title: SmoM2 bcatcLOF cells IFE 4 weeks after TAM administration, rep1

description: 4W K14ER SmoM2 bcatcLOF IFE exp1


title: SmoM2 cells IFE 4 weeks after TAM administration, rep1

status: Public on Sep 06 2012

type: RNA

city: Brussels

first: KHALIL

last: KASS YOUSSEF

address: 808, Route de Lennick

country: Belgium

institute: ULB-IRIBHM

description: 4W K14ER SmoM2 IFE exp1

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix MOE 430 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: The data were analyzed with R (version 2.14.0) Bioconductor fRMA (version 1.6) package with default analysis settings.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: FACS sorted SmoM2+ IFE cells 4wks after tamoxifen administration to K14CREER/Rosa-SmoM2-YFP mice

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

extract_protocol: Microprep kit, RNAeasy, Stratagen

treatment_protocol: K14CREER/Rosa-SmoM2-YFP and K14CREER/Rosa-SmoM2-YFP/b-catenin cKO mice were treated with tamoxifen to activate Cre-mediated recombination.

tag: strain background

value: mixed

tag: genotype/variation

tag: tissue

value: Tail epidermis

tag: cell type

value: basal interfollicular epidermis (IFE) cells


title: SmoM2 cells IFE 1 week after TAM administration, rep1

description: 1W K14ER SmoM2 IFE exp1

source_name: FACS sorted SmoM2+ IFE cells 1wk after tamoxifen administration to K14CREER/Rosa-SmoM2-YFP mice


title: IFE no TAM, rep2

description: WT IFE exp2

source_name: FACS sorted IFE cells from untreated K14CREER/Rosa-SmoM2-YFP mice


title: SmoM2 cells IFE 10 weeks after TAM administration, rep2

description: 10W K14ER SmoM2 exp3

source_name: FACS sorted SmoM2+ IFE cells 10wks after tamoxifen administration to K14CREER/Rosa-SmoM2-YFP mice


title: murine pancreatic cancer cell line PPT-17728

city: München

first: Günter

last: Schneider

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Technische Universität München

description: Gene expression data from murine pancreatic cancer cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the 3 GeneChip Fluidics Station F450.

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

data_processing: Raw data analysis was performed with R and Bioconductor (Gentleman et al. 2004; R Development Core Team 2007). Arrays were assessed for quality and RMA-normalized.

label_protocol: Biotinylated aRNA was prepared according to the standard GeneChip 3' IVT Express Kit (Affymetrix) protocol from 250 ng total RNA.

growth_protocol: Low passage murine pancreatic cancer cells were cultured at 37°C with 5% CO2 in DMEM medium supplemented with 10% fetal calf serum and 1% [vol/vol] P/S/A.

extract_protocol: Extraction of total RNA was performed using QIAGEN QIAshredder (#79656) and the RNeasy Mini kit (#74106) according to the manufacturer's instructions.

treatment_protocol: No special treatment was applied.

tag: cell line

value: pancreatic cancer


title: murine pancreatic cancer cell line B-152727


title: IFE no TAM, rep1

description: WT IFE exp1


title: murine pancreatic cancer cell line PPT-53631


title: murine pancreatic cancer cell line PUL-15272


title: murine pancreatic cancer cell line PPT-5748


title: murine pancreatic cancer cell line HEP1-15272


title: murine pancreatic cancer cell line PPT-6051


title: murine pancreatic cancer cell line LN1-15272


title: murine pancreatic cancer cell line B-6051


title: murine pancreatic cancer cell line ASC-5193


title: murine pancreatic cancer cell line PPT-5671


title: murine pancreatic cancer cell line PPT-3250


title: murine pancreatic cancer cell line ASC-53909


title: murine pancreatic cancer cell line PPT-15272


title: murine pancreatic cancer cell line B-5123


title: murine pancreatic cancer cell line PPT-5320


title: murine pancreatic cancer cell line PPT-5193


title: murine pancreatic cancer cell line PPT1-5123


title: murine pancreatic cancer cell line PPT-16992


title: murine pancreatic cancer cell line PPT2-3202


title: GATA2ff_P41

city: Research Triangle Park

first: Franco

last: DeMayo

state: NC

address: Building 101, Room F191 111 T.W. Alexander Drive

department: Reproductive and Developmental Biology Laboratory

country: USA

institute: National Institute of Environmental Health Sciences

description: Gene expression data from ovariectomized P4 treated Gata2 f/f uterus horn

hyb_protocol: The fragmented, labeled cRNA (15 ug) was hybridized to Affymetrix mouse genome 430 2.0 arrays.

scan_protocol: Scanning was done using an Affymetrix 3000 with autoloading scanner performed using Affymetrix protocols.

data_processing: A DNA-Chip analyzer dChIP version 1.3 was utilized to adjust arrays to a common baseline using invariant set normalization. All Genechips (n=6) were normalized together to the same baseline and modeled together.

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

extract_protocol: QIAGEN RNeasy total RNA isolation kit.

value: GATA2 f/f

tag: gender

value: female

tag: age

value: 8 weeks old

tag: strain

value: mixed background

value: ovariectomized uterus


title: GATA2ff_P42


title: GATA2ff_P43


title: murine pancreatic cancer cell line PPT-5486


title: murine pancreatic cancer cell line PPT-3107


title: GATA2ff_Oil2

description: Gene expression data from ovariectomized Oil treated Gata2 f/f uterus horn


title: GATA2ff_Oil3


title: sleep deprived mouse,biological replicate 8

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

description: sleep deprived mouse

hyb_protocol: cRNA was hybridized for 16 hr at 45C on Mouse 430 2.0 genome arrays (Expression Analysis Technical Manual, 2001, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G at 3um resolution after excitation at 570 nm.

data_processing: The average signal from two sequential scans was calculated for each microarray feature. RMA normalization of signal instensity was performed using the Affy package from R/Bioconductor

source_name: Dissected hippocampus from mouse

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

growth_protocol: Subjects. C57BL/6J adult male mice (2 to 4 months of age) were housed individually on a 12 hr/12 hr light/dark schedule with lights on at 7 am (ZT 0). Food and water were available ad libitum throughout the experiment.

extract_protocol: Samples were homogenized in TRIzol followed by phase separation with 1-bromo-3-chloropropane (BCP). An equal volume of 70% ethanol was added to the aqueous phase, which was then further purified using the RNeasy system according to manufacturer's protocol. The 50ul eluate was supplemented with 1ul SUPERase-In prior to concentration to 20uL by vacuum centrifugation

treatment_protocol: Each animal was handled daily for 6 days prior to sleep deprivation. Starting at approximately ZT 0-5, mice were sleep-deprived (SD) in their home cages for 5 hours by gentle handling[38]. Non-sleep-deprived mice (NSD) were left undisturbed in their home cages.Hippocampal dissections were performed immediately following the behavioral treatment, and alternated between SD and NSD animals.

value: hippocampus

tag: genotype

value: 2 months

tag: treatment

value: sleep deprived mouse


title: murine pancreatic cancer cell line HEP-5123


title: sleep deprived mouse,biological replicate 6

description: sleep deprived mouse


title: GATA2ff_Oil1


title: sleep deprived mouse,biological replicate 7

description: sleep deprived mouse


title: LbrAdeletionMutant vs ScottA rep2

city: Columbus

first: Hua

last: Wang

state: OH

address: 2015 Fyffe CT

department: Food Science and Technology

institute: The Ohio State University

description: Sample 6

hyb_protocol: The Standard Operating Procedures for Hybridization of Labeled cDNA probes (ftp://ftp.jcvi.org/pub/data/PFGRC/MAIN/pdf_files/protocols/M008.pdf) by the J. Craig Venter Institute was followed.

scan_protocol: Microarray slides were scanned on a GenePix 4000B microarray scanner from Molecular Devices. Gain value was acquired in automatic reading mode (3 reads).

data_processing: Scanned data from dried slides were normalized and statistical analysis was conducted using the TM4 microarray software suite from J. Craig Venter Institute.  Briefly, Midas was used to normalize the microarray using LOWESS normalization. The data were then entered into Multi Experiment Viewer (MEV) where T-Tests were performed using a p-value of p = 0.05. The UID column in MEV file corresponds to to ID column in the gpr file and IA represents Cy3 and IB represents Cy5. Please note that the array which was designed for multiple strains (including Listeria moncytogenes 4b F2365, EGD-e, 1/2a F6854, 4bH7858 and HCC23) was used for this study with the ScottA strain, which resulted in no signal/values for a large percentage of the probes on the array.

organism: Listeria monocytogenes

source_name: LbrAdeletion mutant

label_protocol: The Standard Operating Procedures for Aminoallyl Labeling of RNA (ftp://ftp.jcvi.org/pub/data/PFGRC/MAIN/pdf_files/protocols/M007.pdf) from J. Craig Venter Institute was adopted.

growth_protocol: Frozen L. monocytogenes cultures were activated  by incubating in  trypticase soy broth supplemented with 0.5% yeast extract (TSBYE) at 37°C for 18 h, and transferred at least once prior to assessments.

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) following manufacturer’s procedure with slight modification. Briefly, 23.75 ml of fresh TSBYE was inoculated with overnight cultures at 2.5% and grown at 37°C for 6 h until reached at OD600 of 0.6 – 0.7. One mL of aliquots were removed and placed in 4°C refrigerator for 15 min, and the cells were collected by centrifugation at 8000xg for 5 min. The cells were resuspended in 100μL of TE buffer and 6μL of lysozyme (50μg/mL) followed by incubation at 30°C for 30 min. The rest of the procedures followed manufacturer’s instruction .The extracted RNA was used within 30 min of extraction or stored at -80°C until use

treatment_protocol: No treatment was applied before extract preparation.

value: ScottA

value: LbrA deletion

source_name: strong biofilm former


title: MCF10-480min-EGF

city: reovot

first: roi

last: avraham

address: hertzel

country: Israel

institute: weizmann

description: microRNA expression after EGF stimulation

hyb_protocol: Agilent protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting.

data_processing: Samples are in feature extraction format.  The expression value for each miRNA was calculated using Feature Extraction software 9.5.1. miRNAs that were not detected in more than three time points according to GeneView flags were removed. All values lower than 5 were leveled to 5. For each miRNA the intensity values were normalized across the sample set, log transformed, and calculated as fold change from time 0, and are included in the corresponding norm files. MCF10-40 EGF was removed from further analysis due to technical noise.

