title: cancer [4155+]


title: cancer [4083+]

status: Public on Jan 04 2016

type: RNA

city: Shanghai

first: Yi-Zhou

last: Jiang

state: Shanghai

address: No. 270 Dong-An Road

country: China

institute: Fudan University Shanghai Cancer Center

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scaned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G

data_processing:
The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method (ExpressionConsole 1.3.1)
probe group file: HTA-2_0.r1.pgf
meta-probeset file: HTA-2_0.r1.Psrs.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit. WT Expression Kit

extract_protocol: Total RNA was isolated from cells at indicated time point with Trizol

tag: gender

value: female

tag: age (yrs)

tag: menopause status (0=pre, 1=post)

tag: size (cm)

tag: tumor grade

tag: positive lymph nodes

tag: tissue type

value: triple negative breast cancer (TNBC)


title: cancer [4076+]


title: cancer [4162+]


title: cancer [4075+]


title: cancer [4054+]


title: cancer [3979]


title: cancer [3984+]


title: cancer [3595]


title: cancer [3897]


title: cancer [3976]


title: cancer [3983]


title: cancer [3995+]


title: cancer [3415]


title: cancer [3889]


title: cancer [3637]


title: cancer [3419]


title: cancer [3479]


title: cancer [3673]


title: cancer [3626]


title: cancer [3533]


title: cancer [3508]


title: cancer [3420]


title: cancer [3622]


title: cancer [3621]


title: cancer [3538]


title: adjacent cancer [4474-]

source_name: breast_normal tissue

value: normal breast tissue


title: cancer [3400]


title: cancer [3431]


title: cancer [3405]


title: cancer [3336]


title: cancer [3398]


title: cancer [3366]


title: cancer [3392]


title: cancer [3292]


title: cancer [3297]


title: cancer [3383]


title: cancer [3314]


title: cancer [3310]


title: cancer [3241]


title: cancer [3263]


title: cancer [3283]


title: cancer [3262]


title: cancer [3191]


title: cancer [3209]


title: cancer [3222]


title: cancer [3119]


title: U2Os-hyp

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0

source_name: hypoxia exposed U2OS

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: The cells were incubated in Dulbecco's Modified Eagle medium with GlutaMAX supplemented with 10% fetal calf serum (FCS) and 100 U/ml penicillin/streptomycin (Gibco) under a 5% CO2 atmosphere at 37°C, and subcultured twice a week.

extract_protocol: RNA was extracted using RNeasy MiniKit (Quiagen), according to the manufacturers’ instructions.  Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were plated out in plastic dishes (3x105 cells for 6 cm dishes, 9x105 for 10 cm dishes) 24 h prior to exposure to hypoxic (0.2% O2, 5% CO2) or normoxic (95% air, 5% Co2) conditions for 24 h at 37°C. The hypoxia treatment was performed in an Invivo2200 chamber (Ruskinn Technology Ltd, Bridgend, UK) with accurate O2 and CO2 controls.

tag: cell line

tag: cell type

value: Osteosarcoma

tag: histology

value: Epithelial


title: cancer [3180]


title: cancer [3162]


title: cancer [3183]


title: cancer [3169]


title: cancer [3145]


title: cancer [3205]


title: cancer [3266]


title: cancer [3118]


title: cancer [3131]


title: U2OS-O2

source_name: untreated U2OS


title: cancer [3109]


title: cancer [3113]


title: cancer [3083]


title: cancer [3085]


title: KG-P66-14 vs. KG-C66-14

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

description: HT-induced eFS.

hyb_protocol: PREHYBRIDIZATION:  Make 100 ml prehybridization buffer (for a maximum of 4 slides) containing 5xSSC, 25% formamide (Merck Cat# 1.09684.10), 0.1% SDS and 1% bovine serum albumin (BSA; Sigma Cat# A-9418): 25 ml 20x SSC, 25 ml pure formamide, 49 ml ddH2O, 1 ml 10% SDS and 1 g BSA. After BSA has dissolved the solution becomes clear in about 5 minutes. Filter prehybridization buffer through a 0.22 micron syringe filter. Heat the prehybridization solution to 42C in a 100 ml Coplin Jar. Place slides to be analyzed into the preheated prehybridization buffer. Incubate for 45 minutes at 42C. Wash the slides by dipping 5 times in room temperature ddH2O (staining dish). Dip the slides 5 times in room temperature isopropanol (staining dish). Air dry in fume hood (15 ml tube rack upside down). Slides should be used immediately following prehybridization.    HYBRIDIZATION:  (NOTE: The first steps of the hybridization protocol can be completed during the prehybridization step.) The hybridization volume for a whole slide (25x60mm) is 45 ul. Maximum volume of Cy3 and Cy5 combined target is 25 ul! It could be necessary to concentrate in a speed vac until the volume is below 25 ul. Prepare 2x hybridization buffer containing 50% formamide, 10xSSC and 0.2% SDS: 2.5 ml formamide, 2.5 ml 20xSSC and 0.1 ml 10% SDS. Immediately filter the hybridization buffer through a 0.22 micron filter (before SDS precipitates out of solution). Take 250 ul of the 2x hybridization buffer. Add 5 ul Herring sperm DNA (stock 10 ug/ul, sheared). Final concentration in 2x hybridization buffer is 200 ug/ml. In case of Human Gene Arrays add also 5 ul tRNA (stock 20 ug/ul). Preheat to 42C to overcome SDS precipitation. Combine 25 ul target with 25 ul 2x hybridization buffer (preheated to 42C). Heat at 95C for 5 minutes. Spin at 12K for 2 minutes. DO NOT place on ice after the 2 minute spin. Using standard coverslips: To each array add a total of 45 ul target as 3 to 6 separate dots in the center, along the length of the slide. Put a coverslip (25x60mm) on the array by holding the coverslip in place with your fingertips, toward the bottom of the slide. Gently (!) allow the coverslip to drop onto the array by using a needle. Do not move the coverslip after it is in place. Using LifterSlips (Erie Scientific): Place clean LifterSlip, teflon side down, over the array area. Place the pipette tip along an open edge of the LifterSlip and slowly pipette 45 ul target out of the tip. Capillary action will draw the probe mix under the slip. Place the slide in a Corning Hybridization Chamber (Corning Cat# 2551). Add 20 ul of water to each well in the chamber and clamp the hybridization chamber closed. Gently place the hybridization chamber into a 42C water bath for 16-20 hours.    WASHING THE HYBRIDIZED ARRAYS:  Remove the slide from the hybridization chamber, taking care not to disturb the coverslip. Perform the following washes: (i) Low-stringency wash: Place the slides in a Coplin Jar containing 100 ml 1xSSC and 0.2% SDS (= 100 ml 1xSSC and 2 ml of 10% SDS). Gently remove the coverslip while the slide is in solution. LifterSlips are reusable and should be washed in 70% EtOH prior to use. Incubate for 4 minutes at room temperature. (ii) High-stringency wash: Place the slides in a Coplin Jar containing 100 ml 0.1xSSC and 0.2% SDS (= 10 ml 1xSSC, 90 ml water and 2 ml of 10% SDS). Incubate for 4 minutes at room temperature. Wash the slide finally in 100 ml 0.1xSSC to remove particles of SDS. Incubate for 4 minutes at room temperature. Allow the slides to dry by centrifuge 1 minute 500 rpm (do this immediately after the third wash).

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using ImaGene software from BioDiscovery.

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background subtraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.

organism: Mus musculus

label_protocol: aRNA labeling with Cy-dyes    1· In dark micro centrifuge tube; dilute/concentrate required aRNA sample (x ng) to 8 µl.  2· Add 1 µl 0.5 M NaBicarbonate buffer, pH 9. Mix well.  3· Resuspend monofunctional NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): Quickly resuspend entire tube in 10 µl DMSO (Merck 8.02912.10). Add 1.25 µl per sample. Mix immediately and quickly.  4· Incubate 60 min at RT in the dark.  5· Add 4.5 µl 4 M hydroxylamine for quenching to prevent cross-coupling.  6· Incubate 15 min at RT in the dark.    Cleanup using Clontech ChromaSpin-30 columns:    1. Upon removing a CHROMA SPIN Column from the protective plastic bag, invert it several times to resuspend the gel matrix completely. Before removing the top make sure that all the matrix is at the bottom by vigorously flicking the column downwards to remove matrix that is stuck to the top cap.  2. Holding the CHROMA SPIN Column upright, grasp the break-away end between your thumb and index finger and snap off. Place the end of the spin column into one of the 2-ml microcentrifuge (collection) tubes provided, and lift off the top cap. Save the top cap and the white-end cap.  3. Centrifuge at 700 g for 5 min (2700 RPM in Heraeus Megafuge 1.0 Sepatech Centrifuge, 1500 RPM in Eppendorf 5810 centrifuge (prog. 5)). After centrifugation, the column matrix will appear semi-dry. This step purges the equilibration buffer from the column and re-establishes the matrix bed. Make sure that the matrix bed is flat.  4. Remove the spin column and collection tube from the centrifuge rotor, and discard the collection tube and column equilibration buffer.  5. Place the spin column into the second 2-ml microcentrifuge tube. Carefully and slowly apply the sample to the center of the gel bed's flat surface. Drop by drop! Do not allow any sample to flow along the inner wall of the column - this will completely mess up the sample.  6. Centrifuge at 700 g for 5 min.  7. Remove the spin column and collection tube from the rotor and detach them from each other. The purified sample is at the bottom of the collection tube. Immediately keep on ice and in the dark!    Purified sample is about 15-30 µl. Bring sample up to 35 µl with water and take 5 µl eluate for spectrophotometry (190 to 750 nm range).    Samples may be stored at -20 C.

growth_protocol: Mice were bred from pairs of C57BL/6J mice (Jackson Laboratories, ME, USA) and raised by their mothers. Animals were kept in a controlled 12h light-dark cycle with a temperature of 22  ± 1ºC and were given unrestricted access to food (211 RMH-TM diet; Hope Farms, Woerden, NL) and water. Animals were housed in transparent Plexiglas cages with wood-chip bedding and tissue for nest building.

extract_protocol: Trizol RNA isolation of tissue sections:  1. After sectioning, store sections in ice-cold RNAlater (~10 ml RNAlater per 20-mm section). Make sure that the sections do not thaw before they are in ice-cold RNAlater. 50 ml RNAlater.  2. Add X ml Trizol (10x volume of RNAlater) and mix by inverting the tube several times. 500 ml Trizol.  3. Incubate 5 min at room temperature.  4. Pre-incubate Proteinase K (10 mg/ml) at 37 C for at least 10 minutes.  5. Add 10 ml of the pre-heated Proteinase K solution to Trizol mixture. 10 ml Prot-K.  6. Incubate 30 min at 55 C.  7. Add X ml chloroform (20 ml per 100 ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature. 100 ml chloroform.  8. Centrifuge 20 min at 14000 rpm without brake at 4 C. After centrifugation, transfer the water-phase to a new 1.5 ml micro centrifuge tube (~300 ml).  9. Continue with RNeasy columns (Qiagen) for clean-up of RNA.  10. Adjust each sample to a volume of 300 ml with sterile MilliQ water. Add 160 ml buffer RLT to the samples, and mix (= lysis buffer).  11. Add 240 ml ethanol (100% stored at -20 C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipette and work as quickly as possible). Next lysate, and so on.  12. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flow-through and collection tube.  13. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 ml buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in step 5.  14. Pipette 500 ml buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube.  15. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane).  16. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipette 100 ml milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute.  17. Pipette the eluate of step 7 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute.

