title: GROUND CONTROL BRIC A PDFU-1 168 seedlings

source_name: solid media plates; BRIC-16; OES chamber: BRIC-A PDFU-1


title: FLIGHT  BRIC A PDFU-3 113 seedlings

status: Public on Apr 10 2014

type: RNA

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

country: USA

institute: University of Florida

hyb_protocol: Amplified and labeled cDNA (5 µg/sample) was fragmented and hybridized with rotation onto Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays for 16h at 45°C. Arrays were washed on a Fluidics Station 450 (Affymetrix) with the Hybridization Wash and Stain Kit (Affymetrix) and the Washing Procedure FS450_0004.

scan_protocol: scan was performed using Affymetrix GeneChip Scanner 3000 7G

data_processing: The MAS5 data was generated by using the Affymetrix Expression Console software using default analysis settings and global scaling as normalization method.

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: solid media plates; BRIC-16; middeck : BRIC-A PDFU-3

label_protocol: cDNA was synthesized using Ovation Pico WTA System (NuGEN Technologies Inc.) and cDNA was labeled using Encore Biotin Module (NuGEN Technologies Inc.)

growth_protocol: General biology operations   Wild-type (non-transgenic) Arabidopsis plants and Arabidopsis tissue culture cells were planted on 60mm round, nutrient agar Petri plates cultured in a horizontal position until turnover and installation into the BRIC hardware.  All of the sub-culturing on the plates was conducted in the laboratory of the PIs and the University of Florida.  Some planting of the seeded plates was conducted at KSC. Plates were planted in a laminar flow hood and stored in sterile Biotransfer Boxes (BT). Plates with both seeds and cells were kept in the dark, and the seeds vernalized at 4 deg C.  Preparation of specialized plates and biology  Petri plates.   Because of their configuration within the BRIC flight hardware, sterility was maintained on all surfaces (interior and exterior) of the Petri plates. The media in the plates for BRIC had to be 5mm deep or less to accommodate the biology and the PDFU cover hardware. For a 60mm dish, this calculates out to 6.7 mLs. After pouring, the plates are allowed to solidify, and then transferred to a sterile Biotransporter (to maintain sterility of external surface) until planting.  Preparation of seeded plates. Arabidopsis seed was surface sterilized working in a laminar flow hood. Seeds were planted on the surface of the Petri plates at a density of about 75 seeds per plate.  The cover was replaced, but not taped, and transferred to a sterile BT.  The BT was wrapped in black cloth and stored at 4 deg C until Turn Over.  Preparation of cell culture plates.  The liquid media from a sterile cell suspension was decanted, and the cells were washed once with fresh liquid media, and then decanted again. A sterile scoop was used to place about 1 gram of cells in the surface on the plate and disperse evenly across the surface. The cover was replaced, but not taped, and transferred to a sterile BT.  The BT was wrapped in black cloth and stored at room temperature until Turn Over.  BRIC Spaceflight Hardware  The hardware for this experiment was the NASA BRIC-LED (Biological Research In a Canister – Light Emitting Diode). The LED component of the hardware was disabled and all biology was held in the dark for the duration of the experiment. The BRIC-LED canisters hold six 60 mm diameter Petri plates in small sub-compartments called PDFUs (Petri Dish Fixation Units). The PDFUs allow an externally activated fixation step without manipulating the samples. We were allocated 13 PDFUs: 5 in BRIC A, 5 in BRIC B and 3 in BRIC G. The six replicate plates of seedlings and six replicate plates cultured cells (12 plates total) were distributed among three BRIC canisters. We were allocated 13 PDFUs: 5 in BRIC A, 5 in BRIC B and 3 in BRIC G. One of the PDFU slots in each BRIC was used to hold a HOBO™ data logger to record temperature. The HOBO temperature data collection begins immediately after the biology is sealed in the BRICs, 24 hours before launch. The BRICs were contained within a foam-lined tray for launch and stowage in a Shuttle Middeck Locker for the flight.   An additional set of Petri plates within BRIC hardware, identical to that launched for Spaceflight, was prepared for the Ground Control. The Ground Control was housed in the OES (Orbital Environmental Simulator) chamber in the Spaceflight Life Sciences Laboratory (SLSL) at Kennedy Space Center (KSC). The Ground Control was initiated with a precise 24 hour delay to enable the OES environment to be programmed with the environmental profile taken from telemetry of the Space Shuttle. Nominally, the Ground Control BRIC hardware and samples experienced the same external environment profile as the hardware and samples on the Space Shuttle. Environmental parameters that are controlled on the OES and made identical to flight are cabin temperature, humidity and CO2 concentration.

extract_protocol: Total cellular RNA was extracted using RNeasy Mini Kit (QIAGEN)

treatment_protocol: The BRIC-16 experiment was turned over to payload engineers in the SLSL at KSC 24 hours before the scheduled launch time. The payload launched on STS-131 on April 5th, 2010, at 06:25, and achieved orbit approximately eight minutes later. The biology was in orbit 12 days and 21 hours (04/05/10 06:25:28 to 04/18/10 03:37:28) before being fixed on orbit with RNAlater. The orbiter landed on April 20th (04/20/10 07:37:28) and the biology was returned to the PIs at SLSL approximately 7 hours later.

tag: cultivar

tag: material type

value: Etiolated seedlings

tag: organism part

value: germinated seeds

tag: age

value: 7 days old

tag: biosource type

value: in-flight fixed sample


title: GROUND CONTROL BRIC A PDFU-2 315 seedlings

source_name: solid media plates; BRIC-16; OES chamber: BRIC-A PDFU-2

value: fixed sample


title: genomic DNA from formalin fixed paraffin embedded normal kidney 4

status: Public on Jul 08 2014

type: genomic

city: London

first: Jocelyn

last: Charlton

address: 30 Guilford Street

department: Institute of Child Health

country: United Kingdom

institute: University College London

description: SAMPLE 4

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

organism: Homo sapiens

source_name: normal kidney 4

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from formalin fixed paraffin embedded tissue using the Dneasy kit (QIAGEN)

tag: tissue

value: normal kidney

tag: matched trios

tag: matched pairs

tag: Sex

value: F

tag: laterality

tag: overall tumour histology

tag: disease state

value: normal

tag: age (months)


title: GROUND BRIC G PDFU-2 355 tissue

source_name: solid media plates; BRIC-16; OES chamber: BRIC-G PDFU-2

value: Tissue culture cells

value: derived from hypocotyls


title: FLIGHT  BRIC A PDFU-1 052 seedlings

source_name: solid media plates; BRIC-16; middeck : BRIC-A PDFU-1


title: FLIGHT  BRIC A PDFU-2 176 seedlings

source_name: solid media plates; BRIC-16; middeck : BRIC-A PDFU-2


title: GROUNDCONTROL BRIC G PDFU-1 335 seedlings

source_name: solid media plates; BRIC-16; OES chamber: BRIC-G PDFU-1


title: GROUND BRIC B PDFU-4 331 tissue

source_name: solid media plates; BRIC-16; OES chamber: BRIC-B PDFU-4


title: GROUND BRIC B PDFU-3 338 tissue

source_name: solid media plates; BRIC-16; OES chamber: BRIC-B PDFU-3


title: GROUND BRIC B PDFU-2 312 tissue

source_name: solid media plates; BRIC-16; OES chamber: BRIC-B PDFU-2


title: FLIGHT BRIC G PDFU-1 012 seedlings

source_name: solid media plates; BRIC-16; middeck : BRIC-G PDFU-21


title: FLIGHT BRIC B PDFU-3 104 tissue

source_name: solid media plates; BRIC-16; middeck: BRIC-B PDFU-3


title: FLIGHT BRIC B PDFU-4 033 tissue

source_name: solid media plates; BRIC-16; middeck: BRIC-B PDFU-4


title: FLIGHT BRIC B  PDFU-2 083 tissue

source_name: solid media plates; BRIC-16; middeck : BRIC-B PDFU-2


title: GROUND CONTROL BRIC A PDFU-3 320 seedlings

source_name: solid media plates; BRIC-16; OES chamber: BRIC-A PDFU-3


title: FLIGHT BRIC B PDFU-5 153 tissue

source_name: solid media plates; BRIC-16; middeck: BRIC-B PDFU-5


title: GROUND CONTROL TAGES 2B plate4 HYPOCOTYLS Rep2

source_name: solid 0.5x MS media plates; Advanced solid media plates; Advanced Biological Research System (ABRS); GC Unit, OES chamber at KSC