organism: Homo sapiens

label_protocol: Agilent microRNA labelling kit

extract_protocol: microRNAs were prepared using the Qiagen miRneasy kit according to the manufacturer instructions


title: sleep deprived mouse,biological replicate 3

description: sleep deprived mouse


title: sleep deprived mouse,biological replicate 4

description: sleep deprived mouse


title: sleep deprived mouse,biological replicate 5

description: sleep deprived mouse


title: non-sleep deprived mouse control,biological replicate 5

description: non-sleep deprived mouse control

value: non-sleep deprived mouse


title: sleep deprived mouse,biological replicate 2

description: sleep deprived mouse


title: non-sleep deprived mouse control,biological replicate 2

description: non-sleep deprived mouse control


title: non-sleep deprived mouse control,biological replicate 8

description: non-sleep deprived mouse control


title: non-sleep deprived mouse control,biological replicate 7

description: non-sleep deprived mouse control


title: sleep deprived mouse,biological replicate 1

description: sleep deprived mouse


title: non-sleep deprived mouse control,biological replicate 4

description: non-sleep deprived mouse control


title: non-sleep deprived mouse control,biological replicate 3

description: non-sleep deprived mouse control


title: non-sleep deprived mouse control,biological replicate 6

description: non-sleep deprived mouse control


title: non-sleep deprived mouse control,biological replicate 9

description: non-sleep deprived mouse control


title: non-sleep deprived mouse control,biological replicate 1

description: non-sleep deprived mouse control


title: Paxgene total RNA from patient BC355, illness day 18 ,WHO stage 3

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57070.gif

hyb_protocol: not provided

scan_protocol: model: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene Universal Human Reference RNA, 1st rnd amp AW 11/01/01

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: whole blood

tag: individual

value: patient BC355

tag: illness day

tag: disease state

value: WHO stage 3


title: Paxgene total RNA from healthy subject BR407

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57080.gif

value: Stratagene Universal Human Reference RNA

value: healthy subject BR407

value: WHO stage N/A


title: Paxgene total RNA from patient BC325, illness day 90 ,WHO stage indet

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57032.gif

value: patient BC325

value: WHO stage indet


title: Paxgene total RNA from patient BC327, illness day 4 ,WHO stage 1

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57033.gif

value: patient BC327

value: WHO stage 1


title: Paxgene total RNA from patient BC355, illness day 5 ,WHO stage 3

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57066.gif


title: Paxgene total RNA from patient BC338, illness day 31 ,WHO stage 2

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57052.gif

value: patient BC338

value: WHO stage 2


title: Paxgene total RNA from healthy subject BR409

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57082.gif

value: healthy subject BR409


title: Paxgene total RNA from patient BC337, illness day 4 ,WHO stage 3

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57048.gif

value: patient BC337


title: Paxgene total RNA from patient BC333, illness day 5 ,WHO stage 2

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57044.gif

value: patient BC333


title: Paxgene total RNA from patient BC341, illness day 92 ,WHO stage 2

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57053.gif

value: patient BC341


title: Paxgene total RNA from patient BC338, illness day 15 ,WHO stage 2

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57051.gif


title: Paxgene total RNA from patient BC329, illness day 32 ,WHO stage 3

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57039.gif

value: patient BC329


title: Paxgene total RNA from patient BC338, illness day 8 ,WHO stage 2

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57050.gif

value: whole blood


title: Paxgene total RNA from patient BC334, illness day 5 ,WHO stage 2

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57045.gif

value: patient BC334


title: Paxgene total RNA from patient BC325, illness day 4 ,WHO stage indet

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57028.gif


title: Paxgene total RNA from patient BC329, illness day 18 ,WHO stage 3

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57037.gif

value: WHO stage 3


title: Paxgene total RNA from patient BC353, illness day 6 ,WHO stage 3

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57062.gif

value: Stratagene Universal Human Reference RNA

value: patient BC353


title: Paxgene total RNA from healthy subject BR403

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57079.gif

value: healthy subject BR403

value: WHO stage N/A


title: Paxgene total RNA from healthy subject BR408

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57081.gif

value: healthy subject BR408


title: Paxgene total RNA from patient BC355, illness day 10 ,WHO stage 3

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57069.gif

value: patient BC355


title: Paxgene total RNA from patient BC355, illness day 7 ,WHO stage 3

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57068.gif


title: Paxgene total RNA from patient BC355, illness day 33 ,WHO stage 3

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57071.gif


title: SCV, 24h, rep3

city: Nottingham

first: victoria

last: wright

state: Notts

address: University Park

department: MOL

country: United Kingdom

institute: University of Nottingham

description: Gene expression data from PA01-SCV at 24hours, early stationary phase

hyb_protocol: Following fragmentation, 2.7 ug of cRNA were hybridized for 16 hr at 50C at 60rpm on GeneChip Pseudomonas aeruginosa Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: GeneSpring GX7.3.1 was used to process the data using the RMA preprocessing tool. The resultant values were used in downstream analyses.

organism: Pseudomonas aeruginosa

source_name: PA01-SCV early (24h) stationary phase

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12ug total RNA .

growth_protocol: Cultures were grown in triplicate in iron poor casamino acids (CAA) medium (Difco Laboratories)until early (24 h) and late (48 h) stationary phase, respectively, allowing three biological replicates per condition.

extract_protocol: total RNA was extracted using the RNeasy Midi Kit (Qiagen), on-column DNase digestion was performed using the RNase-free DNase Set according to the manufactures instructions.

treatment_protocol: Cells were treated with RNAprotect Bacteria Reagent (Qiagen) as recommended by the manufacturer prior to RNA extraction.

tag: growth phase

value: early stationary


title: Paxgene total RNA from patient BC341, illness day 7 ,WHO stage indet

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57055.gif

value: WHO stage indet


title: SCV, 48h, rep3

description: Gene expression data from PA01-SCV at 48hours, late stationary phase

source_name: PA01-SCV late (48h) stationary phase

value: late stationary


title: WT, 48h, rep3

description: Gene expression data from WT at 48hours, late stationary phase

source_name: WT late (48h) stationary phase

value: WT


title: SCV, 24h, rep1


title: Paxgene total RNA from patient BC330, illness day 6 ,WHO stage 3

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57043.gif

value: patient BC330


title: SCV, 24h, rep2


title: WT, 24h, rep3

description: Gene expression data from WT at 24hours, early stationary phase

source_name: WT early (24h) stationary phase


title: WT, 48h, rep1


title: WT, 24h, rep2


title: Paxgene total RNA from patient BC329, illness day 4 ,WHO stage 3

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57035.gif


title: Paxgene total RNA from patient BC329, illness day 188 ,WHO stage 3

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57041.gif


title: Paxgene total RNA from patient BC325, illness day 6 ,WHO stage indet

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57029.gif

value: patient BC325


title: WT, 24h, rep1


title: Paxgene total RNA from patient BC354, illness day 4 ,WHO stage 2

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57063.gif

value: patient BC354

value: WHO stage 2


title: SCV, 48h, rep2


title: Paxgene total RNA from patient BC328, illness day 5 ,WHO stage 1

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57034.gif

value: whole blood

value: patient BC328

value: WHO stage 1


title: SCV, 48h, rep1


title: Paxgene total RNA from patient BC325, illness day 12 ,WHO stage indet

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57031.gif

value: Stratagene Universal Human Reference RNA


title: Paxgene total RNA from patient BC338, illness day 3 ,WHO stage 2

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57049.gif

value: patient BC338


title: parotid tissue from primary Sjogren syndrome patient 15

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: 15μg of labeled cRNA was fragmented into 50- to 200-bp fragments and assessed for quality with a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)

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

data_processing: Microarray data were processed and normalized using MAS5.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA

growth_protocol: parotid tissue from humans

extract_protocol: Total RNAs were extracted using mirVana PARIS Kit (Ambion/Applied Biosystems).

tag: disease status

value: pSS

tag: batch


title: Paxgene total RNA from patient BC341, illness day 31 ,WHO stage indet

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57056.gif

value: patient BC341


title: parotid tissue from primary Sjogren syndrome patient 19


title: parotid tissue from primary Sjogren syndrome patient 18


title: AD2

city: Jerusalem

first: Amit

last: Berson

address: The Edmond J. Safra Campus, Givat Ram

department: Biological Chemistry

institute: The Hebrew University of Jerusalem

description:
Braak stage 6
J36-98028.CEL

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed and RMA (quantile) normalized using Altanalyse and Matlab softwares.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Entorhinal cortex of AD2

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Total RNA was extracted with miRNeasy (Qiagen) as per the manufacturer's protocol

value: Alzheimer's disease

tag: braak stage


title: parotid tissue from primary Sjogren syndrome patient 14


title: parotid tissue from sicca patient 16

source_name: parotid tissue from sicca patient

value: Sicca


title: Paxgene total RNA from patient BC341, illness day 4 ,WHO stage indet

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57054.gif


title: parotid tissue from primary Sjogren syndrome patient 17


title: Paxgene total RNA from patient BC324, illness day 5 ,WHO stage 4

description:
Simple annotation: Infection, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57025.gif

value: patient BC324

value: WHO stage 4


title: AD3

description:
Braak stage 6
J37-01267.CEL

source_name: Entorhinal cortex of AD3


title: parotid tissue from sicca patient 20


title: parotid tissue from sicca patient 15


title: parotid tissue from sicca patient 19


title: parotid tissue from sicca patient 17


title: parotid tissue from sicca patient 12


title: WT, 48h, rep2

value: late stationary


title: NDC1

description:
Braak stage 1
J32-00036.CEL

source_name: Entorhinal cortex of Non-demented control1

value: Non-demented control


title: parotid tissue from primary Sjogren syndrome patient 13


title: parotid tissue from sicca patient 10


title: NDC2

description:
Braak stage 1
J33-99144.CEL

source_name: Entorhinal cortex of Non-demented control2


title: AD1

description:
Braak stage 5
J35-02234.CEL

source_name: Entorhinal cortex of AD1


title: NDC3

description:
Braak stage 2
J34-00222.CEL

source_name: Entorhinal cortex of Non-demented control3


title: parotid tissue from sicca patient 5


title: parotid tissue from sicca patient 6


title: parotid tissue from sicca patient 9


title: parotid tissue from sicca patient 4


title: parotid tissue from sicca patient 3


title: parotid tissue from primary Sjogren syndrome patient 10


title: parotid tissue from primary Sjogren syndrome patient 9


title: parotid tissue from primary Sjogren syndrome patient 8


title: parotid tissue from primary Sjogren syndrome patient 4


title: parotid tissue from primary Sjogren syndrome patient 3


title: parotid tissue from primary Sjogren syndrome patient 5


title: parotid tissue from sicca patient 13


title: parotid tissue from primary Sjogren syndrome patient 6


title: parotid tissue from primary Sjogren syndrome patient 7


title: parotid tissue from primary Sjogren syndrome patient 2


title: parotid tissue from primary Sjogren syndrome patient 16


title: parotid tissue from primary Sjogren syndrome patient 1


title: adult T-cell leukemia/lymphoma dermis D-A2

city: Kurume

first: Keiko

last: Hashikawa

state: Fukuoka

department: Department of Dermatology

country: Japan

institute: Kurume University School of Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA, which was laser-microdissected from tissue, was isolated according to Ambion RNAqueous-Micro protocal for LCM. Quality control was performed with Experion BIO-RAD automated electrophoresis system.

