title: ∆cspD1 deletion mutant vs. wild type under high oxygen 45 minutes after oxygen sparging

first: Amy

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

description:
This Sample represents 2 dye-swap samples.
cspD1_0045_H_vs_NRC1d.sig
NRC1d_vs_cspD1_0045_H
09233.csv: delta-cspD1=Alexa 546, WT=Alexa 647
09234.csv: WT=Alexa 546, delta-cspD1=Alexa 647

hyb_protocol: See Baliga et al., Genome Res. 2004 Jun;14(6):1025-35.

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See GPL3739 for details.

data_processing:
AnalyzerDG software for spotfinding. Intensities were normalized between the Alexa 546 and Alexa 647 channels by scaling all intensities in one channel such that the 75th percentile in each channel was made equal.
VERA/SAM normalized log10 ratio (test/reference); see also: Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. 2006. SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics. 7:286.

label: Alexa 546,Alexa 647

organism: Halobacterium salinarum

label_protocol: 5 ug quality-checked total RNA was direct-labeled with Alexa 546 and Alexa 647 dyes according to manufacturer's instructions (Kreatech, Alameda, CA).

growth_protocol: ∆cspD1 mutant and NRC-1 wild type control strain of Halobacterium salinarum were grown to mid-logarithmic phase in batch mode in a New Brunswick BioFlo100 modular bench top fermentor (New Brunswick Scientific) in CM medium as described in (Schmid et al., 2007, Genome Res, 17(10):1399-413.

extract_protocol: RNA was prepared the following day using the Absolutely RNA miniprep kit according to manufacturer’s instructions (Agilent Technologies, Santa Clara, CA). RNA quality was measured using an Agilent Bioanalyzer as described (Schmid et al., 2009, Molecular Systems Biology, 5:282). Freedom from DNA contamination was determined on 200 ng samples of RNA in 25 cycles of PCR.

treatment_protocol: At mid-log phase, oxygen sparging and agitation were stopped to induce anoxia. Cultures were incubated anaerobically overnight, then oxygen was sparged and RNA was collected at time points immediately prior to addition of oxygen and 5, 10, 20, 45, and 180 minutes afterwards.

tag: strain/background

tag: oxygen level

value: high

tag: time (min.)

label: Alexa 647,Alexa 546

value: wild type


title: 201048 - Negative

status: Public on Aug 31 2017

type: genomic

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

country: USA

institute: WRAIR

hyb_protocol: we loaded 2.5 to 6µg DNA to the array

scan_protocol: Scanned on a Agilent Technologies SureScan Microarray Scanner G2600D

data_processing: Images were quantified using Agilent Feature Extraction Software (version11.5.1.1). Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole blood

label_protocol: Total Genomic DNA (5µg) was used as starting material, using the SureTag Complete DNA Labeling Kit (Agilent Technologies).  Labeled DNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA). The IP (sample of interest) samples were labeled with Cy5 and the WEC (reference) were labeled with Cy3.

extract_protocol: We extracted DNA from the PAXgene (Agilent, Inc.) tube; whole blood collected from the volenteers stored in Paxgen tube as per the vendor's recommandation.

tag: gender

value: Male

tag: tissue

value: whole blood

tag: sample type

value: reference

value: IP


title: ∆cspD1 deletion mutant vs. wild type under high oxygen 180 minutes after oxygen sparging

type: RNA

city: Durham

middle: K

institute: Duke University

description:
This Sample represents 2 dye-swap samples.
cspD1_0180_H_vs_NRC1d.sig
NRC1d_vs_cspD1_180_H
09235.csv: delta-cspD1=Alexa 546, WT=Alexa 647
09236.csv: WT=Alexa 546, delta-cspD1=Alexa 647

molecule: total RNA

tag: genotype/variation


title: ∆cspD1 deletion mutant vs. wild type under high oxygen 20 minutes after oxygen sparging

description:
This Sample represents 2 dye-swap samples.
cspD1_0020_H_vs_NRC1d.sig
NRC1d_vs_cspD1_0020_H
09231.csv: delta-cspD1=Alexa 546, WT=Alexa 647
09232.csv: WT=Alexa 546, delta-cspD1=Alexa 647


title: 201009 - Negative


title: 201015 - Negative


title: 201012 - Positive


title: 201018 - Negative


title: ∆cspD1 deletion mutant vs. wild type under high oxygen 10 minutes after oxygen sparging

description:
This Sample represents 2 dye-swap samples.
cspD1_0010_H_vs_NRC1d.sig
NRC1d_vs_cspD1_0010_H
09229.csv: delta-cspD1=Alexa 546, WT=Alexa 647
09230.csv: WT=Alexa 546, delta-cspD1=Alexa 647


title: 201011 - Positive


title: 201008 - Negative


title: 201013 - Postive


title: Putida_Heat_Treated

city: Bangalore

first: Rajagopal

last: Rangeshwaran

state: Karnataka

address: Bellary Road

department: Molecular Entomology

country: India

institute: National Bureau of Agricutural Insect resource

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Pseudomonas putida

source_name: cell pellets, 24 hr culture subjected to heat shock at 45 degrees

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared by RNA using the Agilent's Quick -Amp labeling kit (p/n5190-0442) as per manufacturers  instructions, followed by RNAeasy minikit (QIAGEN, Valencia, CA).  RNA concentration and purity was checked with NanoDrop Spectrophotometer.

growth_protocol: Overnight grown culture of P. putida (NBAII-RPF 9) was inoculated to two sets of 250 ml liquid Luria Bertani medium taken in 500 ml conical flask and incubated  overnight.

extract_protocol: RNA was prepared using the Qiagens Rneasy minikit cat #74104 following manufacturers protocol. The RNA quality was checked using Bioanalyzer

treatment_protocol: One of the overnight grown cultures were subjected to heat shock by incubating the culture at 45 degrees for one hour. The other set was used as control. After the treatment, the cells were collected by centrifugation and pellets were resuspended in phosphate buffer.

tag: isolate

value: NBAII-RPF 9

tag: growth phase

value: Exponential culture

tag: exposed to

value: 45°C for 1hr


title: FBG_336h_pI_rep2

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

hyb_protocol: After fragmentation, the maximum amount of labelled cRNA (2.4 µg) was hybridized to Agilent Mycoplasma hominis GE 8x60k Microarrays (OakLabs GmbH, Berlin, Germany/Agilent Technologies, Boeblingen, Germany) for 48 h at 65 °C.

scan_protocol: Microarrays were scanned as described in the manufacturer´s protocol.

data_processing: Signal intensities on 20 bit tiff images were calculated by Feature Extraction (FE, Vers. 11.0.1.1; Agilent Technologies, Waldbronn, Germany) using a custom grid file (061652_D_F_20140129; OakLabs GmbH, Berlin, Germany). After feature extraction and before any normalization, mycoplasma strain specific oligonucleotide signals were extracted using a specific mask file previously defined by genomic DNA hybridization. Data analyses on the strain specific oligo subsets were conducted with GeneSpring GX (Vers. 12.5; Agilent Technologies). Probe signal intensities were quantile normalized across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples.

organism: Metamycoplasma hominis

label_protocol: Synthesis of cDNA and subsequent fluorescent labelling of cRNA was performed on duplicates of each experimental condition according to the manufacturer´s protocol (Agilent One-Color Microarray-Based Exon Analysis/Low Input Quick Amp WT Labelling Kit; Agilent Technologies, Waldbronn, Germany) with some modifications. Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and incorporation of Cy3-CTP into the nascent cRNA. To compensate for the prominent AT content of mycoplasma, equal volumes (0.24 µl) of Cy3-UTP (Enzo Life Sciences, Lörrach, Germany) were added to the labelling reactions.

growth_protocol: The human cervical carcinoma cell line HeLa S3 (both un-infected and infected by FBG) was cultivated in DMEM medium, and M. hominis FBG was cultivated in arginine-medium.

extract_protocol: Nucleic acids were prepared from each 75 cm2 cell culture flask after washing the adherent HeLa cells with 10 ml PBS twice and subsequent lyses in 650 µl RLT Buffer (RNeasy Kit; Qiagen GmbH, Hilden, Germany). 50 µl lysate was used for genomic DNA preparation (Dneasy Blood and Tissue kit, qiagen) and 600 µl lysate for total RNA preparation (RNeasy kit). Before use of the RNA contaminating traces of DNA were digested with DNase I. Total RNA integrity was checked using an Agilent 2100 Bioanalyzer system (Agilent Technologies, Waldbronn, Germany). All samples of this study showed high quality RNA integrity numbers (RIN 9.2 - 9.8). RNA was further analysed by photometric Nanodrop measurements (Thermo Fisher Scientific GmbH, Dreieich, Germany) and quantified by fluorometric Qubit RNA assays (Life Technologies).

treatment_protocol: In 75 cm2 cell culture flask, HeLa cells (10 million cells) were infected with 50 MOI of FBG for 1 h, 4 h, 48 h and 336 h; each time point in duplicates. Total RNA was purified from each infection assay for microarray-based transcriptome analyses.

tag: strain

value: FBG

tag: post infection (pi) time


title: FBG_336h_pI_rep1


title: ∆cspD1 deletion mutant vs. wild type under high oxygen 5 minutes after oxygen sparging

description:
This Sample represents 2 dye-swap samples.
cspD1_0005_H_vs_NRC1d.sig
NRC1d_vs_cspD1_0005_H
09227.csv: delta-cspD1=Alexa 546, WT=Alexa 647
09228.csv: WT=Alexa 546, delta-cspD1=Alexa 647


title: FBG_4h_pI_rep2


title: FBG_48h_pI_rep2


title: FBG_48h_pI_rep1


title: 201061 - Negative


title: FBG_4h_pI_rep1


title: FBG_1h_pI_rep2


title: 201132 - Negative


title: mTECs, E2f4 ko, day4 3

status: Public on Aug 30 2017

city: New York

first: Munemasa

last: Mori

state: New York

address: Black Building 801

department: Department of Medicine

institute: The Columbia Center for Human Development

description: log2-transformed, RMA-normalized Entrez Gene expression values

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450 with streptavidin-R-phycoerythrin (SAPE) and the signal was amplified using a biotinylated goat anti-streptavidin antibody followed by another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix, Santa Clara, CA).

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Raw Affymetrix CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1) and an Entrez Gene-specific probeset mapping (version 16.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan.

label: Biotin

organism: Mus musculus

source_name: mTECs, 4-hydroxytamoxifen, day4

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

growth_protocol: E2f4f/f; R26-CreERT2 derived mTECs were cultured on transwells and treated with vehicle or 4-hydroxytamoxifen from day -5 to day 0.

extract_protocol: Total RNA was extracted from these samples (total 18) using a RNeasy Mini Kit (Qiagen, #74104)  #74104).

treatment_protocol: Triplicate samples (each 2 wells/sample) of each treatment were incubated at 4 degree with RNA-later (Sigma) overnight at each time point (day 0, day 2, day 4).

value: trachea

tag: state

value: healthy

tag: phenotype

tag: cell type

value: Primary culture of mouse tracheal epithelial cells


title: mTECs, E2f4 ko, day0 2

source_name: mTECs, 4-hydroxytamoxifen, day0


title: FBG_1h_pI_rep1


title: mTECs, E2f4 ko, day4 1


title: mTECs, E2f4 ko, day2 2

source_name: mTECs, 4-hydroxytamoxifen, day2


title: mTECs, E2f4 ko, day4 2


title: mTECs, wt, day4 3

source_name: mTECs, vehicle, day4


title: mTECs, E2f4 ko, day2 1


title: mTECs, wt, day4 2


title: day4_adult_fasting

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

description: Gene expression data from day 4 adult worms.

hyb_protocol: Biotin labbeled samples were hybridized for 16 hr at 45C on GeneChip miRNA 4.0 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: Affymetrix Expression Console

label: biotin

organism: Caenorhabditis elegans

label_protocol: FlashTag™ Biotin HSR

growth_protocol: WT worms were maintained at 20 °C on nematode growth medium (NGM) plates seeded with Escherichia coli OP50.