treatment_protocol: For eFS, hyperthermia (HT) in mice was induced by quickly raising core body temperature with a temperature-regulated laminar stream of warm air (41-48ºC) as previously described (Van Gassen/Hessel 2008 Genes Brain Behav.). HT was typically reached within 2.5 minutes. After core temperature of the HT mice had reached 42ºC, air temperature was adjusted to maintain a core body temperature between 41.5ºC and 42ºC. Time and temperature data was logged automatically on a computer (DASHost v1.0, Plexx). HT was maintained for 30 minutes. NT mice were simultaneously treated as HT mice, except that the core body temperature of the animals was kept at 35ºC. The observer scored the stages of behavior and seizures during the experiment, as previously described (van Gassen/Hessel 2008, Genes Brain Behav.). For eFS, only mice showing continued febrile seizures during at least 17.5 minutes were used in the experiment. At one hour, three, fourteen, and fifty-six days after HT, animals were sacrificed by decapitation. Brains were quickly removed and hippocampal tissue was dissected, collected and stored at -80ºC. Total RNA was isolated, purified and checked for quality as described (van Gassen 2007 Epilepsia).

tag: strain/background

tag: tissue

value: hippocampus

tag: treatment

value: hypothermia (HT)

tag: time point

value: 56 days

value: normothermia (NT)


title: pdf-1 KO vs. wild type 5892

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: hermaphrodite young adult sample

hyb_protocol: A mixture of purified and labeled cRNA (Cy3 label: 14 pmol; Cy5 label: 10 pmol) was hybridised on Agilent C. elegans (V2) Gene Expression Microarray followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 9.5.3.1).

data_processing: The Agilent processed signal values (i.e., features gProcessedSignal and rProcessedSignal from Agilent Feature Extraction v9.5.3.1) were used for the data analysis. Base 2 log-ratios (Cy5/Cy3 intensities) were computed and in case of multiple probes for the same Agilent ID, log-intensities were averaged.  Control probes were remove  prior to analysis.

organism: Caenorhabditis elegans

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 1 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

extract_protocol: Qiagen mini kit

tag: strain

tag: stage

value: young adult

value: whole-mount

value: hermaphrodite

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 1 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

value: N2 wild type


title: KG-P66-15 vs. KG-C66-15

description: HT-induced eFS.


title: KG-P66-13 vs. KG-C66-13

description: HT-induced eFS.


title: cancer [3032]


title: KG-P66-16 vs. KG-C66-16

description: HT-induced eFS.


title: KG-P66-12 vs. KG-C66-12

description: HT-induced eFS.


title: cancer [3055]


title: cancer [2965]


title: pdf-1 KO vs. wild type 5891

description: hermaphrodite young adult sample


title: cancer [2963]


title: cancer [2916]


title: pdf-1 KO vs. wild type 5890

description: hermaphrodite young adult sample


title: pdf-1 KO vs. wild type 5889

description: hermaphrodite young adult sample


title: KG-P24-5 vs. KG-C24-5

description: HT-induced eFS.

value: 14 days


title: cancer [3059]


title: cancer [2789]


title: KG-P24-4 vs. KG-C24-4

description: HT-induced eFS.


title: Day 0, QKI shRNA, biological rep2

city: Santa Cruz

first: Lily

last: Shiue

state: CA

address: 1156 High Street

department: MCD Biology

country: USA

institute: UCSC

hyb_protocol: Hybridization was performed as specified, with the GeneChip Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.

source_name: THP cells transfected with QKI shRNA

label_protocol: cDNA synthesis and amplification was performed using the WT Expression Kit (Ambion). Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was extracted using Trizol.

treatment_protocol:
Human THP-1 ‘monocytes’ were stably transduced using lentiviral particles that encode either a QkI-targeting shRNA (sh-QkI) or a scrambled control shRNA (sh-Cont). Stable transductants were selected using 3 µg/mL puromycin for 72h.
For differentiation, THP-1 cells were stimulated with 100 nM PMA for 3 days.

tag: phenotype

value: monocyte

tag: transfected shrna

value: QKI shRNA

tag: differentiation

value: day 0


title: KG-P24-2 vs. KG-C24-2

description: HT-induced eFS.


title: Day 0, QKI shRNA, biological rep3


title: KG-P24-3 vs. KG-C24-3

description: HT-induced eFS.


title: cancer [2742]

tag: gender

value: female

tag: age (yrs)

tag: menopause status (0=pre, 1=post)


title: KG-P66-11 vs. KG-C66-11

description: HT-induced eFS.


title: cancer [2792]

tag: size (cm)

tag: tumor grade

tag: positive lymph nodes

value: triple negative breast cancer (TNBC)


title: Day 0, control shRNA, biological rep3

source_name: THP cells transfected with control shRNA

tag: cell line

value: control shRNA


title: Day 0, control shRNA, biological rep2


title: Day 0, QKI shRNA, biological rep1


title: cancer [2752]

tag: tissue type


title: Day 0, control shRNA, biological rep1


title: cancer [2695]


title: KG-P13-21 vs. KG-C13-21

description: HT-induced eFS.

tag: strain/background

value: 3 days


title: cancer [2688]


title: KG-P24-6 vs. KG-C24-6

description: HT-induced eFS.

tag: tissue


title: KG-P13-22 vs. KG-C13-22

description: HT-induced eFS.

tag: treatment


title: KG-P24-1 vs. KG-C24-1

description: HT-induced eFS.

tag: time point


title: cancer [2729]


title: cancer [2669]


title: Day 3 differentiation, QKI shRNA, biological rep3

source_name: THP cells transfected with QKI shRNA, treated with PMA for 3 days

value: macrophage

value: day 3


title: Day 3 differentiation, control shRNA, biological rep1

source_name: THP cells transfected with control shRNA, treated with PMA for 3 days


title: KG-P13-20 vs. KG-C13-20

description: HT-induced eFS.

value: hippocampus

value: hypothermia (HT)


title: cancer [2682]


title: KG-P13-18 vs. KG-C13-18

description: HT-induced eFS.

value: normothermia (NT)


title: cancer [2617]


title: KG-P13-19 vs. KG-C13-19

description: HT-induced eFS.


title: Day 3 differentiation, control shRNA, biological rep3


title: cancer [2630]


title: cancer [2590]


title: Day 3 differentiation, QKI shRNA, biological rep1


title: cancer [2625]


title: Day 3 differentiation, QKI shRNA, biological rep2


title: cancer [2587]


title: KG-C66-15 vs. KG-P66-15

description: HT-induced eFS.

value: 56 days


title: KG-C66-14 vs. KG-P66-14

description: HT-induced eFS.


title: KG-C66-13 vs. KG-P66-13

description: HT-induced eFS.


title: genomic DNA from saliva Saliva 11

type: genomic

city: Mol

first: Sabine

last: Langie

state: Please Select…

address: Boeretang 200

institute: Flemish Institute of Technological Research (VITO)

description:
saliva from patient with repiratory allergy
Sample 23

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Saliva 11

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from PBMC pellets was extracted using Gentra Puregene Blood Kit (Qiagen, Hilden, Germany); genomic DNAfrom saliva was extracted using the Oragene PrepIT kit (DNA Genotek, Ottawa, Canada)

value: Female

tag: sample type

value: saliva

tag: disease state

value: Respiratory Allergy


title: Day 3 differentiation, control shRNA, biological rep2

tag: phenotype


title: KG-C66-16 vs. KG-P66-16

description: HT-induced eFS.


title: KG-C66-12 vs. KG-P66-12

description: HT-induced eFS.


title: genomic DNA from saliva Saliva 10

description:
saliva from patient with repiratory allergy
Sample 22

source_name: Saliva 10


title: genomic DNA from saliva Saliva 12

description:
saliva from healthy control
Sample 24

source_name: Saliva 12

value: Control


title: cancer [2585]


title: genomic DNA from saliva Saliva 8

description:
saliva from patient with repiratory allergy
Sample 20

source_name: Saliva 8

value: Male


title: KG-C24-6 vs. KG-P24-6

description: HT-induced eFS.

value: 14 days


title: cancer [2557]


title: cancer [2548]


title: cancer [2526]


title: genomic DNA from saliva Saliva 9

description:
saliva from patient with repiratory allergy
Sample 21

source_name: Saliva 9


title: genomic DNA from saliva Saliva 7

description:
saliva from healthy control
Sample 19

source_name: Saliva 7


title: genomic DNA from saliva Saliva 4

description:
saliva from healthy control
Sample 16

source_name: Saliva 4


title: KG-C24-4 vs. KG-P24-4

description: HT-induced eFS.


title: genomic DNA from saliva Saliva 6

description:
saliva from healthy control
Sample 18

source_name: Saliva 6


title: cancer [2522]


title: cancer [2433]


title: KG-C24-1 vs. KG-P24-1

description: HT-induced eFS.


title: genomic DNA from saliva Saliva 2

description:
saliva from healthy control
Sample 14

source_name: Saliva 2


title: genomic DNA from saliva Saliva 5

description:
saliva from patient with repiratory allergy
Sample 17

source_name: Saliva 5


title: cancer [2508]


title: KG-C24-2 vs. KG-P24-2

description: HT-induced eFS.


title: KG-C24-5 vs. KG-P24-5

description: HT-induced eFS.


title: cancer [2392]


title: KG-C24-3 vs. KG-P24-3

description: HT-induced eFS.


title: genomic DNA from saliva Saliva 3

description:
saliva from healthy control
Sample 15

source_name: Saliva 3


title: KG-C13-21 vs. KG-P13-21

description: HT-induced eFS.


title: cancer [2285]


title: cancer [2361]


title: genomic DNA from saliva Saliva 1

description:
saliva from patient with repiratory allergy
Sample 13

source_name: Saliva 1


title: KG-C13-22 vs. KG-P13-22

description: HT-induced eFS.


title: genomic DNA from peripheral blood mononuclear cells PBMC 12

description:
peripheral blood mononuclear cells from healthy control
Sample 12

source_name: PBMC 12

value: peripheral blood mononuclear cells


title: KG-C66-11 vs. KG-P66-11

description: HT-induced eFS.


title: cancer [2272]

value: female


title: cancer [2204]

value: triple negative breast cancer (TNBC)


title: genomic DNA from peripheral blood mononuclear cells PBMC 11

description:
peripheral blood mononuclear cells from patient with repiratory allergy
Sample 11

source_name: PBMC 11


title: KG-P13-17 vs. KG-C13-17

description: HT-induced eFS.


title: KG-C13-17 vs. KG-P13-17

description: HT-induced eFS.