value: skin

tag: region

value: dermis

value: adult T-cell leukemia/lymphoma

value: female

tag: Stage

value: IB

tag: rna extraction

value: laser microdissection


title: polymorphonuclear leukocyte cells treated with iPVL time 180 replicate 1

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description:
3610_SFG_1_human_28_Denat PVL-180-1_01_3922
Gene expression data from PMN leukocyte cells treated with iPVL time 180 replicate 1

hyb_protocol: Samples from 3 different PMN donors were hybridized on HU133+2 GeneChips (Affymetrix, Santa Clara, CA) according to manufacturer's recommendations

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. The trimmed mean target intensity of each array was arbitrarily set to 1250.

source_name: polymorphonuclear leukocyte cells treated with iPVL time 180 min

label_protocol: 12 µg of biotin-labeled cRNA target as previously described [PMID:11983860]

growth_protocol: PMNs were isolated from venous whole blood of healthy individuals as described [PMID:11983860]. Each subject gave informed consent prior to participation in the study and all work was approved by the Institutional Review Board for Human Subjects, National Institute of Allergy and Infectious Diseases, National Institutes of Health, USA.

extract_protocol: At each indicated time point, PMNs were lysed with RLT buffer and RNA was purified

treatment_protocol: PMNs (1 × 107) in RPMI/H were cultured with 1 nM PVL or iPVL at 37°C for 30, 60, or 180 min.

tag: cell type

value: polymorphonuclear leukocyte


title: parotid tissue from sicca patient 8


title: adult T-cell leukemia/lymphoma epidermis E-A5

tag: tissue

value: epidermis

tag: gender

value: male

value: IIB


title: mycosis fungoides dermis D-M3

value: mycosis fungoides

tag: age


title: adult T-cell leukemia/lymphoma epidermis E-A3


title: mycosis fungoides dermis D-M1

value: IA


title: polymorphonuclear leukocyte cells treated with iPVL time 30 replicate 1

description:
3604_SFG_1_human_22_Denat PVL-30-1_01_3932
Gene expression data from PMN leukocyte cells treated with iPVL time 30 replicate 1

source_name: polymorphonuclear leukocyte cells treated with iPVL time 30 min


title: adult T-cell leukemia/lymphoma epidermis E-A2


title: mycosis fungoides epidermis E-M3


title: polymorphonuclear leukocyte cells treated with iPVL time 30 replicate 2

description:
3605_SFG_1_human_23_Denat PVL-30-2_01_5731
Gene expression data from PMN leukocyte cells treated with iPVL time 30 replicate 2


title: polymorphonuclear leukocyte cells treated with iPVL time 30 replicate 3

description:
3606_SFG_1_human_24_Denat PVL-30-3_01_5765
Gene expression data from PMN leukocyte cells treated with iPVL time 30 replicate 3


title: polymorphonuclear leukocyte cells treated with iPVL time 60 replicate 2

description:
3608_SFG_1_human_26_Denat PVL-60-2_01_8449
Gene expression data from PMN leukocyte cells treated with iPVL time 60 replicate 2

source_name: polymorphonuclear leukocyte cells treated with iPVL time 60 min


title: polymorphonuclear leukocyte cells treated with iPVL time 60 replicate 1

description:
3607_SFG_1_human_25_Denat PVL-60-1_01_3937
Gene expression data from PMN leukocyte cells treated with iPVL time 60 replicate 1


title: adult T-cell leukemia/lymphoma epidermis E-A4


title: mycosis fungoides dermis D-M2


title: polymorphonuclear leukocyte cells treated with iPVL time 180 replicate 3

description:
3612_SFG_1_human_30_Denat PVL-180-3_01_5759
Gene expression data from PMN leukocyte cells treated with iPVL time 180 replicate 3


title: mycosis fungoides epidermis E-M4


title: mycosis fungoides epidermis E-M5


title: polymorphonuclear leukocyte cells treated with iPVL time 180 replicate 2

description:
3611_SFG_1_human_29_Denat PVL-180-2_01_8501
Gene expression data from PMN leukocyte cells treated with iPVL time 180 replicate 2


title: adult T-cell leukemia/lymphoma dermis D-A1


title: adult T-cell leukemia/lymphoma epidermis E-A1

source_name: E_9 (ATL)

value: IIA


title: polymorphonuclear leukocyte cells treated with iPVL time 60 replicate 3

description:
3609_SFG_1_human_27_Denat PVL-60-3_01_5764
Gene expression data from PMN leukocyte cells treated with iPVL time 60 replicate 3


title: polymorphonuclear leukocyte cells treated with PVL time 180 replicate 2

description:
3602_SFG_1_human_20_PVL-180-2_01_5756
Gene expression data from PMN leukocyte cells treated with PVL time 180 replicate 2

source_name: polymorphonuclear leukocyte cells treated with PVL time 180 min


title: polymorphonuclear leukocyte cells treated with PVL time 180 replicate 3

description:
3603_SFG_1_human_21_PVL-180-3_01_5747
Gene expression data from PMN leukocyte cells treated with PVL time 180 replicate 3


title: mycosis fungoides epidermis E-M2


title: mycosis fungoides epidermis E-M1


title: polymorphonuclear leukocyte cells treated with PVL time 60 replicate 3

description:
3600_SFG_1_human_18_PVL-60-3_01_3913
Gene expression data from PMN leukocyte cells treated with PVL time 60 replicate 3

source_name: polymorphonuclear leukocyte cells treated with PVL time 60 min


title: Test-biological replicate4

city: Hyderabad

first: kotakonda

last: Arunasri

state: Andhra Pradesh

address: Habsiguda

country: India

institute: Centre for Cellular and Molecular biology

description: Gene expression data from E.coli grown under Microgravity conditions

hyb_protocol: DNA micro array chips were hybridized with the labelled cDNA using the Affymetrix protocol (www.affymetrix.com).

scan_protocol: Microarray slides were then scanned using Affymetrix 428 Array Scanner and GCOS software to obtain images of the chips and further processed to get intensity cell files for the probe sets.

data_processing: The intensity cell files were then imported, normalized for background correction and data analysed using GCOS. MAS algorithm was used to normalize the data.

label: Biotin

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E.coli culture that reached 0.8OD under Microgravity conditions

label_protocol: The cDNA was fragmented with DNAse 1 (Promega Corporation, Madison, USA) and then labeled with biotin at the 3’ end using the labeling reagent from Affymetrix (CA, USA) and Terminal transferase enzyme (Promega).

growth_protocol: E.coli was cultured in both noraml amd microgravity conditions. Three biological replicates were maintained under each condition.

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

treatment_protocol: When the OD600nm reached 0.8, 10 ml of the culture was suspended in 3 volumes of RNAlater solution (Ambion Inc., USA) and stored at 4 degrees centigrade until use.

tag: growth protocol

value: E.coli culture grown in LB broth supplemented with 10%v/v glycerol

tag: stress

value: Microgravity


title: polymorphonuclear leukocyte cells treated with PVL time 180 replicate 1

description:
3601_SFG_1_human_19_PVL-180-1_01_3946
Gene expression data from PMN leukocyte cells treated with PVL time 180 replicate 1


title: polymorphonuclear leukocyte cells treated with PVL time 60 replicate 2

description:
3599_SFG_1_human_17_PVL-60-2_01_8459
Gene expression data from PMN leukocyte cells treated with PVL time 60 replicate 2


title: polymorphonuclear leukocyte cells treated with PVL time 60 replicate 1

description:
3598_SFG_1_human_16_PVL-60-1_01_3962
Gene expression data from PMN leukocyte cells treated with PVL time 60 replicate 1


title: polymorphonuclear leukocyte cells treated with PVL time 30 replicate 3

description:
3597_SFG_1_human_15_PVL-30-3_01_8483
Gene expression data from PMN leukocyte cells treated with PVL time 30 replicate 3

source_name: polymorphonuclear leukocyte cells treated with PVL time 30 min


title: Sertraline_25_rep3

city: Knoxville

first: Julia

last: Gouffon

state: TN

address: 1215 West Cumberland Ave, RM 229

department: Nutrition

institute: Univ. of TN

hyb_protocol: Protocol follows the Affymetrix Hybridization, Wash and Stain kit for Eukaryotic Target Hybridization for 49 Format Array using 15 ug fragmented cRNA and 45C hyb temp for 16 hours at 60 rpm.  Washed with Affymetrix 450 Fluidics Station using FS450_001 script.

scan_protocol: Affymetrix 7G Scanner/GCOS

data_processing: Partek Genomics Suite GCRMA Algorithm

organism: Danio rerio

source_name: Danio rerio Larvae exposed to Sertraline 25 ug/L for 96 h

label_protocol: Affymetrix 3' labeling kit 5 ug total RNA

growth_protocol: Zebrafish (Danio rerio) were obtained from the Zebrafish Research Facility maintained at the Center for Environmental Biotechnology at the University of Tennessee.  Fish husbandry, spawning, and experimental procedures were conducted with approval from the UT Insititutional Animal Care and Use Committee (Protocol #1690-1007).  Water for holding fish and conducting experiments (hereafter referred to as fish water) consisted of MilliQ water (Millipore, Bedford, MA) with ions added: 19 mg/L NaHCO3, 1 mg/L sea salt (Instant Ocean Synthetic Sea Salt, Mentor, OH), 10 mg/L CaSO4, 10 mg/L MgSO4, 2 mg/L KCl. Embroyos were obtained by spawning adult fish with no history of contaminant exposure.  Fertilization of embryos took place at the same time (<15 minutes), such that larvae used in experiments were of similar age at the time of exposure.  All activities (maintenance of adult fish, spawning, and experiments) were conducted in an environmental chamber with a temperature of 27 +/- 1 C and 14:10h light:dark photoperiod.

extract_protocol: Larvae were centrifuged for 10 min. at 13,000 rpm to separate larvae from exposure water, and pellets containing larvae were stored at <-80C until RNA extraction was performed.  Total Larval RNA was extracted using the Rneasy mini extraction kit for animal tissues (Qiagen, Valencia, CA) and quantified using a spectrophotometer (Nanodrop, Wilmington, DE).

treatment_protocol: Larval zebrafish (72 hpf) were exposed for 96 h in 200ml fish water containing appropirate amount of SSRI stock (i.e. fluoxetine or sertraline).  There were four SSRIs treatments (25 and 250 ug/L fluoxetine and 25 and 250 ug/L sertraline) and one control (no SSRIs) with triplicate beakers and each beaker contained about 100 larval fish.  During exposure for 96 hours, beakers were kept covered to prevent water evaporation and fish were not fed (i.e., fish consumed their yolk sac).

