one competition where no queens survived, we designated the winning colony as the queen donor colony from which the winning queen or queens originated. We thus retained the results for six pairs of colonies.

tag: colony

value: colony T

tag: rna source

value: pooled RNA from five sister virgin queens

source_name: Reference RNA

tag: reference

value: pooled RNA from many S. invicta ants of all castes and stage


title: Competition VII: t24 colony F vs Ref

description: Competition VII. won

source_name: won

value: colony F


title: Competition III: t24 colony A vs Ref

description: Competition III. lost

value: colony A


title: Competition V: t24 colony R vs Ref

description: Competition V. lost

value: colony R


title: Competition VIII: t24 colony U vs Ref

description: Competition VIII. won

value: colony U


title: Competition V: t24 colony C vs Ref

description: Competition V. won

value: colony C


title: Patient 14 visit 1

description: total RNA


title: Competition I: t24 colony K vs Ref

description: Competition I. lost

value: colony K


title: Patient 15 visit 2

description: total RNA


title: Patient 17 visit 1

description: total RNA


title: Patient 16 visit 2

description: total RNA


title: Competition II: t24 colony D vs Ref

description: Competition II. won

value: colony D


title: Competition II: t24 colony H vs Ref

description: Competition II. lost

value: colony H


title: Patient 15 visit 1

description: total RNA

value: PBMC


title: Patient 14 visit 2

description: total RNA


title: CPE7

source_name: CPE7, YPD, 24h

value: Traditional cachaça fermentations in Brazil

value: reference strain


title: Patient 13 visit 1

description: total RNA


title: Competition VIII: t24 colony E vs Ref

description: Competition VIII. lost

value: colony E


title: Patient 12 visit 1

description: total RNA


title: LmycKO2_CD8anegDC

city: Saint Louis

first: Kenneth

middle: M

last: Murphy

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine

hyb_protocol: Hybed onto Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: standard Affymetrix protocol

data_processing: Data was analyzed using DNASTAR Arraystar software.

label_protocol: Ambion WT Expression kit, Genechip WT Terminal Labeling and Controls Kit

growth_protocol: Primary splenocytes were harvested by digestion with Collagenase B and DNAse1

extract_protocol: Bone marrow pDCs were sorted as CD11c+SiglecH+B220+, splenic CD8a+ DCs were sorted as CD11c+MHCII+CD24+CD172a-B220-, splenic CD8a- DCs were sorted as CD11c+MHCII+CD172a+CD24-B220-

treatment_protocol: Mice were analyzed at steady-state unless indicated. For short-term ex vivo culture and stimulation, CD8a+ DCs were purified by cell sorting and plated in flat-bottom tissue-culture treated plates at a density of 105 per 200 microL; CD8a+ DCs were stimulated with 10 ng/ml GM-CSF (Peprotech) for 24 hours.

value: CD8a- DCs

tag: genetic background

tag: genotype

value: Spleen


title: LmycKO_BMpDC

tag: cell type

value: DC

value: Bone marrow


title: Patient 13 visit 2

description: total RNA

value: flare


title: Competition III: t24 colony N vs Ref

description: Competition III. won

value: colony N

value: pooled RNA from five sister virgin queens

value: pooled RNA from many S. invicta ants of all castes and stage


title: Patient 12 visit 2

description: total RNA


title: Patient 11 visit 2

description: total RNA


title: Competition I: t24 colony Q vs Ref

description: Competition I. won

value: colony Q


title: Patient 11 visit 1

description: total RNA

value: no flare


title: WT_BMpDC

value: wt


title: WT2_CD8anegDC


title: WT1_CD8anegDC


title: LmycKO1_CD8anegDC


title: Patient 7 visit 2

description: total RNA


title: Patient 9 visit 1

description: total RNA


title: WT2_CD8aDC

value: CD8a+ DCs


title: Patient 10 visit 1

description: total RNA


title: Patient 8 visit 2

description: total RNA


title: Patient 9 visit 2

description: total RNA


title: LmycKO2_CD8aDC


title: LmycKOCD8aDC_GM1

value: GM-CSF


title: Patient 7 visit 1

description: total RNA

value: PBMC


title: Patient 8 visit 1

description: total RNA


title: WTCD8aDC_GM3


title: Patient 6 visit 2

description: total RNA


title: LmycKO1_CD8aDC


title: LmycKOCD8aDC_Media

value: media


title: LmycKOCD8aDC_GM2


title: Patient 4 visit 2

description: total RNA


title: LmycKOCD8aDC_GM3


title: Patient 5 visit 2

description: total RNA


title: WTCD8aDC_Media


title: Patient 6 visit 1

description: total RNA


title: WTCD8aDC_GM1


title: Patient 5 visit 1

description: total RNA


title: Patient 4 visit 1

description: total RNA


title: E18 retina ECCM treated (biological Rep 2)