title: KG-C13-20 vs. KG-P13-20

description: HT-induced eFS.


title: cancer [2139]


title: KG-C13-18 vs. KG-P13-18

description: HT-induced eFS.


title: KG-C13-19 vs. KG-P13-19

description: HT-induced eFS.


title: genomic DNA from peripheral blood mononuclear cells PBMC 9

description:
peripheral blood mononuclear cells from patient with repiratory allergy
Sample 9

source_name: PBMC 9


title: KG-B-8 vs. KG-A-7

description: HT-induced eFS.

value: 1 hour


title: cancer [2111]


title: genomic DNA from peripheral blood mononuclear cells PBMC 7

description:
peripheral blood mononuclear cells from healthy control
Sample 7

source_name: PBMC 7


title: genomic DNA from peripheral blood mononuclear cells PBMC 10

description:
peripheral blood mononuclear cells from patient with repiratory allergy
Sample 10

source_name: PBMC 10


title: genomic DNA from peripheral blood mononuclear cells PBMC 8

description:
peripheral blood mononuclear cells from patient with repiratory allergy
Sample 8

source_name: PBMC 8


title: cancer [2170]


title: KG-B-26 vs. KG-A-19

description: HT-induced eFS.


title: cancer [2110]


title: genomic DNA from peripheral blood mononuclear cells PBMC 6

description:
peripheral blood mononuclear cells from healthy control
Sample 6

source_name: PBMC 6


title: KG-B-6 vs. KG-A-5

description: HT-induced eFS.


title: genomic DNA from peripheral blood mononuclear cells PBMC 4

description:
peripheral blood mononuclear cells from healthy control
Sample 4

source_name: PBMC 4


title: KG-B-23 vs. KG-A-13

description: HT-induced eFS.


title: C2aMxcys3_ V72cys5R2

city: Saint-Genès Champanelle

last: Leroy

address: Clermont-Ferrand Theix Research Center

department: MICA

country: France

institute: INRA

hyb_protocol: The experimentation was realized in dye swap. Cyanine 3/cDNA and cyanine 5/cDNA were mixed with  Agilent hybridization buffer, and hybridized at a temperature of 60°C for 18 hours in a dedicated hybridization oven.

scan_protocol: Microarrays were scanned in a SYS-SN-ARRAY Agilent Microarray Scanner (5-µm resolution) with a coefficient of photomultiplication of 30%.

data_processing:
Global lowess within array normalization.
Normalized log2 ratio representing Mx/V (Cy3/Cy5 for samples  2, 4, 6, 8, 10, 12 and Cy5/Cy3 for samples 1, 3, 5, 7, 9, 11)

organism: Staphylococcus xylosus

source_name: strain  C2a

label_protocol: RNA from each sample was reverse transcribed to cDNA according to the manufacturer’s instructions (Invitrogen, Superscript Reverse Transcriptase). The RNA was digested by RNAse H (Invitrogen). The cDNA was labeled by cyanine 3 or cyanine 5 by the kit Bioprime DNA according to the manufacturer’s instructions (Invitrogen). Unincorporated Cy-dye was removed using CentriSep column (Applied Biosystem).

growth_protocol: S.xylosus was precultured 24 h in a minimum medium Mx, cultured 21 h in Mx and then inoculated at 107 CFU/g of meat model. S. xylosus was finally incubated in meat model during 24, 48 or 72hours.

extract_protocol: Bacteria were lysed in 1.25 ml of Trizol reagent (Invitrogen Life Technologie) with 800mg of zirconia-silica beads (0.1 mm-diameter) in a FastPrep instrument (MP Biomedicals). RNA was purified with the kit Nucleospin RNA II (Macherey Nagel) according to the manufacturer’s instructions. A supplementary treatment is performed with Turbo DNAse (Ambion) to remove all traces of contaminated DNA.

treatment_protocol: S.xylosus was incubated in a meat model containing per kg: 5 g of glucose and 27.7 g of NaCl

value: Inoculum at 72hours of incubation

value: Meat model at 72hours of incubation


title: C2aV72cys3_ Mxcys5R3


title: C2aMxcys3_ V72cys5R3


title: cancer [2095]


title: KG-A-7 vs. KG-B-8

description: HT-induced eFS.


title: C2aV48cys3_ Mxcys5R3

value: Meat model at 48hours of incubation

value: Inoculum at 48hours of incubation


title: genomic DNA from peripheral blood mononuclear cells PBMC 2

description:
peripheral blood mononuclear cells from healthy control
Sample 2

source_name: PBMC 2


title: KG-B-20 vs. KG-A-15

description: HT-induced eFS.

value: hippocampus

value: hypothermia (HT)


title: C2aMxcys3_ V48cys5R3


title: genomic DNA from peripheral blood mononuclear cells PBMC 1

description:
peripheral blood mononuclear cells from patient with repiratory allergy
Sample 1

source_name: PBMC 1


title: C2aV48cys3_ Mxcys5R1


title: cancer [2084]


title: cancer [2093]


title: cancer [1803]


title: KG-A-5 vs. KG-B-6

description: HT-induced eFS.

value: normothermia (NT)


title: C2aMxcys3_ V24cys5R3

value: Inoculum at 24hours of incubation

value: Meat model at 24hours of incubation


title: KG-B-18 vs. KG-A-14

description: HT-induced eFS.


title: genomic DNA from peripheral blood mononuclear cells PBMC 3

description:
peripheral blood mononuclear cells from healthy control
Sample 3

source_name: PBMC 3


title: KG-B-25 vs. KG-A-24

description: HT-induced eFS.


title: cancer [1814]


title: KG-A-24 vs. KG-B-25

description: HT-induced eFS.


title: C2aMxcys3_ V48cys5R2


title: cancer [1758]


title: cancer [2445]


title: cancer [1723]


title: genomic DNA from peripheral blood mononuclear cells PBMC 5

description:
peripheral blood mononuclear cells from patient with repiratory allergy
Sample 5

source_name: PBMC 5

value: Female

value: Respiratory Allergy


title: KG-A-19 vs. KG-B-26

description: HT-induced eFS.


title: C2aV24cys3_ Mxcys5R3


title: cancer [1545]


title: KG-A-13 vs. KG-B-23

description: HT-induced eFS.


title: C2aV24cys3_ Mxcys5R1


title: cancer [1709]


title: WB1-scr_H_8 vs. CRR

hyb_protocol: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA  * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan)  * Priming: 5xSSC, 0.1%SDS  * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul  * Hybridization: 45 min at 42C.  * Wash 2x: milliQ  * Wash: 5xSSC, 0.1%SDS  * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul)  * Hybridization: 16 hours at 42C.  * Wash 2x: 1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC at 23C  * Drying: blow with nitrogen for 3min at 30C

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using ImaGene software from BiodDiscovery.

data_processing:
Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background subtraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.
The supplementary *derived.txt file includes the normalized Cy5 and Cy3 signal intensities.

label_protocol: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrophotometer (Molecular Devices), and a magnetic bead-locator (Beckman).    mRNA amplification protocol description:  * all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script.  * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well.  * plate is incubated @ 70C for 10 mins, cooled to 48C.  * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNase Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well.  * plate is incubated @ 48C for 2 hours and cooled to room temperature.  * 106 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNaseH (Promega) is added and mixed in each well.  * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul .  * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems).  * Plate is incubated @37C for 4 hours.  * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol.   * Concentration is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot.  * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.    Labeling protocol description:   * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).   All subsequent steps are performed by the robot script :  * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ).  * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells.  * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour.  * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes.  * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol.  * RNA concentration and labeling incorporation are measured (SpectraMax 190).  * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C.  * Samples are stored at -20C until hybridization.

growth_protocol: The cervical cancer (HeLa) cell line was cultured in DMEM (Invitrogen, 41966-052) supplemented with 10% FBS (Lonza, DE14-802F) and 1% Penicillin/Streptomycin (Lonza, DE17-602E). For hypoxia treatment, cells were incubated in the H35 Hypoxystation (Don Whitley Scientific) at 1% O2 for 16 hours.

extract_protocol: 1. Add 1 ml Trizol per 5x 10^6 cells in suspension (1 ml Trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube.   2. Incubate 5 min at room temperature.   3. Add chloroform (200 µl per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature.   4. Centrifuge 20 min at 14000 rpm 4°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube.   5. add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml Trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min.   6. wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Airdry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 µg/column)   7. Adjust each sample to a volume of 300 µl with sterile MilliQ water. Add 160 µl buffer RLT to the samples, and mix (= lysis buffer).   8. Add 240 µl ethanol (100% stored at -20 °C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on.   9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at room temperature! DNase treatment: D1. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 µl/reaction): add 10 µl DNase I stock solution to 70 µl Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 µl) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 µl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube.   10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 µl buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps.  11. Pipet 500 µl buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube.   12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane).   13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 µl milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 µl milliQ.   14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80 °C.

treatment_protocol: HeLa cells were grown to confluence and re-seeded at 150k/well (6 well plate, Greiner). Next day, cells were siRNA transfected as specified by the manufacturer using 5mL/well RNAIMAX (Invitrogen, 13778-075) and a final siRNA concentration of 50nM. Medium was replaced the next day and cells were grown overnight in normoxia or hypoxia and harvested 48h after transfection. siRNAs used in this study: hHIF1-alpha(L-004018-00-0005, Thermo Scientific ), non-targeting siRNA #2 (D-001210-02, Thermo Scientific). hE2F7 (HSS135118, HSS135119, HSS175354, Invitrogen), hE2F8 (HHS128758, HSS128759, HSS128760, Invitrogen), Negative control medium (Invitrogen, 12935-300). The negative control siRNAs from Thermo and Invitrogen were mixed and used at a 1:1 ratio. For double transfection, half of the amounts applied for the single siRNA transfections were used, ensuring a final concentration of 50nM.

value: HeLa

tag: sirna

value: scr

tag: growth condition

value: hypoxia

value: normoxia


title: WB1-siHif1a_H_14 vs. CRR


title: C2aMxcys3_ V24cys5R2


title: C2aV72cys3_ Mxcys5R1


title: cancer [1365]

tag: gender

value: female

value: triple negative breast cancer (TNBC)


title: WB1-si7_H_12 vs. CRR


title: WB1-si7+Hif1a_H_16 vs. CRR


title: CRR vs. WB1-siHif1a_H_13


title: cancer [1503]

tag: age (yrs)


title: cancer [1268]

tag: menopause status (0=pre, 1=post)


title: cancer [1507]

tag: size (cm)


title: WB1-si7+8_H_10 vs. CRR


title: cancer [1302]

tag: tumor grade


title: cancer [1304]

tag: positive lymph nodes


title: cancer [1355]


title: cancer [1271]


title: cancer [1303]


title: CRR vs. WB1-si7_H_11

tag: cell line


title: CRR vs. WB1-si7+Hif1a_H_15


title: cancer [1253]

tag: tissue type


title: CRR vs. WB1-scr_H_7


title: CRR vs. WB1-si7+8_H_9


title: TUM-OS0115R2

status: Public on Jan 03 2016

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

country: Germany

institute: Charité - Universitätsmedizin Berlin

description: osteosarcoma, 3rd relapse

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: GCS 3000 7G scanner (Affymetrix) using the standard Affymetrix protocol.