tag: developmental stage

value: larval


title: Sertraline_250_rep3

source_name: Danio rerio Larvae exposed to Sertraline 250 ug/L for 96 h


title: Fluoxetine_250_rep3

source_name: Danio rerio Larvae exposed to Fluoxetine 250ug/L for 96 h


title: Sertraline_25_rep2


title: Control_rep2

source_name: Danio rerio Larvae exposed to Control Fish Water for 96 h


title: Test-biological replicate2


title: polymorphonuclear leukocyte cells treated with PVL time 30 replicate 2

description:
3596_SFG_1_human_14_PVL-30-2_01_5779
Gene expression data from PMN leukocyte cells treated with PVL time 30 replicate 2


title: polymorphonuclear leukocyte cells treated with PVL time 30 replicate 1

description:
3595_SFG_1_human_13_PVL-30-1_01_5758
Gene expression data from PMN leukocyte cells treated with PVL time 30 replicate 1


title: Sertraline_25_rep1


title: Control_rep3


title: Sertraline_250_rep1


title: Control_rep1


title: Fluoxetine_250_rep2


title: Sertraline_250_rep2


title: control-biological replicate4

description: Gene expression data from E.coli grown under normal gravity conditions

source_name: E.coli culture that reached 0.8OD under normal gravity conditions

value: control


title: control-biological replicate3


title: Test-biological replicate1


title: Fluoxetine_25_rep2

source_name: Danio rerio Larvae exposed to Fluoxetine 25 ug/L for 96 h


title: Fluoxetine_250_rep1


title: Fluoxetine_25_rep3


title: control-biological replicate2


title: control-biological replicate1


title: Fluoxetine_25_rep1


title: matched control 3

city: Augusta

first: Yen-Hao

last: Chen

state: GA

address: 1459 Laney-Walker Blvd

department: OB/Gyn

institute: Georgia Health Sciences University

description: miRNA expression data from sc adipose of control women

hyb_protocol: Following labeling, RNAs were hybridized for 16 hr at 48C on GeneChip miRNA(1_0) Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner

data_processing: The data was analyzed using Partek and normalized with RMA

source_name: sc adipose tissue from control women

label_protocol: Biotinylated RNAs were prepared according to the standard FlashTag HSR protocol from 250 ng total RNA (FlashTag Biotin HSR RNA Labeling Kit, Genisphere).

extract_protocol: Total RNA was extracted using miRACLE Isolation Kit for CELLS/TISSUES (Jinfiniti Biosciences) according to the manufacturer's instructions.

treatment_protocol: Subcutaneous adipose tissue was excised from patients lower abdomen and frozen in liquid nitrogen

value: subcutaneous (sc) adipose tissue

tag: diagnosis

value: healthy control


title: matched control 2


title: PCOS patient 2

description: miRNA expression data from sc adipose of lean PCOS patients

source_name: sc adipose tissue from lean PCOS patients

value: PCOS


title: matched control 1

value: female


title: PCOS patient 1


title: Cyp1a1_1b1_16_1

city: Cincinnati

first: Mario

last: Medvedovic

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description:
N28
Gene expression from Cyp1a1_1b1 KO at 16 weeks.

hyb_protocol: Used the Affymetrix GeneChip hybridization and stain kit following the manufacturer's instructions.

scan_protocol: The GeneChips are scanned with Affymetrix GeneChip Scanner 3000 7G Plus using Affymetrix GeneChip Command Console 3.2.3.1515 software and Affymetrix preset settings.

data_processing: Microarray data was preprocessed using RMA implemented in R with a BrainArray custom CDF (Entrez Gene, version 13).

source_name: Cyp1a1_1b1 DKO mouse at week 16

label_protocol: Ovation Pico WTA System (NuGEN, San Carlos, CA) following the manufacturer's instructions.

extract_protocol: Snap-frozen preputial glands (N=2 mice per group) from WT, Cyp1a1KO and Cyp1a1/1b1 DKO males treated with BaP at 0, 4, 8, 12, and 16 weeks were allowed to thaw overnight at -20oC with RNAlater®-ICE reagent prior to homogenization using Tri-Reagent. RNA isolation was performed using Qiagen RNeasy mini-kits.

treatment_protocol: Male mice of the three genotypes (75 mice total per genotype) were begun on the benzo[a]pyrene (BaP) diet at 6 weeks of age. BaP was added with the corn oil-soaked food such that the mice ingested approximately 12.5 mg/kg/day. Groups of N=15 for each genotype were killed at zero, 4, 8, 12 and 16 weeks, and preputial glands were dissected free of surrounding tissue.

tag: strain/background

tag: genotype

value: Cyp1a1 Cyp1b1 double-knockout

value: preputial gland duct

tag: treatment

value: oral benzo[a]pyrene (BaP)

tag: treatment duration

value: 16 weeks


title: PCOS patient 3


title: Cyp1a1_1b1_16_2

description:
N33
Gene expression from Cyp1a1_1b1 KO at 16 weeks.

value: male


title: Cyp1a1_1b1_12_2

description:
N27
Gene expression from Cyp1a1_1b1 KO at 12 weeks.

source_name: Cyp1a1_1b1 DKO mouse at week 12

value: 12 weeks


title: Ring 13b IR

city: Heidelberg

first: Peter

last: Schmezer

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

data_processing: Illumina’s BeadStudio software was used to extract raw data and to produce an average intensity value for each bead type after outliers have been excluded and background has been removed. To correct for differences in expression level across a chip and between chips quantile normalisation of log2 transformed data was applied to achieve gene expression values.

source_name: Ring 13b

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina’s recommended sample labeling procedure based on the modified Eberwine protocol (Methods Enzymol 216, 1992)

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.

value: lymphocytes

value: irradiated with 5Gy (IR)

tag: tumor type

value: Head and neck

tag: age at radiation

tag: clinical radiosensitivity

value: Sensitive

value: Female

tag: chemotherapy

value: No


title: adult T-cell leukemia/lymphoma dermis D-A3

value: skin

tag: region

value: dermis

tag: disease state

value: adult T-cell leukemia/lymphoma

tag: Stage

value: IIB

tag: rna extraction

value: laser microdissection


title: mutant K-ras off 24h [4825641012_C]

city: Dallas

first: Kimberly

last: Batten

state: TX

address: 5323 Harry Hines Blvd

department: Cell biology

institute: UT Southwestern Medical Center

description: replicate 1

data_processing: Data was background corrected, quantile normalized, and log2 transformed using MBCB in R

source_name: mutant K-ras off 24h

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

growth_protocol: The mice were fed ad libitum until the time of the lung removal

treatment_protocol: The lungs were excised form mice and tumor were immediately microdissected and snap-frozen

tag: tissue

value: lung

tag: age

value: 19 weeks old

tag: strain


title: Ring 13a IR

source_name: Ring 13a

tag: cell type

value: Not sensitive

tag: gender


title: mutant K-ras off 24h [4825641012_F]

description: replicate 4


title: Cyp1a1_1b1_4_1

description:
N22
Gene expression from Cyp1a1_1b1 KO at 4 weeks.

source_name: Cyp1a1_1b1 DKO mouse at week 4

tag: strain/background

value: Cyp1a1 Cyp1b1 double-knockout

value: preputial gland duct

value: oral benzo[a]pyrene (BaP)

value: 4 weeks


title: Ring 14a IR

source_name: Ring 14a

value: lymphocytes

value: irradiated with 5Gy (IR)

value: Breast


title: Cyp1a1_1b1_8_2

description:
N25
Gene expression from Cyp1a1_1b1 KO at 8 weeks.

source_name: Cyp1a1_1b1 DKO mouse at week 8

tag: genotype

value: male

value: 8 weeks


title: Cyp1a1_1b1_8_1

description:
N24
Gene expression from Cyp1a1_1b1 KO at 8 weeks.

tag: treatment


title: Cyp1a1_1b1_4_2

description:
N23
Gene expression from Cyp1a1_1b1 KO at 4 weeks.

tag: treatment duration


title: mutant K-ras off 24h [4825641012_E]

description: replicate 3


title: Cyp1a1_1b1_12_1

description:
N26
Gene expression from Cyp1a1_1b1 KO at 12 weeks.

value: 12 weeks


title: mutant K-ras off 24h [4825641012_D]

description: replicate 2


title: mutant K-ras off 48h [4825641012_A]

description: replicate 3

source_name: mutant K-ras off 48h


title: mutant K-ras off 48h [4825641012_B]

description: replicate 4


title: Cyp1a1_1b1_0_2

description:
N31
Gene expression from Cyp1a1_1b1 KO at 0 weeks.

source_name: Cyp1a1_1b1 DKO mouse at week 0

value: 0 weeks


title: Ring 14b IR

source_name: Ring 14b

tag: tumor type

value: Female

value: No


title: mutant K-ras off 48h [4825641011_F]

description: replicate 2


title: Cyp1a1_16_2

description:
N19
Gene expression from Cyp1a1 KO at 16 weeks.

source_name: Cyp1a1 KO mouse at week 16

value: Cyp1a1 knockout

value: 16 weeks


title: Ring 12a IR

source_name: Ring 12a

value: Head and neck

tag: age at radiation

value: Male


title: Ring 11b IR

source_name: Ring 11b

tag: clinical radiosensitivity

value: Not sensitive


title: Cyp1a1_1b1_0_1

description:
N20
Gene expression from Cyp1a1_1b1 KO at 0 weeks.

value: Cyp1a1 Cyp1b1 double-knockout

value: preputial gland duct


title: mutant K-ras on [4825641011_D]

description: replicate 4

source_name: mutant K-ras on

value: lung

value: 19 weeks old


title: mutant K-ras off 48h [4825641011_E]

description: replicate 1


title: Cyp1a1_12_2

description:
N30
Gene expression from Cyp1a1 KO at 12 weeks.

source_name: Cyp1a1 KO mouse at week 12

value: oral benzo[a]pyrene (BaP)


title: Ring 10a IR

source_name: Ring 10a

value: lymphocytes

value: irradiated with 5Gy (IR)

value: Breast

value: Sensitive

tag: chemotherapy


title: Ring 11a IR

source_name: Ring 11a


title: mutant K-ras on [4825641011_C]

description: replicate 3


title: Cyp1a1_12_1

description:
N17
Gene expression from Cyp1a1 KO at 12 weeks.