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

treatment_protocol: The day on which the animals were transferred to FUDR-containing NGM plates was defined as t = 0 day. On day 2, the animals were transferred to FUDR-containing NGM plates that were seeded with or without UV-killed OP50.

tag: age

value: day 4 adult worm

value: wild type (N2)

tag: condition

value: fasting


title: day2_adult

description: Gene expression data from day 2 adult worms.

value: day 2 adult worm


title: mTECs, wt, day2 1

source_name: mTECs, vehicle, day2


title: mTECs, E2f4 ko, day2 3


title: mTECs, wt, day2 2


title: mTECs, E2f4 ko, day0 1


title: mTECs, E2f4 ko, day0 3


title: day4_adult_fed

value: fed


title: mTECs, wt, day2 3

value: wild type


title: mTECs, wt, day0 3

source_name: mTECs, vehicle, day0


title: gland cistern 3 h S. aureus infected, animal 12

city: Dummerstorf

first: Juliane

last: Guenther

address: Wilhelm-Stahl-Allee 2

institute: Leibniz-Institute for Farm Animal Biology (FBN)

description: 3 h infected gland cistern of an animal whose three udder quarter were sequentially infected for 1, 2 and 3 h with S. aureus

hyb_protocol: Samples were hybridized to the microarray using the Affymetrix® GeneChip® WT Hybridization Wash and Stain Kit following the Affymetrix standard protocols. The fluidic station protocol FS540_0001 was used.

scan_protocol: Slides were scanned with the GeneChip® Scanner 3000 7G system (Affymetrix, Santa Clara, USA).

data_processing:
Quality of the data was controlled with the Expression Console 1.2 software (Affymetrix, Santa Clara, USA) in accordance with the pertinent Affymetrix technical note (Affymetrix 2007). Background was adjusted with the robust multi-array average (RMA) algorithm which also served for quantile normalization, and summarization. Transcripts with significant (P < 0.05) expression levels were identified with the detection above background (DABG) algorithm.
probe group file: BovGene-1_0-v1.pgf
meta-probeset file: BovGene-1_0-v1.mps

organism: Bos taurus

source_name: gland cistern Sa3h

label_protocol: Samples containing 5.5 μg of the resultant cDNA were fragmented, labelled (Affymetrix GeneChip WT Terminal Labelling Kit)

growth_protocol: The animal experiments included 12 healthy, first-lactating Holstein cows, 26–35 mo of age and 59–185 d in milk. Only animals without previous diagnosis of clinical or subclinical mastitis and a reported somatic cell count <50,000/ml were included in the study.

extract_protocol: At the end of the trial, the cows were slaughtered with a penetrating captive bolt gun, followed by exsanguination. Tissue samples were collected aseptically from the gland cistern from the slaughtered cows within 10 min after killing. Small tissue pieces (0.5 × 0.5 × 0.5 cm) were taken after the right and the left udder side was cut open sagittally. All tissue samples were immediately snap frozen in liquid nitrogen and stored at −80℃ until further processing.Tissue samples from the gland cistern (50–200 mg) were powdered under liquid nitrogen. 500 ng RNA was subsequently extracted with RNeasy kit (Qiagen, Hilden, Germany) and amplified with the Ambion WT Expression Kit (Ambion, Grand Island, NY, USA).

treatment_protocol: The animals were randomly enrolled into two different treatment groups. In the Ec3h group six cows were experimentally challenged with E. coli, and in the Sa3h group six cows were challenged with S. aureus. At trial start the udder was entirely milked out after i.v. application of 20 IU Oxytocin. After cleaning and disinfecting the teat end thoroughly with 70% ethanol, the first challenge dose (5 × E+06 CFU/2 ml) was instilled into the hind left quarter intra-cisternally with a sterile syringe and teat cannula via the teat canal. One h later, the front left udder quarters were challenged and after another h the hind right quarters were challenged as described above. The front right quarters received no challenge and served as control quarters. The trial ended 3 h after the first challenge. At this time point the duration of pathogen presence was 1 h for hind right quarters, 2 h for front left quarters and 3 h for hind left quarters.

tag: breed

value: Holstein

tag: animal no.

value: gland cistern

tag: infection

value: 3 h S. aureus


title: gland cistern 1 h S. aureus infected, animal 12

description: 1 h infected gland cistern of an animal whose three udder quarter were sequentially infected for 1, 2 and 3 h with S. aureus

source_name: gland cistern Sa1h

value: 1 h S. aureus


title: mTECs, wt, day0 1


title: gland cistern 2 h S. aureus infected, animal 12

description: 2 h infected gland cistern of an animal whose three udder quarter were sequentially infected for 1, 2 and 3 h with S. aureus

source_name: gland cistern Sa2h

value: 2 h S. aureus


title: mTECs, wt, day4 1


title: uninfected gland cistern, animal 12

description: uninfected gland cistern of an animal whose three udder quarters were sequentially infected for 1, 2 and 3 h with S. aureus

source_name: gland cistern control

value: control


title: mTECs, wt, day0 2


title: metastasized cells

city: Tokyo

first: Mariko

last: Honda

address: 3-19-18, Nishishimbashi, Minato-ku

department: urology department

institute: The Jikei University School of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Llabeled PC3 prostate cancer cells were injected into the heart of nude mice and 5-7 weeks later, cancer cells of metastasis site were extractedwith cell sorter.

extract_protocol: The total RNA was isolated from cells using RNeasy (Quiagen) according to the manufacturer's instructions.

tag: cell line

value: bone marrow


title: ∆cspD1 deletion mutant vs. wild type under low oxygen 1 minute prior to oxygen sparging

description:
This Sample represents 2 dye-swap samples.
cspD1_-0001_L_H_vs_NRC1d.sig
NRC1d_vs_cspD1_-0001_L_H
09225.csv: delta-cspD1=Alexa 546, WT=Alexa 647
09226.csv: WT=Alexa 546, delta-cspD1=Alexa 647

tag: strain/background

tag: oxygen level

value: low to high transition

tag: time (min.)

source_name: NRC-1d reference sample


title: gland cistern 3 h S. aureus infected, animal 9

tag: tissue


title: gland cistern 2 h S. aureus infected, animal 10


title: gland cistern 1 h S. aureus infected, animal 10


title: gland cistern 2 h S. aureus infected, animal 8


title: gland cistern 3 h E. coli infected, animal 7

description: 3 h infected gland cistern of an animal whose three udder quarter were sequentially infected for 1, 2 and 3 h with E. coli

source_name: gland cistern Ec3h

value: 3 h E. coli


title: uninfected gland cistern, animal 8


title: gland cistern 1 h E. coli infected, animal 11

description: 1 h infected gland cistern of an animal whose three udder quarter were sequentially infected for 1, 2 and 3 h with E. coli

source_name: gland cistern Ec1h

value: 1 h E. coli


title: uninfected gland cistern, animal 9


title: gland cistern 2 h S. aureus infected, animal 9


title: uninfected gland cistern, animal 10, technical replicate


title: gland cistern 2 h E. coli infected, animal 7

description: 2 h infected gland cistern of an animal whose three udder quarter were sequentially infected for 1, 2 and 3 h with E. coli

source_name: gland cistern Ec2h

value: 2 h E. coli


title: gland cistern 2 h E. coli infected, animal 11


title: gland cistern 3 h S. aureus infected, animal 8


title: gland cistern 1 h S. aureus infected, animal 8


title: uninfected gland cistern, animal 7

description: uninfected gland cistern of an animal whose three udder quarters were sequentially infected for 1, 2 and 3 h with E. coli


title: gland cistern 1 h E. coli infected, animal 6


title: gland cistern 3 h E. coli infected, animal 5


title: uninfected gland cistern, animal 11


title: uninfected gland cistern, animal 6


title: gland cistern 2 h E. coli infected, animal 5


title: gland cistern 1 h S. aureus infected, animal 9


title: gland cistern 1 h E. coli infected, animal 7


title: gland cistern 3 h S. aureus infected, animal 10


title: gland cistern 1 h E. coli infected, animal 5


title: gland cistern 3 h E. coli infected, animal 6


title: uninfected gland cistern, animal 10


title: gland cistern 2 h E. coli infected, animal 6


title: uninfected gland cistern, animal 5


title: gland cistern 2 h S. aureus infected, animal 4


title: gland cistern 3 h S. aureus infected, animal 4


title: gland cistern 1 h S. aureus infected, animal 4


title: gland cistern 1 h S. aureus infected, animal 3


title: uninfected gland cistern, animal 4


title: gland cistern 1 h E. coli infected, animal 2


title: uninfected gland cistern, animal 2


title: gland cistern 2 h S. aureus infected, animal 3


title: gland cistern 2 h E. coli infected, animal 2


title: gland cistern 3 h E. coli infected, animal 1


title: uninfected gland cistern, animal 3


title: ain-1_fed

description: Gene expression data from ain-1 mutant in the fed conditions.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip  C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: genespring GX

label_protocol: 3` IVT

growth_protocol: All strains were maintained at 20 °C on nematode growth medium (NGM) plates seeded with Escherichia coli OP50.

value: day 4 adult


title: daf-16_fasting

description: Gene expression data from daf-16 mutant in the fasting conditions.


title: drsh-1_fasting

description: Gene expression data from drsh-1 mutant in the fasting conditions.


title: WT_fed

description: Gene expression data from WT worms in the fed conditions.

value: wild type (N2)


title: WT_fasting

description: Gene expression data from WT worms in the fasting conditions.

value: fasting


title: drsh-1_fed

description: Gene expression data from drsh-1 mutant in the fed conditions.


title: uninfected gland cistern, animal 1


title: gland cistern 1 h E. coli infected, animal 1


title: gland cistern 2 h E. coli infected, animal 1


title: gland cistern 3 h E. coli infected, animal 2


title: daf-16_fed

description: Gene expression data from daf-16 mutant in the fed conditions.


title: gland cistern 3 h S. aureus infected, animal 3


title: ain-1_fasting

description: Gene expression data from ain-1 mutant in the fasting conditions.


title: 201044 - Negative

tag: gender

value: Male

value: whole blood

tag: sample type

value: reference

value: IP


title: WB 99C B0099CV1 HEALTHY

city: Cambridge

first: Andrew

last: Hill

state: MA

address: 300 Technology Square

department: Research Business Technology

institute: Pfizer

data_processing: Batch corrected delta Ct values are reported. Ct values were reported by the AppliedBiosystems SDS software.  Delta Ct values were computed using the median of endogenous control transcripts.  Finally, Delta Ct values were batch corrected using a linear model.