data_processing: RMA normalization using Expression Console, Version 1.1 (Affymetrix).

source_name: osteosarcoma

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

extract_protocol: Total RNA was isolated using the RNeasy RNA isolation kit according to the manufacturer's instructions.

value: osteosarcoma


title: TUM-OS0115R3

description: osteosarcoma, 4th relapse


title: TUM-OS0100A

description: osteosarcoma lung metastase B

value: osteosarcoma lung metastase


title: TUM-OS0100B

description: osteosarcoma lung metastase, relapse


title: TUM-ES0062

description: Ewing sarcoma, temporal bone

source_name: advanced Ewing sarcoma

value: Ewing sarcoma

value: Ewing sarcoma, temporal bone


title: TUM-OS0048

description: osteosarcoma lung metastase


title: TUM-OS0115R

description: osteosarcoma, relapse


title: TUM-OS0051

description: osteosarcoma lung metastase A


title: TUM-OS0100M

description: osteosarcoma lung metastase


title: TUM-ES0138

description: Ewing sarcoma relapse


title: TUM-ES0099

description: osteoid Ewing sarcoma

value: osteoid Ewing sarcoma


title: TUM-ES0021

description: Ewing sarcoma, lung metastase

value: Ewing sarcoma, lung metastase


title: 7 days post injury - rep 3

city: Woods hole

first: Karen

last: Echeverri

state: MA

address: 7 MBL ST

department: Eugene Bell Center for Regeneration Biology and Tissue Engineering

institute: MARINE BIOLOGICAL LAB

description:
gene expression data from axolotl spinal cord 7 day post injury
7 days post injury
white axolotls

hyb_protocol: Hybridizations were performed according to the Affymetric's GeneChip 3’IVT Express Kit User Manual,    12.5µg fragmented and labelled aRNA were hybridized for 17 hours at 45 degrees and 60 rpm.

scan_protocol: The Arrays were scanned using the Affymetrix GCS3000 System (Scanner). (Affymetrix).

data_processing: Cel files containing normalized intensity data (RMA normalization) were generated using the Gene Expression Console (Affymetrix)

organism: Ambystoma mexicanum

source_name: 7 days post injury axolotl spinal cord

label_protocol: 150ng of total RNA was used toreverse  transcribe double stranded cDNA and Biotinylation was carried out according to the instructions in Affymetrix's 3'IVT Reagent Kit user's manual

growth_protocol: axolotl was maintained at the University of Minnesota in 20% Holtfreters solution and fed daily with axolotl pellets

extract_protocol: Total RNA was extracted using Trizol (Invitrogen)

treatment_protocol: All axolotls used in these experiments were bred in the axolotl facility at the University of Minnesota under the IACUC protocol #1201A08381. Axolotls of 2–3 cm were used for all in vivo experiments, and animals were kept in separate containers and fed daily with artemia; water was changed daily. Animals were anesthetized in 0.01% p-amino benzocaine (Sigma) before microinjection was performed.      Experimental Design: Ivermectin injection  Ivermectin or vehicle only (water) was pressure injected into the central canal of the spinal cord, and this was visualized by the addition of Fast Green into the solution. Directly after injection, a portion of the spinal cord was surgically removed and the animals were placed back into water in individual containers. One day post injury (1dpi) animals were anesthetized again and the area of the injury was removed. Tissue from 10 animals were pooled for each microarray replicate.

tag: age

value: 1month old

tag: stress

value: spinal cord injury

tag: time

value: 7 days post injury

value: spinal cord


title: ivermectin treated 1 day post injury - rep 1

description:
gene expression data from ivermection injected injured spinal cord 1 day post injury
Ivermectin 1
white axolotls

source_name: drug treated injured axolotl spinal cord

tag: agent

value: ivermection

value: 1 day post injury

tag: tissue


title: TUM-ES0068

description: Ewing sarcoma, L4 vertebra

tag: disease state

value: Ewing sarcoma, L4 vertebra


title: TUM-ES0073

description: Ewing sarcoma, metastase

value: Ewing sarcoma, metastase


title: ivermectin treated 1 day post injury - rep 2

description:
gene expression data from ivermection injected injured spinal cord 1 day post injury
Ivermectin 2
white axolotls


title: TUM-OS0015M

description: osteosarcoma metastase

value: osteosarcoma metastase


title: TUM-ES0031

description: Ewing sarcoma relapse


title: ivermectin treated 1 day post injury - rep 3

description:
gene expression data from ivermection injected injured spinal cord 1 day post injury
Ivermectin 3
white axolotls


title: TUM-OS0015M2

description: osteosarcoma 2nd lung metastase


title: 7 days post injury - rep 2


title: 7 days post injury - rep 1


title: TUM-ES0082

description: Ewing sarcoma, mandible late relapse

value: Ewing sarcoma, mandible


title: 3 days post injury - rep 3

description:
gene expression data from axolotl spinal cord 3 day post injury
3 days post injury
white axolotls

source_name: 3 days post injury axolotl spinal cord

value: 3 days post injury


title: 3 days post injury - rep 2


title: NDMA-silica_AC_3

city: Pamplona

first: Daniel

last: Ajona

address: Pio XII, 55

country: Spain

institute: CIMA

hyb_protocol: Samples were added for 17 h at 60 ° C using hybridization chambers G2534-60002, G2534A (Agilent) and DNA hybridization oven G2545A

scan_protocol: Raw data were obtained using DNA Microarray Scanner scanner G2505B (Agilent) and Feature Extraction software v10.1.

data_processing: Normalization of every individual array was performed using the lowess scatterplot smoother implemented in Matlab software. All the probes of the array, except controls, were used for normalization purposes and the fraction of the data used for smoothing at each point was set to 5 %. After calculation of the fold-change values a filtering process was applied to eliminate low expression spots. The criterion of |FC| > 2 in at least one of the samples reduced the number of probes for the statistical analysis to 33611.

source_name: Adenocarcinoma observed 12 months after NDMA-silica treatment

label_protocol: RNA was retrotranscribed in Cy3 or Cy5 labeled cDNA using the TargetAmp 2-Round aRNA Amplification Kit 2.0 (Epicenter, Madison-Wisconsin, USA) following manufacturer’s protocol

growth_protocol: Eight-week-old female Balb/c mice were purchased from Harlan laboratories and maintained in a pathogen free environment. They were fed with laboratory rodent chow and water ad libitum. Mice were maintained on a 12-hour light/day cycle.

extract_protocol: RNA from LCM microdissected tissue of at least 8 consecutive 20 µm sections from each frozen tissue block was extracted using RNeasy kit (Qiagen).

treatment_protocol: Both NDMA (Sigma, St. Louis, MO) and silica 99% pure α-quartz with a particle size of < 5 µm (Min-U-Sil 5; US Silica Co., Berkeley Springs, WV) were resuspended in neutral-buffered saline and sonicated during 30 seconds. Mice were treated via oropharyngeal aspiration with a single dose of 7.5 mg/kg NDMA, 9 mg of silica, a combination of both or saline in a final of 90 µl as previously described24. NDMA dose was determined as the minimal amount of carcinogen able to induce lung tumorigenesis in mice without toxic side effects

value: female

tag: strain

value: balb/c

value: Lung adenocarcinoma

source_name: normal lung

value: Lung


title: 3 days post injury - rep 1


title: NDMA-silica_AC_1


title: NDMA-silica_AD_9m_2

source_name: Adenoma observed 9 months after NDMA-silica treatment

value: Lung adenoma


title: cancer [1777]

value: triple negative breast cancer (TNBC)


title: NDMA-silica_AC_2


title: 1 day post injury - rep 3

description:
gene expression data from axolotl spinal cord 1 day post injury
1 day post injury
white axolotls

source_name: 1 day post injury axolotl spinal cord

value: 1month old


title: uninjured tissue - rep 3

description:
gene expresion dat from mature uninjured axolotl spinal cord tissue
Mature 3
white axolotls

source_name: axolotl spinal cord

value: uninjured

value: control


title: NDMA-silica_AD_9m_1


title: NDMA-silica_AD_4m_1

source_name: Adenoma observed 4 months after NDMA-silica treatment


title: 1 day post injury - rep 1

value: spinal cord injury

value: spinal cord


title: NDMA-silica_AD_6m_3

source_name: Adenoma observed 6 months after NDMA-silica treatment


title: NDMA_AC_3

source_name: Adenocarcinoma observed 12 months after NDMA treatment


title: NDMA-silica_AD_6m_2


title: NDMA_AC_2


title: Lung_HPAIV (H5N1) Clade 2.2_Bird3

status: Public on Jan 02 2016

city: bhopal

first: Anamika

last: Mishra

state: Madhya Pradesh

address: Anand Nagar

department: Animal Genetics

country: India

institute: NIHSAD

description:
Gene expression after 5dpi in  HPAIV (H5N1) clade 2.2 virus-challenged duck lung tissue
BB3

hyb_protocol: 600ng of the labeled Cyanine 3-CTP cRNAs were fragmented to an average size of approximately 50 to 100 nucleotides with fragmentation buffer at 60°C for 30 minutes and the reaction was stopped by adding 2X GE HI-RPM hybridization buffer (Agilent Technologies, In situ Hybridization kit, Part Number5190-0404).The samples were pipetted onto the gasket slide and hybridized on to arrays .The hybridization was carried out at 65°C for 16 hours.After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 1 minute and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37 oC for 1 minute.

scan_protocol: The microarray slide was scanned using Agilent Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method

organism: Anas platyrhynchos

source_name: Lung_5dpi_HPAIV (H5N1) Clade 2.2

label_protocol: The sample labeling was performed using Quick-Amp Labeling Kit, One Color (Agilent Technologies, Part Number: 5190-0442). 500ng of total RNA was denatured along with appropriate diluted Spike In controls; Spike A Mix/cyanine 3-CTP (Agilent Technologies, RNA Spike In Kit, One Color, Part Number 5188-5282) and oligodT primers tagged to T7 promoter region at 65°C for 10 min followed by snap chilling on ice for 5 minutes.The cDNA master mix was added to the denatured RNA sample and incubated at 40°C for 2 hours.The cDNA sample mix was denatured at 65°C for 15 min to denature the enzymes in the cDNA reaction. The in vitro transcription master mix was added to the cDNA samples and incubated at 40°C for 2.30 hours. Cy3-CTP present in the reaction mix gets incorporated into the newly synthesized strands. The Cyanine 3-CTP labeled cRNA samples were purified using Qiagen RNeasy column (Qiagen, Cat No: 74106). The concentration of cRNA and dye incorporation was determined using Nanodrop-1000 (JH Bio) and the specific activity was estimated.

extract_protocol: Total RNA isolated from the lung tissues of three birds from each infected group and two birds from non-infected group. Total RNA was isolate using TRIzol® Reagent (Invitrogen, USA) with the Qiagen’s RNeasy mini kit (Qiagen, Germany). The integrity of RNA was analyzed on the Bioanalyzer.