value: male

value: 12 weeks


title: Ring 10b IR

source_name: Ring 10b

value: Female

value: No


title: Ring 12b IR

source_name: Ring 12b


title: mutant K-ras on [4825641011_B]

description: replicate 2


title: Cyp1a1_16_1

description:
N18
Gene expression from Cyp1a1 KO at 16 weeks.

value: Cyp1a1 knockout

value: 16 weeks


title: Ring 9a IR

source_name: Ring 9a

value: Head and neck

value: Male


title: Ring 9b IR

source_name: Ring 9b


title: Cyp1a1_4_2

description:
N14
Gene expression from Cyp1a1 KO at 4 weeks.

source_name: Cyp1a1 KO mouse at week 4

value: 4 weeks


title: Ring 8b IR

source_name: Ring 8b

value: Not sensitive

value: Yes


title: mutant K-ras on [4825641011_A]

description: replicate 1

value: lung

value: 19 weeks old


title: Ring 6a IR

source_name: Ring 6a

value: lymphocytes


title: Cyp1a1_4_1

description:
N11
Gene expression from Cyp1a1 KO at 4 weeks.

value: preputial gland duct

value: oral benzo[a]pyrene (BaP)


title: Cyp1a1_8_1

description:
N15
Gene expression from Cyp1a1 KO at 8 weeks.

source_name: Cyp1a1 KO mouse at week 8

value: 8 weeks


title: Cyp1a1_8_2

description:
N16
Gene expression from Cyp1a1 KO at 8 weeks.

value: male


title: Test-biological replicate3

description: Gene expression data from E.coli grown under Microgravity conditions

source_name: E.coli culture that reached 0.8OD under Microgravity conditions

tag: growth protocol

value: E.coli culture grown in LB broth supplemented with 10%v/v glycerol

tag: stress

value: Microgravity


title: Ring 8a IR

source_name: Ring 8a

value: irradiated with 5Gy (IR)

value: Breast

value: Sensitive

value: Female


title: Spleen 0.1 56

city: buffalo

state: NY

address: Elm & Carlton Streets

institute: RPCI

hyb_protocol: The labeled probes were then mixed with hybridization reagents and hybridized overnight to the MouseWG-6 v2 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

data_processing: The data were normalised using quantile normalization with GenomeStudio Software (V1.6.0)

source_name: spleen from mouse drinking water with 0.1mg/ml of Curaxin-137 during 10 weeks

label_protocol: Initially, we converted 250-500 ng total RNA to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA (Illumina TotalPrep RNA Amplification Kit, Ambion Inc., Austin, TX).

extract_protocol: Total RNA was isolated from frozen tissue samples using TRIZOL reagent (Invitrogen).

value: Spleen


title: Ring 4a IR

source_name: Ring 4a

value: No


title: Cyp1a1_0_2

description:
N13
Gene expression from Cyp1a1 KO at 0 weeks.

source_name: Cyp1a1 KO mouse at week 0

value: Cyp1a1 knockout

value: 0 weeks


title: Spleen 0.2 62_86

source_name: spleen from mouse drinking water with 0.2mg/ml of Curaxin-137 during 10 weeks


title: Ring 5b IR

source_name: Ring 5b


title: Spleen 0.2 62

value: water with 0.2mg/ml of Curaxin-137 during 10 weeks


title: B6_16_1

description:
N10
Gene expression from WT at 16 weeks.

source_name: WT mouse at week 16

value: wild-type

value: 16 weeks


title: B6_16_2

description:
N9
Gene expression from WT at 16 weeks.

value: preputial gland duct


title: Liver 0.1 55

source_name: liver from mouse drinking water with 0.1mg/ml of Curaxin-137 during 10 weeks

value: Liver


title: Spleen 0.1 32

value: water with 0.1mg/ml of Curaxin-137 during 10 weeks


title: Ring 6b IR

source_name: Ring 6b

value: lymphocytes

value: Not sensitive

value: Yes


title: Ring 2a IR

source_name: Ring 2a

value: irradiated with 5Gy (IR)


title: Ring 2b IR

source_name: Ring 2b

value: Breast


title: B6_12_1

description:
N7
Gene expression from WT at 12 weeks.

source_name: WT mouse at week 12

value: male

value: oral benzo[a]pyrene (BaP)

value: 12 weeks


title: Ring 4b IR

source_name: Ring 4b

value: Sensitive

value: Female

value: No


title: Liver 0.2 73

source_name: liver from mouse drinking water with 0.2mg/ml of Curaxin-137 during 10 weeks


title: Ring 1a IR

source_name: Ring 1a


title: Liver control 25

source_name: liver from mouse drinking plain water during 10 weeks


title: diamide B 46440202

type: genomic

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE - Université Paris-Saclay

hyb_protocol: Hybridization was done by Roche Nimblegen (Madison, WI, USA) following the standard Nimblegen protocol.

scan_protocol: Scanning was done by Roche Nimblegen (Madison, WI, USA) following the standard Nimblegen protocol.

data_processing:
Identification of peaks corresponding to Spx binding sites on the Bacillus subtilis chromosome was done as described previously (Reppas et al., 2006, Mol Cell 24: 747-757 [PMID 17157257]).
Signal intensities were converted as log2 ratio (ChIP-DNA/Control-DNA) and corrected for dye bias using Loess regression on the MA plot.
The signal was smoothed by two rounds of sliding window averaging. The sliding window contained 29 probes (the middle probe and 14 probes on each side) corresponding to approximately 320 bp.

molecule: genomic DNA

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis cells

label_protocol: Labelling was done by Roche Nimblegen (Madison, WI, USA) using the standard Nimblegen protocol. ChIP DNA was labelled with Cy5 and control DNA was labelled with Cy3.

growth_protocol: Cells were grown in a flask of 2 L LB medium until OD600nm reached 0.6. Then 0.5 mM diamide was added for 5 min.

extract_protocol: 0.6 % formaldehyde was added in the flasks for 20 min at room temperature before quenching with 125 mM glycine. Cells were harvested by centrifugation at 6000g for 10 min, washed twice with 200 mL of buffer A (10 mM Tris-HCl pH=7.5, 150 mM NaCl), and then lysed in 12 mL of buffer B (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.2 mM EDTA, 0.1 % (v/v) TritonX-100) supplemented with 0.1 mg/mL RNase A and 1 mg/mL lysozyme for 15 min at 37°C. DNA was then sheared by sonication in order to obtain 0.2 to 1 kb fragments. An aliquot of 50 µL of the whole cell extract (WCE) volume was saved for use as control DNA. The rest was used for immuno-precipitation DNA (IP): 400 μL of anti-FLAG M2 agarose beads (Sigma A2220) were incubated 2 h with cell lysates under gentle agitation. Then IP beads were washed 3 times in buffer B before being resuspended into 500 µL of buffer C (100 mM Tris-HCl pH=8, 100 g/L, 1% SDS, 10 mM EDTA) to reverse cross-linking for 18 h at 65°C. WCE and IP DNA fragments were recovered and purified using QIAquick PCR purification kit (Qiagen). Remaining RNA was removed by RNase A treatment followed by a second DNA purification step.

tag: replicate

value: B

value: diamide

tag: dna fraction

value: IP DNA

value: Control DNA


title: Liver 0.1 43

tag: tissue

value: Liver


title: B6_12_2

description:
N8
Gene expression from WT at 12 weeks.

value: wild-type

value: preputial gland duct


title: Cyp1a1_0_1

description:
N12
Gene expression from Cyp1a1 KO at 0 weeks.

value: Cyp1a1 knockout

value: 0 weeks


title: Liver 0.2 85

value: water with 0.2mg/ml of Curaxin-137 during 10 weeks


title: B6_4_2

description:
N4
Gene expression from WT at 4 weeks.

source_name: WT mouse at week 4

value: 4 weeks


title: B6_4_1

description:
N3
Gene expression from WT at 4 weeks.

value: male


title: Ring 14b C

source_name: Ring 14b

value: lymphocytes

value: untreated (C)

value: Breast

value: Not sensitive


title: B6_0_2

description:
N2
Gene expression from WT at 0 weeks.

source_name: WT mouse at week 0

value: oral benzo[a]pyrene (BaP)


title: Mek\NestinCre mutant dorsal cortex_E18.5_rep2

city: Chapel Hill

first: xiaoyan

last: li

address: 115 Mason Farm Road

department: Neuroscience Center

institute: University of North Carolina

hyb_protocol: Hybridization were carried out according to  GeneChip®WT hybridization mannual from Affymetrix

scan_protocol: The arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G Plus

data_processing: The data were analyzed with Partex Genomics Suite 6.6. The gene level RMA-sketch algorithm was used to generate the intensity data for the Mouse Gene 1.0 ST arrays. Differences in gene expression were expressed as fold changes (down-regulated genes are expressed as -fold value). Fold-change was calculated based on log2 ratio. Transcripts down-regulated >-2 fold were considered interesting candidates and some were further validated with IHC and western blotting.

source_name: E18.5 dorsal cortex

label_protocol: RNA were labeled using standard GeneChip®WT Terminal labeling protocal from Affymetrix

growth_protocol: Tissue were directly taken from animals

extract_protocol: RNA was extracted using Trizol (Invitrogen) and purified using RNAeasy plus mini kit (QIAGEN).

treatment_protocol: no treatment were applied before extraction of RNA

value: dorsal cortex

tag: genotype/variation

value: Mek1fl/fl, Mek2-/- ,NestinCre

tag: age


title: Ring 13a C

source_name: Ring 13a

tag: cell type

value: Head and neck

value: Female

value: No


title: Ring 14a C

source_name: Ring 14a

value: Sensitive

tag: gender


title: Mek\NestinCre mutant dorsal cortex_E18.5_rep1


title: B6_8_1

description:
N5
Gene expression from WT at 8 weeks.

source_name: WT mouse at week 8

tag: strain/background

value: wild-type

value: preputial gland duct

value: 8 weeks


title: Liver control 1

value: Liver


title: Ring 1b IR

source_name: Ring 1b

value: irradiated with 5Gy (IR)

value: Yes


title: diamide A 46439602

value: A

value: diamide

value: IP DNA

value: Control DNA


title: B6_8_2

description:
N6
Gene expression from WT at 8 weeks.

tag: genotype

value: male

value: oral benzo[a]pyrene (BaP)


title: Spleen control 8

source_name: spleen from mouse drinking plain water during 10 weeks

value: Spleen

tag: treatment


title: B6_0_1

description:
N1
Gene expression from WT at 0 weeks.

tag: treatment duration

value: 0 weeks


title: control dorsal cortex_E18.5_rep1

value: dorsal cortex

value: Mek1fl/wt, Mek2-/-


title: no-diamide B 46443102

growth_protocol: Cells were grown in a flask of 2 L LB medium until OD600nm reached 0.6.

value: B

value: no-diamide


title: Ring 12a C

source_name: Ring 12a

value: lymphocytes

value: untreated (C)

tag: tumor type

value: Head and neck

value: Not sensitive

value: Male

value: No


title: no-diamide A 46445702

value: A


title: TscWT3_brain

city: Boston

first: Sek Won

last: Kong

state: MA

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: Tsc2 wildtype mouse 3, cerebellum

hyb_protocol: The cRNA was quantified (using A260) and fragmented. Fragmented cRNA was hybridized on the GeneChips according to the manufacturer's standard protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000 at 2.5 μm resolution.

data_processing: The data were analyzed with Probe Logarithmic Intensity Error (PLIER) estimation method using Affymetrix Power Tools.

source_name: Tsc2 wildtype mouse, cerebellum

label_protocol: A total of 250 ng was processed using established Affymetrix protocols for the generation of biotin-labeled cRNA.