growth_protocol: Plant Lines and Seed Dormancy: Arabidopsis thaliana (Arabidopsis) plants were grown in a vertical configuration on the surface of 10 cm2 solid media plates.  Three GFP (Green fluorescent Protein reporter gene lines were used:  Adh::GFP (alcohol dehydrogenase promoter), DR5::GFP (synthetic auxin response element) and UB::GFP (35sCaMV constitutive promoter). Seeds, and the seeded plates, were prepared in such a way as to maintain dormancy until the initiation of the experiment on orbit. Seeds were surface sterilized with 75% ethanol for 10 minutes, dried on sterile filter paper and stored at 4°C until use. Immediately before planting onto media plates, a small amount of seed was suspended in sterile water and the seeds were dispersed individually to the surface of the plate.  The plate was then immediately wrapped in light-tight black cloth (Duvatyne) and stored at room temperature until launch. After launch (Shuttle launch STS-131, Orbiter Discovery, April, 2010) and transition to the International Space Station (ISS), the wrapped plates were stowed at ambient temperature for 12 days until the initiation of the experiment on orbit.  The dry-sterilized seeds remained dormant until activated by exposure to light.

treatment_protocol: Experiment Unique Equipment and Environmental Conditions:Both the flight and ground control components of the experiment were grown in specialized growth chamber units developed by Kennedy Space Center referred to as ABRS (Advanced Biological Research System) growth chamber.  Seeded plates were unwrapped from their light-tight coverings and installed in a specialized GFP imaging system (GIS) designed to hold six plates – one in the direct line of fluorescent excitation LEDs and the imaging camera, plus five additional plates. GFP expression data were collected on orbit form the imaging plate, and after 12 days of growth, all plates were harvested on orbit to RNAlater-filled KSC Fixation Tubes (KFTs) and then stowed below -40°C on station.  The Ground Control was housed in the Orbital Environmental Simulator (OES) chamber in the Spaceflight Life Sciences Laboratory at Kennedy Space Center. The Ground Control was initiated with a precise 48 hour delay to enable the OES environment to be programed with those environmental conditions that can be replicated on the ground, such as cabin temperature and CO2 levels, taken from ISS telemetry. Sample Preparation: Plants harvested to RNAlater-filled KFTs were returned from ISS stowage with Orbiter Atlantis for the return flight of STS-132 and transferred to the PIs. Total RNA was isolated form sets of intact 12 day old seedlings, and from seedlings separated into three tissue types: leaves (cut from the plant at base of each petiole), hypocotyls (the region between the root/shoot junction and the start of the leaf rosette) and roots.

value: plant tissue

value: hypocotyls

value: seeds germinated with light stimulus 12 days into the flight


title: FLIGHT BRIC G PDFU-2 018 tissue

source_name: solid media plates; BRIC-16; middeck: BRIC-G PDFU-2


title: FLIGHT BRIC G PDFU-3 159 tissue

source_name: solid media plates; BRIC-16; middeck: BRIC-G PDFU-3


title: GROUND CONTROL TAGES 2B plate4

value: WS

value: whole plant


title: 72.9 DF2 D5

status: Public on Mar 01 2013

city: Stanford

first: Stephen

last: Popper

state: CA

department: Division of Infectious Diseases, Dept. of Medicine

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88807.gif

hyb_protocol: not provided

scan_protocol: Agilent Feature Extraction

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

source_name: Stratagene Universal Human Reference RNA: 8 ug input

label_protocol: not provided

extract_protocol: not provided

tag: reference

source_name: 72.9 DF2 D5 amino-allyl amplified PBMC total RNA

value: PBMC

tag: disease state (nth day of fever)

value: 5 d

tag: individual

tag: replicate


title: 379.4 Healthy

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88777.gif

scan_protocol: Agilent Feature Extraction Scanner Model: G2505B

value: Stratagene Universal Human Reference RNA

source_name: 379.4 Healthy amino-allyl amplified PBMC total RNA

value: Healthy

value: N/A d


title: 63.1 DF1 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88746.gif

source_name: 63.1 DF1 D4 amino-allyl amplified PBMC total RNA

value: 4 d


title: 47.1 DF1 D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88789.gif

source_name: 47.1 DF1 D3 amino-allyl amplified PBMC total RNA

value: 3 d


title: 70.9 DSS D8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88852.gif

source_name: 70.9 DSS D8 amino-allyl amplified PBMC total RNA

value: DSS

value: 8 d


title: 26.1 DF2 D5

description: Image: http://smd.stanford.edu/MicroArray/gifs//88813.gif

source_name: 26.1 DF2 D5 amino-allyl amplified PBMC total RNA


title: 18.4 DF2 D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/88782.gif

source_name: 18.4 DF2 D5 amino-allyl amplified PBMC total RNA


title: 18.2 DF2 D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88799.gif

source_name: 18.2 DF2 D3 amino-allyl amplified PBMC total RNA


title: 70.1 DSS D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88747.gif

scan_protocol: Agilent Feature Extraction Scanner Model: GenePix 4000A

source_name: 70.1 DSS D4 amino-allyl amplified PBMC total RNA


title: 174.1 DHF D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88742.gif

source_name: 174.1 DHF D4 amino-allyl amplified PBMC total RNA

value: DHF


title: 46.1 DF2 D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/88819.gif

source_name: 46.1 DF2 D3 amino-allyl amplified PBMC total RNA


title: 84.1 DF2 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88763.gif

scan_protocol: Agilent Feature Extraction Scanner Model: GenePix 4200A

source_name: 84.1 DF2 D4 amino-allyl amplified PBMC total RNA


title: 47.9 DF1 D7

description: Image: http://smd.stanford.edu/MicroArray/gifs//88816.gif

source_name: 47.9 DF1 D7 amino-allyl amplified PBMC total RNA

value: 7 d


title: 54.1 DSS D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88869.gif

source_name: 54.1 DSS D3 amino-allyl amplified PBMC total RNA


title: 134.9 DHF D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88800.gif

source_name: 134.9 DHF D6 amino-allyl amplified PBMC total RNA

value: 6 d


title: 44.3 DSS D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88853.gif

source_name: 44.3 DSS D6 amino-allyl amplified PBMC total RNA


title: 85.3 DF2 D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88793.gif

source_name: Stratagene Universal Human Reference RNA: 8 ug input

source_name: 85.3 DF2 D5 amino-allyl amplified PBMC total RNA


title: 85.9 DF2 D7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88824.gif

source_name: 85.9 DF2 D7 amino-allyl amplified PBMC total RNA


title: 189.9 DHF D12

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88814.gif

source_name: 189.9 DHF D12 amino-allyl amplified PBMC total RNA


title: 21.3 DHF D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88805.gif

source_name: 21.3 DHF D6 amino-allyl amplified PBMC total RNA


title: 41.4 DF1 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88835.gif

source_name: 41.4 DF1 D4 amino-allyl amplified PBMC total RNA


title: 54.4 DSS D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88788.gif

source_name: 54.4 DSS D6 amino-allyl amplified PBMC total RNA


title: 37.9 DF2 D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88859.gif

source_name: 37.9 DF2 D6 amino-allyl amplified PBMC total RNA


title: 2873.4 Healthy

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88757.gif

source_name: 2873.4 Healthy amino-allyl amplified PBMC total RNA


title: 37.3 DF2 D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88780.gif

source_name: 37.3 DF2 D5 amino-allyl amplified PBMC total RNA


title: 174.2 DHF D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88803.gif

source_name: 174.2 DHF D5 amino-allyl amplified PBMC total RNA


title: 121.4 DSS D6

description: Image: http://smd.stanford.edu/MicroArray/gifs//88809.gif

source_name: 121.4 DSS D6 amino-allyl amplified PBMC total RNA


title: 134.2 DHF D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88847.gif

source_name: 134.2 DHF D5 amino-allyl amplified PBMC total RNA


title: 52.9 DF1 D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88834.gif

source_name: 52.9 DF1 D6 amino-allyl amplified PBMC total RNA


title: 31.3 DHF D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/88823.gif

source_name: 31.3 DHF D5 amino-allyl amplified PBMC total RNA


title: 68.1 DHF D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88758.gif

source_name: 68.1 DHF D4 amino-allyl amplified PBMC total RNA


title: 189.2 DHF D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/88769.gif