treatment_protocol: Six weeks old AIV seronegative domestic ducks were divided into three groups and each group containing 4 birds. In group 1ducks was intranasally inoculated with 106 EID50 of HPAI H5N1  virus isolate and the group 2 was inoculated with 106 EID50 of HPAI H5N1  virus isolate. The group 3 was inoculated with PBS. Birds were observed daily for clinical signs. The birds were sacrificed from all groups at 5 days of post infection (dpi) and lung tissues collected in RNA latter and stored at -800C.

value: 6 weeks

tag: challenged with

value: HPAIV (H5N1) Clade 2.2

tag: time point

value: 5 dpi

value: lung


title: NDMA-silica_AD_4m_2

tag: gender


title: NDMA_AD_2

source_name: Adenoma observed 12 months after NDMA treatment


title: 1 day post injury - rep 2

value: 1 day post injury


title: uninjured tissue - rep 2

description:
gene expresion dat from mature uninjured axolotl spinal cord tissue
Mature 2
white axolotls


title: KG-A-17 vs. KG-B-21

description: HT-induced eFS.

tag: strain/background

value: hippocampus

tag: treatment

value: hypothermia (HT)

value: 1 hour

value: normothermia (NT)


title: uninjured tissue - rep 1

description:
gene expresion dat from mature uninjured axolotl spinal cord tissue
Mature 1
white axolotls


title: NDMA-silica_AD_9m_3

value: female

value: balb/c

value: Lung


title: NDMA-silica_AD_6m_1

value: Lung adenoma


title: NDMA_AC_1

value: Lung adenocarcinoma


title: NDMA_AD_1


title: Lung_HPAIV (H5N1) Clade 2.2_Bird2

description:
Gene expression after 5dpi in HPAIV (H5N1) clade 2.2 virus-challenged duck lung tissue
BB2


title: Lung_HPAIV (H5N1) Clade 2.3.2_Bird1

description:
Gene expression after 5dpi in HPAIV (H5N1) clade 2.3.2 virus-challenged duck lung tissue
AA1

source_name: Lung_5dpi,HPAIV (H5N1) Clade 2.3.2

value: HPAIV (H5N1) Clade 2.3.2


title: 0.5Gy3h_+24hPAXgene_Donor6_Hyb1

city: Fontenay aux Roses Cedex

first: Gaetan

last: GRUEL

address: BP 17

department: Service de RadioBiologie et d'Epidemiologie

institute: Institut de Radioprotection et de Surete Nucleaire

description: Gene expression after 3hr at 37°C in 0.5Gy-irradiated human blood and 24h of storage at room temperature in Paxgene

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl following the manufacturers instructions (Agilent Technologies). On completion of the fragmentation reaction, 55 µl of 2x GEx Hybridization Buffer HI-RPM (Agilent Technologies) was added to the fragmentation mixture and hybridized to 4x44K Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm double pass, Dye channel is set to Green, Green PMT is set to 100%, XDR is set to 0.10).

data_processing: The TIFF images were imported into Feature Extraction v10.5 software (Agilent Technologies). The data for each slide were imported into a statistical data analysis system R (http://www.R-project.org). The data (without any background subtraction) were then normalized, using the quantile normalization approach implemented in the BioConductor Agi4x44Preprocess package. The probes with little or no signal and obvious defects were flagged as unusable and excluded from further analysis. After filtering, 19835 probes with high-quality signals remained.

source_name: Peripheral Blood, 3hr, 0.5Gy, +24h in Paxgene at RT, Donor 3, Hybridization 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug of total RNA using the Quick Amp Labeling one-color Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy mini column purification (QIAGEN). Dye incorporation and cRNA yield and quality were checked with the NanoDrop ND-1000 Spectrophotometer and a Bioanalyzer RNA nano assay (Agilent Technologies).

extract_protocol: RNA from leukocytes were prepared using the qiagen miRNEASY kit (Qiagene) following the manufacturer's recommendations. RNA from samples stored in Paxgene buffer were prepared using the PAXgene™ Blood RNA kit (PreAnalytix) following the manufacturer's recommendations. Globin message was further reduced using GLOBINclear (Ambion Inc.) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies)

treatment_protocol: Venous blood was collected from 6 healthy volunteers in buffered sodium-citrate tubes.These whole blood samples were irradiated at 0 Gy (sham irradiation, the sample undergoing the same handling except exposure) and 0.5 Gy respectively with 137Cs γ-rays (Eγ =661 keV) and incubated for 3 hours post-irradiation at 37°C  in a humidified incubator with 5% CO2. The dose rate was 0.5 Gy.min-1. Uncertainty regarding the kerma rate was 6%. Following the incubation of 3 hours at 37°C, the blood samples of 6 donors were split into 2 sets of 3 donors. For each donor of the first set, the blood sample was split in 2 parts. The total RNA of the leukocytes of the first part was extracted immediately. The second part was incubated for 24 hours at room temperature (as for transportation of blood sample in anticoagulant) and then the total RNA of the leukocytes was extracted. For each donor of the second set, the blood sample was brought in 2 tubes of the PAXgene™ Blood RNA System (PreAnalytix). The total RNA of the first PAXgene™ tube was extracted immediately with the PAXgene™ Blood RNA kit (PreAnalytix). The total RNA of the second tube was extracted after 24 hours of incubation at room temperature (as for transportation of blood sample in PAXgene™ solution).

value: whole blood

value: male


title: Lung_Control_Bird2

description:
Gene expression after  5dpi in PBS-challenged duck lung tissue
C2

value: 6 weeks

value: PBS (control)


title: Lung_Control_Bird1

description:
Gene expression after 5dpi in PBS-challenged duck lung tissue
C1

value: 5 dpi


title: 0.5Gy3h_+24hPAXgene_Donor6_Hyb2

source_name: Peripheral Blood, 3hr, 0.5Gy, +24h in Paxgene at RT, Donor 3, Hybridization 2


title: 0.5Gy3h_+24hPAXgene_Donor5_Hyb2

source_name: Peripheral Blood, 3hr, 0.5Gy, +24h in Paxgene at RT, Donor 2, Hybridization 2


title: Lung_HPAIV (H5N1) Clade 2.2_Bird1

description:
Gene expression after 5 dpi in HPAIV (H5N1) clade 2.2 virus-challenged duck lung tissue
BB1

value: HPAIV (H5N1) Clade 2.2

value: lung


title: Lung_HPAIV (H5N1) Clade 2.3.2_Bird2

description:
Gene expression after 5 dpi in HPAIV (H5N1) clade 2.3.2 virus-challenged duck lung tissue
AA2

source_name: Lung_5dpi_HPAIV (H5N1) Clade 2.3.2


title: 0.5Gy3h_+24hPAXgene_Donor4_Hyb2

source_name: Peripheral Blood, 3hr, 0.5Gy, +24h in Paxgene at RT, Donor 1, Hybridization 2


title: WT Control, rep3

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

description: Gene expression after 20h CONTROL vehicle treatment

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >11.5 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4852A-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green at 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 028005_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities. Data was uploaded into Genespring version 11.5.1 where it was log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filted by flags in a way that at least 75% of the samples in any of the experimental groups had DETECTED flags. Then, differentially expressed genes were determined.

source_name: Control Macrophage replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

growth_protocol: Macrophages were isoltated from C57BL/6 mice and plated with DMEM+10% FBS. Non-adherent cells were washed away 2 hours after plating and cells were culture overnight in serum free DMEM prior to treatment.

extract_protocol: Total RNA was isolated using Qiagen miRNeasy mini kit.

treatment_protocol: Macrophages were stimulated with LPS (100 ng/ml) and IFNg (20 ng/ml) with or without emodin (50 μM) overnight. Cells were lysed with Qiazol.

value: Peritoneal macrophage

value: Male

value: 8 weeks


title: 0Gy3h_+24hPAXgene_Donor5_Hyb1

description: Gene expression after 3hr at 37°C in 0Gy-irradiated human blood and 24h of storage at room temperature in Paxgene

source_name: Peripheral Blood, 3hr, 0Gy, +24h in Paxgene at RT, Donor 2, Hybridization 1


title: 0Gy3h_+24hPAXgene_Donor6_Hyb1

source_name: Peripheral Blood, 3hr, 0Gy, +24h in Paxgene at RT, Donor 3, Hybridization 1


title: 0Gy3h_+24hPAXgene_Donor6_Hyb2

source_name: Peripheral Blood, 3hr, 0Gy, +24h in Paxgene at RT, Donor 3, Hybridization 2


title: WT Control, rep1

source_name: Control Macrophage replicate 1

value: Female


title: 0.5Gy3h_+24hPAXgene_Donor5_Hyb1

source_name: Peripheral Blood, 3hr, 0.5Gy, +24h in Paxgene at RT, Donor 2, Hybridization 1


title: WT LPS_IFNg, rep1

description: Gene expression after 20h LPS-IFNg treatment

source_name: LPS+IFNg Treated Macrophage replicate 1

value: 9 weeks


title: 0.5Gy3h_+0hPAXgene_Donor6_Hyb2

description: Gene expression after 3hr at 37°C in 0.5Gy-irradiated human blood and 0h of storage at room temperature in Paxgene

source_name: Peripheral Blood, 3hr, 0.5Gy, +0h in Paxgene at RT, Donor 3, Hybridization 2


title: 0Gy3h_+24hPAXgene_Donor4_Hyb1

source_name: Peripheral Blood, 3hr, 0Gy, +24h in Paxgene at RT, Donor 1, Hybridization 1


title: WT LPS_IFNg, rep4

source_name: LPS+IFNg Treated Macrophage replicate 4


title: WT LPS_IFNg, rep2

source_name: LPS+IFNg Treated Macrophage replicate 2


title: WT LPS_IFNg, rep3

source_name: LPS+IFNg Treated Macrophage replicate 3


title: WT Control, rep2

source_name: Control Macrophage replicate 2


title: WT LPS_IFNg+Emodin, rep4

description: Gene expression after 20h LPS-IFNg-Emodin treatment

source_name: LPS+IFNg+Emodin Treated Macrophage replicate 4


title: 0Gy3h_+24hPAXgene_Donor4_Hyb2

source_name: Peripheral Blood, 3hr, 0Gy, +24h in Paxgene at RT, Donor 1, Hybridization 2


title: 0.5Gy3h_+24hPAXgene_Donor4_Hyb1

source_name: Peripheral Blood, 3hr, 0.5Gy, +24h in Paxgene at RT, Donor 1, Hybridization 1


title: 0.5Gy3h_+0hPAXgene_Donor6_Hyb1

source_name: Peripheral Blood, 3hr, 0.5Gy, +0h in Paxgene at RT, Donor 3, Hybridization 1


title: WT Control, rep4

source_name: Control Macrophage replicate 4


title: WT LPS_IFNg+Emodin, rep3

source_name: LPS+IFNg+Emodin Treated Macrophage replicate 3


title: 0.5Gy3h_+0hPAXgene_Donor4_Hyb1

source_name: Peripheral Blood, 3hr, 0.5Gy, +0h in Paxgene at RT, Donor 1, Hybridization 1


title: 0.5Gy3h_+0hPAXgene_Donor4_Hyb2

source_name: Peripheral Blood, 3hr, 0.5Gy, +0h in Paxgene at RT, Donor 1, Hybridization 2


title: WT LPS_IFNg+Emodin, rep1

source_name: LPS+IFNg+Emodin Treated Macrophage replicate 1


title: WT LPS_IFNg+Emodin, rep2

source_name: LPS+IFNg+Emodin Treated Macrophage replicate 2


title: WT IL4+EMODIN, rep 3

description: Gene expression after 6h IL4-Emodin treatment

source_name: IL4+Em treated Macrophage replicate 3

treatment_protocol: Macrophages were stimulated with IL4 (10 ng/ml) with or without emodin (50 μM) overnight. Cells were lysed with Qiazol.