city: Omaha

first: Iqbal

last: Ahmad

state: Nebraska

address: 985840 Nebraska Medical Center

department: Ophthalmology and Visual Sciences

institute: University of Nebraska Medical Center

description: Gene expression data from retinal neurospheres obtained from embryonic day 18 retina cells cultured in EGF and endothelial cell conditioned medium.

hyb_protocol: The samples were hybridized on Rat Affymetrix 230 2.0 gene chip as per manufacturer's instruction.

scan_protocol: Gene chips were scanned as per manufacturer's protocol using Affymetrix Genechip 3000 7G scanner to generate .CEL files.

data_processing: The data were processed using GenePattern. CEL files were subjected to RMA normalization and log2 transformation.

source_name: E18 retinal neurospheres treated with Endothelial cell conditioned medium

label_protocol: Biotinylated cRNA were prepared as per manufacturers suggestion with the Genechip 3'IVT expression kit (Affymetrix).

growth_protocol: Timed pregnant Sprague dawley  rats were obtained from Charles River Laboratory. Embryonic day 18 embryos were harvested

extract_protocol: Total RNA was extracted with Qiagen Rneasy mini kit according to the manufacturer's instructions.Concentration and integrity were tested by spectrophotometry and Bioanalyzer analyses.

treatment_protocol: Embryos were enucleated and retinae dissected out. Retinal cells were obtained by treating retinae with trypsin -EDTA digestion followed by mechanical tituration. Retinal cell dissociates were grown as neurospheres.

value: embryonic day 18 retina

tag: strain

value: Sprague Dawley

value: ECCM

value: retinal cells


title: E18 retina ECCM treated (biological Rep 1)


title: WTCD8aDC_GM2

value: Spleen


title: Patient 3 visit 2

description: total RNA


title: Patient 2 visit 1

description: total RNA


title: Patient 3 visit 1

description: total RNA


title: Patient 2 visit 2

description: total RNA


title: Patient 1 visit 2

description: total RNA


title: Patient 1 visit 1

description: total RNA


title: E18 retina EGF treated (biological Rep 1)

description: Gene expression data from retinal neurospheres obtained from embryonic day 18 retina cells cultured in EGF.

source_name: E18 retinal neurospheres treated with EGF

value: EGF


title: MN_UT_96h_ROC-UPS_3

status: Public on Dec 13 2013

city: Duluth

first: Jason

last: Berninger

address: 6201 Congdon Blvd

department: NHEERL

institute: US EPA

hyb_protocol: Microarrays were hybridized following the manufacturer’s guidelines for One-Color Microarray-Based Gene Expression Analysis (version 5.7; Agilent)

scan_protocol: Microarrays were scanned with a SureScan High-Resolution Microarray scanner G2505 C (Agilent).

data_processing: Data were extracted from microarray images using Feature Extraction Software (Agilent).

organism: Pimephales promelas

source_name: ovary from female fish exposed to upstream Site R 4d

label_protocol: One μg of total RNA from each sample was used in complementary RNA synthesis, complementary RNA labeling, amplification, and hybridizations as recommended in the manufacturer’s kits and protocols (Quick Amp labeling kit; Agilent).

growth_protocol: The fish were held in a mini-mobile experimental unit at 25+1ºC, with aeration, and were fed frozen adult brine shrimp twice daily (San Francisco Bay Brand, Newark, CA, USA).  Fish used for the experiment were from an on-site culture, and all procedures involving animals conformed to guidelines approved by the local Animal Care and Use Committee.

extract_protocol: Total RNA was isolated from ovary tissue of fathead minnow using RNeasy kits (Qiagen, Valencia, CA). RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) and RNA was quantified spectrophotometrically (Nanodrop, Wilmington, DE). Total RNA samples were stored at -80°C until used for microarray analyses.

treatment_protocol: The fish were expose to site water based on one of three locations, upstream, effluent, or downstream.  For site R and H, site water was pumped through the system at a rate of 2-3 exchanges per day for 4 days.  For Site E, flow through was not logistically possible, so water exchanges (>95%) were done twice daily, so that the total water exchange rate between flow throught and static systems were equivalent.