source_name: 189.2 DHF D4 amino-allyl amplified PBMC total RNA


title: 55.3 DF1 D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88786.gif

source_name: Stratagene Universal Human Reference RNA: 8 ug input

source_name: 55.3 DF1 D5 amino-allyl amplified PBMC total RNA


title: 67.9 DF2 D9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88862.gif

source_name: 67.9 DF2 D9 amino-allyl amplified PBMC total RNA

value: 9 d


title: 121.2 DSS D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88848.gif

source_name: 121.2 DSS D4 amino-allyl amplified PBMC total RNA


title: 205.1 DF1 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88776.gif

source_name: 205.1 DF1 D4 amino-allyl amplified PBMC total RNA


title: 128.9 DHF D8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/88865.gif

source_name: 128.9 DHF D8 amino-allyl amplified PBMC total RNA


title: 29.9 DHF D7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88867.gif

source_name: 29.9 DHF D7 amino-allyl amplified PBMC total RNA


title: 44.1 DSS D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88744.gif

source_name: 44.1 DSS D4 amino-allyl amplified PBMC total RNA


title: 191.1 DHF D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88760.gif

source_name: 191.1 DHF D4 amino-allyl amplified PBMC total RNA


title: 25.9 DF2 D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88795.gif

source_name: 25.9 DF2 D5 amino-allyl amplified PBMC total RNA


title: 42.4 DF1 D7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88797.gif

source_name: 42.4 DF1 D7 amino-allyl amplified PBMC total RNA


title: 128.2 DHF D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88830.gif

source_name: 128.2 DHF D3 amino-allyl amplified PBMC total RNA


title: 39.1 DF2 D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88817.gif

source_name: 39.1 DF2 D3 amino-allyl amplified PBMC total RNA


title: 39.9 DF2 D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/88820.gif

source_name: 39.9 DF2 D6 amino-allyl amplified PBMC total RNA


title: 125.1 DSS D2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/88828.gif

source_name: 125.1 DSS D2 amino-allyl amplified PBMC total RNA

value: 2 d


title: 1640.4 Healthy

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88771.gif

source_name: 1640.4 Healthy amino-allyl amplified PBMC total RNA


title: 173.1 DF1 D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88790.gif

source_name: 173.1 DF1 D3 amino-allyl amplified PBMC total RNA


title: 4469.4 Healthy

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88745.gif

source_name: Stratagene Universal Human Reference RNA: 8 ug input

source_name: 4469.4 Healthy amino-allyl amplified PBMC total RNA


title: 37.1 DF2 D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88794.gif

source_name: 37.1 DF2 D3 amino-allyl amplified PBMC total RNA


title: 185.1 DHF D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/88762.gif

source_name: 185.1 DHF D4 amino-allyl amplified PBMC total RNA


title: 41.3 DF1 D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/88784.gif

source_name: 41.3 DF1 D3 amino-allyl amplified PBMC total RNA


title: 42.2 DF1 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88756.gif

source_name: 42.2 DF1 D4 amino-allyl amplified PBMC total RNA


title: 191.9 DHF D12

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88849.gif

source_name: 191.9 DHF D12 amino-allyl amplified PBMC total RNA


title: 42.3 DF1 D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88855.gif

source_name: 42.3 DF1 D6 amino-allyl amplified PBMC total RNA


title: 18.3 DF2 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88796.gif

source_name: 18.3 DF2 D4 amino-allyl amplified PBMC total RNA


title: 132.1 DSS D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/88857.gif

source_name: 132.1 DSS D3 amino-allyl amplified PBMC total RNA


title: 18.9 DF2 D7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88868.gif

source_name: 18.9 DF2 D7 amino-allyl amplified PBMC total RNA


title: 178.1 DHF D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88832.gif

source_name: 178.1 DHF D3 amino-allyl amplified PBMC total RNA


title: 42.1 DF1 D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88781.gif

source_name: 42.1 DF1 D3 amino-allyl amplified PBMC total RNA


title: 121.1 DSS D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/88864.gif

source_name: 121.1 DSS D3 amino-allyl amplified PBMC total RNA


title: 44.2 DSS D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/88818.gif

source_name: 44.2 DSS D5 amino-allyl amplified PBMC total RNA


title: 72.2 DF2 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/88750.gif

source_name: 72.2 DF2 D4 amino-allyl amplified PBMC total RNA


title: 39.3 DF2 D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88801.gif

source_name: 39.3 DF2 D5 amino-allyl amplified PBMC total RNA


title: 46.9 DF2 D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88858.gif

source_name: Stratagene Universal Human Reference RNA: 8 ug input

source_name: 46.9 DF2 D6 amino-allyl amplified PBMC total RNA


title: 47.4 DF1 D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88845.gif

source_name: 47.4 DF1 D6 amino-allyl amplified PBMC total RNA


title: 86.2 DHF D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88764.gif

source_name: 86.2 DHF D4 amino-allyl amplified PBMC total RNA


title: 558.4 Healthy

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/88759.gif

source_name: 558.4 Healthy amino-allyl amplified PBMC total RNA


title: 42.9 DF1 D29

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88854.gif

source_name: 42.9 DF1 D29 amino-allyl amplified PBMC total RNA


title: 189.1 DHF D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88837.gif

source_name: 189.1 DHF D3 amino-allyl amplified PBMC total RNA


title: 68.3 DHF D7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88841.gif

source_name: 68.3 DHF D7 amino-allyl amplified PBMC total RNA


title: 174.9 DHF D9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88843.gif

source_name: 174.9 DHF D9 amino-allyl amplified PBMC total RNA


title: 185.9 DHF D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88821.gif

source_name: 185.9 DHF D6 amino-allyl amplified PBMC total RNA


title: 72.1 DF2 D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88825.gif

source_name: 72.1 DF2 D3 amino-allyl amplified PBMC total RNA


title: 63.9 DF1 D10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88812.gif

source_name: 63.9 DF1 D10 amino-allyl amplified PBMC total RNA


title: 50.2 DF2 D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88808.gif

source_name: 50.2 DF2 D5 amino-allyl amplified PBMC total RNA


title: 1922.4 Healthy

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88761.gif

source_name: 1922.4 Healthy amino-allyl amplified PBMC total RNA


title: 63.2 DF1 D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/88829.gif

source_name: 63.2 DF1 D5 amino-allyl amplified PBMC total RNA


title: 31.2 DHF D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88772.gif

source_name: 31.2 DHF D4 amino-allyl amplified PBMC total RNA


title: 121.3 DSS D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88851.gif

source_name: 121.3 DSS D5 amino-allyl amplified PBMC total RNA


title: 50.9 DF2 D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88811.gif

source_name: Stratagene Universal Human Reference RNA: 8 ug input

source_name: 50.9 DF2 D6 amino-allyl amplified PBMC total RNA


title: 70.2 DSS D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88844.gif

source_name: 70.2 DSS D5 amino-allyl amplified PBMC total RNA


title: 67.2 DF2 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88778.gif

source_name: 67.2 DF2 D4 amino-allyl amplified PBMC total RNA


title: 132.2 DSS D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88770.gif

source_name: 132.2 DSS D4 amino-allyl amplified PBMC total RNA


title: 52.2 DF1 D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88850.gif

source_name: 52.2 DF1 D5 amino-allyl amplified PBMC total RNA


title: 29.1 DHF D4

description: Image: http://smd.stanford.edu/MicroArray/gifs//88752.gif

source_name: 29.1 DHF D4 amino-allyl amplified PBMC total RNA


title: 55.1 DF1 D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88787.gif

source_name: 55.1 DF1 D3 amino-allyl amplified PBMC total RNA


title: 54.2 DSS D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/88774.gif

source_name: 54.2 DSS D4 amino-allyl amplified PBMC total RNA


title: 31.9 DHF D8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88802.gif

source_name: 31.9 DHF D8 amino-allyl amplified PBMC total RNA


title: 85.2 DF2 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/88767.gif

source_name: 85.2 DF2 D4 amino-allyl amplified PBMC total RNA


title: 46.3 DF2 D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88839.gif

source_name: 46.3 DF2 D5 amino-allyl amplified PBMC total RNA


title: 37.2 DF2 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88748.gif

source_name: 37.2 DF2 D4 amino-allyl amplified PBMC total RNA


title: 128.3 DHF D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88822.gif

source_name: 128.3 DHF D4 amino-allyl amplified PBMC total RNA


title: 31.1 DHF D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-03/88840.gif