title: WT IL4+EMODIN, rep 4

source_name: IL4+Em treated Macrophage replicate 4


title: 0.5Gy3h_+0hPAXgene_Donor5_Hyb1

source_name: Peripheral Blood, 3hr, 0.5Gy, +0h in Paxgene at RT, Donor 2, Hybridization 1


title: 0.5Gy3h_+0hPAXgene_Donor5_Hyb2

source_name: Peripheral Blood, 3hr, 0.5Gy, +0h in Paxgene at RT, Donor 2, Hybridization 2


title: 0Gy3h_+0hPAXgene_Donor6_Hyb1

description: Gene expression after 3hr at 37°C in 0Gy-irradiated human blood and 0h of storage at room temperature in Paxgene

source_name: Peripheral Blood, 3hr, 0Gy, +0h in Paxgene at RT, Donor 3, Hybridization 1


title: 0Gy3h_+0hPAXgene_Donor5_Hyb1

source_name: Peripheral Blood, 3hr, 0Gy, +0h in Paxgene at RT, Donor 2, Hybridization 1


title: 0Gy3h_+0hPAXgene_Donor6_Hyb2

source_name: Peripheral Blood, 3hr, 0Gy, +0h in Paxgene at RT, Donor 3, Hybridization 2


title: 0.5Gy3h_+24hAntiCoag_Donor2_Hyb2

description: Gene expression after 3hr at 37°C in 0.5Gy-irradiated human blood and 24h of storage at room temperature in anticoagulant

source_name: Peripheral Blood, 3hr, 0.5Gy, +24h in Anticoagulant at RT, Donor 2, Hybridization 2

value: female


title: 0Gy3h_+0hPAXgene_Donor5_Hyb2

source_name: Peripheral Blood, 3hr, 0Gy, +0h in Paxgene at RT, Donor 2, Hybridization 2


title: 0.5Gy3h_+24hAntiCoag_Donor3_Hyb1

source_name: Peripheral Blood, 3hr, 0.5Gy, +24h in Anticoagulant at RT, Donor 3, Hybridization 1


title: 0Gy3h_+0hPAXgene_Donor4_Hyb2

source_name: Peripheral Blood, 3hr, 0Gy, +0h in Paxgene at RT, Donor 1, Hybridization 2


title: WT IL4+EMODIN, rep 2

source_name: IL4+Em treated Macrophage replicate 2


title: WT CTRL, rep 2

description: Gene expression after 6h CONTROL vehicle treatment

source_name: Control Macrophage replicate 2


title: WT IL4+EMODIN, rep 1

source_name: IL4+Em treated Macrophage replicate 1


title: WT CTRL, rep 3

source_name: Control Macrophage replicate 3


title: Lung_LPAIV (H9N2)_Bird3

description:
Gene expression after  6dpi in LPAIV (H9N2)-challenged chicken lung tissue
LPAI_BB3

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method.

organism: Gallus gallus

source_name: Lung_6dpi_LPAIV (H9N2)

extract_protocol: TRIzol method for RNA extraction used for tissues

treatment_protocol: Six weeks old specific pathogen free (SPF) chickens were divided into three groups of 4 birds each. Chickens of group 1 were intranasally inoculated with 106 EID50 of the HPAIV H5N1 virus (A/duck/India/02CA10/2011). Group 2 was inoculated with 106EID50 of the LPAIV H9N2 virus (A/duck/India/249800/2010). A control group of chickens was inoculated with PBS. The birds were observed daily for clinical signs. At 2 days of post infection (dpi), 3 birds from HPAIV H5N1 virus infected group and at 6 dpi, 3 birds from LPAIV H9N2 virus infected group were sacrificed and necropsied to evaluate gross lesions and lungs tissues collected in RNA later. 3 birds from control group were also sacrificed.

value: LPAIV (H9N2)

value: 6 dpi

value: Lung


title: 0.5Gy3h_+24hAntiCoag_Donor3_Hyb2

source_name: Peripheral Blood, 3hr, 0.5Gy, +24h in Anticoagulant at RT, Donor 3, Hybridization 2


title: 0.5Gy3h_+24hAntiCoag_Donor1_Hyb2

source_name: Peripheral Blood, 3hr, 0.5Gy, +24h in Anticoagulant at RT, Donor 1, Hybridization 2


title: WT IL4, rep 3

description: Gene expression after 6h IL4 treatment

source_name: IL4 treated Macrophage replicate 3


title: Lung_HPAIV(H5N1)_Bird3

description:
Gene expression after 2dpi in HPAIV (H5N1)-challenged chicken lung tissue
HPAI_AA3

value: 2 dpi


title: Lung_LPAIV (H9N2)_Bird2

description:
Gene expression after 6dpi in LPAIV (H9N2)-challenged chicken lung tissue
LPAI_BB2


title: 0.5Gy3h_+24hAntiCoag_Donor1_Hyb1

source_name: Peripheral Blood, 3hr, 0.5Gy, +24h in Anticoagulant at RT, Donor 1, Hybridization 1

value: whole blood


title: 0.5Gy3h_+24hAntiCoag_Donor2_Hyb1

source_name: Peripheral Blood, 3hr, 0.5Gy, +24h in Anticoagulant at RT, Donor 2, Hybridization 1


title: 0Gy3h_+0hPAXgene_Donor4_Hyb1

source_name: Peripheral Blood, 3hr, 0Gy, +0h in Paxgene at RT, Donor 1, Hybridization 1

value: male


title: WT CTRL, rep 4

source_name: Control Macrophage replicate 4


title: WT IL4, rep 1

description: Gene expression after 6h IL4 treatment

source_name: IL4 treated Macrophage replicate 1


title: WT IL4, rep 2

description: Gene expression after 6h IL4 treatment

source_name: IL4 treated Macrophage replicate 2


title: Lung_LPAIV (H9N2)_Bird1

description:
Gene expression after 6dpi in LPAIV (H9N2)-challenged chicken lung tissue
LPAI_BB1

value: 6 weeks


title: WT IL4, rep 4

description: Gene expression after 6h IL4 treatment

source_name: IL4 treated Macrophage replicate 4


title: WT CTRL, rep 1

source_name: Control Macrophage replicate 1


title: Lung_HPAIV(H5N1)_Bird2

description:
Gene expression after 2dpi in HPAIV (H5N1)-challenged chicken lung tissue
HPAI_AA2


title: Lung_HPAIV(H5N1)_Bird1

description:
Gene expression after 2dpi in  HPAIV (H5N1)-challenged chicken lung tissue
HPAI_AA1


title: 0Gy3h_+24hAntiCoag_Donor3_Hyb1

description: Gene expression after 3hr at 37°C in 0Gy-irradiated human blood and 24h of storage at room temperature in anticoagulant

source_name: Peripheral Blood, 3hr, 0Gy, +24h in Anticoagulant at RT, Donor 3, Hybridization 1


title: Lung_Control_Bird2

description:
Gene expression after PBS-challenged chicken lung tissue
C2

value: PBS (control)


title: RNA Pol II_CPE-DC Repl 2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description:
Comparision of Stem/progenitor cells and differentiated retinal neuronal cells
Diff_35+455_RNA Pol II_IP_Cy5_b Vs Diff_35+455_RNA Pol II_WCE_Cy3_b

hyb_protocol: 4 micrograms of Cy3 and Cy5 labeled samples were hybridized. Hybridizations were done using the Agilent Hybridization kit of (Part Number: 5188-6420) Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 40 hours. The hybridized slides were washed using Agilent aCGH wash buffers

scan_protocol: Agilent Microarray Scanner G2505C

data_processing: Data extraction from Images was done using Feature Extraction software v 10.7 of Agilent. Feature extracted raw data was analyzed using Agilent Genomic Workbench Lite Edition 6.5 (Liner loess normalization).

source_name: Input DNA from the CPE differentiated progeny

label_protocol: The IP and WCE DNA samples were blunted at 12°C for 20 minutes using T4 DNA polymerase as per the Mammalian Chip on Chip Protocol of Agilent Technologies. The blunted DNA was cleaned, precipitated and resuspended in 25 microlitres of Nuclease free water. The entire DNA was then ligated to linkers at 16°C for 16 hours. The linker-ligated DNA was subjected to two rounds of LMPCR and resuspended in Nuclease free water. Two micrograms of each IP and WCE sample was labeled using Agilent Genomic DNA Labeling Kit with Cy5 and Cy3 dUTP ( 5190-0453). DNA yield and incorporation of label (specific activity) was measured using NanoDrop spectrophotometer.

extract_protocol: Chromatin immunoprecipitation was performed according to the Agilent ChIP-chip protocol. Briefly, the chromatin was immunoprecipitated by treating 2 × 10^7 cells with 1% formaldehyde at room temperature for 10 min followed by addition of 0.125 M glycine for quenching formaldehyde. The chromatin DNA fragments ranging from 200 to 800 base pairs was obtained by sonication of the lysed cells.

tag: cell type

value: Differentiated retinal neuronal cells

tag: chip antibody

value: none, input DNA

source_name: RNA Pol II_ChIP DNA from the CPE differentiated progeny

value: RNA Pol II

tag: chip antibody vendor

value: Santa cruz

tag: chip antibody cat. #

tag: chip antibody lot #


title: Lung_HPAIV (H5N1) Clade 2.3.2_Bird3

description:
Gene expression after 5dpi in  HPAIV (H5N1) clade 2.3.2 virus-challenged duck lung tissue
AA3

source_name: Lung_5dpi_HPAIV (H5N1) Clade 2.3.2

tag: age

value: HPAIV (H5N1) Clade 2.3.2

value: 5 dpi

value: lung


title: 0Gy3h_+24hAntiCoag_Donor3_Hyb2

source_name: Peripheral Blood, 3hr, 0Gy, +24h in Anticoagulant at RT, Donor 3, Hybridization 2


title: 0Gy3h_+24hAntiCoag_Donor1_Hyb2

source_name: Peripheral Blood, 3hr, 0Gy, +24h in Anticoagulant at RT, Donor 1, Hybridization 2


title: 0Gy3h_+24hAntiCoag_Donor2_Hyb2

source_name: Peripheral Blood, 3hr, 0Gy, +24h in Anticoagulant at RT, Donor 2, Hybridization 2


title: 0Gy3h_+24hAntiCoag_Donor2_Hyb1

source_name: Peripheral Blood, 3hr, 0Gy, +24h in Anticoagulant at RT, Donor 2, Hybridization 1


title: 0.5Gy3h_+0hAntiCoag_Donor3_Hyb2

description: Gene expression after 3hr at 37°C in 0.5Gy-irradiated human blood and 0h of storage at room temperature in anticoagulant

source_name: Peripheral Blood, 3hr, 0.5Gy, +0h in Anticoagulant at RT, Donor 3, Hybridization 2


title: Lung_Control_Bird1

description:
Gene expression after PBS-challenged chicken lung tissue
C1


title: sensitive to Dnr_Group 3 [A-15]

city: Vellore

first: Poonkuzhali

last: Balasubramanian

state: Tamil Nadu

address: Ida Scudder Road

department: Department of Haematology

institute: Christian Medical College Vellore

description: Gene expression at diagnosis

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Hi-RPM large Hybridization Kit (Part No: 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression Wash Buffers Set (Part No: 5188-5327).  The hybridized, washed microarray slides were then scanned on a G2505C scanner (Agilent Technologies)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.7)

data_processing: Data extraction from Images was done using Feature Extraction software and Percentile shift Normalization of the data was done in GeneSpring GX.