value: ovary


title: MN_UT_96h_ROC-UPS_5


title: MN_UT_96h_ROC-UPS_1


title: E18 retina EGF treated (biological Rep 2)


title: MN_UT_96h_ROC-EFFL_6

source_name: ovary from female fish exposed to effluent Site R 4d


title: MN_UT_96h_ROC-EFFL_5


title: MN_UT_96h_ROC-DNS_4

source_name: ovary from female fish exposed to downstream Site R 4d


title: MN_UT_96h_HUT-UPS_6

source_name: ovary from female fish exposed to upstream Site H 4d


title: MN_UT_96h_ROC-DNS_1


title: MN_UT_96h_ROC-EFFL_4


title: MN_UT_96h_ROC-EFFL_2


title: MN_UT_96h_ROC-UPS_2


title: MN_UT_96h_ROC-EFFL_3


title: MN_UT_96h_HUT-UPS_5


title: MN_UT_96h_ROC-UPS_4


title: MN_UT_96h_ROC-DNS_2


title: MN_UT_96h_ROC-EFFL_1


title: MN_UT_96h_ROC-DNS_6


title: MN_UT_96h_ROC-DNS_3


title: MN_UT_96h_ROC-DNS_5


title: MN_UT_96h_ROC-UPS_6


title: MN_UT_96h_HUT-UPS_3


title: MN_UT_96h_HUT-UPS_4


title: MN_UT_96h_HUT-UPS_2


title: MN_UT_96h_HUT-UPS_1


title: MN_UT_96h_HUT-EFFL_5

source_name: ovary from female fish exposed to effluent Site H 4d


title: MN_UT_96h_HUT-DNS_4

source_name: ovary from female fish exposed to downstream Site H 4d


title: MN_UT_96h_HUT-DNS_2


title: MN_UT_96h_HUT-DNS_3


title: MN_UT_96h_HUT-DNS_6


title: MN_UT_96h_HUT-EFFL_4


title: MN_UT_96h_HUT-EFFL_6


title: Patient 10 visit 2

description: total RNA

value: flare


title: MN_UT_96h_HUT-DNS_5


title: MN_UT_96h_HUT-EFFL_3


title: MN_UT_24h_ELY-UPS_1

source_name: ovary from female fish exposed to upstream Site E 4d


title: MN_UT_24h_ELY-UPS_4


title: MN_UT_96h_HUT-DNS_1


title: MN_UT_24h_ELY-UPS_5


title: MN_UT_96h_HUT-EFFL_2


title: MN_UT_24h_ELY-UPS_3


title: MN_UT_24h_ELY-EFFL_6

source_name: ovary from female fish exposed to effluent Site E 4d


title: MN_UT_24h_ELY-UPS_2


title: MN_UT_24h_ELY-EFFL_2


title: WT1_CD8aDC


title: MN_UT_96h_HUT-EFFL_1


title: MN_UT_24h_ELY-EFFL_5


title: MN_UT_24h_ELY-EFFL_3


title: MN_UT_24h_ELY-UPS_6


title: MN_UT_24h_ELY-DNS_3

source_name: ovary from female fish exposed to downstream Site E 4d


title: MN_UT_24h_ELY-DNS_5


title: MN_UT_24h_ELY-DNS_2


title: MN_UT_24h_ELY-EFFL_1


title: MN_UT_24h_ELY-EFFL_4


title: MN_UT_24h_ELY-DNS_4


title: 118-7h-sample4-BLOCK4

city: Nijmegen

first: Jeroen

middle: Daniel

last: Langereis

address: PO Box 9101

department: Department of Pediatrics

country: Netherlands

institute: Radboud University Medical Centre

description:
118_7h_4_4
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416654_A03_118_7_4_2011-05-13_532_gridded.pair
416654_A03_118_7_4_2011-05-13_532_gridded_norm_RMA.pair

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Haemophilus influenzae R2866

source_name: R2866Δ112 mutant  7 hours

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: NTHi strain R2866 was grown in supplemented brain-heart infusion medium for 7 hours.

extract_protocol: Bacteria were washed with PBS and total RNA was extracted with the RNeasy minikit (Qiagen) and was DNase treated (Ambion).

treatment_protocol: Growth of the R2866 wild-type and R2866Δ0112 gene mutant was compared.