label: FAM

molecule: polyA RNA

source_name: Whole Blood

label_protocol: Applied Biosystems Viia7 protocol

extract_protocol: mRNA was extracted from whole blood

value: C

tag: rin

value: No

value: Control

value: 99C B0099CV1 HEALTHY

tag: nicevisit

value: HEALTHY

tag: neutrophils

tag: lymphocytes

tag: monocytes

tag: eosinophils

tag: basophils


title: WB 98C B0098CV2 HEALTHY

value: 98C B0098CV2 HEALTHY


title: WB 99C B0099CV2 HEALTHY

value: 99C B0099CV2 HEALTHY


title: WB 94C B0094CV2 HEALTHY

value: 94C B0094CV2 HEALTHY


title: WB 96C B0096CV2 HEALTHY

value: 96C B0096CV2 HEALTHY


title: WB 96C B0096CV1 HEALTHY

value: 96C B0096CV1 HEALTHY


title: WB 98C B0098CV1 HEALTHY

value: 98C B0098CV1 HEALTHY


title: WB 90C B0090CV1 HEALTHY

value: 90C B0090CV1 HEALTHY


title: WB 93C B0093CV1 HEALTHY

value: 93C B0093CV1 HEALTHY


title: WB 93C B0093CV2 HEALTHY

value: 93C B0093CV2 HEALTHY


title: WB 8C B0008CV2 HEALTHY

value: 8C B0008CV2 HEALTHY


title: WB 84C B0084CV2 HEALTHY

value: 84C B0084CV2 HEALTHY


title: WB 89C B0089CV1 HEALTHY

value: 89C B0089CV1 HEALTHY


title: WB 87C B0087CV2 HEALTHY

value: C

value: 87C B0087CV2 HEALTHY


title: WB 88C B0088CV1 HEALTHY

value: No

value: Control

value: 88C B0088CV1 HEALTHY


title: WB 88C B0088CV2 HEALTHY

value: Yes

value: 88C B0088CV2 HEALTHY

value: HEALTHY


title: WB 94C B0094CV1 HEALTHY

value: 94C B0094CV1 HEALTHY


title: WB 83C B0083CV1 HEALTHY

value: 83C B0083CV1 HEALTHY


title: WB 84C B0084CV1 HEALTHY

value: 84C B0084CV1 HEALTHY


title: WB 77C B0077CV1 HEALTHY

value: 77C B0077CV1 HEALTHY


title: WB 7C B0007CV2 HEALTHY

value: 7C B0007CV2 HEALTHY


title: WB 82C B0082CV2 HEALTHY

value: 82C B0082CV2 HEALTHY


title: WB 83C B0083CV2 HEALTHY

value: 83C B0083CV2 HEALTHY


title: WB 90C B0090CV2 HEALTHY

value: 90C B0090CV2 HEALTHY


title: WB 77C B0077CV2 HEALTHY

value: 77C B0077CV2 HEALTHY


title: WB 8C B0008CV1 HEALTHY

value: C

value: 8C B0008CV1 HEALTHY


title: WB 75C B0075CV2 HEALTHY

value: No

value: 75C B0075CV2 HEALTHY


title: WB 75C B0075CV1 HEALTHY

value: Control

value: 75C B0075CV1 HEALTHY


title: WB 73C B0073CV2 HEALTHY

value: 73C B0073CV2 HEALTHY


title: WB 73C B0073CV1 HEALTHY

value: 73C B0073CV1 HEALTHY

value: HEALTHY


title: WB 6C B0006CV2 HEALTHY

value: 6C B0006CV2 HEALTHY


title: WB 70C B0070CV1 HEALTHY

value: 70C B0070CV1 HEALTHY


title: WB 70C B0070CV2 HEALTHY

value: 70C B0070CV2 HEALTHY


title: WB 68C B0068CV2 HEALTHY

value: 68C B0068CV2 HEALTHY


title: WB 64C B0064CV1 HEALTHY

value: 64C B0064CV1 HEALTHY


title: WB 62C B0062CV1 HEALTHY

value: 62C B0062CV1 HEALTHY


title: WB 5C B0005CV2 HEALTHY

value: 5C B0005CV2 HEALTHY


title: WB 5C B0005CV1 HEALTHY

value: 5C B0005CV1 HEALTHY


title: WB 57C B0057CV1 HEALTHY

value: C

value: 57C B0057CV1 HEALTHY


title: WB 57C B0057CV2 HEALTHY

value: No

value: 57C B0057CV2 HEALTHY


title: gland cistern 3 h E. coli infected, animal 11

tag: breed

value: Holstein

value: gland cistern

value: 3 h E. coli


title: WB 4C B0004CV1 HEALTHY

value: Control

value: 4C B0004CV1 HEALTHY


title: WB 49C B0049CV1 HEALTHY

value: 49C B0049CV1 HEALTHY

value: HEALTHY


title: WB 4C B0004CV2 HEALTHY

value: 4C B0004CV2 HEALTHY


title: WB 49C B0049CV2 HEALTHY

value: 49C B0049CV2 HEALTHY


title: WB 54C B0054CV2 HEALTHY

value: 54C B0054CV2 HEALTHY


title: WB 55C B0055CV1 HEALTHY

value: 55C B0055CV1 HEALTHY


title: WB 43C B0043CV1 HEALTHY

value: 43C B0043CV1 HEALTHY


title: WB 42C B0042CV2 HEALTHY

value: 42C B0042CV2 HEALTHY


title: WB 3C B0003CV1 HEALTHY

value: C

value: 3C B0003CV1 HEALTHY


title: WB 42C B0042CV1 HEALTHY

value: No

value: 42C B0042CV1 HEALTHY


title: WB 38C B0038CV1 HEALTHY

value: 38C B0038CV1 HEALTHY


title: WB 3C B0003CV2 HEALTHY

value: 3C B0003CV2 HEALTHY


title: WB 41C B0041CV1 HEALTHY

value: 41C B0041CV1 HEALTHY


title: WB 38C B0038CV2 HEALTHY

value: Control

value: 38C B0038CV2 HEALTHY


title: WB 41C B0041CV2 HEALTHY

value: 41C B0041CV2 HEALTHY


title: WB 35C B0035CV2 HEALTHY

value: 35C B0035CV2 HEALTHY

value: HEALTHY


title: WB 35C B0035CV1 HEALTHY

value: 35C B0035CV1 HEALTHY


title: WB 33C B0033CV1 HEALTHY

value: 33C B0033CV1 HEALTHY


title: WB 31C B0031CV1 HEALTHY

value: 31C B0031CV1 HEALTHY


title: WB 33C B0033CV2 HEALTHY

value: 33C B0033CV2 HEALTHY


title: WB 31C B0031CV2 HEALTHY

value: 31C B0031CV2 HEALTHY


title: WB 54C B0054CV1 HEALTHY

value: C

value: 54C B0054CV1 HEALTHY


title: WB 2C B0002CV2 HEALTHY

value: No

value: 2C B0002CV2 HEALTHY


title: WB 2C B0002CV1 HEALTHY

value: 2C B0002CV1 HEALTHY


title: WB 29C B0029CV2 HEALTHY

value: 29C B0029CV2 HEALTHY


title: WB 27C B0027CV2 HEALTHY

value: 27C B0027CV2 HEALTHY


title: WB 29C B0029CV1 HEALTHY

value: Control

value: 29C B0029CV1 HEALTHY


title: WB 28C B0028CV2 HEALTHY

value: 28C B0028CV2 HEALTHY


title: WB 26C B0026CV1 HEALTHY

value: 26C B0026CV1 HEALTHY


title: WB 23C B0023CV1 HEALTHY

value: 23C B0023CV1 HEALTHY

value: HEALTHY


title: WB 23C B0023CV2 HEALTHY

value: 23C B0023CV2 HEALTHY


title: WB 28C B0028CV1 HEALTHY

value: 28C B0028CV1 HEALTHY


title: WB 25C B0025CV1 HEALTHY

value: 25C B0025CV1 HEALTHY


title: WB 1C B0001CV2 HEALTHY

value: 1C B0001CV2 HEALTHY


title: WB 27C B0027CV1 HEALTHY

value: C

value: 27C B0027CV1 HEALTHY


title: WB 26C B0026CV2 HEALTHY

value: No

value: 26C B0026CV2 HEALTHY


title: WB 25C B0025CV2 HEALTHY

value: 25C B0025CV2 HEALTHY


title: WB 17C B0017CV2 HEALTHY

value: 17C B0017CV2 HEALTHY


title: WB 16C B0016CV2 HEALTHY

value: 16C B0016CV2 HEALTHY


title: WB 1C B0001CV1 HEALTHY

value: Control

value: 1C B0001CV1 HEALTHY


title: WB 20C B0020CV2 HEALTHY

value: 20C B0020CV2 HEALTHY


title: WB 19C B0019CV2 HEALTHY

value: 19C B0019CV2 HEALTHY


title: WB 20C B0020CV1 HEALTHY

value: 20C B0020CV1 HEALTHY


title: WB 17C B0017CV1 HEALTHY

value: 17C B0017CV1 HEALTHY

value: HEALTHY


title: WB 16C B0016CV1 HEALTHY

value: 16C B0016CV1 HEALTHY


title: WB 13C B0013CV2 HEALTHY

value: 13C B0013CV2 HEALTHY


title: WB 14C B0014CV1 HEALTHY

value: 14C B0014CV1 HEALTHY


title: WB 14C B0014CV2 HEALTHY

value: C

value: 14C B0014CV2 HEALTHY


title: WB 15C B0015CV1 HEALTHY

value: No

value: 15C B0015CV1 HEALTHY


title: WB 13C B0013CV1 HEALTHY

value: 13C B0013CV1 HEALTHY


title: WB 19C B0019CV1 HEALTHY

value: 19C B0019CV1 HEALTHY


title: WB 12C B0012CV2 HEALTHY

value: 12C B0012CV2 HEALTHY


title: WB 11C B0011CV2 HEALTHY

value: Control

value: 11C B0011CV2 HEALTHY


title: WB 11C B0011CV1 HEALTHY

value: 11C B0011CV1 HEALTHY


title: WB 10C B0010CV2 HEALTHY

value: 10C B0010CV2 HEALTHY


title: WB 10C B0010CV1 HEALTHY

value: 10C B0010CV1 HEALTHY


title: WB 99 B0099V1 BASELINE

value: A

value: Baseline

value: Patient

value: 99 B0099V1 BASELINE

value: BASELINE


title: WB 94 B0094V1 BASELINE

value: B

value: 94 B0094V1 BASELINE


title: WB 99 B0099VF FLARE

value: Flare visit

value: No

value: 99 B0099VF FLARE

value: FLARE


title: WB 95 B0095V1 BASELINE

value: Yes

value: 95 B0095V1 BASELINE


title: WB 98 B0098V6 IMPROVING

value: improving visit

value: 98 B0098V6 IMPROVING

value: IMPROVING


title: WB 99 B0099V5 IMPROVING

value: 99 B0099V5 IMPROVING


title: WB 96 B0096V6 IMPROVING

value: A

value: 96 B0096V6 IMPROVING


title: WB 12C B0012CV1 HEALTHY

value: C

value: Control

value: 12C B0012CV1 HEALTHY

value: HEALTHY


title: WB 93 B0093V5 IMPROVING

value: Patient

value: 93 B0093V5 IMPROVING


title: WB 98 B0098V1 BASELINE

value: Baseline

value: No

value: 98 B0098V1 BASELINE

value: BASELINE


title: WB 93 B0093VF OTHER

value: pre-Flare visit

value: 93 B0093VF OTHER

value: OTHER


title: WB 96 B0096V5 OTHER

value: 96 B0096V5 OTHER


title: WB 97 B0097V1 BASELINE

value: B

value: 97 B0097V1 BASELINE


title: WB 93 B0093VF2 FLARE

value: A

value: Flare visit

value: 93 B0093VF2 FLARE

value: FLARE


title: WB 96 B0096V1 BASELINE

value: 96 B0096V1 BASELINE


title: WB 93 B0093V1 BASELINE

value: Patient

value: 93 B0093V1 BASELINE


title: WB 92 B0092V5 IMPROVING

value: improving visit

value: 92 B0092V5 IMPROVING

value: IMPROVING


title: WB 91 B0091VF FLARE

value: No

value: 91 B0091VF FLARE


title: WB 91 B0091V6 OTHER

value: 91 B0091V6 OTHER


title: WB 92 B0092VF FLARE

value: Yes

value: 92 B0092VF FLARE


title: WB 91 B0091V5 IMPROVING

value: 91 B0091V5 IMPROVING


title: WB 91 B0091V1 BASELINE

value: Baseline

value: 91 B0091V1 BASELINE

value: BASELINE


title: WB 98 B0098VF FLARE

value: A

value: Flare visit

value: 98 B0098VF FLARE


title: WB 90 B0090V9 OTHER

value: Patient

value: 90 B0090V9 OTHER

value: OTHER


title: WB 82C B0082CV1 HEALTHY

value: C

value: Control

value: 82C B0082CV1 HEALTHY

value: HEALTHY


title: WB 90 B0090V6 IMPROVING

value: improving visit

value: No

value: 90 B0090V6 IMPROVING

value: IMPROVING


title: WB 90 B0090V5 OTHER

value: 90 B0090V5 OTHER


title: WB 90 B0090V11 OTHER


title: WB 90 B0090V10 OTHER


title: WB 8 B0008V8 OTHER

value: 8 B0008V8 OTHER


title: WB 8 B0008VF FLARE

value: 8 B0008VF FLARE

value: FLARE


title: WB 8 B0008V1 BASELINE

value: A

value: Baseline

value: 8 B0008V1 BASELINE

value: BASELINE


title: WB 88 B0088VF FLARE

value: Flare visit

value: Patient

value: 88 B0088VF FLARE


title: WB 92 B0092V1 BASELINE

value: Yes

value: 92 B0092V1 BASELINE


title: WB 8 B0008V6 IMPROVING

value: improving visit

value: 8 B0008V6 IMPROVING


title: WB 89 B0089V1 BASELINE

value: No

value: 89 B0089V1 BASELINE


title: WB 89 B0089VF FLARE

value: 89 B0089VF FLARE


title: WB 8 B0008V3 OTHER

value: 8 B0008V3 OTHER

value: OTHER


title: WB 87 B0087V9 OTHER

value: 87 B0087V9 OTHER


title: WB 87 B0087VF FLARE

value: A

value: 87 B0087VF FLARE

value: FLARE


title: WB 89 B0089V5 IMPROVING

value: 89 B0089V5 IMPROVING

value: IMPROVING


title: WB 90 B0090V8 OTHER

value: Patient

value: 90 B0090V8 OTHER


title: WB 87 B0087V6 OTHER

value: 87 B0087V6 OTHER


title: WB 87 B0087V1 BASELINE

value: Baseline

value: Yes

value: 87 B0087V1 BASELINE

value: BASELINE


title: WB 87 B0087V8 OTHER

value: No

value: 87 B0087V8 OTHER


title: WB 86 B0086V1 BASELINE

value: B

value: 86 B0086V1 BASELINE


title: WB 87 B0087V5 IMPROVING

value: improving visit

value: 87 B0087V5 IMPROVING


title: WB 84 B0084VF FLARE

value: A

value: Flare visit

value: 84 B0084VF FLARE


title: WB 90 B0090V1 BASELINE

value: 90 B0090V1 BASELINE


title: WB 8 B0008V5 OTHER

value: Patient

value: 8 B0008V5 OTHER

value: OTHER