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

value: Tsc2 wildtype

value: cerebellum

value: Female


title: Ring 12b C

source_name: Ring 12b

tag: age at radiation

value: Sensitive


title: Ring 13b C

source_name: Ring 13b

tag: clinical radiosensitivity


title: TscWT1_brain

description: Tsc2 wildtype mouse 1, cerebellum


title: Ring 10a C

source_name: Ring 10a

value: Breast

tag: chemotherapy


title: Ring 11b C

source_name: Ring 11b


title: TscWT3_blood

description: Tsc2 wildtype mouse 3, blood

source_name: Tsc2 wildtype mouse, blood

value: blood


title: TscHet3_brain

description: Tsc2 +/- mouse 3, cerebellum

source_name: Tsc2 +/- mouse, cerebellum

value: Tsc2 +/- mouse


title: TscHet2_brain

description: Tsc2 +/- mouse 2, cerebellum


title: control dorsal cortex_E18.5_rep2

value: dorsal cortex

value: Mek1fl/wt, Mek2-/-


title: TscWT2_brain

description: Tsc2 wildtype mouse 2, cerebellum


title: Ring 5a IR

source_name: Ring 5a

value: irradiated with 5Gy (IR)


title: TscHet3_blood

description: Tsc2 +/- mouse 3, blood

source_name: Tsc2 +/- mouse, blood


title: TscHet1_brain

description: Tsc2 +/- mouse 1, cerebellum


title: Ring 11a C

source_name: Ring 11a

value: lymphocytes


title: TscWT2_blood

description: Tsc2 wildtype mouse 2, blood


title: Ring 8a C

source_name: Ring 8a

value: untreated (C)

value: Yes


title: Ring 10b C

source_name: Ring 10b

value: Not sensitive


title: PBMC 15B

first: Claudia

last: Macaubas

department: Pediatrics

institute: SUMC

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53005.gif

scan_protocol: Scanner Model: GenePix 4000B

source_name: Universal human reference (Stratagene)

tag: reference

value: Universal human reference (Stratagene)

source_name: patient

value: PBMC

tag: phenotype (number of affected joint)

value: 13.88 years

tag: iv solumedrol treatment

value: no

tag: Sex

value: M


title: TscWT1_blood

description: Tsc2 wildtype mouse 1, blood

value: Tsc2 wildtype

tag: tissue

value: Female


title: PBMC 16O

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53008.gif

value: 11.47 years

value: F


title: PBMC 04E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52988.gif

value: 18.88 years


title: PBMC 28D

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53016.gif

value: 8.48 years


title: PBMC 03S

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52985.gif

value: 10.01 years


title: Ring 9a C

source_name: Ring 9a

value: Head and neck

value: Male

value: No


title: Ring 6b C

source_name: Ring 6b

value: lymphocytes

value: untreated (C)

value: Breast

value: Yes


title: Ring 5b C

source_name: Ring 5b

value: Sensitive


title: PBMC 03R

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52984.gif

value: Universal human reference (Stratagene)

value: PBMC

value: 9.55 years

value: no


title: FmrWT4_brain

description: Fmr1 wildtype mouse 4, cerebellum

source_name: Fmr1 wildtype mouse, cerebellum

tag: genotype/variation

value: Fmr1 wildtype

value: cerebellum

value: Female


title: FmrWT5_brain

description: Fmr1 wildtype mouse 5, cerebellum


title: Ring 9b C

source_name: Ring 9b


title: FmrWT3_brain

description: Fmr1 wildtype mouse 3, cerebellum


title: Ring 4a C

source_name: Ring 4a

value: Not sensitive


title: TscHet1_blood

description: Tsc2 +/- mouse 1, blood

value: Tsc2 +/- mouse

value: blood


title: Ring 5a C


title: TscHet2_blood

description: Tsc2 +/- mouse 2, blood


title: PBMC 22E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53014.gif

tag: age

value: 8.88 years

value: M


title: PBMC 43J

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53022.gif

value: 4.93 years


title: FmrWT2_brain

description: Fmr1 wildtype mouse 2, cerebellum


title: PBMC 21S

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53012.gif

value: 10.21 years

value: F


title: PBMC 19D

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53010.gif

value: 9.20 years


title: FmrWT5_blood

description: Fmr1 wildtype mouse 5, blood

source_name: Fmr1 wildtype mouse, blood


title: PBMC 41A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53019.gif

value: 4.71 years


title: PBMC 10O

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52997.gif

value: Universal human reference (Stratagene)

value: 8.22 years


title: PBMC 05B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52989.gif

value: PBMC

value: 14.35 years


title: PBMC 11A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53001.gif

value: 8.97 years

value: no


title: Ring 6a C

source_name: Ring 6a

tag: cell type

value: lymphocytes

value: untreated (C)

value: Breast

value: Sensitive

value: Female

value: Yes


title: Ring 4b C

source_name: Ring 4b

tag: gender

value: No


title: Ring 8b C

source_name: Ring 8b

value: Not sensitive


title: FmrWT1_brain

description: Fmr1 wildtype mouse 1, cerebellum

value: Fmr1 wildtype

value: cerebellum


title: FmrWT1_blood

description: Fmr1 wildtype mouse 1, blood

value: blood


title: Ring 2a C

source_name: Ring 2a


title: PBMC 21A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53011.gif

value: Universal human reference (Stratagene)

value: 9.07 years

value: F


title: Ring 2b C

source_name: Ring 2b


title: PBMC 16A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53007.gif

value: PBMC

value: 9.51 years


title: FmrWT2_blood

description: Fmr1 wildtype mouse 2, blood


title: FmrKO2_brain

description: Fmr1 knockout mouse 2, cerebellum

source_name: Fmr1 knockout mouse, cerebellum

value: Fmr1 knockout


title: Ring 1a C

source_name: Ring 1a

value: lymphocytes


title: FmrWT3_blood

description: Fmr1 wildtype mouse 3, blood


title: Bifidobacterium breve UCC2003 phoP knockout versus wildtype under 90 minutes phosphate starvation

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures.

scan_protocol: Microarrays were scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: The scanning results were converted to data files with Agilent's Feature Extraction software (version 9.5). DNA microarray data was processed as previously described (Zomer et al., J. Bacteriol. November 2009 vol. 191 no. 22 7039-7049 (PMID 19734308)). The data were Loess normalized using the default settings of Agilent's Feature Extraction software (version 9.5).

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003 grown in CDM with low phosphate

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC200 was grown in MRS or CDM supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany). Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5.

extract_protocol: RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

tag: background strain

value: wildtype

value: 90 minutes phosphate starvation


title: Bifidobacterium breve UCC2003 phoP knockout versus wildtype under 45 minutes phosphate starvation

tag: genotype

value: 45 minutes phosphate starvation


title: Bifidobacterium breve UCC2003 PhoP overexpression 2

source_name: Bifidobacterium breve UCC2003 phoP overexpression grown in MRS

value: UCC2003 pNZ44:phoP

tag: treatment

value: normal phosphate

source_name: Bifidobacterium breve UCC2003 grown in MRS


title: Bifidobacterium breve UCC2003 phoP knockout phosphate starvation

source_name: Bifidobacterium breve UCC2003 phoP knockout grown in CDM with low phosphate


title: Ring 1b C

source_name: Ring 1b

value: untreated (C)

value: Breast

value: Sensitive

value: Female

value: Yes


title: FmrKO3_brain

description: Fmr1 knockout mouse 3, cerebellum

value: cerebellum


title: FmrKO5_brain

description: Fmr1 knockout mouse 5, cerebellum


title: FmrKO4_brain

description: Fmr1 knockout mouse 4, cerebellum


title: Bifidobacterium breve UCC2003 PhoP overexpression 3


title: FmrWT4_blood

description: Fmr1 wildtype mouse 4, blood

value: Fmr1 wildtype

value: blood


title: PBMC 14A

city: Stanford

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53003.gif

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Universal human reference (Stratagene)

label_protocol: not provided

value: Universal human reference (Stratagene)

source_name: patient

value: PBMC

value: 5.80 years

value: no

value: M


title: PBMC 35A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53017.gif

value: 3.34 years

value: F


title: PBMC 10A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52993.gif

value: 4.61 years


title: Bifidobacterium breve UCC2003 90 minutes phosphate starvation 3

value: wildtype

value: 90 minutes phosphate starvation

source_name: Bifidobacterium breve UCC2003 grown in CDM

value: normal phosphate


title: FmrKO1_brain

description: Fmr1 knockout mouse 1, cerebellum

value: Fmr1 knockout


title: PBMC 05F

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52991.gif

value: 15.54 years


title: Bifidobacterium breve UCC2003 90 minutes phosphate starvation 1


title: Bifidobacterium breve UCC2003 PhoP overexpression 1

value: UCC2003 pNZ44:phoP


title: FmrKO4_blood

description: Fmr1 knockout mouse 4, blood

source_name: Fmr1 knockout mouse, blood

value: Female


title: PBMC 04A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52986.gif

value: 16.59 years


title: FmrKO3_blood

description: Fmr1 knockout mouse 3, blood

value: blood


title: Bifidobacterium breve UCC2003 45 minutes phosphate starvation 3

value: 45 minutes phosphate starvation


title: FmrKO5_blood

description: Fmr1 knockout mouse 5, blood


title: Bifidobacterium breve UCC2003 90 minutes phosphate starvation 2


title: Bifidobacterium breve UCC2003 45 minutes phosphate starvation 2


title: FmrKO2_blood

description: Fmr1 knockout mouse 2, blood


title: Bifidobacterium breve UCC2003 45 minutes phosphate starvation 1


title: PBMC 15L

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53006.gif

value: Universal human reference (Stratagene)

value: PBMC

value: 17.10 years


title: FmrKO1_blood

description: Fmr1 knockout mouse 1, blood


title: PBMC 19A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53009.gif

value: 9.06 years

value: no

value: M


title: PBMC 28A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53015.gif

value: 8.16 years

value: F


title: US_BM_37_M022

status: Public on Sep 05 2012

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

description:
PBMC gene expression data
US_BM_37_M022.CEL

hyb_protocol: 25 ng/ul fragmented and labeled DNA target was hybridized according to the protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Images were processed using the Affymetrix Microarray Suite 5.0, cel files were normalized with RMA and further analyzed using Bioconductor software based on R language.