tag: genotype/variation

value: R2866_0112 gene deletion mutant

value: 7 hours


title: 118-7h-sample4-BLOCK3

description:
118_7h_4_3
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416654_A03_118_7_4_2011-05-13_532_gridded.pair
416654_A03_118_7_4_2011-05-13_532_gridded_norm_RMA.pair


title: 118-7h-sample4-BLOCK2

description:
118_7h_4_2
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416654_A03_118_7_4_2011-05-13_532_gridded.pair
416654_A03_118_7_4_2011-05-13_532_gridded_norm_RMA.pair


title: 118-7h-sample4-BLOCK1

description:
118_7h_4_1
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416654_A03_118_7_4_2011-05-13_532_gridded.pair
416654_A03_118_7_4_2011-05-13_532_gridded_norm_RMA.pair


title: 118-7h-sample3-BLOCK4

description:
118_7h_3_4
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416694_A03_118_7_3_2011-05-13_532_gridded.pair
416694_A03_118_7_3_2011-05-13_532_gridded_norm_RMA.pair


title: MN_UT_24h_ELY-DNS_1


title: 118-7h-sample3-BLOCK3

description:
118_7h_3_3
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416694_A03_118_7_3_2011-05-13_532_gridded.pair
416694_A03_118_7_3_2011-05-13_532_gridded_norm_RMA.pair


title: 118-7h-sample3-BLOCK2

description:
118_7h_3_2
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416694_A03_118_7_3_2011-05-13_532_gridded.pair
416694_A03_118_7_3_2011-05-13_532_gridded_norm_RMA.pair


title: Wild-type mouse at 24 months, biological replicate 1

city: Stony Brook

first: Dmitri

middle: V

last: GNATENKO

address: T15/053 HSC SUNY

department: Medicine

institute: Stony Brook University

description:
Mouse-HCC_WT4
Gene expression data in liver of 24-month-old wild-type mouse.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix 7G scanner.

data_processing: The data were analyzed using R bioconductor Simpleaffy package based on Robust Multichip Average (RMA) method. Data were further converted to gene symbols by averaging over duplicated probes later.

source_name: Mouse wild-type control at 24 months

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

growth_protocol: Both IQGAP2 -/- and wild-type mouse lines were maintained on 129J background, fed regular diet, housed in pathogen-free rooms in an environment with controlled temperature, humidity, and a 12 h light/dark cycle. The study was approved by the Stony Brook University Institutional Animal Care and Use Committee.

treatment_protocol: At the age specified, mice were humanely euthanized in accordance with the institutional guidelines, their livers immediately excised and submerged in liquid nitrogen until total RNA isolation.

tag: strain/background

value: wild-type

value: male

value: 24 months

value: normal liver


title: Wild-type mouse at 6 months, biological replicate 1

description:
Mouse-HCC_WT1
Gene expression data in liver of 6-month-old wild-type mouse.

source_name: Mouse wild-type control at 6 months

value: 6 months


title: Wild-type mouse at 24 months, biological replicate 2

description:
Mouse-HCC_WT5
Gene expression data in liver of 24-month-old wild-type mouse.


title: Wild-type mouse at 6 months, biological replicate 3

description:
Mouse-HCC_WT3
Gene expression data in liver of 6-month-old wild-type mouse.


title: Wild-type mouse at 6 months, biological replicate 2

description:
Mouse-HCC_WT2
Gene expression data in liver of 6-month-old wild-type mouse.


title: Knockout mouse at 24 months, biological replicate 1

description:
Mouse-HCC_KO4
Gene expression data in HCC tumor in liver of 24-month-old IQGAP2 knockout mouse.

source_name: Mouse IQ-GAP2 knockout liver at 24 months

value: IQGAP2 knockout

value: hepatocellular carcinoma (HCC) tumor


title: Knockout mouse at 6 months, biological replicate 3

description:
Mouse-HCC_KO3
Gene expression data in liver of 6-month-old IQGAP2 knockout mouse.

source_name: Mouse IQ-GAP2 knockout liver at 6 months


title: Knockout mouse at 6 months, biological replicate 2

description:
Mouse-HCC_KO2
Gene expression data in liver of 6-month-old IQGAP2 knockout mouse.