source_name: Bone Marrow MNC at diagnosis

label_protocol: The samples were labeled using Agilent Quick Amp Labeling Kit one color (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using  RNeasy Mini Kit(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

extract_protocol: Bone marrow mononuclear cells (BM MNCs) from each patient at diagnosis were separated using Ficoll-Paque (GE Healthcare) separation. RNA was isolated from BM MNCsusing Tri Reagent (Sigma), following the manufacturer's recommendations.


title: 0Gy3h_+24hAntiCoag_Donor1_Hyb1

source_name: Peripheral Blood, 3hr, 0Gy, +24h in Anticoagulant at RT, Donor 1, Hybridization 1


title: sensitive to Dnr_Group 3 [A-13]

description: Gene expression at diagnosis


title: 0.5Gy3h_+0hAntiCoag_Donor3_Hyb1

source_name: Peripheral Blood, 3hr, 0.5Gy, +0h in Anticoagulant at RT, Donor 3, Hybridization 1


title: sensitive to Dnr_Group 3 [A-12]

description: Gene expression at diagnosis


title: 0.5Gy3h_+0hAntiCoag_Donor2_Hyb2

source_name: Peripheral Blood, 3hr, 0.5Gy, +0h in Anticoagulant at RT, Donor 2, Hybridization 2


title: sensitive to Dnr_Group 3 [A-11]

description: Gene expression at diagnosis


title: sensitive to Dnr_Group 3 [A-14]

description: Gene expression at diagnosis


title: 0Gy3h_+24hPAXgene_Donor5_Hyb2

description: Gene expression after 3hr at 37°C in 0Gy-irradiated human blood and 24h of storage at room temperature in Paxgene

source_name: Peripheral Blood, 3hr, 0Gy, +24h in Paxgene at RT, Donor 2, Hybridization 2


title: 0.5Gy3h_+0hAntiCoag_Donor2_Hyb1

source_name: Peripheral Blood, 3hr, 0.5Gy, +0h in Anticoagulant at RT, Donor 2, Hybridization 1


title: sensitive to AraC_Group 1 [A-05]

description: Gene expression at diagnosis


title: H3K27me3_CPE-DC Repl 2

description:
Comparision of Stem/progenitor cells and differentiated retinal neuronal cells
Diff_47+65_H3K27_IP_Cy5_b Vs Diff_47+65_H3K27_WCE_Cy3_b

source_name: H3K27me3_ChIP DNA from the CPE differentiated progeny

value: Diagenode


title: sensitive to AraC_Group 1 [A-04]

description: Gene expression at diagnosis

value: female


title: RNA Pol II_CPE-DC Repl 1

description:
Comparision of Stem/progenitor cells and differentiated retinal neuronal cells
Diff_35+455_RNA Pol II_IP_Cy5_a Vs Diff_35+455_RNA Pol II_WCE_Cy3_a


title: 0.5Gy3h_+0hAntiCoag_Donor1_Hyb2

source_name: Peripheral Blood, 3hr, 0.5Gy, +0h in Anticoagulant at RT, Donor 1, Hybridization 2


title: 0.5Gy3h_+0hAntiCoag_Donor1_Hyb1

source_name: Peripheral Blood, 3hr, 0.5Gy, +0h in Anticoagulant at RT, Donor 1, Hybridization 1


title: sensitive to AraC_Group 1 [A-01]

description: Gene expression at diagnosis


title: sensitive to AraC_Group 1 [A-02]

description: Gene expression at diagnosis


title: 0Gy3h_+0hAntiCoag_Donor3_Hyb1

description: Gene expression after 3hr at 37°C in 0Gy-irradiated human blood and 0h of storage at room temperature in anticoagulant

source_name: Peripheral Blood, 3hr, 0Gy, +0h in Anticoagulant at RT, Donor 3, Hybridization 1


title: 0Gy3h_+0hAntiCoag_Donor3_Hyb2

source_name: Peripheral Blood, 3hr, 0Gy, +0h in Anticoagulant at RT, Donor 3, Hybridization 2


title: 0Gy3h_+0hAntiCoag_Donor2_Hyb2

source_name: Peripheral Blood, 3hr, 0Gy, +0h in Anticoagulant at RT, Donor 2, Hybridization 2


title: drug resistant_Group 2 [A-10]

description: Gene expression at diagnosis


title: 0Gy3h_+0hAntiCoag_Donor1_Hyb2

source_name: Peripheral Blood, 3hr, 0Gy, +0h in Anticoagulant at RT, Donor 1, Hybridization 2


title: H3K4me3_CPE-DC Repl 2

description:
Comparision of Stem/progenitor cells and differentiated retinal neuronal cells
Diff_69+79_H3K4_IP_Cy5_b Vs Diff_69+79_H3K4_WCE_Cy3_b

source_name: Input DNA from the CPE differentiated progeny

source_name: H3K4me3_ChIP DNA from the CPE differentiated progeny

value: Invitrogen


title: sensitive to AraC_Group 1 [A-03]

description: Gene expression at diagnosis


title: drug resistant_Group 2 [A-08]

description: Gene expression at diagnosis


title: RNA Pol II_CPE-NS Repl 2

description:
Comparision of Stem/progenitor cells and differentiated retinal neuronal cells
Neuro_59+447_RNA Pol II_IP_Cy5_b Vs Neuro_59+447_RNA Pol II_WCE_Cy3_b

source_name: Input DNA from CPE derived neurospheres

value: Stem/Progenitor cells

source_name: RNA Pol II_ChIP DNA from CPE derived neurospheres


title: H3K4me3_CPE-DC Repl 1

description:
Comparision of Stem/progenitor cells and differentiated retinal neuronal cells
Diff_69+79_H3K4_IP_Cy5_a Vs Diff_69+79_H3K4_WCE_Cy3_a


title: H3K27me3_CPE-DC Repl 1

description:
Comparision of Stem/progenitor cells and differentiated retinal neuronal cells
Diff_47+65_H3K27_IP_Cy5_a Vs Diff_47+65_H3K27_WCE_Cy3_a


title: drug resistant_Group 2 [A-09]

description: Gene expression at diagnosis

source_name: Bone Marrow MNC at diagnosis


title: 0Gy3h_+0hAntiCoag_Donor2_Hyb1

source_name: Peripheral Blood, 3hr, 0Gy, +0h in Anticoagulant at RT, Donor 2, Hybridization 1


title: 0Gy3h_+0hAntiCoag_Donor1_Hyb1

source_name: Peripheral Blood, 3hr, 0Gy, +0h in Anticoagulant at RT, Donor 1, Hybridization 1


title: RNA Pol II_CPE-NS Repl 1

description:
Comparision of Stem/progenitor cells and differentiated retinal neuronal cells
Neuro_59+447_RNA Pol II_IP_Cy5_a Vs Neuro_59+447_RNA Pol II_WCE_Cy3_a


title: HeK27me3_CPE-NS Repl 2

description:
Comparision of Stem/progenitor cells and differentiated retinal neuronal cells
Neuro_48+76_H3K27_IP_Cy5_b Vs Neuro_48+76_H3K27_WCE_Cy3_b

source_name: H3K27me3_ChIP DNA from CPE derived neurospheres


title: HeK27me3_CPE-NS Repl 1

description:
Comparision of Stem/progenitor cells and differentiated retinal neuronal cells
Neuro_48+76_H3K27_IP_Cy5_a Vs Neuro_48+76_H3K27_WCE_Cy3_a


title: 5-mC_CPE-DC Repl 3

description: Comparision of Stem/progenitor cells and differentiated retinal neuronal cells

hyb_protocol: For the hybridization, Cy3-labeled Input was mixed with Cy5-labeled IP DNA.  Hybridizations were performed with the Hybridization kit of Agilent (Part Number 5188-6420). Hybridization was carried out in Agilent’s Surehyb Chambers at 67º C for 40 hours.

data_processing: Data extraction from Images was done using Feature Extraction software v 10.7 of Agilent.Feature extracted raw data was analyzed using Data analysis was done using Agilent Genomic Workbench Lite Edition 6.5

source_name: Input DNA from CPE derived differentiated progeny

label_protocol: The Input DNA and IP samples were labeled using Agilent Genomic DNA Labeling Kit.  Random primer labeling using Exo-Klenow to label IP and Input DNA samples (Agilent Methylation Protocol )DNA yield and incorporation of labeled nucleotide (specific activity) were measured by NanoDrop estimation

extract_protocol: 2 × 107 cells form the Neurosphere cultures and the Differentiated cultures were colleted and the genomic DNA was isolated and purified using QIAamp DNA mini kit (Qiagen). The purified genomic DNA was sonicated into 200-600bp. 30μg sonicated DNA was incubated with 200μl pan-mouse IgG Dynal magnetic beads (Invitrogen) coupled to 20μg antibody against 5’-methylcytosine (Eurogentec, Seraing, Belgium) overnight at 4°C. The genomic DNA-beads-antibody complex was washed and methylated DNA was eluted using the Dynal Magnetic Particle Concentrator. Eluted DNA and WCE (Whole cell extract) DNA (Reference DNA) were extracted/purified using phenol: chloroform: isoamylalcohol and precipitated with ethanol.

value: Differentiated Retinal neuronal cells

source_name: 5-mC MeDIP DNA from CPE derived differentiated progeny


title: H3K4me3_CPE-NS Repl 1

description:
Comparision of Stem/progenitor cells and differentiated retinal neuronal cells
Neuro_37+88_H3K4_IP_Cy5_a Vs Neuro_37+88_H3K4_WCE_Cy3_a

source_name: H3K4me3_ChIP DNA from CPE derived neurospheres


title: AG83 (Control S)

status: Public on Jan 01 2016

city: Kolkata

first: Syamal

last: Roy

state: West Bengal

address: 4, Raja SC Mullick Road

department: Infectious Disease and Immunology

institute: Indian Institute of Chemical Biology

description: Drug sensitive parasite

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to custome Agilent leishmania donovani  for 16 hours at 65°C  in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The hybridized.washed microarray slides were then scanned on a Agilent G2565C scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software10.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  In next step raw data was analyzed using Genesprong GX v. 12.0 software from Agilent. The percentile shift algorithm was used for the data normalization.