source_name: bacterial meningitis_peripheral blood

label_protocol: 100 ng Total RNA Labeling protocol, whole transcript sense target labeling assay

growth_protocol: RNA was extracted from whole blood of bacterial meningitis patients and healthy controls.

extract_protocol: Tempus blood extraction

treatment_protocol: Samples are from bactreial meningitis patients and healthy controls.

tag: sample group

value: bacterial meningitis

value: whole blood

tag: bacteria

value: Streptococcus pneumoniae (Spn)

tag: outcome

value: good


title: US_BM_34_M046

description:
PBMC gene expression data
US_BM_34_M046.CEL


title: US_BM_35_M041

description:
PBMC gene expression data
US_BM_35_M041.CEL

value: bad


title: US_BM_32_M029

description:
PBMC gene expression data
US_BM_32_M029.CEL


title: PBMC 43G

address: 300 Pasteur Drive

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53021.gif

extract_protocol: not provided

value: 4.45 years


title: US_BM_18_M004

description:
PBMC gene expression data
US_BM_18_M004.CEL

value: A2 (non-Spn)


title: PBMC 14I

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53004.gif

value: 9.50 years

value: prior week


title: US_BM_24_M002

description:
PBMC gene expression data
US_BM_24_M002.CEL


title: US_BM_20_M006

description:
PBMC gene expression data
US_BM_20_M006.CEL


title: US_BM_29_M023

description:
PBMC gene expression data
US_BM_29_M023.CEL


title: US_BM_16_M047

description:
PBMC gene expression data
US_BM_16_M047.CEL


title: US_BM_26_M028

description:
PBMC gene expression data
US_BM_26_M028.CEL


title: PBMC 41D

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53020.gif

value: Universal human reference (Stratagene)

value: 5.32 years


title: US_BM_27_M027

description:
PBMC gene expression data
US_BM_27_M027.CEL


title: PBMC 11S

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53002.gif

value: PBMC

value: 10.66 years


title: US_BM_23_M014

description:
PBMC gene expression data
US_BM_23_M014.CEL


title: US_BM_13_M031

description:
PBMC gene expression data
US_BM_13_M031.CEL


title: PBMC 35K

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53018.gif

value: 4.22 years

value: no


title: US_BM_09_M032

description:
PBMC gene expression data
US_BM_09_M032.CEL


title: US_BM_19_M039

description:
PBMC gene expression data
US_BM_19_M039.CEL


title: US_BM_05_M025

description:
PBMC gene expression data
US_BM_05_M025.CEL


title: PBMC 22A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53013.gif

value: 6.70 years

value: M


title: US_BM_22_M036

description:
PBMC gene expression data
US_BM_22_M036.CEL

value: bacterial meningitis


title: siRNA3_96_3

source_name: HEK_WFS1 siRNA3_96h

label_protocol: 100 ng Total RNA Labeling protocol, whole transcript sense target labeling assay.

growth_protocol: HEK celle were grown in standard media.

extract_protocol: Trizol extracted RNA

treatment_protocol: Cells were treated with 3 different siRNAs against WFS1 gene, RNA was collected 24, 48, 72 and 96 hours later.

value: HEK cells

tag: time after transfection (hr)

tag: transfected with

value: WFS1 siRNA3

tag: replicate


title: PBMC 03B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52982.gif

tag: reference

tag: phenotype (number of affected joint)

value: 6.44 years

value: yes

tag: disease state

value: Macrophage Activation Syndrome


title: US_BM_04_M042

description:
PBMC gene expression data
US_BM_04_M042.CEL

tag: tissue

value: whole blood

value: Streptococcus pneumoniae (Spn)

value: good


title: siRNA3_72_5

source_name: HEK_WFS1 siRNA3_72h


title: US_BM_08_M040

description:
PBMC gene expression data
US_BM_08_M040.CEL

value: A2 (non-Spn)


title: PBMC 03D

description: Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52983.gif

value: Universal human reference (Stratagene)

value: 6.92 years

tag: iv solumedrol treatment

tag: Sex


title: siRNA3_72_1

tag: cell type


title: siRNA3_72_2


title: US_BM_01_M038

description:
PBMC gene expression data
US_BM_01_M038.CEL


title: siRNA3_96_2


title: siRNA3_48_4

source_name: HEK_WFS1 siRNA3_48h


title: siRNA3_48_2


title: siRNA3_72_4


title: siRNA3_96_1


title: siRNA3_48_3


title: siRNA3_48_1


title: siRNA2_72_4

source_name: HEK_WFS1 siRNA2_72h

value: WFS1 siRNA2


title: siRNA2_96_1

source_name: HEK_WFS1 siRNA2_96h


title: siRNA2_72_1


title: siRNA3_24_4

source_name: HEK_WFS1 siRNA3_24h


title: siRNA3_72_3


title: siRNA2_96_2


title: siRNA2_72_2


title: siRNA2_72_5


title: siRNA2_48_3

source_name: HEK_WFS1 siRNA2_48h


title: siRNA2_48_4


title: siRNA2_48_1


title: siRNA2_48_2


title: BreastTumor_Invasive_rep3

city: Bronx

first: Antonia

last: Patsialou

address: 1301 Morris Park Ave

department: Anatomy and Structural Biology

institute: Albert Einstein College of Medicine

hyb_protocol: 2.5 micrograms of each labeled cDNA sample together with Cy3-labeled cDNA reference sample were added to hybridization buffe and then hybridized to a single microarray chip (detailed protocol for cDNA chip hybridization in  http://microarray1k.aecom.yu.edu/).  After hybridization, slides were washed sequential.

scan_protocol: Scanned on a AXON GenePix 4000A Microarray Scanner

data_processing:
1. LOWESS normalized using the Einstein Microaray Facility pipeline (http://microarray1k.aecom.yu.edu/pipeline.html).
2. Filter out data with more than 1 Flag (spot flagged as bad quality; so keep data with at least 3 good spots) and data with low signal intensity (< 200)
3. A ratio was calculated of the normalized sample signal over the original reference signal (reference signals do not change with normalization, since sample was normalized over the reference)
4. Finally, log2 transformed ratios of processed Sample signal/processed Reference signal were calculated and used in SAM (Significance Analysis of Microarrays).

source_name: invasive cell subpopulation from MDA-MB-231 orthotopic tumors

label_protocol: 2.5 micrograms of total amplified cDNA was labeled with Cy5 using the Mirus Label-IT kit, according to the manufacturer's instructions

growth_protocol: orthotopic tumors were grown in SCID mice by injection in the mammary fat pad of 2 million MDA-MB-231 cells (ATTC cell line).

extract_protocol: total RNA was extracted using a Qiagen RNeasy Micro kit. Because of the low number of invasive cells typically collected with the in vivo invasion assay per mouse (less than 500 cells), an amplification step was included. The procedure was previously published in Wang et al., 2003, BMC Biotechnology (http://www.biomedcentral.com/1472-6750/3/13). Briefly, total RNA was transcribed to cDNA and then amplified to dsDNA by the Clontech SMART kit (PCR-based method).

value: invasive (INV) tumor cells

source_name: Human reference RNA (Clontech)

label_protocol: 2.5 micrograms of total amplified cDNA was labeled with Cy3 using the Mirus Label-IT kit, according to the manufacturer's instructions

tag: reference type

value: Human reference RNA (Clontech)


title: siRNA1_96_2

source_name: HEK_WFS1 siRNA1_96h

value: WFS1 siRNA1


title: BreastTumor_Average_rep3

source_name: average tumor cell population from MDA-MB-231 orthotopic tumors

value: average primary tumor cells (APTC)


title: siRNA2_24_2

source_name: HEK_WFS1 siRNA2_24h


title: BreastTumor_Invasive_rep2


title: BreastTumor_Invasive_rep4


title: BreastTumor_Invasive_rep1


title: siRNA1_72_4

source_name: HEK_WFS1 siRNA1_72h


title: BreastTumor_Average_rep4


title: siRNA1_48_4

source_name: HEK_WFS1 siRNA1_48h


title: siRNA2_24_4


title: siRNA1_96_3


title: siRNA1_72_1


title: siRNA1_96_1


title: siRNA1_72_3


title: BreastTumor_Average_rep2


title: BreastTumor_Average_rep1


title: genome s04 hybrid male rep3

city: Iowa City

first: Ana

last: Llopart

address: 469 Biology Building

institute: University of Iowa

description: Biological replicate 3 out of 3

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185) as implemented in the NimbleScan software package, version 2.3.78 (Roche NimbleGen, Inc.).  Additional normalization was done using 5 control genes [Gapdh2, RpL32(rp49), Actin 42A, Eif-4a and RpII140], with 10 replicates each

organism: Drosophila yakuba x Drosophila santomea

source_name: F1 hybrids (genome project x ST04)

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

extract_protocol: Total RNA from ~30 males was isolated using the RNeasy kit with DNAse I treatment (Qiagen, Valencia, CA) and verified to be of high quality and molecular weight using the Bio-Rad Experion Automated Electrophoresis station (RNA Standard Sens kit; RNA StdSens chips; Bio-Rad Laboratories, Hercules, CA).