source_name: 31.1 DHF D3 amino-allyl amplified PBMC total RNA


title: 49.2 DF1 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88751.gif

source_name: 49.2 DF1 D4 amino-allyl amplified PBMC total RNA


title: 86.3 DHF D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88798.gif

source_name: 86.3 DHF D6 amino-allyl amplified PBMC total RNA


title: 3014.4 Healthy

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88749.gif

source_name: Stratagene Universal Human Reference RNA: 8 ug input

source_name: 3014.4 Healthy amino-allyl amplified PBMC total RNA


title: 18.1 DF2 D2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88826.gif

source_name: 18.1 DF2 D2 amino-allyl amplified PBMC total RNA


title: 21.2 DHF D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88863.gif

source_name: 21.2 DHF D5 amino-allyl amplified PBMC total RNA


title: 120.2 DSS D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88860.gif

source_name: 120.2 DSS D5 amino-allyl amplified PBMC total RNA


title: blood-cd1c-dc-1

status: Public on Jul 12 2012

city: Singapore

first: Pavandip Singh

last: Wasan

address: 8A Biomedical Grove, #03-06, Immunos

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

description:
BD_CD1c_DC_I
healthy donor, dendritic cell, CD1c,Homo sapiens,blood,dendritic cell,CD1c,total RNA,biotin

hyb_protocol: According to BeadChip array manufacturer's protocol.

data_processing: Array data were extracted at the probeset level with no background correction using Illumina's BeadStudio software. These raw data were normalised using the Loess method within the LUMI package in R/Bioconductor v2.13.1. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate, and probesets with corrected p-value less than 0.05 were considered.

source_name: healthy donor, dendritic cell, CD1c

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: Monocytes and dendritic cell subsets were purified by FACS sorting from primary samples for transcription analysis.

extract_protocol: RNA was extracted from monocytes using an RNeasy Mini Kit (Qiagen) as per manufacturer's specifications. Extracted RNA was runned and quantified on a Bioanalyser (Agilent) for quality control and used subsequently in a microarray assay.

treatment_protocol: None.

value: blood

tag: cell type

value: dendritic cell

tag: cell subtype

value: healthy


title: 99.1 DSS D3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88856.gif

source_name: 99.1 DSS D3 amino-allyl amplified PBMC total RNA

value: PBMC


title: blood-cd141-dc-3

description:
BD_CD141_DC_VI
healthy donor, dendritic cell, CD141,Homo sapiens,blood,dendritic cell,CD141,total RNA,biotin

scan_protocol: According to BeadChip array manufacturer's protocol.

source_name: healthy donor, dendritic cell, CD141


title: blood-cd141-dc-2

description:
BD_CD141_DC_II
healthy donor, dendritic cell, CD141,Homo sapiens,blood,dendritic cell,CD141,total RNA,biotin


title: 39.2 DF2 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/88775.gif

source_name: 39.2 DF2 D4 amino-allyl amplified PBMC total RNA


title: 136.1 DHF D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88753.gif

source_name: 136.1 DHF D5 amino-allyl amplified PBMC total RNA

value: 5 d


title: 932.4 Healthy

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88765.gif

value: Stratagene Universal Human Reference RNA

source_name: 932.4 Healthy amino-allyl amplified PBMC total RNA


title: 178.9 DHF D25

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88783.gif

source_name: 178.9 DHF D25 amino-allyl amplified PBMC total RNA


title: 191.2 DHF D5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88870.gif

source_name: 191.2 DHF D5 amino-allyl amplified PBMC total RNA


title: 46.2 DF2 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/88766.gif

source_name: 46.2 DF2 D4 amino-allyl amplified PBMC total RNA


title: 44.9 DSS D7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/88861.gif

source_name: 44.9 DSS D7 amino-allyl amplified PBMC total RNA


title: 99.2 DSS D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/88755.gif

source_name: 99.2 DSS D4 amino-allyl amplified PBMC total RNA


title: blood-cd1c-dc-2

description:
BD_CD1c_DC_II
healthy donor, dendritic cell, CD1c,Homo sapiens,blood,dendritic cell,CD1c,total RNA,biotin


title: 68.2 DHF D5

description: Image: http://smd.stanford.edu/MicroArray/gifs//88810.gif

source_name: 68.2 DHF D5 amino-allyl amplified PBMC total RNA


title: blood-cd14-mono-3

description:
BD_CD14_Mono_VI
healthy donor, monocyte, CD14,Homo sapiens,blood,monocyte,CD14,total RNA,biotin

source_name: healthy donor, monocyte, CD14

value: monocyte


title: 63.3 DF1 D6

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-12/88815.gif

source_name: Stratagene Universal Human Reference RNA: 8 ug input

source_name: 63.3 DF1 D6 amino-allyl amplified PBMC total RNA


title: blood-cd14-mono-2

description:
BD_CD14_Mono_II
healthy donor, monocyte, CD14,Homo sapiens,blood,monocyte,CD14,total RNA,biotin


title: blood-cd14-mono-1

description:
BD_CD14_Mono_V
healthy donor, monocyte, CD14,Homo sapiens,blood,monocyte,CD14,total RNA,biotin


title: 47.2 DF1 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs//88743.gif

source_name: 47.2 DF1 D4 amino-allyl amplified PBMC total RNA


title: blood-cd14_cd16-mono-4

description:
BD_CD14CD16_Mono_VI
healthy donor, monocyte, CD14_CD16,Homo sapiens,blood,monocyte,CD14_CD16,total RNA,biotin

source_name: healthy donor, monocyte, CD14_CD16


title: 173.2 DF1 D4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-09/88768.gif

source_name: 173.2 DF1 D4 amino-allyl amplified PBMC total RNA


title: bd-cd14-mono-1

description:
BD_CD14_Mono_I
healthy donor, monocyte, CD14,Homo sapiens,blood,monocyte,CD14,total RNA,biotin


title: blood-cd1c-dc-3

description:
BD_CD1c_DC_VI
healthy donor, dendritic cell, CD1c,Homo sapiens,blood,dendritic cell,CD1c,total RNA,biotin

source_name: healthy donor, dendritic cell, CD1c


title: blood-dc1c-dc-6

description:
BD_CD1c_DC_V
healthy donor, dendritic cell, CD1c,Homo sapiens,blood,dendritic cell,CD1c,total RNA,biotin


title: blood-cd14_cd16-mono-1

description:
BD_CD14_CD16_Mono_V
healthy donor, monocyte, CD14_CD16,Homo sapiens,blood,monocyte,CD14_CD16,total RNA,biotin


title: blood-cd14_cd16-mono-2

description:
BD_CD14CD16_Mono_I
healthy donor, monocyte, CD14_CD16,Homo sapiens,blood,monocyte,CD14_CD16,total RNA,biotin


title: blood-cd14_cd16-mono-3

description:
BD_CD14CD16_Mono_II
healthy donor, monocyte, CD14_CD16,Homo sapiens,blood,monocyte,CD14_CD16,total RNA,biotin


title: liver western diet 0.05% quercetin rep4

status: Public on May 30 2012

city: Tsukuba

first: Masuko

last: Kobori

state: Ibaraki

address: 2-1-13 Kannondai

country: Japan

institute: Food Research Institute, National Agriculture and Food Research Organization

description: Gene expression data from liver after 20 week feeding of western diet containing 0.05% quercetin

hyb_protocol: Fragmented cRNA were hybridized to an array (Mouse Genome 430 2.0 array, Affymetrix) at 45°C for 16 h.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).