title: 118-7h-sample3-BLOCK1

description:
118_7h_3_1
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416694_A03_118_7_3_2011-05-13_532_gridded.pair
416694_A03_118_7_3_2011-05-13_532_gridded_norm_RMA.pair

tag: time


title: Wild-type mouse at 24 months, biological replicate 3

description:
Mouse-HCC_WT6
Gene expression data in liver of 24-month-old wild-type mouse.


title: Knockout mouse at 24 months, biological replicate 2

description:
Mouse-HCC_KO5
Gene expression data in HCC tumor in liver of 24-month-old IQGAP2 knockout mouse.


title: Soybean_imbibition_8hr_1

city: Tokyo

first: Tomoko

last: TAMURA

address: 1-1-1 Sakuragaoka Setagaya-ku

department: Nutritional Science and Food Safety

country: Japan

institute: Tokyo University of Agriculture

description: Gene expression after 8hr imbibed seed

hyb_protocol: Cy3-labeled cRNA (1.65 μg) was fragmented to an average size of about 50–100 nucleotides and then hybridized for 17 h at 65°C to an soybean oligonucleotide microarray slide. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned in Cy3 channel with the Agilent DNA Microarray Scanner (Agilent).

data_processing: Signal intensity per spot was generated from the scanned image with Agilent scan control 8.0 software according to Agilent Technologies standard operation procedures. Spots that did not pass quality control procedures were flagged as Not Detected. The scanned images were analyzed using commercial software (Gene spring GX11.5) as follows: (i) Gene expression more than seven of eight samples were Not detect, the gene was excluded, (ii) threshold raw signals were set at unify, and (iii) submitted to 75th percentile normalization.

organism: Glycine max

label_protocol: Total RNAs (200 ng) of 0-, 8-, and 16-h imbibed-samples were amplified with a low RNA Input Quick Amp Labeling Kit fluorescent linear amplification kit, one-color (Agilent Technologies).

growth_protocol: About 30 dry seeds of Glycine max (cv. Suzumaru) were soaked in 1 % hypochlorous acid, and then washed in water. They were then placed on moistened absorbent cotton and made to germinate in the dark at 25 °C.

extract_protocol: Total RNA (3 samples/stage) was extracted from frozen samples using an RNeasy plant mini kit (Qiagen, Tokyo, Japan) and purified using the same kit. RNA quality and quantification were checked using the Agilent 2100 bioanalyzer (Agilent Technologies) and NanoDrop ND-2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

treatment_protocol: The beans were imbibed more than 0.06 g water, the 8 h-imbibed-seeds were used for sample. Whether beans were germinated or imbibed more than 0.33 g, the 16 h-imbibed-seeds were used for sample. The 24, 32, 40, and 48 h-imbibed-seeds were collected, which grew up to more than 2, 5, 15, and 20 mm in radicle length, respectively. About 20-25 seeds at each imbibition stage were collected, trichotomized, and milled with solid CO2 individually. All the samples were stored at -80°C to being used.

value: whole seed

tag: cultivar

value: Suzumaru


title: Knockout mouse at 24 months, biological replicate 3

description:
Mouse-HCC_KO6
Gene expression data in HCC tumor in liver of 24-month-old IQGAP2 knockout mouse.


title: Soybean_imbibition_16hr_1

description: Gene expression after 16hr imbibed seed


title: Soybean_dryseed_1

description: Gene expression after 0hr imbibed seed


title: Soybean_imbibition_16hr_2

description: Gene expression after 16hr imbibed seed


title: Soybean_imbibition_16hr_3

description: Gene expression after 16hr imbibed seed


title: Soybean_dryseed_2

description: Gene expression after 0hr imbibed seed


title: 118-7h-sample2-BLOCK2

description:
118_7h_2_2
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416566_A03_118_7_2_2011-05-13_532_gridded.pair
416566_A03_118_7_2_2011-05-13_532_gridded_norm_RMA.pair


title: 118-7h-sample2-BLOCK1

description:
118_7h_2_1
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416566_A03_118_7_2_2011-05-13_532_gridded.pair
416566_A03_118_7_2_2011-05-13_532_gridded_norm_RMA.pair


title: 118-7h-sample2-BLOCK4

description:
118_7h_2_4
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416566_A03_118_7_2_2011-05-13_532_gridded.pair
416566_A03_118_7_2_2011-05-13_532_gridded_norm_RMA.pair


title: Knockout mouse at 6 months, biological replicate 1

description:
Mouse-HCC_KO1
Gene expression data in liver of 6-month-old IQGAP2 knockout mouse.