tag: origin

value: Laboratory-obtained

tag: gender

value: male

tag: genetic background

value: F1 hybrids (genome project x ST04)

value: whole organism


title: Reciprocal hybrid male rep1

description: Biological replicate 1 out of 3

source_name: Reciprocal F1 hybrids (ST04 x genome project)


title: siRNA1_72_2

value: HEK cells


title: siRNA1_48_2


title: siRNA1_72_5


title: siRNA1_48_3


title: US_BM_25_M012

description:
PBMC gene expression data
US_BM_25_M012.CEL

source_name: bacterial meningitis_peripheral blood

tag: sample group

value: bacterial meningitis


title: siRNA2_96_3


title: Reciprocal hybrid male rep2

description: Biological replicate 2 out of 3

value: Reciprocal F1 hybrids (ST04 x genome project)


title: genome s04 hybrid male rep1

description: Biological replicate 1 out of 3


title: siRNA1_48_1


title: nc_96_1

value: negative control siRNA


title: nc_96_3


title: siRNA1_24_3

source_name: HEK_WFS1 siRNA1_24h


title: Dsan male s04 rep1

description: Biological replicate 1 out of 2

organism: Drosophila santomea

source_name: Drosophila santomea ST04 strain

value: Hybrid zone, Sao Tome

tag: strain

value: Drosophila santomea ST04 strain


title: nc_72_5


title: genome s04 hybrid male rep2

description: Biological replicate 2 out of 3


title: siRNA1_24_4


title: Dsan male s04 rep2

description: Biological replicate 2 out of 2


title: Dyak male bosu rep1

description: Biological replicate 1 out of 2

organism: Drosophila yakuba

source_name: Drosophila yakuba Bosu strain

value: Drosophila yakuba Bosu strain


title: Dsan male Quija rep2

description: Biological replicate 2 out of 2

source_name: Drosophila santomea Quija strain

value: Rio Quija, Sao Tome

value: Drosophila santomea Quija strain


title: nc_72_3


title: nc_96_2


title: Dsan male s18 rep2

description: Biological replicate 2 out of 2

source_name: Drosophila santomea ST18 strain

value: Drosophila santomea ST18 strain


title: nc_48_2


title: nc_72_4


title: Dsan male Quija rep1

description: Biological replicate 1 out of 2


title: Dsan male s18 rep1

description: Biological replicate 1 out of 2


title: nc_72_1


title: Dyak male cam rep1

description: Biological replicate 1 out of 2

source_name: Drosophila yakuba Cameroon 115 strain

value: Cameroon

value: Drosophila yakuba Cameroon 115 strain


title: Dyak male bosu rep2

description: Biological replicate 2 out of 2


title: Reciprocal hybrid male rep3

description: Biological replicate 3 out of 3


title: nc_48_4


title: Dyak male cam rep2

description: Biological replicate 2 out of 2


title: Dyak male genome rep2

description: Biological replicate 2 out of 2

source_name: Drosophila yakuba genome project strain

value: Ivory Coast

value: Drosophila yakuba genome project strain


title: nc_72_2


title: nc_48_3


title: Dyak male genome rep1

description: Biological replicate 1 out of 2

value: male


title: nc_48_1


title: nc_24_4


title: thymic CD8+ T-cell prep1_vs_OP9 CD8+ T-cell prep2

city: Toronto

first: Dzana

middle: Dzenetdina

last: Dervovic

state: Ontario

address: 2075 Bayview Av.

department: Molecular and Cellular Biology

country: Canada

institute: Sunnybrook Research Institute

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

scan_protocol: The images were scanned using an Aglient G2505B scanner.

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.  For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis.

source_name: thymic CD8+ T-cells prep 1

label_protocol: For the linear T7-based amplification step, 1ug of each total RNA sample was used as starting material. To produce Cy3- and Cy5- labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (agilent Technologies) following the manufacturer's protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 spectrophotometer (Nano Drop technologies). In general, control samples were labeled with Cy3 (CD8+ T-cells derived from B6 thymi), and experimental samples were labeled with Cy5 (in vitro-derived CD8+ T cells).

growth_protocol: In vitro-derived CD8+ T cells were differentiated from 100,000 Lin-Sca1+CD117+ sorted hematopoietic cells (HSCs) isolated from bone marrow (BM) of 6-8 weeks old B6 mice. These were cultured with OP9-DL1 cells in OP9 media (made of alpha-MEM + 20% FBS) with addition of Flt3 (5ng/ml) and IL7 (1ng/ml) cytokines for 35 days. After d35 in vitro derived and thymic CD8+TCR(beta)hi cells were FACS purified.

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

treatment_protocol: No treatment was done with either CD8+ in vitro-derived cells or thymocytes.

tag: age

value: 4-5 weeks

source_name: OP9DL1-derived CD8+ T-cells prep 2

tag: co-culture length


title: nc_24_2

tag: time after transfection (hr)

tag: transfected with


title: Nkx2-1_2

first: Yutaka

last: Maeda

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cincinnati Children's Hospital

description: Gene expression data from human A549 lung carcinoma cells

hyb_protocol: We created a hybridization cocktail for a single probe array that contains 2.5 micrograms of fragmented cRNA. We incubated at 45C for 17 hours in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. The probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.

scan_protocol: The Genechip 1.0 ST arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G. The Scanning software was Affymetrix Genechip Command Console version 3.2.

data_processing: RMA was used to normalize all samples. The means of replicate samples were averaged to create interpretations to compare the different groups, and the raw data was filtered to remove entities not being expressed. We performed fold change analysis to create a list of genes with a fold change 2.0 or higher and used a T-Test unpaired with a p-value cutoff of 0.05 and multiple testing correction (FDR) to create a list of genes with statistical significance.

source_name: Nkx2-1 lentivirus vector-infected A549 cells

label_protocol: The Ambion® WT Expression Kit (Life Technologies) combined with the GeneChip® WT Terminal Labeling Kit (Affymetrix), was used to create biotin–labeled sense-strand cDNA targets from 300 ng of total RNA.

growth_protocol: A549 cells were grown in F-12K media containing 10% fetal bovine serum and penicillin/streptomycin at 37oC with 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  The RNA was further purified using Qiagen Rneasy MinElute Cleanup Kit according to the manufacturer's instructions.

treatment_protocol: A549 cells were infected with control or Nkx2-1-expressing lentivirus and harvested for the analysis.

tag: genotype

tag: cell line


title: thymic CD8+ T-cell prep2_vs_OP9 CD8+ T-cell prep1

source_name: thymic CD8+ T-cells prep 2

source_name: OP9DL1-derived CD8+ T-cells prep 1


title: Control_3

source_name: Control lentivirus vector-infected A549 cells

value: Control


title: HK_Resistant_family5463_day5

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

description: Head kidney gene expression in resistant family ID 5463 at 5 days post-infection

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Atlantic salmon oligonucleotide microarrays (GPL10679) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature (RT) with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 45 seconds at RT Acetonitrile (Sigma), and 30 seconds at RT with Stabilization and drying solution (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Spot intensities and other quality control features were extracted with Feature Extraction software version 10.4.0.0 (Agilent). Nofima’s bioinformatic package STARS was used for data processing, lowess normalization, and mining.

organism: Salmo salar

source_name: Head kidney, resistant family (5463), day 5 post-infection

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the LowInput Quick Amp Labelling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: This study was realized with 30 different families mantained each one in different freshwater tanks (146.1±14.85 fish/family) with a total of 4,457 fry. Fish were fed with commercial pellet twice a day (1% of body weight) and acclimated for 10 d at a biomass of 12 kg/m3, 10-12°C and controled conditions of pH, oxygen and ammonia levels.

extract_protocol: Total RNA was extracted from head kidney (HK) using RNeasy Lipid tissue mini kit (Qiagen), following the manufacturer’s instructions, and resuspended in free nuclease water (Invitrogen). RNA was quantified using a NanoDrop-1000 spectrophotometer (Thermo Scientific) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies). All RNA samples employed in this work were selected with a criteria of RIN value >7.

treatment_protocol: Before the challenge the fish was starved for 24 h. Fish was challenged in the tank with 1x106 PFU/ml of Sp and He IPNV strain. Fish were kept in the bath for 2 h, after wich the water was supplied at normal level and 24 hpi the water was replaced in all tanks and were offered feed.

value: Head kidney

tag: phenotype against ipnv infection

value: Resistant

tag: family id

tag: time point

value: 5 days post-infection


title: thymic CD8+ T-cell prep1_vs_OP9 CD8+ T-cell prep1


title: HK_Susceptible_family5637_day5

description: Head kidney gene expression in susceptible family 5637 at 5 days post-infection

source_name: Head kidney, susceptible family (5637), day 5 post-infection

tag: tissue

value: Susceptible


title: Control_2


title: thymic CD8+ T-cell prep2_vs_OP9 CD8+ T-cell prep2


title: HK_Susceptible_family5629_day5

description: Head kidney gene expression in susceptible family 5629 at 5 days post-infection

source_name: Head kidney, susceptible family (5629), day 5 post-infection


title: HK_Susceptible_family5469_day1

description: Head kidney gene expression in susceptible family ID 5469 at 1 day post-infection

source_name: Head kidney, susceptible family (5469), day 1 post-infection

value: 1 day post-infection


title: Nkx2-1_1


title: Nkx2-1_3


title: HK_Susceptible_family5352_day1

description: Head kidney gene expression in susceptible family ID 5352 at 1 day post-infection

source_name: Head kidney, susceptible family (5352), day 1 post-infection


title: HK_Resistant_family5764_day5

description: Head kidney gene expression in resistant family ID 5764 at 5 days post-infection

source_name: Head kidney, resistant family (5764), day 5 post-infection


title: Control_1


title: Granulocytic monocytic progenitors_-7AML_16683A

first: Boris

last: Bartholdy

address: 1300 Morris Park Ave

department: Cell Biology

hyb_protocol: Following fragmentation, labeled cRNA of each individual sample was hybridized to Affymetrix Affymetrix Human Gene 1.0 ST microarrays (Affymetrix) and stained according to the manufacturer's instructions.

scan_protocol: Arrays were scanned according to the manufacturer's instructions.

data_processing: Data were normalized normalized with the Expression Console Software  version 1.1 from Affymetrix using Robust Multi-array Average (RMA) algorithm. MeV software was used to select differentially expressed genes by applying the following criteria: (a)Absolute value of the group mean difference greater than 1.5, and (b) p value smaller than 0.05 (Welch's t test)

source_name: AML_granulocytic monocytic progenitors (GMP)

label_protocol: 10 ng of total RNA were used for linear amplification of cDNA using the Ovation Pico RNA Amplification Systm (Nugen), according to the manufacturer's instructions. 5 µg of cRNA were biotin-labeled using the FL-Ovation cDNA Biotin Module V2 (NuGen).

growth_protocol: primary cells

extract_protocol: human bone marrow mononuclear cells were enriched for CD34 expression using Miltenyi MACS technology. Afterwards, cells were stained with antibodies against lineage-antigens (CD2, CD3,CD4, CD7, CD8, CD10, CD11b, CD14, CD19, CD20 CD56, Glycophorin A),CD34, CD38, CD90, as well as CD123 and CD45R  in order to distinguish LT-HSC (Lin-/CD34+/CD38-/CD90+), ST-HSC (Lin-/CD34+/CD38-/CD90-), CMP (Lin-/CD34+/CD38+/CD123+/CD45R -), GMP (Lin-/CD34+/CD38+/CD123+/CD45R+) and MEP (Lin-/CD34+/CD38+/CD123-/CD45R -). Cells were subjected to 7-color 5 waysorting utilizing a high-speed cell sorter as previously described (Steidl, et al. Nature Medicine, 2006). Total RNA was extracted using a denaturing buffer containing guanidine isothiocyanate (ALLprep Kit, Qiagen) from sorted cell populations.

treatment_protocol: primary cells

value: bone marrow

tag: karyotype


title: Granulocytic monocytic progenitors_-7AML_10209A