title: WB 83 B0083VF FLARE

value: 83 B0083VF FLARE

value: FLARE


title: WB 84 B0084V5 OTHER

value: 84 B0084V5 OTHER


title: WB 83 B0083V5 IMPROVING

value: 83 B0083V5 IMPROVING

value: IMPROVING


title: WB 83 B0083V1 BASELINE

value: Baseline

value: No

value: 83 B0083V1 BASELINE

value: BASELINE


title: WB 82 B0082V5 OTHER

value: 82 B0082V5 OTHER


title: WB 82 B0082V1 BASELINE

value: A

value: 82 B0082V1 BASELINE


title: WB 7 B0007V6 OTHER

value: 7 B0007V6 OTHER


title: WB 84 B0084V6 IMPROVING

value: improving visit

value: 84 B0084V6 IMPROVING


title: WB 7 B0007V7 OTHER

value: Patient

value: 7 B0007V7 OTHER


title: WB 7 B0007V5 OTHER

value: 7 B0007V5 OTHER

value: OTHER


title: WB 80 B0080V1 BASELINE

value: B

value: 80 B0080V1 BASELINE


title: WB 7 B0007V8 IMPROVING

value: 7 B0007V8 IMPROVING

value: IMPROVING


title: WB 7 B0007V1 BASELINE

value: Baseline

value: No

value: 7 B0007V1 BASELINE


title: WB 79 B0079V1 BASELINE

value: 79 B0079V1 BASELINE

value: BASELINE


title: WB 87C B0087CV1 HEALTHY

value: C

value: Control

value: 87C B0087CV1 HEALTHY

value: HEALTHY


title: WB 78 B0078V1 BASELINE

value: Patient

value: 78 B0078V1 BASELINE


title: WB 77 B0077V6 IMPROVING

value: A

value: improving visit

value: 77 B0077V6 IMPROVING


title: WB 77 B0077V8 OTHER

value: 77 B0077V8 OTHER

value: OTHER


title: WB 75 B0075V1 BASELINE

value: B

value: 75 B0075V1 BASELINE


title: WB 77 B0077V1 BASELINE

value: Baseline

value: No

value: 77 B0077V1 BASELINE


title: WB 77 B0077V5 OTHER

value: 77 B0077V5 OTHER


title: WB 74 B0074V1 BASELINE

value: 74 B0074V1 BASELINE

value: BASELINE


title: WB 73 B0073VF FLARE

value: Flare visit

value: 73 B0073VF FLARE

value: FLARE


title: WB 77 B0077VF FLARE

value: Patient

value: 77 B0077VF FLARE


title: WB 7 B0007VF FLARE

value: A

value: 7 B0007VF FLARE


title: WB 81 B0081V1 BASELINE

value: 81 B0081V1 BASELINE


title: WB 73 B0073V8 OTHER

value: 73 B0073V8 OTHER

value: OTHER


title: WB 7 B0007V3 OTHER

value: 7 B0007V3 OTHER


title: WB 73 B0073V6 IMPROVING

value: improving visit

value: 73 B0073V6 IMPROVING

value: IMPROVING


title: sc1_10

city: Nashville

first: Shilin

last: Zhao

state: TN

address: 2200 Pierce Ave, PRB building 571

department: Center for Quantitative Sciences

institute: Vanderbilt University

description: exp 1174

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array (HG-U133_Plus_2). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: We performed Robust Multichip Average (RMA) to normalize the 6 samples. Consistent difference between SC and CC were computed by combining time points from the same cell type together.

source_name: sc1 cells, grown for 10 days

label_protocol: Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 3μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)

growth_protocol: CC and SC cells were grown in 3D collagen in 12-well dishes using 50,000 cells/ml.

extract_protocol: On day 5, 10, or 15, total RNA was extracted from the middle, cell-containing collagen layers using TRIzol Reagent (Life Technologies, Grand Island, NY) according to the manufacturer’s instructions. The RNeasy Mini Kit (Qiagen, Valencia, CA) was used to clean up 50 to 100 μg of each total RNA sample. Samples were then submitted for microarray analysis.

tag: cell type

value: colorectal cancer

tag: colony morphology

value: spiky

tag: day


title: sc1_15

description: exp 1174

source_name: sc1 cells, grown for 15 days

tag: cell line


title: WB 70 B0070VF FLARE

value: No

value: 70 B0070VF FLARE


title: WB 76 B0076V1 BASELINE

value: B

value: Baseline

value: 76 B0076V1 BASELINE

value: BASELINE


title: WB 73 B0073V1 BASELINE

value: A

value: Patient

value: 73 B0073V1 BASELINE


title: sc1_5

description: exp 1174

source_name: sc1 cells, grown for 5 days


title: WB 70 B0070V8 IMPROVING

value: 70 B0070V8 IMPROVING


title: WB 70 B0070V9 OTHER

value: 70 B0070V9 OTHER

value: OTHER


title: WB 70 B0070V5 OTHER

value: 70 B0070V5 OTHER


title: WB 73 B0073V9 OTHER

value: 73 B0073V9 OTHER


title: WB 70 B0070V1 BASELINE

value: 70 B0070V1 BASELINE


title: WB 69 B0069V6 OTHER

value: 69 B0069V6 OTHER


title: WB 68 B0068VF FLARE

value: Flare visit

value: 68 B0068VF FLARE

value: FLARE


title: WB 68 B0068V6 IMPROVING

value: improving visit

value: No

value: 68 B0068V6 IMPROVING

value: IMPROVING


title: WB 73 B0073V5 OTHER

value: A

value: 73 B0073V5 OTHER


title: cc3_15

description: exp 1174

source_name: cc3 cells, grown for 15 days

value: colorectal cancer

value: cystic


title: WB 69 B0069V1 BASELINE

value: Baseline

value: Patient

value: 69 B0069V1 BASELINE

value: BASELINE


title: WB 66 B0066V1 BASELINE

value: B

value: 66 B0066V1 BASELINE


title: WB 68 B0068V1 BASELINE

value: 68 B0068V1 BASELINE


title: WB 67 B0067V1 BASELINE

value: 67 B0067V1 BASELINE


title: WB 65 B0065V1 BASELINE

value: 65 B0065V1 BASELINE


title: WB 64 B0064V1 BASELINE

value: 64 B0064V1 BASELINE


title: WB 63 B0063V1 BASELINE

value: No

value: 63 B0063V1 BASELINE


title: WB 62 B0062V1 BASELINE

value: 62 B0062V1 BASELINE


title: WB 5 B0005V7F FLARE

value: A

value: Flare visit

value: 5 B0005V7F FLARE

value: FLARE


title: WB 5 B0005V6 IMPROVING

value: improving visit

value: 5 B0005V6 IMPROVING

value: IMPROVING


title: WB 60 B0060V1 BASELINE

value: Baseline

value: Patient

value: 60 B0060V1 BASELINE

value: BASELINE


title: WB 5 B0005V5 OTHER

value: 5 B0005V5 OTHER

value: OTHER


title: WB 69 B0069V5 IMPROVING

value: 69 B0069V5 IMPROVING


title: WB 6 B0006V1 BASELINE

value: B

value: No

value: 6 B0006V1 BASELINE


title: WB 61 B0061V1 BASELINE

value: 61 B0061V1 BASELINE


title: WB 68 B0068V5 OTHER

value: A

value: 68 B0068V5 OTHER


title: WB 59 B0059V1 BASELINE

value: 59 B0059V1 BASELINE


title: WB 58 B0058V1 BASELINE

value: 58 B0058V1 BASELINE


title: WB 57 B0057VF FLARE

value: Flare visit

value: Yes

value: 57 B0057VF FLARE

value: FLARE


title: WB 57 B0057V5 OTHER

value: Patient

value: 57 B0057V5 OTHER


title: WB 56 B0056V1 BASELINE

value: Baseline

value: 56 B0056V1 BASELINE

value: BASELINE


title: DGM-10948_M0_sm

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: small airway epithelium brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: smoker


title: DGM-00127_M0_sm


title: WB 57 B0057V1 BASELINE

value: No

value: 57 B0057V1 BASELINE


title: cc3_10

description: exp 1174

source_name: cc3 cells, grown for 10 days

value: colorectal cancer

value: cystic


title: WB 57 B0057V6 IMPROVING

value: A

value: improving visit

value: 57 B0057V6 IMPROVING

value: IMPROVING


title: WB 5 B0005V3 OTHER

value: 5 B0005V3 OTHER

value: OTHER


title: cc3_5

description: exp 1174

source_name: cc3 cells, grown for 5 days


title: WB 55 B0055V6 IMPROVING

value: 55 B0055V6 IMPROVING


title: WB 55 B0055V5 OTHER

value: Yes

value: Patient

value: 55 B0055V5 OTHER


title: WB 5 B0005V1 BASELINE

value: Baseline

value: 5 B0005V1 BASELINE


title: WB 69 B0069VF FLARE

value: Flare visit

value: 69 B0069VF FLARE

value: FLARE


title: WB 55 B0055V1 BASELINE

value: No

value: 55 B0055V1 BASELINE

value: BASELINE


title: gly/gln; M_r_217_2

city: Bethesda

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description: Gly/Gln expt1 (reverse)

hyb_protocol: standard Agilent sure-print hybridization protocol

scan_protocol: Agilent microarray scanner

data_processing: Feature extraction protocol v. dec08, followed by loess normalization using JMP/Genomics v4.1

source_name: trigeminal ganglia; glutamine

label_protocol: amino-allyl cDNA

growth_protocol: Six-week-old Balb/c mice were inoculated with HSV-1 onto both scarified cornea at 4 x105 pfu/mouse. Human IgG (0.5 ml, 1:8 dilution in PBS, Gammagard, Baxter, Deerfield, IL) was injected intraperitoneally into each mouse shortly after infection, so most animals would survive acute infection. Fourteen days after infection, mice were divided into 2  groups. Each group was given glutamine (3g/dL), or glycine (3 g/dl) in the drinking water.

extract_protocol: RNA was extracted from pooled trigeminal ganglia using a mirVana RNA isolation kit (Ambion, Applied Biosystems, Foster City, CA)

treatment_protocol: Four weeks after corneal infection with HSV-1 (2 weeks on glutamine or glycine) mice were sacrificed and trigeminal ganglia were harvested.

tag: diet

value: glutamine

value: trigeminal ganglia

tag: strain

value: Balb/c

source_name: trigeminal ganglia; glycine

value: glycine


title: gln/gly; M_r_214_2

description: Gln/Gly expt1

tag: tissue


title: gln/gly; M_r_216_3

description: Gln/Gly expt1


title: WB 54 B0054V5 IMPROVING

value: A

value: improving visit

value: 54 B0054V5 IMPROVING

value: IMPROVING


title: WB 54 B0054VF FLARE

value: Patient

value: 54 B0054VF FLARE


title: WB 54 B0054V3 OTHER

value: 54 B0054V3 OTHER

value: OTHER


title: WB 54 B0054V1 BASELINE

value: Baseline

value: Yes

value: 54 B0054V1 BASELINE


title: WB 53 B0053V1 BASELINE

value: B

value: No

value: 53 B0053V1 BASELINE


title: WB 52 B0052V1 BASELINE

value: 52 B0052V1 BASELINE

value: BASELINE


title: gln/gly; M_r_216_4

description: Gln/Gly expt1

value: glycine

value: trigeminal ganglia

value: Balb/c

value: glutamine


title: WB 50 B0050V1 BASELINE

value: 50 B0050V1 BASELINE


title: WB 4 B0004V1 BASELINE

value: Patient

value: 4 B0004V1 BASELINE


title: WB 48 B0048V1 BASELINE

value: 48 B0048V1 BASELINE


title: WB 46 B0046V1 BASELINE

value: 46 B0046V1 BASELINE


title: WB 45 B0045V1 BASELINE

value: Baseline

value: 45 B0045V1 BASELINE


title: 044_2015_8_uM_T

first: Hui

last: Shi

address: Downing Street

department: Department of Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Illumina HumanHT-12 v4 expression beadchip standard

data_processing: Preprocessing of Illumina microarray data and quality control (QC) were performed using R/Bioconductor packages BeadArray (Dunning et al, 2007) and Lumi (Du et al, 2008). QC steps undertaken i) exclusion of unexpressed genes/probes if their detection p-val ≤ 0.05 in all samples and ii) quantile normalisation of data, followed by log2 and variance-stablizing transformation (VST) implemented in Lumi Bioconductor package. In the circumstance of genes represented by multiple distinct oligonucleotide probes, the probe with the highest average expression across all samples was selected for use in further analyses. Normalised data were exported directly from Lumi Bioconductor package.