data_processing: Data analysis was performed with a GeneChip Operating Software (Ver. 1.4) using Affymetrix default analysis settings and global scaling as normalization method..

organism: Mus musculus

source_name: liver, fed Western diet containing 0.05% quercetin for 20 weeks

label_protocol: Double-stranded cDNA was synthesized from the total RNA of each mouse using the One-Cycle cDNA Synthesis Kit (Affymetrix Japan KK, Tokyo, Japan) with a T7-(dT)24 primer. Biotin-labeled cRNA was then synthesized using an IVT Labeling Kit (Affymetrix). The biotin-labeled cRNA was further purified and fragmented using the Sample Cleanup Module (Affymetrix).

growth_protocol: Five-week-old male C57BL/6J mice were obtained from the Institute for Animal Reproduction, Charles River Japan Inc. (Ibaraki, Japan). The mice were housed under conditions of 24± 1°C, 55 ± 5% humidity, and 12 hour light/dark photocycles (dark period from 0800 to 2000) with free access to water and a standard nonpurified diet (NMF, Oriental Yeast Co., Tokyo, Japan) for a week prior to the experiment.

extract_protocol: The mice were killed under anesthesia with pentobarbital, and blood and liver tissue were immediately collected. Total RNA was extracted from liver tissues using an RNeasy Midi Kit (Qiagen KK, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: The mice were divided into 10 groups of 6 mice each, housed in groups of 3 per cage and fed one of the following diets for 20 weeks : AIN93G (control), AIN93G containing 0.05% quercetin (0.05% quercetin, (Funakoshi, Tokyo, Japan)), a high fat, high cholesterol and high sucrose Western-style diet (39.9% of energy from fat (20% unsalted butter, 1% soy oil, 0.15% cholesterol) and 34.0% of energy from sucrose) (Oriental Yeast) or this Western diet supplemented with 0.05% quercetin.

tag: gender

value: male

tag: strain

value: liver

tag: diet


title: liver western diet 0.05% quercetin rep6

tag: tissue

value: Western diet containing 0.05% quercetin for 20 weeks


title: liver western diet 0.05% quercetin rep1


title: liver western diet 0.05% quercetin rep3


title: liver western diet 0.05% quercetin rep5


title: liver western diet rep1

description: Gene expression data from liver after 20 week feeding of western diet

source_name: liver, fed Western diet for 20 weeks

value: Western diet for 20 weeks


title: liver western diet rep4


title: liver western diet rep5


title: non-western liver control diet rep2

description: Gene expression data from liver after 20 week feeding of control AIN93G diet

source_name: liver, fed control AIN93G diet for 20 weeks

value: AIN93G diet for 20 weeks


title: non-western liver control diet rep1


title: liver western diet rep6


title: wild-type, 37 degrees, t=165

status: Public on Feb 03 2012

city: Durham

first: Laura

middle: Anne

last: Simmons Kovacs

state: NC

department: Biology

institute: Duke University

description: 165 minutes after synchronization, CDK activity

hyb_protocol: Hybridization was preformed at the Duke Institute for Genome Sciences and Policy DNA Microarray Core Facility (www.genome.duke.edu/cores/microarray)

scan_protocol: Scanning was preformed at the Duke Institute for Genome Sciences and Policy DNA Microarray Core Facility (www.genome.duke.edu/cores/microarray)

data_processing: CEL files from samples 1-48 were normalized and summarized alongside previously published arrays (GSE8799) according to the dChip method as implemented in the affy package of BioConductor using standard parameters.

organism: Saccharomyces cerevisiae

source_name: CDC28, 37 degrees, t=165

label_protocol: Samples 1-33 were labeled using the Affymetrix GeneChip One Cycle Labeling procedure.  Samples 34-48 were labeled using the Ambion MessageAmp Premier kit.

growth_protocol: Cells were grown at 25°C in YEPD to a final concentration of 3-5x107 cells/mL.  Small daughter cells were collected by centrofugal elutriation.  The synchronized population was resuspended in YEPD prewarmed to 37°C at time=0.  Samples were taken at each time indicated.

extract_protocol: Total RNA was extracted using a standard hot acid phenol protocol and cleaned with a Qiagen RNeasy MinElute Cleanup Kit.

tag: genotype

value: BF264-15DU; mat a; bar1

tag: time

value: 165 minutes after synchronization

tag: cdk activity

value: yes


title: non-western liver control diet rep6


title: wild-type, 37 degrees, t=150

description: 150 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=150

value: 150 minutes after synchronization


title: wild-type, 37 degrees, t=225

description: 225 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=225

value: 225 minutes after synchronization


title: liver western diet rep2


title: non-western liver control diet rep4


title: wild-type, 37 degrees, t=135

description: 135 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=135

value: 135 minutes after synchronization


title: wild-type, 37 degrees, t=180

description: 180 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=180

value: 180 minutes after synchronization


title: non-western liver control diet rep5


title: wild-type, 37 degrees, t=105

description: 105 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=105

value: 105 minutes after synchronization


title: liver western diet 0.05% quercetin rep2


title: non-western liver control diet rep3


title: wild-type, 37 degrees, t=120

description: 120 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=120

value: 120 minutes after synchronization


title: liver western diet rep3


title: wild-type, 37 degrees, t=30

description: 30 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=30

value: 30 minutes after synchronization


title: wild-type, 37 degrees, t=60

description: 60 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=60

value: 60 minutes after synchronization


title: wild-type, 37 degrees, t=90

description: 90 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=90

value: 90 minutes after synchronization


title: wild-type, 37 degrees, t=45

description: 45 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=45

value: 45 minutes after synchronization


title: wild-type, 37 degrees, t=210

description: 210 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=210

value: 210 minutes after synchronization


title: wild-type, 37 degrees, t=15

description: 15 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=15

value: 15 minutes after synchronization


title: Naive CD4+ T-cell, sample 7

status: Public on Jan 21 2011

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: The cDNA was fragmented, labeled and hybridized to Affymetrix HG_U133AAofAv2 microarrays (Affymetrix, Santa Clara, CA)

scan_protocol: standard Affymetrix protocol

data_processing: Transcript levels were processed from data image files using RMA method, implemented by Bioconductor R package. To reduce batch effects, transcript levels were further corrected with the ComBat method (Johnson, 2007), which applies empirical Bayes framework for adjusting data for batch effects. Final dataset which was used in the paper and contains 8968 genes is included in the supplementary file GSE24759_data.sort.txt.

source_name: peripheral blood

label_protocol: Ten nanograms of total RNA were amplified using the Ovation Biotin RNA Amplification and Labeling System (NuGEN, San Carlos, CA).