title: 118-7h-sample1-BLOCK2

description:
118_7h_1_2
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416693_A03_118_7_1_2011-05-13_532_gridded.pair
416693_A03_118_7_1_2011-05-13_532_gridded_norm_RMA.pair


title: Soybean_imbibition_8hr_3

description: Gene expression after 8hr imbibed seed


title: 118-7h-sample2-BLOCK3

description:
118_7h_2_3
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416566_A03_118_7_2_2011-05-13_532_gridded.pair
416566_A03_118_7_2_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample4-BLOCK4

description:
WT_7h_4_4
This sample is wild-type Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416654_A01_WT_7_4_2011-05-13_532_gridded.pair
416654_A01_WT_7_4_2011-05-13_532_gridded_norm_RMA.pair

source_name: Wild-type 7 hours

value: Wild-type


title: 118-7h-sample1-BLOCK1

description:
118_7h_1_1
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416693_A03_118_7_1_2011-05-13_532_gridded.pair
416693_A03_118_7_1_2011-05-13_532_gridded_norm_RMA.pair


title: 118-7h-sample1-BLOCK3

description:
118_7h_1_3
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416693_A03_118_7_1_2011-05-13_532_gridded.pair
416693_A03_118_7_1_2011-05-13_532_gridded_norm_RMA.pair


title: 118-7h-sample1-BLOCK4

description:
118_7h_1_4
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416693_A03_118_7_1_2011-05-13_532_gridded.pair
416693_A03_118_7_1_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample4-BLOCK2

description:
WT_7h_4_2
This sample is wild-type Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416654_A01_WT_7_4_2011-05-13_532_gridded.pair
416654_A01_WT_7_4_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample4-BLOCK1

description:
WT_7h_4_1
This sample is wild-type Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416654_A01_WT_7_4_2011-05-13_532_gridded.pair
416654_A01_WT_7_4_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample2-BLOCK4

description:
WT_7h_2_4
This sample is wild-type Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416566_A01_WT_7_2_2011-05-13_532_gridded.pair
416566_A01_WT_7_2_2011-05-13_532_gridded_norm_RMA.pair


title: Soybean_imbibition_8hr_2

description: Gene expression after 8hr imbibed seed


title: WT-7h-sample2-BLOCK3

description:
WT_7h_2_3
This sample is wild-type Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416566_A01_WT_7_2_2011-05-13_532_gridded.pair
416566_A01_WT_7_2_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample3-BLOCK1

description:
WT_7h_3_1
This sample is wild-type Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416694_A01_WT_7_3_2011-05-13_532_gridded.pair
416694_A01_WT_7_3_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample1-BLOCK2

description:
WT_7h_1_2
This sample is wild-type Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416693_A01_WT_7_1_2011-05-13_532_gridded.pair
416693_A01_WT_7_1_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample2-BLOCK2

description:
WT_7h_2_2
This sample is wild-type Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416566_A01_WT_7_2_2011-05-13_532_gridded.pair
416566_A01_WT_7_2_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample3-BLOCK2

description:
WT_7h_3_2
This sample is wild-type Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416694_A01_WT_7_3_2011-05-13_532_gridded.pair
416694_A01_WT_7_3_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample3-BLOCK4

description:
WT_7h_3_4
This sample is wild-type Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416694_A01_WT_7_3_2011-05-13_532_gridded.pair
416694_A01_WT_7_3_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample3-BLOCK3

description:
WT_7h_3_3
This sample is wild-type Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416694_A01_WT_7_3_2011-05-13_532_gridded.pair
416694_A01_WT_7_3_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample1-BLOCK3

description:
WT_7h_1_3
This sample is wild-type Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416693_A01_WT_7_1_2011-05-13_532_gridded.pair
416693_A01_WT_7_1_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample4-BLOCK3

description:
WT_7h_4_3
This sample is wild-type Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416654_A01_WT_7_4_2011-05-13_532_gridded.pair
416654_A01_WT_7_4_2011-05-13_532_gridded_norm_RMA.pair


title: 118-4h-sample4-BLOCK2

description:
118_4h_4_2
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416654_A03_118_4_4_2011-05-13_532_gridded.pair
416654_A03_118_4_4_2011-05-13_532_gridded_norm_RMA.pair

source_name: R2866Δ112 mutant  4 hours

growth_protocol: NTHi strain R2866 was grown in supplemented brain-heart infusion medium for 4 hours.

value: 4 hours