source_name: ESC 8µM Rep2

label_protocol: not provided

growth_protocol: Human embryonic stem cells (hESCs) were first cultured on a feeder layer of mouse embryonic fibroblasts (MEFs) inactivated by mitomycin C (Sigma–Aldrich, Milan, Italy) in KO-DMEM medium (Gibco Invitrogen, Milan, Italy) supplemented with 10% serum replacement (Gibco Invitrogen, Milan, Italy), 4.3 mg/ml bovine serum albumin (BSA) (Sigma–Aldrich, Milan, Italy), 2 mM glutamine (L-alanyl- L-glutamine, Sigma–Aldrich, Milan, Italy), 1% non-essential amino acids (Gibco Invitrogen, Milan, Italy), 0.055 mM beta-mercaptoethanol (Gibco Invitrogen, Milan, Italy), 50 units/ml penicillin, 50 mg/ml streptomycin, and 10 ng/ml bFGF (Pepro-tech, Milan, Italy). To perform the experiments, hESCs were adapted to grow in feeder-free conditions in mTeSRTM1 medium (Stemcell Technologies, obtained from Voden medical instruments, Milan, Italy). The medium was changed daily and cells were passaged 1:4 with PBS/EDTA every 3 or 4 days.

extract_protocol: RNA was extracted from the cells treated with the different H2O2 concentrations, from three different biological replicates, using the RNeasy Mini Kit (Qiagen, Milan, Italy) following the manufacturer’s instructions.

treatment_protocol: Human ESCs were exposed to 0µM, 4µM, 8µM and 16µM of H2O2 started 24 hours (h) after plating and medium was changed daily during the following 72 h, ending at day 4 after plating.

value: Human embryonic stem cells (hESCs)


title: WB 43 B0043V8 OTHER

value: A

value: 43 B0043V8 OTHER

value: OTHER


title: 044_2015-II_4_uM_T

scan_protocol: Illumina HumanHT-12 v4 expression beadchip standard

source_name: ESC 4µM Rep3


title: 044_2015_16_uM_T

source_name: ESC 16µM Rep2


title: 044_2015-II_16_uM_T

source_name: ESC 16µM Rep3


title: 044_2015_CTR_NT

source_name: ESC Control Rep2


title: 044_2015-II_8_uM_T

source_name: ESC 8µM Rep3


title: 033_2015_16_uM_T

source_name: ESC 16µM Rep1


title: 044_2015-II_CTR_NT

source_name: ESC Control Rep3


title: 044_2015_4_uM_T

source_name: ESC 4µM Rep2


title: PSI 10 days after Tx

city: Oviedo

first: Alvaro

middle: J

last: Obaya

state: Asturias

address: Julian Claveria s/n

department: Biología Funcional

country: Spain

institute: Universidad de Oviedo

description: Scaffold biopsia from PSI day 10

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix GeneChip® Mouse genome 430 2,0 array according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit (PN900720)

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: The data were normalized with Bioconductor (R 2.15.0, Bioconductor 2.11 and affy package 1.36.0) software using RMA algorithm.

source_name: Scaffold biopsia

label_protocol: GeneChip IVT Labeling Kit

growth_protocol: Tissue growth was in the subcutaneous space of nude mice

extract_protocol: Whole RNA was isolated using TRIzol (Invitrogen) and purified with Rneasy Mini Kit (Qiagen)

tag: sample type

value: PSI

tag: time point


title: WB 43 B0043V6 IMPROVING

source_name: Whole Blood

tag: rin

value: improving visit

value: No

value: 43 B0043V6 IMPROVING

tag: nicevisit

value: IMPROVING


title: gln/gly; M_r_214_1

description: Gln/Gly expt1

value: glycine

value: trigeminal ganglia

value: Balb/c

value: glutamine


title: PSI-F 7 days after Tx

description: Scaffold biopsia from PSI-F day 7

value: PSI-F


title: PSI 7 days after Tx

description: Scaffold biopsia from PSI day 7


title: PSI-F 10 days after Tx

description: Scaffold biopsia from PSI-F day 10


title: PSI 1 days after Tx

description: Scaffold biopsia from PSI day 1


title: 033_2015_4_uM_T

source_name: ESC 4µM Rep1


title: WB 43 B0043V5 OTHER

value: Patient

value: 43 B0043V5 OTHER

tag: neutrophils

tag: lymphocytes


title: PSI-F 1 days after Tx

description: Scaffold biopsia from PSI-F day 1


title: 033_2015_CTR_NT

source_name: ESC Control Rep1


title: PSI 3 days after Tx

description: Scaffold biopsia from PSI day 3


title: WB 44 B0044V1 BASELINE

value: B

value: Baseline

value: 44 B0044V1 BASELINE

value: BASELINE

tag: monocytes

tag: eosinophils


title: WB 43 B0043V1 BASELINE

value: A

value: 43 B0043V1 BASELINE

tag: basophils


title: WB 42 B0042VF FLARE

value: Flare visit

value: 42 B0042VF FLARE

value: FLARE


title: MRC5 fibroblasts, day 5, replicate 1

first: Mark

last: Ptashne

address: 1275 York Ave

department: Molecular Biology Program

institute: Sloan Kettering Institute

description:
MRC5 fibroblasts replicate 1
Male, MRC5 fibroblasts, five days following mock infection

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing:
The data were analyzed with GenomeStudio using Illumina default analysis settings
Quantile normalized and analyzed using Partek's Genomics Suite

source_name: MRC5 fibroblasts, day 5

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

growth_protocol: MRC5 (mock and infected) cells were maintained in Eagle's Minimal Essential Medium (EMEM, ATCC Cat # 30-2003) supplemented with 10% FBS

extract_protocol: Total RNA was extracted with the Trizol reagent (1ml/ 6 well; ThermoFisher Cat # 15596-018) according to manufacturer's instructions

treatment_protocol: On day 0, about 1-1.2 x 10^5 cells grown on 6-well plates were infected with a combination of lentiviruses separately encoding O,S,K and M (OSKM samples) or O, S(v), K and M (OS(v)KM samples) with 4 ug/ml polybrene. Mock- infected MRC5 cells were treated with 4 ug/ml polybrene alone. 16-18 hours later, media was replaced with EMEM + 10% FBS and changed thereafter daily. Cells were harvested on day 5 by adding 1 ml Trizol to each well.

tag: gender

value: male

value: MRC5 cells (ATCC Ca # CCL-171, Lot 59474707) of passages 7-10.

tag: protocol

value: mock infection

tag: time

value: five days following mock infection


title: WB 42 B0042V5 IMPROVING

value: improving visit

value: No

value: 42 B0042V5 IMPROVING

value: IMPROVING


title: WB 40 B0040VF FLARE

value: Patient

value: 40 B0040VF FLARE


title: WB 41 B0041V1 BASELINE

value: B

value: Baseline

value: 41 B0041V1 BASELINE


title: WB 40 B0040V8 IMPROVING

value: A

value: 40 B0040V8 IMPROVING


title: WB 40 B0040V6 OTHER

value: 40 B0040V6 OTHER

value: OTHER


title: WB 40 B0040V5 OTHER

value: 40 B0040V5 OTHER


title: WB 40 B0040V1 BASELINE

value: 40 B0040V1 BASELINE

value: BASELINE


title: OSKM, day 5, replicate 1

description:
OSKM replicate 1
Male, OSKM infected MRC5 fibroblasts, five days following lentiviral infection

source_name: OSKM, day 5

value: male

tag: cell line

value: MRC5 cells (ATCC Ca # CCL-171, Lot 59474707) of passages 7-10.

value: OSKM infection


title: Control mouse

description: Subcutaneous biopsia from control mouse

source_name: Subcutaneous biopsia

value: Control mouse


title: MRC5 fibroblasts, day 5, replicate 2

description:
MRC5 fibroblasts replicate 2
Male, MRC5 fibroblasts, five days following mock infection

value: mock infection

value: five days following mock infection


title: Diabetic mouse

description: Subcutaneous biopsia from diabetic mouse

value: Diabetic mouse


title: WB 39 B0039V1 BASELINE

value: B

value: No

value: Patient

value: 39 B0039V1 BASELINE


title: WB 38 B0038V5 IMPROVING

value: A

value: improving visit

value: 38 B0038V5 IMPROVING

value: IMPROVING


title: PSI-F 3 days after Tx

description: Scaffold biopsia from PSI-F day 3

value: PSI-F


title: OSKM, day 5, replicate 3

description:
OSKM replicate 3
Male, OSKM infected MRC5 fibroblasts, five days following lentiviral infection


title: WB 38 B0038VF FLARE

value: Flare visit

value: 38 B0038VF FLARE

value: FLARE


title: WB 38 B0038V1 BASELINE

value: Baseline

value: 38 B0038V1 BASELINE

value: BASELINE


title: OSKM, day 5, replicate 2

description:
OSKM replicate 2
Male, OSKM infected MRC5 fibroblasts, five days following lentiviral infection

value: male

value: MRC5 cells (ATCC Ca # CCL-171, Lot 59474707) of passages 7-10.

value: OSKM infection


title: 033_2015_8_uM_T

source_name: ESC 8µM Rep1

value: Human embryonic stem cells (hESCs)


title: WB 37 B0037V1 BASELINE

value: B

value: No

value: Patient

value: 37 B0037V1 BASELINE


title: OS(v)KM, day 5, replicate 3

description:
OS(v)KM replicate 3
Male, OS(v)KM infected MRC5 fibroblasts, five days following lentiviral infection

source_name: OS(v)KM, day 5

value: OS(v)KM infection


title: OS(v)KM, day 5, replicate 1

description:
OS(v)KM replicate 1
Male, OS(v)KM infected MRC5 fibroblasts, five days following lentiviral infection


title: OS(v)KM, day 5, replicate 2

description:
OS(v)KM replicate 2
Male, OS(v)KM infected MRC5 fibroblasts, five days following lentiviral infection


title: H1 hESC (Feeder free)

description:
H1-hES
Male, H1 (WA01), passage 39, grown in feeder-free conditions (vitronectin-coated plates and Essential 8 media)

source_name: H1 hESC (Feeder free)

value: H1 (WA01) ESC line obtained from WiCell. Grown in feeder-free conditions

tag: passage


title: hiPS R4 (Feeder free)

description:
hiPS-R4
Male, hiPSC, passage 20, derived using lentiviral constructs separately expressing OSKM, grown in feeder-free conditions (vitronectin-coated plates and Essential 8 media)

source_name: hiPS R4 (Feeder free)

value: R4 iPSC line derived from MRC5 cells using lentiviral constructs separately expressing OSKM. Grown in feeder-free conditions


title: WB 36 B0036V1 BASELINE

value: 36 B0036V1 BASELINE


title: WB 3 B0003V1 BASELINE

value: 3 B0003V1 BASELINE


title: WB 35 B0035V1 BASELINE

value: 35 B0035V1 BASELINE


title: hiPS S1 (on MEFs)

description:
hiPS-S1
Male, hiPSC, passage 5, derived using lentiviral constructs separately expressing OSKM, grown on feeders (mitomycin treated MEFs)

source_name: hiPS S1 (on MEFs)

value: S1 iPSC line derived from MRC5 cells using lentiviral constructs separately expressing OSKM. Grown on feeders (mitomycin treated MEFs)