extract_protocol: Total RNA was isolated from TriZol.  The concentration of RNA was quantified using the RiboGreen© RNA Quantitation Kit (Invitrogen, San Diego, CA)

value: Naive CD4+ T-cell

tag: batch


title: Naive CD4+ T-cell, sample 2


title: Naive CD4+ T-cell, sample 3


title: CD8+ Central Memory, sample 1

value: CD8+ Central Memory


title: CD8+ Central Memory, sample 7


title: Naive CD4+ T-cell, sample 1


title: Naive CD4+ T-cell, sample 5


title: CD8+ Central Memory, sample 2


title: Naive CD4+ T-cell, sample 4


title: CD8+ Central Memory, sample 5


title: CD8+ Effector Memory, sample 6

value: CD8+ Effector Memory


title: CD8+ Effector Memory, sample 4


title: CD8+ Central Memory, sample 4


title: CD8+ Effector Memory, sample 3


title: CD8+ Central Memory, sample 6


title: Naive CD4+ T-cell, sample 6


title: CD8+ Effector Memory, sample 2


title: CD8+ Effector Memory, sample 1


title: CD8+ Effector Memory, sample 5


title: wild-type, 37 degrees, t=195

description: 195 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=195

value: BF264-15DU; mat a; bar1

value: 195 minutes after synchronization


title: Naive CD8+ T-cell, sample 7

value: Naive CD8+ T-cell


title: Naive CD8+ T-cell, sample 5


title: CD8+ Central Memory, sample 3


title: wild-type, 37 degrees, t=75

description: 75 minutes after synchronization, CDK activity

source_name: CDC28, 37 degrees, t=75

value: 75 minutes after synchronization

value: yes


title: Naive CD8+ T-cell, sample 2


title: Naive CD8+ T-cell, sample 3


title: Naive CD8+ T-cell, sample 6


title: blood-cd141-dc-1

description:
BD_CD141_DC_I
healthy donor, dendritic cell, CD141,Homo sapiens,blood,dendritic cell,CD141,total RNA,biotin

source_name: healthy donor, dendritic cell, CD141

value: blood

value: dendritic cell

value: healthy


title: Naive CD8+ T-cell, sample 4


title: Naive CD8+ T-cell, sample 1


title: CD8+ Effector Memory RA, sample 1

value: CD8+ Effector Memory RA


title: Pro B-cell, sample 5

source_name: umbilical cord blood

value: Pro B-cell


title: CD8+ Effector Memory RA, sample 2


title: Pro B-cell, sample 3


title: Pro B-cell, sample 4


title: CD8+ Effector Memory RA, sample 3


title: Early B-cell, sample 1

value: Early B-cell


title: Early B-cell, sample 4


title: CD4+ Effector Memory, sample 1

value: CD4+ Effector Memory


title: Early B-cell, sample 2


title: NKT, sample 2

value: NKT


title: Mature NK cell_CD56- CD16- CD3-, sample 4

value: Mature NK cell_CD56- CD16- CD3-


title: Pro B-cell, sample 1


title: Mature NK cell_CD56- CD16- CD3-, sample 3


title: Mature NK cell_CD56- CD16- CD3-, sample 5


title: Mature NK cell_CD56+ CD16+ CD3-, sample 2

value: Mature NK cell_CD56+ CD16+ CD3-


title: Early B-cell, sample 3


title: Mature NK cell_CD56- CD16- CD3-, sample 1


title: Mature NK cell_CD56+ CD16+ CD3-, sample 1


title: NKT, sample 4


title: Mature NK cell_CD56+ CD16+ CD3-, sample 3


title: Mature NK cell_CD56+ CD16+ CD3-, sample 5


title: Mature NK cell_CD56- CD16+ CD3-, sample 4

value: Mature NK cell_CD56- CD16+ CD3-


title: Pro B-cell, sample 2


title: Mature NK cell_CD56+ CD16+ CD3-, sample 4


title: Mature NK cell_CD56- CD16+ CD3-, sample 3


title: Mature NK cell_CD56- CD16+ CD3-, sample 1


title: Monocyte, sample 5

value: Monocyte


title: CD8+ Effector Memory RA, sample 4


title: Monocyte, sample 2


title: Monocyte, sample 4


title: Mature NK cell_CD56- CD16- CD3-, sample 2


title: Mature NK cell_CD56- CD16+ CD3-, sample 2


title: Colony Forming Unit-Monocyte , sample 3

value: Colony Forming Unit-Monocyte


title: Monocyte, sample 3


title: Megakaryocyte/ erythroid progenitor, sample 9

value: Megakaryocyte/ erythroid progenitor


title: Megakaryocyte/ erythroid progenitor, sample 2


title: Colony Forming Unit-Monocyte , sample 1


title: Colony Forming Unit-Monocyte , sample 2


title: Colony Forming Unit-Monocyte , sample 4


title: Megakaryocyte/ erythroid progenitor, sample 3


title: Megakaryocyte/ erythroid progenitor, sample 1


title: Megakaryocyte/ erythroid progenitor, sample 6


title: Megakaryocyte/ erythroid progenitor, sample 7


title: Megakaryocyte/ erythroid progenitor, sample 4


title: Megakaryocyte, sample 3

value: Megakaryocyte


title: NKT, sample 3


title: Megakaryocyte, sample 1


title: Megakaryocyte, sample 6


title: Megakaryocyte, sample 7


title: Colony Forming Unit-Megakaryocytic , sample 5

value: Colony Forming Unit-Megakaryocytic


title: Megakaryocyte, sample 5


title: Megakaryocyte, sample 4


title: Megakaryocyte/ erythroid progenitor, sample 8


title: Colony Forming Unit-Megakaryocytic , sample 4


title: NKT, sample 1


title: Megakaryocyte/ erythroid progenitor, sample 5


title: Hematopoietic stem cell_CD38- CD34+, sample 2

value: Hematopoietic stem cell_CD38- CD34+


title: Granulocyte (Neutrophilic Metamyelocyte), sample 3


title: Hematopoietic stem cell_CD38- CD34+, sample 3


title: Hematopoietic stem cell_CD133+ CD34dim, sample 6

value: Hematopoietic stem cell_CD133+ CD34dim


title: Megakaryocyte, sample 2


title: Colony Forming Unit-Megakaryocytic , sample 1


title: Colony Forming Unit-Megakaryocytic , sample 3


title: Hematopoietic stem cell_CD133+ CD34dim, sample 8


title: Granulocyte (Neutrophil), sample 3

value: Granulocyte (Neutrophil)