organism: Leishmania donovani

source_name: cell

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

growth_protocol: 10 million parasites were grown in 50 ml M199 medium supplemented with 10% FCS and Penicillin Streptomycin at 22 degree C on a shaker for 5 days

extract_protocol: Cells were harvested by centrifugation of the medium containing the parasites at 3000 rpm for 10 mins. The supernatent was discarded and the pellet was resuspended in Phosphate buffered saline. Cells were washed in PBS for 3 times and the pellet was dried on a tissue paper as much as possible. The cells were used to quantify total RNA.

value: kinetoplastid protozoan parasite

tag: sample source

value: Clinical isolate from patient

tag: drug resistant status

value: sensitive


title: BPK 206

description: Drug sensitive parasite


title: BHU 138 (Control R)

description: Drug resistant parasite

value: resistant


title: BHU 777

description: Drug sensitive parasite


title: H3K4me3_CPE-NS Repl 2

description:
Comparision of Stem/progenitor cells and differentiated retinal neuronal cells
Neuro_37+88_H3K4_IP_Cy5_b Vs Neuro_37+88_H3K4_WCE_Cy3_b


title: BHU 814

description: Drug resistant parasite


title: BHU 581

description: Drug sensitive parasite


title: BHU 138

description: Drug resistant parasite


title: 5-mC_CPE-DC Repl 1


title: 5-mC_CPE-DC Repl 2


title: drug resistant_Group 2 [A-07]

description: Gene expression at diagnosis


title: iPS-PB20_rep2

city: Castanet-Tolosan

first: Herve

last: Acloque

address: 24 chemin de Borde Rouge

description:
Gene expression in iPS-like cells derived from normal amniocytes
PB20_B

hyb_protocol: Microarray hybridation oven according to manufacturer's instruction

scan_protocol: Image analysis using the Feature Extraction software (Agilent).

data_processing: Data were filtered to keep only spots of sufficient intensity and quality for at least 2 out of 3 technical replicates. Intensity values were log-transformed and normalized by the quantile normalization method. Differential analysis was then performed using the Limma package (Bioconductor). Threshold parameters were defined as follow: maximal adjusted p-value (Benjamini& Hochberg) of 0.01 and minimal log-fold change (lfc) of 2.

organism: Sus scrofa

source_name: Cultured cells

label_protocol: Label, hybridation , scan and data extraction were performed by the GeT-Biopuces platform following manufacturer's intruction. Samples were then marked by Cyanine-3 fluorochrome and converted in cDNA before hybridization on the 60K customized chip from Agilent (Voillet et al., 2014).

growth_protocol: PEF were culture in F medium, all iPS-like cells were culture in piPS medium.  Floating embryoïd bodies were cultured 10 days in in DIFF medium. For medium composition see the Material and Methods section of the associated publication.

extract_protocol: Total RNA from cell pellets of each sample was extracted in triplicate using the Nucleospin RNA kit (Macherey-Nagel). Quantity and quality of RNA was evaluated by NanoDrop dosage and Bioanalyser analysis (Agilent Technologies).

tag: reprogramming technique

value: Integrative

tag: starting cell type

value: normal amniocytes

tag: resulting cell type

value: iPS-like cell

tag: culture conditions

value: piPS medium

tag: cell line


title: PEF_rep1

description:
Gene expression in porcine embryonic fibroblasts
PEF_A

value: Non reprogrammed

value: Normal embryonic fibroblast

value: F medium

value: PEF


title: PEF_rep2

description:
Gene expression in porcine embryonic fibroblasts
PEF_B


title: iPS-NI20_rep3

description:
Gene expression in NI-iPS-like cells
NI20_C

value: Non integrative

value: t(Y;14) fibroblasts

value: NI-iPS-like cells


title: iPS-PB20_rep1

description:
Gene expression in iPS-like cells derived from normal amniocytes
PB20_A


title: 5-mC_CPE-NS Repl 2

value: Stem/progenitor cells

value: none, input DNA

source_name: 5-mC MeDIP DNA from CPE derived neurospheres


title: BHU 575

description: Drug resistant parasite

value: kinetoplastid protozoan parasite


title: iPS-NI20_rep2

description:
Gene expression in NI-iPS-like cells
NI20_B


title: iPS-NI20_rep1

description:
Gene expression in NI-iPS-like cells
NI20_A


title: iPS-NI12_rep1

description:
Gene expression in NI-iPS-like cells
NI12_A


title: iPS-NI12_rep2

description:
Gene expression in NI-iPS-like cells
NI12_B


title: iPS-NI13_rep2

description:
Gene expression in NI-iPS-like cells
NI13_B


title: iPS-NI13_rep1

description:
Gene expression in NI-iPS-like cells
NI13_A


title: iPS-I4-lp_rep3

description:
Gene expression in I-iPS-like cells at late passages
I4lp_C

value: I-iPS-like cells

tag: passage

value: late


title: iPS-I4-lp_rep2

description:
Gene expression in I-iPS-like cells at late passages
I4lp_B


title: iPS-I4-ep_rep3

description:
Gene expression in I-iPS-like cells at early passages
I4ep_C

value: early


title: iPS-I4-ep_rep2

description:
Gene expression in I-iPS-like cells at early passages
I4ep_B

value: Integrative


title: iPS-I4-lp_rep1

description:
Gene expression in I-iPS-like cells at late passages
I4lp_A


title: iPS-I3-lp_rep2

description:
Gene expression in I-iPS-like cells at late passages
I3lp_B


title: iPS-PB20_rep3

description:
Gene expression in iPS-like cells derived from normal amniocytes
PB20_C

value: normal amniocytes


title: 5-mC_CPE-NS Repl 3

description: Comparision of Stem/progenitor cells and differentiated retinal neuronal cells


title: iPS-NI12_rep3

description:
Gene expression in NI-iPS-like cells
NI12_C


title: FLS ob/ob

city: Yonago-city

first: Kinya

last: Okamoto

state: Tottori

address: 36-1, Nishi-cho

department: Second Dept. Internal Medicine

country: Japan

institute: Tottori University

data_processing:
For the normalization it uses the average of endogenous control genes: Small nuclear U6 RNA.
Target gene signals normalized to endogenous control genes; ΔCt = (Ct_Target gene − Ct_Endogenous control gene)
Relative value; ΔΔCt = (ΔCt_Test sample − ΔCt_Control sample)
Fold Change worksheet reports ratio (against control sample): 2^-ΔΔCt, where -ΔΔCt = -(ΔCt_Test sample − ΔCt_Control sample).

label: FAM

source_name: Fatty Liver Sionogi ob/ob mouse, Non-alcoholic steatohepatitis model

label_protocol: We followed protocol of manual that is TaqMan® Array Micro Fluidic Cards.

growth_protocol: Animals were housed in a room maintained at a controlled temperature of 24 ± 2 ˚C under a 12-h light-dark cycle. Animals were provided ad libitum access to water and standard pellet feed.

extract_protocol: mirVanaTM miRNA Isolation Kit was used.

tag: strain

value: Fatty Liver Sionogi ob/ob mouse

tag: gender

value: Male

tag: tissue

value: Liver


title: iPS-I3-ep_rep2

description:
Gene expression in I-iPS-like cells at early passages
I3ep_B

value: piPS medium


title: FLS W

source_name: Fatty Liver Sionogi wild type mouse, Simple steatosis model

value: Fatty Liver Sionogi wild type mouse


title: EB-NI13_rep3

description:
Gene expression in embryoïd bodies derives from NI-iPS-like cells
EB13_C

source_name: Embryoid body

value: DIFF medium

tag: resulting embryoid body


title: EB-NI20_rep2

description:
Gene expression in embryoïd bodies derives from NI-iPS-like cells
EB20_B

value: Non integrative


title: iPS-I3-lp_rep3

description:
Gene expression in I-iPS-like cells at late passages
I3lp_C

value: t(Y;14) fibroblasts


title: EB-NI12_rep1

description:
Gene expression in embryoïd bodies derives from NI-iPS-like cells
EB12_A

value: NI-iPS-like cells


title: EB-NI12_rep3

description:
Gene expression in embryoïd bodies derives from NI-iPS-like cells
EB12_C


title: EB-NI12_rep2

description:
Gene expression in embryoïd bodies derives from NI-iPS-like cells
EB12_B


title: EB-NI13_rep1

description:
Gene expression in embryoïd bodies derives from NI-iPS-like cells
EB13_A


title: EB-NI13_rep2

description:
Gene expression in embryoïd bodies derives from NI-iPS-like cells
EB13_B


title: iPS-I3-ep_rep3

description:
Gene expression in I-iPS-like cells at early passages
I3ep_C


title: EB-NI20_rep3

description:
Gene expression in embryoïd bodies derives from NI-iPS-like cells
EB20_C


title: DS

source_name: DD Shionogi mouse, normal control

value: DD Shionogi mouse


title: Cells after adipogenic differentation with MDI, treated with forskolin, biological replicate 2

city: Worcester

first: Silvia

last: Corvera

address: 373 Platantion Street

department: Molecular Medicine

institute: UMASS Medical School

description:
FSK_2
Cells after adipogenic differentation with MDI (methylisobutylxanthine, dexamethasone, insulin), treated with forskolin, biological replicate 2

hyb_protocol: Affymetrix protocols were followed for the preparation of cRNA, which was hybridized to HTA-v2.0 Chips.

scan_protocol: Raw expression data collected from an Affymetrix HP GeneArrayScanner

data_processing:
The data were analyzed with Affymetrix Expression Console_1_4_0
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0

source_name: adipocytes from human vascular progenitors treated with forskolin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Adipose tissue from three individuals was cultured in matrigel under pro-angiogenic conditions. Capillary networks emerging from the explants were subcultured on plastic, grown to confluence, subjected to adipogenic differentiation and after 12 days treated with vehicle or forskolin for 7 days

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

treatment_protocol: No differentiation, differentation and vehicle, or differentation plus forskolin 50 uM for 7 days

tag: cell type

tag: treatment

value: forskolin


title: iPS-NI13_rep3

description:
Gene expression in NI-iPS-like cells
NI13_C


title: iPS-I3-ep_rep1

description:
Gene expression in I-iPS-like cells at early passages
I3ep_A


title: Cells after adipogenic differentation with MDI, biological replicate 1

description:
MDI_1
Cells after adipogenic differentation with MDI (methylisobutylxanthine, dexamethasone, insulin), biological replicate 1

source_name: adipocytes from human vascular progenitors


title: Cells after adipogenic differentation with MDI, treated with forskolin, biological replicate 3

description:
FSK_3
Cells after adipogenic differentation with MDI (methylisobutylxanthine, dexamethasone, insulin), treated with forskolin, biological replicate 3

value: adipocytes from human vascular progenitors