title: WB 34 B0034V1 BASELINE

value: Baseline

value: 34 B0034V1 BASELINE


title: WB 33 B0033V7 OTHER

value: A

value: 33 B0033V7 OTHER

value: OTHER


title: WB 42 B0042V1 BASELINE

value: 42 B0042V1 BASELINE

value: BASELINE


title: WB 33 B0033V9 OTHER

value: No

value: 33 B0033V9 OTHER


title: WB 33 B0033V5 OTHER

value: Patient

value: 33 B0033V5 OTHER


title: WB 33 B0033V6 IMPROVING

value: improving visit

value: 33 B0033V6 IMPROVING

value: IMPROVING


title: WB 33 B0033VF FLARE

value: Flare visit

value: Yes

value: 33 B0033VF FLARE

value: FLARE


title: WB 2 B0002V1 BASELINE

value: B

value: Baseline

value: 2 B0002V1 BASELINE


title: WB 33 B0033V1 BASELINE

value: A

value: 33 B0033V1 BASELINE


title: WB 29 B0029V8 IMPROVING

value: 29 B0029V8 IMPROVING


title: WB 29 B0029V1 BASELINE

value: No

value: 29 B0029V1 BASELINE

value: BASELINE


title: WB 29 B0029V3 OTHER

value: Patient

value: 29 B0029V3 OTHER

value: OTHER


title: WB 28 B0028V1 BASELINE

value: 28 B0028V1 BASELINE


title: WB 29 B0029V5 OTHER

value: 29 B0029V5 OTHER


title: WB 27 B0027V1 BASELINE

value: 27 B0027V1 BASELINE


title: WB 26 B0026V1 BASELINE

value: 26 B0026V1 BASELINE


title: WB 26 B0026V8 OTHER

value: 26 B0026V8 OTHER


title: WB 26 B0026V6 IMPROVING

value: improving visit

value: 26 B0026V6 IMPROVING

value: IMPROVING


title: WB 26 B0026VF FLARE

value: A

value: Flare visit

value: 26 B0026VF FLARE

value: FLARE


title: WB 26 B0026V5 OTHER

value: No

value: 26 B0026V5 OTHER


title: WB 26 B0026V3 OTHER

value: Patient

value: 26 B0026V3 OTHER


title: WB 33 B0033V10 OTHER

value: Yes

value: OTHER


title: WB 33 B0033V3 OTHER

value: 33 B0033V3 OTHER


title: WB 25 B0025V1 BASELINE

value: B

value: Baseline

value: 25 B0025V1 BASELINE

value: BASELINE


title: WB 21 B0021V1 BASELINE

value: 21 B0021V1 BASELINE


title: WB 20 B0020VF FLARE

value: 20 B0020VF FLARE


title: WB 22 B0022V1 BASELINE

value: 22 B0022V1 BASELINE


title: WB 1 B0001V6 IMPROVING

value: A

value: improving visit

value: 1 B0001V6 IMPROVING

value: IMPROVING


title: WB 20 B0020V1 BASELINE

value: No

value: 20 B0020V1 BASELINE


title: WB 20 B0020V3 OTHER

value: Patient

value: 20 B0020V3 OTHER


title: WB 18 B0018V1 BASELINE

value: 18 B0018V1 BASELINE


title: WB 19 B0019VF FLARE

value: Flare visit

value: 19 B0019VF FLARE

value: FLARE


title: WB 1 B0001V1 BASELINE

value: Baseline

value: 1 B0001V1 BASELINE


title: WB 19 B0019V1 BASELINE

value: 19 B0019V1 BASELINE

value: BASELINE


title: WB 1 B0001V8F FLARE

value: 1 B0001V8F FLARE


title: WB 17 B0017V7 OTHER

value: A

value: 17 B0017V7 OTHER

value: OTHER


title: WB 20 B0020V5 OTHER

value: Yes

value: 20 B0020V5 OTHER


title: WB 17 B0017VF2 FLARE

value: No

value: 17 B0017VF2 FLARE


title: WB 20 B0020V6 IMPROVING

value: improving visit

value: Patient

value: 20 B0020V6 IMPROVING

value: IMPROVING


title: WB 17 B0017V3 OTHER

value: 17 B0017V3 OTHER


title: WB 17 B0017V5 OTHER

value: 17 B0017V5 OTHER


title: WB 19 B0019V3 OTHER

value: 19 B0019V3 OTHER


title: WB 1 B0001V5 OTHER

value: 1 B0001V5 OTHER


title: WB 17 B0017V1 BASELINE

value: Baseline

value: 17 B0017V1 BASELINE

value: BASELINE


title: WB 16 B0016VF FLARE

value: A

value: Flare visit

value: 16 B0016VF FLARE

value: FLARE


title: WB 19 B0019V5 IMPROVING

value: No

value: 19 B0019V5 IMPROVING


title: WB 17 B0017VF OTHER

value: pre-Flare visit

value: 17 B0017VF OTHER

value: OTHER


title: WB 16 B0016V8 IMPROVING

value: improving visit

value: Patient

value: 16 B0016V8 IMPROVING

value: IMPROVING


title: WB 16 B0016V5 OTHER

value: 16 B0016V5 OTHER


title: WB 16 B0016V3 OTHER

value: 16 B0016V3 OTHER


title: WB 16 B0016V1 BASELINE

value: Baseline

value: Yes

value: 16 B0016V1 BASELINE


title: WB 15 B0015V7 OTHER

value: A

value: 15 B0015V7 OTHER


title: WB 15 B0015VF FLARE

value: Flare visit

value: 15 B0015VF FLARE

value: FLARE


title: A2262_G technical replicate

description:
Glycine expt3 technical replicate
_4818547055_F

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with JMP/Genomics after dropping probes with detection p-value greater than 0.1 in all arrays

source_name: HSV-1 latently infected trigeminal ganglia after 2weeks supplemental glutamine (drinking water)

label_protocol: Biotinylated cRNA were prepared with the AB TotalPrep kit for Illumina arrays

extract_protocol: RNA was extracted from pooled trigeminal ganglia (four harvested from two mice) using a mirVana RNA isolation kit (Ambion, Applied Biosystems, Foster City, CA)

value: trigeminal ganglia

tag: diet

value: Glycine

tag: prep batch

value: Balb/c


title: A2254_Q technical replicate

description:
glutamine expt3 technical replicate
_4818547055_E

tag: tissue

value: glutamine

tag: strain


title: A2268_G

description:
Glycine expt3
_4818547055_D


title: A2260_Q

description:
glutamine expt3
_4818547055_C


title: A2263_G

description:
Glycine expt3
_4818547055_B


title: WB 15 B0015V6 IMPROVING

value: improving visit

value: No

value: Patient

value: 15 B0015V6 IMPROVING


title: WB 23 B0023V1 BASELINE

value: B

value: 23 B0023V1 BASELINE

value: BASELINE


title: WB 15 B0015V3 OTHER

value: 15 B0015V3 OTHER

value: OTHER


title: A2266_G

description:
Glycine expt3
_4818547003_F


title: A2265_G

description:
Glycine expt3
_4818547003_D


title: WB 14 B0014V6F FLARE

value: A

value: 14 B0014V6F FLARE


title: WB 14 B0014V5 IMPROVING

value: 14 B0014V5 IMPROVING

value: IMPROVING


title: A2258_Q

description:
glutamine expt3
_4818547003_E

value: trigeminal ganglia


title: WB 15 B0015V1 BASELINE

value: Baseline

value: 15 B0015V1 BASELINE


title: A2255_Q

description:
glutamine expt3
_4818547055_A

value: glutamine

value: Balb/c


title: WB 15 B0015V5 OTHER

value: No

value: 15 B0015V5 OTHER


title: WB 14 B0014V3 OTHER

value: Patient

value: 14 B0014V3 OTHER


title: A2262_G

description:
Glycine expt3
_4818547003_B

source_name: HSV-1 latently infected trigeminal ganglia after 2weeks supplemental glycine (drinking water)

value: Glycine


title: A2269_G

description:
Glycine expt3
_4658547084_F


title: A2261_Q

description:
glutamine expt3
_4658547084_E


title: A2257_Q

description:
glutamine expt3
_4818547003_C


title: A2254_Q

description:
glutamine expt3
_4818547003_A


title: WB 14 B0014V1 BASELINE

value: 14 B0014V1 BASELINE

value: BASELINE


title: WB 12 B0012V6 IMPROVING

value: improving visit

value: 12 B0012V6 IMPROVING


title: WB 13 B0013V1 BASELINE

value: B

value: 13 B0013V1 BASELINE


title: WB 12 B0012VF FLARE

value: A

value: Flare visit

value: 12 B0012VF FLARE

value: FLARE


title: A2267_G

description:
Glycine expt3
_4658547084_D

value: trigeminal ganglia


title: WB 11 B0011VF FLARE

value: Yes

value: 11 B0011VF FLARE


title: WB 12 B0012V5 OTHER

value: No

value: 12 B0012V5 OTHER

value: OTHER


title: WB 12 B0012V3 OTHER

value: Patient

value: 12 B0012V3 OTHER


title: WB 12 B0012V1 BASELINE

value: Baseline

value: 12 B0012V1 BASELINE

value: BASELINE


title: A2264_G

description:
Glycine expt3
_4658547084_B

value: Glycine

value: Balb/c


title: #30_L-gln_0h

description:
Gln expt2
_4658547022_E

value: glutamine


title: A2259_Q

description:
glutamine expt3
_4658547084_C


title: #29_L-gln_0h

description:
Gln expt2
_4658547022_D


title: #28_L-gln_0h

description:
Gln expt2
_4658547022_B


title: #40_L-gln_0h

description:
Gln expt2
_4658547018_E


title: #36_L-gln_0h technical replicate

description:
Gln expt2 technical repeat of #36
_4658547018_F


title: WB 10 B0010VF FLARE

value: A

value: Flare visit

value: 10 B0010VF FLARE


title: WB 11 B0011V1 BASELINE

value: 11 B0011V1 BASELINE


title: #38_L-gln_0h

description:
Gln expt2
_4658547018_A

value: trigeminal ganglia


title: WB 11 B0011V5 OTHER

value: 11 B0011V5 OTHER


title: A2256_Q

description:
glutamine expt3
_4658547084_A


title: WB 11 B0011V6 IMPROVING

value: improving visit

value: No

value: 11 B0011V6 IMPROVING

value: IMPROVING


title: WB 10 B0010V6 IMPROVING

value: Patient

value: 10 B0010V6 IMPROVING


title: WB 10 B0010V5 OTHER

value: 10 B0010V5 OTHER

value: OTHER


title: #37_L-gln_0h

description:
Gln expt2
_4658547017_D


title: #20_Gly_0

description:
Gly expt2
_4658547022_C

value: glycine


title: WB 10 B0010V3 OTHER

value: 10 B0010V3 OTHER


title: #36_L-gln_0h

description:
Gln expt2
_4658547017_B

value: glutamine

value: Balb/c


title: #20_Gly_0 technical replicate

description:
Gly expt2 technical repeat of #20
_4658547022_F


title: WB 108 B0108V1 BASELINE

value: B

value: Baseline

value: 108 B0108V1 BASELINE

value: BASELINE


title: #19_Gly_0

description:
Gly expt2
_4658547022_A

value: trigeminal ganglia


title: WB 109 B0109V1 BASELINE

value: 109 B0109V1 BASELINE


title: WB 10 B0010V1 BASELINE

value: A

value: No

value: 10 B0010V1 BASELINE


title: #15_Gly_0

description:
Gly expt2
_4658547018_D


title: #11_Gly_0 technical replicate

description:
Gly expt2 technical repeat of #11
_4658547017_F


title: WB 107 B0107V1 BASELINE

value: Patient

value: 107 B0107V1 BASELINE


title: #14_Gly_0

description:
Gly expt2
_4658547018_B


title: WB 106 B0106V1 BASELINE

value: 106 B0106V1 BASELINE


title: #11_Gly_0

description:
Gly expt2
_4658547017_A


title: #12_Gly_0

description:
Gly expt2
_4658547017_C


title: WB 102 B0102V1 BASELINE

value: Yes

value: 102 B0102V1 BASELINE


title: WB 103 B0103V1 BASELINE

value: 103 B0103V1 BASELINE


title: WB 104 B0104V1 BASELINE

value: 104 B0104V1 BASELINE


title: WB 105 B0105V1 BASELINE

value: 105 B0105V1 BASELINE


title: WB 29 B0029VF FLARE

value: Flare visit

value: 29 B0029VF FLARE

value: FLARE


title: WB 32 B0032V1 BASELINE

value: B

value: Baseline

value: 32 B0032V1 BASELINE

value: BASELINE


title: WB 100 B0100V1 BASELINE

value: No

value: 100 B0100V1 BASELINE


title: WB 101 B0101V1 BASELINE

value: Patient

value: 101 B0101V1 BASELINE


title: TAC_BIX_rep2

city: Rozzano

first: Simone

last: Serio

state: Milano

address: Via Alessandro Manzoni, 56

department: Cardiovascular Medicine

country: Italy

institute: Humanitas Research Hospital

description: SAMPLE 4

data_processing: The data exported from GenomeStudio V2011.1  were analysed with Lumi/Limma in R.                 Data preprocessing was performed using lumi package:                                                                          - Background Correction: bgAdjust  - Variance Stabilizing Transform method: vst  - Normalization method: quantile                                                                                The differentianly expressed genes were identified using limma package.