title: Hematopoietic stem cell_CD133+ CD34dim, sample 3


title: Hematopoietic stem cell_CD38- CD34+, sample 4


title: Hematopoietic stem cell_CD133+ CD34dim, sample 7


title: Colony Forming Unit-Granulocyte , sample 5

value: Colony Forming Unit-Granulocyte


title: Hematopoietic stem cell_CD133+ CD34dim, sample 2


title: Hematopoietic stem cell_CD133+ CD34dim, sample 1


title: Granulocyte (Neutrophil), sample 2


title: Granulocyte (Neutrophil), sample 4


title: Granulocyte (Neutrophilic Metamyelocyte), sample 4


title: Colony Forming Unit-Megakaryocytic , sample 2


title: Hematopoietic stem cell_CD133+ CD34dim, sample 5


title: Granulocyte (Neutrophilic Metamyelocyte), sample 1


title: Hematopoietic stem cell_CD133+ CD34dim, sample 10


title: Hematopoietic stem cell_CD133+ CD34dim, sample 9


title: Granulocyte (Neutrophilic Metamyelocyte), sample 2


title: Hematopoietic stem cell_CD38- CD34+, sample 1


title: Hematopoietic stem cell_CD133+ CD34dim, sample 4


title: Granulocyte (Neutrophil), sample 1


title: Colony Forming Unit-Granulocyte , sample 3


title: Erythroid_CD34- CD71- GlyA+, sample 6

value: Erythroid_CD34- CD71- GlyA+


title: Erythroid_CD34- CD71lo GlyA+, sample 2

value: Erythroid_CD34- CD71lo GlyA+


title: Monocyte, sample 1


title: Colony Forming Unit-Granulocyte , sample 4


title: Granulocyte/monocyte progenitor, sample 4

value: Granulocyte/monocyte progenitor


title: Granulocyte/monocyte progenitor, sample 1


title: Colony Forming Unit-Granulocyte , sample 2


title: Granulocyte/monocyte progenitor, sample 2


title: Erythroid_CD34- CD71- GlyA+, sample 3


title: Erythroid_CD34- CD71lo GlyA+, sample 1


title: Erythroid_CD34- CD71+ GlyA+, sample 6

value: Erythroid_CD34- CD71+ GlyA+


title: Erythroid_CD34- CD71lo GlyA+, sample 7


title: Granulocyte/monocyte progenitor, sample 3


title: Erythroid_CD34- CD71- GlyA+, sample 1


title: Erythroid_CD34- CD71- GlyA+, sample 2


title: Erythroid_CD34- CD71lo GlyA+, sample 6


title: Erythroid_CD34- CD71lo GlyA+, sample 3


title: Erythroid_CD34- CD71+ GlyA+, sample 5


title: Erythroid_CD34- CD71lo GlyA+, sample 5


title: Erythroid_CD34- CD71+ GlyA+, sample 4


title: Colony Forming Unit-Granulocyte , sample 1


title: Erythroid_CD34- CD71- GlyA+, sample 4


title: Erythroid_CD34- CD71+ GlyA-, sample 6

value: Erythroid_CD34- CD71+ GlyA-


title: Erythroid_CD34- CD71lo GlyA+, sample 4


title: Erythroid_CD34- CD71- GlyA+, sample 5


title: Erythroid_CD34- CD71+ GlyA+, sample 2


title: Erythroid_CD34- CD71+ GlyA+, sample 1


title: Erythroid_CD34- CD71+ GlyA-, sample 7


title: Erythroid_CD34- CD71+ GlyA+, sample 3


title: Erythroid_CD34- CD71+ GlyA-, sample 3


title: Erythroid_CD34- CD71+ GlyA-, sample 1


title: Erythroid_CD34+ CD71+ GlyA-, sample 5

value: Erythroid_CD34+ CD71+ GlyA-


title: Erythroid_CD34- CD71+ GlyA-, sample 5


title: Erythroid_CD34+ CD71+ GlyA-, sample 6


title: Erythroid_CD34- CD71+ GlyA-, sample 2


title: Erythroid_CD34+ CD71+ GlyA-, sample 4


title: Erythroid_CD34+ CD71+ GlyA-, sample 3


title: Erythroid_CD34+ CD71+ GlyA-, sample 1


title: Erythroid_CD34+ CD71+ GlyA-, sample 2


title: Myeloid Dendritic Cell, sample 5

value: Myeloid Dendritic Cell


title: Eosinophill, sample 3

value: Eosinophill


title: Eosinophill, sample 1


title: Eosinophill, sample 2


title: Eosinophill, sample 5


title: Erythroid_CD34- CD71+ GlyA-, sample 4


title: Eosinophill, sample 4


title: Erythroid_CD34+ CD71+ GlyA-, sample 7


title: Myeloid Dendritic Cell, sample 3


title: Myeloid Dendritic Cell, sample 2


title: Common myeloid progenitor, sample 2

value: Common myeloid progenitor


title: Myeloid Dendritic Cell, sample 1


title: Plasmacytoid Dendritic Cell, sample 1

value: Plasmacytoid Dendritic Cell


title: Common myeloid progenitor, sample 3


title: Plasmacytoid Dendritic Cell, sample 4


title: Common myeloid progenitor, sample 4


title: Myeloid Dendritic Cell, sample 4


title: Common myeloid progenitor, sample 1


title: Mature B-cell class switched, sample 5

value: Mature B-cell class switched


title: Mature B-cell class switched, sample 3


title: Mature B-cell class switched, sample 1


title: Mature B-cell class switched, sample 2


title: Plasmacytoid Dendritic Cell, sample 2


title: Plasmacytoid Dendritic Cell, sample 3


title: Mature B-cell class switched, sample 4


title: Mature B-cells, sample 5

value: Mature B-cells


title: Mature B-cell class able to switch, sample 4

value: Mature B-cell class able to switch


title: Mature B-cells, sample 4


title: Mature B-cell class able to switch, sample 3


title: Mature B-cells, sample 2


title: Mature B-cells, sample 3


title: Mature B-cell class able to switch, sample 5


title: Mature B-cells, sample 1


title: Mature B-cell class able to switch, sample 2


title: Mature B-cell class able to switch, sample 1


title: Basophils, sample 6

value: Basophils


title: Basophils, sample 5


title: Naïve B-cells, sample 4

value: Naïve B-cells


title: Naïve B-cells, sample 1


title: Basophils, sample 3


title: Basophils, sample 2


title: Naïve B-cells, sample 3


title: Naïve B-cells, sample 2


title: CD4+ Central Memory, sample 7

value: CD4+ Central Memory


title: Basophils, sample 1


title: CD4+ Central Memory, sample 6


title: Naïve B-cells, sample 5


title: Basophils, sample 4


title: Plasmacytoid Dendritic Cell, sample 5


title: CD4+ Central Memory, sample 4


title: CD4+ Central Memory, sample 3


title: CD4+ Central Memory, sample 5


title: CD4+ Central Memory, sample 2


title: CD4+ Effector Memory, sample 7

value: CD4+ Effector Memory


title: CD4+ Central Memory, sample 1


title: CD4+ Effector Memory, sample 5


title: CD4+ Effector Memory, sample 6


title: CD4+ Effector Memory, sample 4


title: CD4+ Effector Memory, sample 2


title: CD4+ Effector Memory, sample 3


title: 25 ng/hr leptin_7

status: Public on Nov 25 2009

city: New York

first: Kristina

last: Hedbacker

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description:
adult male mouse
4240351001_G

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: adult male liver, treated with 25 ng/hr leptin

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

extract_protocol: Livers were extracted and flash frozen and later processed for RNA using a Trizol protocol.

treatment_protocol: Animals were treated for 12 days with leptin at defined doses.

value: liver

tag: agent

value: untreated

tag: dose

value: 25 ng/hr

value: 12 days


title: 25 ng/hr leptin_6

description:
adult male mouse
4240351001_F


title: 12.5 ng/hr leptin_5

description:
adult male mouse
4240351001_E

source_name: adult male liver, treated with 12.5 ng/hr leptin

value: leptin


title: Cerevisiae_CyclinMutant_126min_rep2

status: Public on May 07 2008

first: Steven

middle: B

last: Haase

address: Duke University, Department of Biology, Box 90338

description: Cell cycle gene expression data from B-cyclin mutant yeast synchronized by elutration

hyb_protocol: DNA microarray hybridization was performed according to standard Affymetrix protocols by the Duke Micorarray Core Facility.

scan_protocol: Array scanning was carried by the Duke Micorarray Core Facility using standard Affymetrix protocols.

data_processing: Data from all 60 chips was normalized together using the dChip implementation with default paramaters from the affy package (v1.8.1) within Bioconductor in the R statistical environment.

source_name: Cerevisiae culture, cyclin mutant,  126 min

label_protocol: Amplification and labeling using the GeneChip One-Cycle target Labeling (Affymetrix, Santa Clara, CA).

growth_protocol: YEPDextrose /1M Sorbitol at 30c

extract_protocol: RNA was extracted using standard yeast methods.

treatment_protocol: synchronous G1 populations collected by elutration.

tag: Strain

value: BF264-15DU MATa; clb1::URA3; clb2::LEU2; clb3::TRP1; clb4::HIS2; clb5::ARG4; clb6::APE1; GAL1-CLB1:LEU2


title: Cerevisiae_CyclinMutant_222min_rep2

source_name: Cerevisiae culture, cyclin mutant,  222 min


title: Cerevisiae_CyclinMutant_30min_rep2

source_name: Cerevisiae culture, cyclin mutant,  30 min


title: Cerevisiae_CyclinMutant_46min_rep2

source_name: Cerevisiae culture, cyclin mutant, 46 min


title: Cerevisiae_CyclinMutant_254min_rep2

source_name: Cerevisiae culture, cyclin mutant,  254 min


title: Cerevisiae_CyclinMutant_238min_rep2

source_name: Cerevisiae culture, cyclin mutant,  238 min


title: Cerevisiae_CyclinMutant_190min_rep2

source_name: Cerevisiae culture, cyclin mutant,  190 min


title: Cerevisiae_CyclinMutant_110min_rep2

source_name: Cerevisiae culture, cyclin mutant,  110 min


title: Cerevisiae_CyclinMutant_62min_rep2

source_name: Cerevisiae culture, cyclin mutant,  62 min


title: Cerevisiae_CyclinMutant_142min_rep2

source_name: Cerevisiae culture, cyclin mutant,  142 min


title: Cerevisiae_CyclinMutant_246min_rep1

source_name: Cerevisiae culture, cyclin mutant,  246 min


title: Cerevisiae_CyclinMutant_262min_rep1

source_name: Cerevisiae culture, cyclin mutant,  262 min


title: Cerevisiae_CyclinMutant_78min_rep2

source_name: Cerevisiae culture, cyclin mutant,  78 min


title: 0 ng/hr leptin_3

description:
adult male mouse
4240351001_C

source_name: adult male liver, control

value: 0 ng/hr


title: LCCTam_p8

status: Public on Nov 01 2008

city: Washington

first: Rebecca

middle: B.