source_name: cardiomyocyte

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: C57BL/6J mice subject to TAC (transverse aortic constriction) were treated with BIX-01294 for 1 week via subcutaneous mini-osmotic pumps. The control groups included cardiomyocyte-enriched populations isolated from DMSO-treated mice after TAC and from sham surgery mice.


title: #13_Gly_0

description:
Gly expt2
_4658547017_E

value: trigeminal ganglia

value: glycine

value: Balb/c


title: sham_rep2

description: SAMPLE 2

value: sham


title: TAC_DMSO_rep2

description: SAMPLE 6


title: TAC_DMSO_rep1

description: SAMPLE 5


title: sham_rep1

description: SAMPLE 1


title: TAC_BIX_rep1

description: SAMPLE 3


status: Public on Aug 29 2017

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_Staphylococcus aureus MRSA3407 PSM-E replicate 2

hyb_protocol: All cDNAs were hybridized to a custom Affymetrix GeneChip

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis

organism: Staphylococcus aureus

label_protocol: Biotin-labeled cDNA was synthesized and labeled according to the manufacturer’s suggestions for Affymetrix antisense genome arrays

growth_protocol: All bacteria were grown in tryptic soy broth (TSB)

extract_protocol: RNA was isolated using an RNeasy Mini Kit (Qiagen)

treatment_protocol: A single base mutation of the start codon was introduced into psm-mec (resulting in psm-mec*).

value: Staphylococcus aureus 3407 PSM-E


description: Gene expression data from_Staphylococcus aureus MRSA3407 PSM-E replicate 1


description: Gene expression data from_Staphylococcus aureus MRSA3407 replicate 3

value: Staphylococcus aureus 3407 Wt


description: Gene expression data from_Staphylococcus aureus MRSA3407 replicate 1


description: Gene expression data from_Staphylococcus aureus MRSA3407 replicate 2


description: Gene expression data from_Staphylococcus aureus MRSA252 replicate 1

value: Staphylococcus aureus MRSA 252 Wt


description: Gene expression data from_Staphylococcus aureus MRSA252 PSM-E replicate 3

value: Staphylococcus aureus MRSA 252 PSM-E


description: Gene expression data from_Staphylococcus aureus MRSA252 replicate 3


description: Gene expression data from_Staphylococcus aureus MRSA3407 PSM-E replicate 3


description: Gene expression data from_Staphylococcus aureus MRSA252 PSM-E replicate 2


description: Gene expression data from_Staphylococcus aureus MRSA252 replicate 2


description: Gene expression data from_Staphylococcus aureus MRSA252 PSM-E replicate 1


title: Stk11 deletion_rep4

city: Memphis

first: Geoffrey

last: Neale

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Mouse Gene 2.0 ST GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.6

source_name: LKB1-deficient Treg cells from mixed BM chimeras

label_protocol: One to five nanograms of total RNA were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Treg cells were sorted from mixed BM chimeras without additional culture.

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted Treg cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

value: mixed bone marrow (BM) chimeras

tag: genotype/variation

tag: cell type

value: Treg cells


title: WT_rep5

source_name: WT Treg cells from mixed BM chimeras

value: wild type


title: #39_L-gln_0h

description:
Gln expt2
_4658547018_C

value: glutamine


title: Stk11 deletion_rep2


title: Stk11 deletion_rep5


title: Stk11 deletion_rep1


title: WT_rep4


title: WT_rep3


title: ATLL

city: Kawasaki

first: Yoshihisa

last: Yamano

address: 2-16-1 Sugao, Miyamae-ku

institute: St. Marianna University School of Medicine

description: mRNA expression in CD4+CD25+CCR4+ from the ATLL patient.

hyb_protocol: Agilent one-color gene expression hyb/wash protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CD4+CD25+CCR4+ T-lymphocytes, peripheral blood ATLL

label_protocol: Agilent one-color Quick-Amp Labeling Kit labeling protocol.

extract_protocol: RNA was prepared using ISOGEN (Nippon gene, Toyama, Japan) following the manufacturer's recommendations.

treatment_protocol: Freshly drawn peripheral blood from a HAM/TSP patient, an ATLL patient and a healthy donor was subjected to peripheral blood mononuclear cells (PBMCs) isolation (Pancoll; PAN-Biotech, Aidenbach, Germany). For cell sorting, CD4+ T cells were negatively selected from PBMCs using MACS beads (Miltenyi Biotec, Germany) according to the manufacturer's instructions. The purified CD4+ T cells were stained with anti-CD4, anti-CD25 and anti-CCR4 antibodies, then CD4+CD25+CCR4+ and CD4+CD25-CCR4- T cells were separated using a cell sorter (JSAN, Bay Bioscience, Japan). The purity exceeded 95%.

tag: disease status

value: adult T-cell leukemia/lymphoma

value: CD4+CD25+CCR4+ blood cells

value: female


title: HD

description: mRNA expression in CD4+CD25+CCR4+ from the healthy donor.

source_name: CD4+CD25+CCR4+ T-lymphocytes, peripheral blood healthy donor

value: healthy

value: male


title: HAM/TSP

description: mRNA expression in CD4+CD25+CCR4+ from the HAM/TSP patient.

source_name: CD4+CD25+CCR4+ T-lymphocytes, peripheral blood HAM/TSP

value: HTLV-1 associated myelopathy/tropical spastic paraparesis


title: WT_rep1


title: HAM/TSP-negative

description: mRNA expression in CD4+CD25-CCR4- from the HAM/TSP patient.

source_name: CD4+CD25-CCR4- T-lymphocytes, peripheral blood HAM/TSP

value: CD4+CD25-CCR4- blood cells


title: WT_rep2


title: Stk11 deletion_rep3


title: Monasterium D2: Donor 6 Sandalore 500μM

city: Muenster

first: Jérémy

last: Cheret

address: Heisenbergstrasse 11

institute: Monasterium Laboratory

description: Monasterium D2: Donor 6 Sandalore 500μM

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Hair follicles cultured with Sandalore 500μM in William's E medium for 6 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Eukaryote Total RNA Nano 2.6; Total RNA Analysis ng sensitivity (Eukaryote)

treatment_protocol: For samples 1 to 8, human hair follicles were transfected for 6 hours with siRNA transfection reagent (Santa cruz) followed by 18 hours culture with normal William's E medium.

value: Hair follicle

value: Female


title: Monasterium B1: Donor 2 Scrambled Oligos

source_name: Hair follicle transfected with scrambled oligos for 6 hours followed by 18 hours culture with normal William's E medium.


title: HF 16-137 scramble: Donor 4 Scrambled Oligos


title: Monasterium A2: Donor 1 siRNA OR2AT4

description: Monasterium A2: Donor 1 siRNA OR2AT4

source_name: Hair follicle transfected with siRNA OR2AT4 for 6 hours followed by 18 hours culture with normal William's E medium.


title: Monasterium C1: Donor 5 Vehicle

description: Monasterium C1: Donor 5 Vehicle

source_name: Hair follicles cultured with 0.1% DMSO in William's E medium for 6 hours


title: HF 16-137 si OR: Donor 4 siRNA OR2AT4

description: HF 16-137 si OR: Donor 4 siRNA OR2AT4


title: Monasterium C2: Donor 5 Sandalore 500μM

description: Monasterium C2: Donor 5 Sandalore 500μM


title: Monasterium D1: Donor 6 Vehicle

description: Monasterium D1: Donor 6 Vehicle


title: HF 16-127 vehicle: Donor 8 Vehicle

description: HF 16-127 vehicle: Donor 8 Vehicle


title: Monasterium B2: Donor 2 siRNA OR2AT4

description: Monasterium B2: Donor 2 siRNA OR2AT4


title: HF 16-115 scramble: Donor 3 Scrambled Oligos


title: HF 16-116 vehicle: Donor 7 Vehicle

description: HF 16-116 vehicle: Donor 7 Vehicle


title: HF 16-116 sandalore: Donor 7 Sandalore 500μM


title: Monasterium A1: Donor 1 Scrambled Oligos


title: HF 16-127 sandalore: Donor 8 Sandalore 500μM


title: last third leaf at stage4, biological rep1

city: Shanghai

first: Hong-Wei

last: Xue

address: 300 Fenglin Road

country: China

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences

description: Gene expression data from last third leaf at stage4

hyb_protocol: Array hybridization and wash was performed using GeneChip Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 and Fluidics Station 450 (Affymetrix) followed the manufacturer’s instructions.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: Analyses were performed using the R software package and packages by Bioconductor.  After comparing the performances of popular methods on our data, the RMA method was used to obtain summary expression values for each probe set. Gene expression intensities were analyzed on a logarithmic scale.

organism: Oryza sativa

source_name: rice last third leaf at stage4

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Sata Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Rice plants (Oryza sativa, japonica cultivar Zhonghua 11)  were cultivated in a greenhouse with a light/dark cycle of 12 h at 28°C/12 h at 22°C, 85% relative humidity regime.

treatment_protocol: Lamina joint and leaf tissues were manually cut and immediately put into liquid nitrogen.

value: last third leaf

tag: age

value: stage4 (55 days after sowing)

tag: morphology

value: green


title: last third lamina joint at stage4, biological rep1

description: Gene expression data from last third lamina joint at stage4

source_name: rice last third lamina joint at stage4

value: last third lamina joint

value: mature, white, leaf angle is 0


title: last second lamina joint at stage5, biological rep2

description: Gene expression data from last second lamina joint at stage5

source_name: rice last second lamina joint at stage5

value: last second lamina joint

value: stage5 (65 days after sowing)

value: leaf angle increase, white


title: HF 16-115 si OR: Donor 3 siRNA OR2AT4

description: HF 16-115 si OR: Donor 3 siRNA OR2AT4

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).


title: last third lamina joint at stage6, biological rep1

description: Gene expression data from last third lamina joint at stage6

source_name: rice last third lamina joint at stage6

value: stage6 (70 days after sowing)

value: senescence, white, dehydrated and distorted


title: last third lamina joint at stage6, biological rep2


title: last third lamina joint at stage4, biological rep2


title: last second lamina joint at stage6, biological rep2

description: Gene expression data from last second lamina joint at stage6

source_name: rice last second lamina joint at stage6

value: stage6 (75 days after sowing)


title: last second lamina joint at stage5, biological rep1


title: last third lamina joint at stage2, biological rep2

description: Gene expression data from last third lamina joint at stage2

source_name: rice last third lamina joint at stage2

value: stage2 (50 days after sowing)

value: young, white or creamy yellow


title: last second lamina joint at stage6, biological rep1


title: last third leaf at stage4, biological rep2


title: last third lamina joint at stage5, biological rep1

description: Gene expression data from last third lamina joint at stage5

source_name: rice last third lamina joint at stage5

value: stage5 (60 days after sowing)


title: last third lamina joint at stage5, biological rep2


title: last third lamina joint at stage2, biological rep1


title: last second lamina joint at stage4, biological rep1

description: Gene expression data from last second lamina joint at stage4

source_name: rice last second lamina joint at stage4

value: stage4 (60 days after sowing)


title: last second lamina joint at stage2, biological rep2

description: Gene expression data from last second lamina joint at stage2

source_name: rice last second lamina joint at stage2

value: stage2 (55 days after sowing)


title: last second lamina joint at stage4, biological rep2


title: last lamina joint at stage5, biological rep2

description: Gene expression data from last lamina joint at stage5

source_name: rice last lamina joint at stage5

value: last lamina joint

value: stage5 (70 days after sowing)


title: last lamina joint at stage6, biological rep2

description: Gene expression data from last lamina joint at stage6

source_name: rice last lamina joint at stage6

value: stage6 (80 days after sowing)


title: last lamina joint at stage2, biological rep1

description: Gene expression data from last lamina joint at stage2

source_name: rice last lamina joint at stage2

value: stage2 (60 days after sowing)


title: last lamina joint at stage4, biological rep2

description: Gene expression data from last lamina joint at stage4

source_name: rice last lamina joint at stage4

value: stage4 (65 days after sowing)


title: last lamina joint at stage2, biological rep2


title: last lamina joint at stage4, biological rep1

value: mature, white, leaf angle is 0


title: EGC tissue sample 15

city: Beijing

first: Xue

last: Xu

state: Beijing

address: ShuaiFuYuan 1

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description: gene expression of gastric early-stage adenocarcinoma

hyb_protocol: cRNA was hybridized to Agilent 4×44K Whole Human Genome microarray.

scan_protocol: Slides were washed and then scanned with the Agilent G2505B Microarray Scanner System. Fluorescence intensities of the scanned images were extracted and preprocessed with the Agilent Feature Extraction Software (v9.1).

data_processing: Data normalization, Quality Control, Principal component analysis(PCA) and Filter by Flags were performed using the GeneSpring software GX 12.6(Agilent Technologies).

source_name: EGC

label_protocol: Initially 100ng of total RNA was added into the reaction to generate 1.65µg Cy3-labeled cRNA using Low Input Quick Amp Labeling Kit(Agilent).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit(Qiagen, MD, USA). The concentration was measured by ND-1000 UV-VIS spectrophotometer(NanoDrop Technologies, DE, USA). The quality of purified RNA(RNA integrity number, RIN) was detected by the RNA 6000 Labchip Kit and Agilent 2100 Bioanalyzer(Agilent, CA, USA).

value: Male

tag: disease state

value: gastric early-stage adenocarcinoma

value: gastric tissue


title: EGC tissue sample 18

value: Female


title: last lamina joint at stage6, biological rep1

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

value: senescence, white, dehydrated and distorted


title: EGC tissue sample 19


title: EGC tissue sample 14


title: last second lamina joint at stage2, biological rep1

value: last second lamina joint


title: EGC tissue sample 17


title: last lamina joint at stage5, biological rep1

value: leaf angle increase, white


title: EGC tissue sample 16


title: EGC tissue sample 9


title: EGC tissue sample 12


title: EGC tissue sample 10


title: EGC tissue sample 13


title: EGC tissue sample 11


title: EGC tissue sample 8


title: EGC tissue sample 4


title: EGC tissue sample 2


title: EGC tissue sample 5


title: EGC tissue sample 3


title: EGC tissue sample 1


title: EGC tissue sample 6


title: EGC tissue sample 7


title: HGIN tissue sample 20

description: gene expression of gastric high-grade intraepithelial neoplasia

source_name: HGD


title: HGIN tissue sample 16

value: gastric high-grade intraepithelial neoplasia


title: HGIN tissue sample 19


title: HGIN tissue sample 17


title: HGIN tissue sample 18


title: HGIN tissue sample 10


title: HGIN tissue sample 15


title: HGIN tissue sample 8


title: HGIN tissue sample 5


title: HGIN tissue sample 14


title: HGIN tissue sample 13


title: HGIN tissue sample 4


title: HGIN tissue sample 11


title: hCC at passage 6

city: Montpellier

first: Said

last: Assou

address: 80, av. Augustin Fliche

department: Institute for Regenerative Medecine and Biotherapy

country: France

institute: University Hospital of Montpellier, Inserm

description: Gene expression data from hCC at passage 6

hyb_protocol: After fragmentation, the labeled antisense aRNA (15 μg) was hybridized to HG-U133 Plus 2.0 GeneChip pan-genomic oligonucleotide arrays (Affymetrix)

scan_protocol: GeneChips were scanned using the

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.

source_name: human cumulus cells

label_protocol: Biotinylated nucleotide analog was incorporated during in vitro transcription step according to the Affymetrix protocol.

growth_protocol: Human cumulus cells were collected from patients consulting in our centre for intra-cytoplasmic sperm injection (ICSI) after written informed consent. Cumulus–oocyte complex (COC) retrieval was performed by vaginal puncture under ultrasound echo-guidance 36 h after hCG administration

extract_protocol: Rneasy Micro-kit was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: The fresh cumulus cells were mechanically separated from the oocytes using needles, (<40 h after hCG administration). They were then transferred to dish coated with a matrix of human collagen.

value: ovary

value: cumulus cell


title: HGIN tissue sample 6


title: HGIN tissue sample 12


title: hCC at passage 3

description: Gene expression data from hCC at passage 3


title: HGIN tissue sample 3


title: HGIN tissue sample 9


title: HGIN tissue sample 7


title: hCC at passage 9

description: Gene expression data from hCC at passage 9


title: HGIN tissue sample 2


title: MC-AD_F?_BB_01

city: Houston

first: Mario

last: Sirito

state: TX

address: 1515 Holcombe blvd

department: Cancer Genetics

institute: M. D. Anderson Cancer Center

data_processing: from CEL files we genereated DCP files uing dChip 2006 (DNA-Chip Analyzer), Build date: Feb 16 2006 (MBEI analysis model)

source_name: Skeletal Muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix GeneChip Expression Analysis Technical Manual, Rev5, using 5 ug total RNA

tag: biopsy site

value: Biceps brachii

tag: Myotonia Congenita Autosomal Dominant patient

tag: age unknown

tag: Gender

value: F


title: TMD_F88_EDL_03

hyb_protocol: standard Affymetrix GeneChip Expression Analysis Technical Manual, Rev5

value: Extensor hallucis/Digitorum longus

tag: Tibial Muscular Dystropy patient

tag: age 88


title: TMD_M58_TA_04

scan_protocol: standard Affymetrix GeneChip Expression Analysis Technical Manual, Rev5

value: Tibialis anterior

tag: age 58

value: M


title: LGIN tissue sample 18

description: gene expression of gastric low-grade intraepithelial neoplasia

source_name: LGD

tag: gender


title: HGIN tissue sample 1


title: LGIN tissue sample 19

value: gastric low-grade intraepithelial neoplasia


title: DMD_M8_BB_02

tag: Duchenne Muscular Dystrophy patient

tag: age 8


title: DMD_M20_G_03

value: Gastrocnemius

tag: age 20


title: TMD_M58_EDL_02


title: LGIN tissue sample 17

value: Male

tag: tissue


title: LGIN tissue sample 15


title: TMD_M64_G_01

tag: age 64


title: LGIN tissue sample 12


title: LGIN tissue sample 16


title: LGIN tissue sample 13


title: LGIN tissue sample 11


title: LGIN tissue sample 6


title: BMD_M45_BB_04

tag: Baker Myotonic Dystrophy patient

tag: age 45


title: BMD_M?_BB_02


title: LGIN tissue sample 9

tag: age


title: LGIN tissue sample 8

tag: disease state


title: LGIN tissue sample 10


title: DMD_M5_BB_01

tag: biopsy site

tag: age 5


title: LGIN tissue sample 14


title: LGIN tissue sample 7


title: LGIN tissue sample 2


title: BMD_M50_D_03

value: Deltoid

tag: age 50


title: BMD_M26_BB_05

tag: age 26

tag: Gender


title: BMD_M?_TB_01

value: Triceps brachii

tag: age unknown


title: LGIN tissue sample 4

value: Female

value: gastric tissue


title: LGIN tissue sample 5


title: N_Mf_?_09

value: unknown

tag: Normal fetus patient

tag: age f


title: chronic gastritis tissue sample 19

description: gene expression of chronic gastritis

source_name: inflammation

tag: gender

value: chronic gastritis


title: LGIN tissue sample 1


title: N_Ff_?_08


title: N_Ff_?_07


title: chronic gastritis tissue sample 18

description: gene expression of chronic gastritis


title: chronic gastritis tissue sample 15

description: gene expression of chronic gastritis


title: N_MF43-46_?_06_b

tag: Normal adult patient

tag: Gender M/F pool


title: chronic gastritis tissue sample 16

description: gene expression of chronic gastritis

tag: tissue


title: chronic gastritis tissue sample 13

description: gene expression of chronic gastritis


title: LGIN tissue sample 3


title: N_M26_?_05_b


title: chronic gastritis tissue sample 14

description: gene expression of chronic gastritis


title: chronic gastritis tissue sample 17

description: gene expression of chronic gastritis


title: chronic gastritis tissue sample 12

description: gene expression of chronic gastritis


title: chronic gastritis tissue sample 5

description: gene expression of chronic gastritis


title: DMx_M69_?_15

tag: DMX patient

tag: age 69


title: chronic gastritis tissue sample 11

description: gene expression of chronic gastritis


title: chronic gastritis tissue sample 2

description: gene expression of chronic gastritis


title: chronic gastritis tissue sample 9

description: gene expression of chronic gastritis


title: N_M43_?_04_b

tag: age 43


title: chronic gastritis tissue sample 10

description: gene expression of chronic gastritis

tag: age


title: chronic gastritis tissue sample 4

description: gene expression of chronic gastritis

tag: disease state


title: chronic gastritis tissue sample 6

description: gene expression of chronic gastritis


title: DMx_M48_G_14

tag: biopsy site

tag: age 48


title: N_M85_?_02_b

tag: age 85


title: chronic gastritis tissue sample 8

description: gene expression of chronic gastritis


title: chronic gastritis tissue sample 1

description: gene expression of chronic gastritis


title: chronic gastritis tissue sample 3

description: gene expression of chronic gastritis


title: N_M43_?_03_b


title: DMx_M46_VL_13

value: Vastus lateralis

tag: age 46


title: N_F61_?_01_b

tag: age 61

tag: Gender


title: chronic gastritis tissue sample 7

description: gene expression of chronic gastritis


title: 480 - 48hrs

city: Curitiba

first: Guilherme

middle: Ferreira

last: Silveira

address: Prof Algacyr Munhoz Máder

country: Brazil

institute: Instituto Carlos Chagas

hyb_protocol: Samples were hybridized with GeneChip Human Gene 1.0 ST Arrays (Affymetrix) and scanned at the LNLS- Campinas Brazil facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
RMA expression value derived from Expression Console software; core-gene analysis
The generated files were analyzed for quality by the software Expression Console (Affymetrix, Santa Clara, CA). The same software was used to normalize the data by the RMA method. Log-ratio between DENV1/60, DENV1 435, or DENV1 480 infected-mdDCs and mock-infected-mdDCs intensity signal values were generated and a list of differential expressed genes was obtained by using a 2 our higher fold-change. Data clustering was performed by the Cluster 3.0 software with a Euclidian’s distance. Tool for Analysis of GO Enrichments (TANGO), in Expander software was used to obtain a GO with statistical enhancer values of 0.05, and, NCBIEntrez Gene database (www.ncbi.nih.gov) and the Gene Ontology database (www.geneontology.org), to define the most relevant cell signaling and metabolic pathways during mdDC infection with DENV1 60, DENV1 435, or DENV1 480.

source_name: DENV1/480-infected, 48hr

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Monocyte-derived dendritic cells (mdDCs) were generated using peripheral blood from healthy volunteers after informed consent and approval of the FIOCRUZ Research Ethics Committee (number 514/09). Mononuclear cells were separated by density gradient using Lymphocyte Separation Medium (Lonza, Walkersville, USA) and CD14+ cells were purified by magnetic immunosorting (Miltenyi Biotec, Auburn, CA), according to the manufacturer’s recommendations. CD14+ cells were cultured for 6-7 days in RPMI 1640 medium containing 100 ng/mL interleukin-4 (IL-4) and 50 ng/mL granulocyte-monocyte colony stimulating factor (GM-CSF; PeproTech, Rocky Hill, NJ), 10% fetal bovine serum (FBS) and 100 IU/µg/mL of penicillin/streptomycin and 2 mM of L-Glutamine (Gibco-BRL, Grand Island, NY). The cultures were assessed by flow cytometry and only cultures with more than 80% of CD1a+ and less than 5% of CD14+ purity were used. C6/36 cells were grown in Leibovitz-15 medium supplemented with 5% FBS and 0.26% of tryptose and 25 µg/mL of gentamicin (all reagents from Gibco-BRL, Grand Island, NY).

extract_protocol: Cells were collected at 8, 24 and 48 hours post infection (hpi) and used to extract total RNA using RNaesy Mini Kit according to the manufacturer’s recommendations (QIAGEN, Valencia, CA). The RNA of all ten mdDC cultures was pooled (75 µg of each) for microarray experiments and compared to mock infected cells using Human Gene 1.0 st v. 1 array GeneChip slides from Affymetrix (Santa Clara, CA). The RNA pool was processed as according to the manufacturer’s recommendations (Affymetrix, Santa Clara, CA) for the amplification and in vitro transcription, purification, tagging, hybridization and scanning of the slides (GeneChip® Scanner 3000).

treatment_protocol: Ten mdDCs cultures were mock-infected or infected with DENV1/60, DENV1/435 or DENV1/480 at an MOI of 5 for two hours in the absence of FBS. The viral inoculum was removed and cells were washed and cultured in RPMI 1640 plus 10% of FBS and 100 IU/µg/mL of penicillin/streptomycin (Gibco-BRL, Grand Island, NY).

tag: cell type

value: Dendrític Cells

tag: infection

value: DENV1/480 (mutated strain)

tag: time


title: Mock - 8hrs

source_name: Mock-infected, 8hr

value: control