last: Riggins

state: DC

address: E412 Research Building, 3970 Reservoir Rd. NW

department: Oncology, and Lombardi Comprehensive Cancer Center

institute: Georgetown University

description: comparison of invasive lobular breast carcinoma cell line SUM44 and its TAM-resistant variant, LCCTam

hyb_protocol: standard Affymetrix protocol

scan_protocol: Standard Protocol for Affymetrix GeneChip Scanner 3000

data_processing: RMA

source_name: LCCTam breast cancer cell line, passage 8

label_protocol: standard one-cycle Affymetrix protocol

growth_protocol: cultured in SFIH (Ham's F12) to 70% confluence with the addition of 500 nM 4-hydroxytamoxifen

extract_protocol: Trizol (Invitrogen; Carlsbad, CA), 2 ml per T-25 cm^2 flask, followed by Qiagen RNeasy cleanup protocol

tag: variant

value: Tamoxifen-resistant variant of SUM44


title: 25 ng/hr leptin_8

description:
adult male mouse
4240351001_H

source_name: adult male liver, treated with 25 ng/hr leptin


title: 0 ng/hr leptin_2

description:
adult male mouse
4240351001_B


title: Cerevisiae_CyclinMutant_94min_rep2

source_name: Cerevisiae culture, cyclin mutant,  94 min


title: 12.5 ng/hr leptin_4

description:
adult male mouse
4240351001_D

source_name: adult male liver, treated with 12.5 ng/hr leptin


title: Cerevisiae_CyclinMutant_158min_rep2

source_name: Cerevisiae culture, cyclin mutant,  158 min


title: 0 ng/hr leptin_1

description:
adult male mouse
4240351001_A


title: Cerevisiae_CyclinMutant_174min_rep2

source_name: Cerevisiae culture, cyclin mutant,  174 min


title: Cerevisiae_CyclinMutant_230min_rep1

source_name: Cerevisiae culture, cyclin mutant,  230 min


title: Cerevisiae_CyclinMutant_214min_rep1

source_name: Cerevisiae culture, cyclin mutant,  214 min


title: LCCTam_p9

source_name: LCCTam breast cancer cell line, passage 9


title: LCCTam_p10

source_name: LCCTam breast cancer cell line, passage 10


title: Cerevisiae_CyclinMutant_206min_rep2

source_name: Cerevisiae culture, cyclin mutant,  206 min


title: Cerevisiae_CyclinMutant_198min_rep1

source_name: Cerevisiae culture, cyclin mutant,  198 min


title: Cerevisiae_CyclinMutant_182min_rep1

source_name: Cerevisiae culture, cyclin mutant,  182 min


title: Cerevisiae_CyclinMutant_118min_rep1

source_name: Cerevisiae culture, cyclin mutant,  118 min


title: Cerevisiae_CyclinMutant_70min_rep1

source_name: Cerevisiae culture, cyclin mutant,  70 min


title: Cerevisiae_WildType_198min_rep2

description: Cell cycle gene expression data from wild type yeast synchronized by elutration

source_name: Cerevisiae culture, wild type, 198 min

value: BF264-15DU MATa; bar1


title: Cerevisiae_WildType_166min_rep2

source_name: Cerevisiae culture, wild type, 166 min


title: Cerevisiae_CyclinMutant_134min_rep1

source_name: Cerevisiae culture, cyclin mutant,  134 min


title: Cerevisiae_WildType_238min_rep1

source_name: Cerevisiae culture, wild type, 238 min


title: Cerevisiae_WildType_262min_rep2

source_name: Cerevisiae culture, wild type, 262 min


title: Cerevisiae_WildType_254min_rep1

source_name: Cerevisiae culture, wild type, 254 min


title: Cerevisiae_WildType_86min_rep2

source_name: Cerevisiae culture, wild type, 86 min


title: Cerevisiae_CyclinMutant_86min_rep1

source_name: Cerevisiae culture, cyclin mutant,  86 min


title: Cerevisiae_WildType_102min_rep2

source_name: Cerevisiae culture, wild type, 102 min


title: Cerevisiae_CyclinMutant_166min_rep1

source_name: Cerevisiae culture, cyclin mutant,  166 min


title: Cerevisiae_WildType_214min_rep2

source_name: Cerevisiae culture, wild type, 214 min


title: Cerevisiae_CyclinMutant_102min_rep1

source_name: Cerevisiae culture, cyclin mutant,  102 min


title: Cerevisiae_WildType_246min_rep2

source_name: Cerevisiae culture, wild type, 246 min


title: Cerevisiae_CyclinMutant_54min_rep1

source_name: Cerevisiae culture, cyclin mutant,  54 min


title: Cerevisiae_WildType_38min_rep2

source_name: Cerevisiae culture, wild type, 38 min


title: Cerevisiae_WildType_230min_rep2

source_name: Cerevisiae culture, wild type, 230 min


title: Cerevisiae_CyclinMutant_150min_rep1

source_name: Cerevisiae culture, cyclin mutant,  150 min


title: Cerevisiae_WildType_70min_rep2

source_name: Cerevisiae culture, wild type, 70 min


title: Cerevisiae_WildType_54min_rep2

source_name: Cerevisiae culture, wild type, 54 min


title: Cerevisiae_CyclinMutant_38min_rep1

source_name: Cerevisiae culture, cyclin mutant,  38 min


title: Cerevisiae_WildType_118min_rep2

source_name: Cerevisiae culture, wild type, 118 min


title: Cerevisiae_WildType_150min_rep2

source_name: Cerevisiae culture, wild type, 150 min


title: Cerevisiae_WildType_134min_rep2

source_name: Cerevisiae culture, wild type, 134 min


title: Cerevisiae_WildType_222min_rep1

source_name: Cerevisiae culture, wild type, 222 min


title: Cerevisiae_WildType_190min_rep1

source_name: Cerevisiae culture, wild type, 190 min


title: Cerevisiae_WildType_174min_rep1

source_name: Cerevisiae culture, wild type, 174 min


title: Cerevisiae_WildType_182min_rep2

source_name: Cerevisiae culture, wild type, 182 min


title: Cerevisiae_WildType_206min_rep1

source_name: Cerevisiae culture, wild type, 206 min


title: Cerevisiae_WildType_158min_rep1

source_name: Cerevisiae culture, wild type, 158 min


title: Cerevisiae_WildType_126min_rep1

source_name: Cerevisiae culture, wild type, 126 min


title: Cerevisiae_WildType_142min_rep1

source_name: Cerevisiae culture, wild type, 142 min


title: Cerevisiae_WildType_110min_rep1

source_name: Cerevisiae culture, wild type, 110 min


title: Cerevisiae_WildType_94min_rep1

source_name: Cerevisiae culture, wild type, 94 min


title: Cerevisiae_WildType_46min_rep1

source_name: Cerevisiae culture, wild type, 46 min


title: Cerevisiae_WildType_78min_rep1

source_name: Cerevisiae culture, wild type, 78 min


title: Cerevisiae_WildType_62min_rep1

source_name: Cerevisiae culture, wild type, 62 min


title: Cerevisiae_WildType_30min_rep1

source_name: Cerevisiae culture, wild type,  30 min