title: CpG ODN 2

source_name: IGROV-1 cells treated with ascitic fluid from CpG-ODN-treated mice

tag: treatment

value: CpG ODN


title: MGH_Liver_pool vs MGH_Liver_75

status: Public on Apr 01 2011

type: RNA

city: Seattle

first: Radu

last: Dobrin

state: WA

address: 401 Terry Ave N

country: USA

institute: Merck and Co. Inc.

description: Gene expression data from Human livers, biopsies taken during RY gastric bypass surgery. All individuals were compared to a common pool created from equal portions of RNA.

hyb_protocol: Microarrays are incubated at 40?C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver? system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

molecule: total RNA

organism: Homo sapiens

source_name: liver

label_protocol: Samples were amplified and labeled using a custom automated two-cycle version of the MessageAmp II kit from Ambion. Hybridizations to custom Agilent microarrays were completed as described in by Hughes et al. Nat Biotech (2001), 19(4):342-7. Sample amplification, labeling, and microarray processing were performed by the Rosetta Inpharmatics Gene Expression Laboratory in Seattle, Wash.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: reference

tag: tissue

value: liver

tag: ID


title: AVC control 2 vs. mutant 2

city: Salt Lake City

first: Deborah

last: Frank

state: UT

address: 15 North 2030 East

department: Pediatrics

institute: University of Utah

description: Biological replicate 2 of 4.

hyb_protocol: Agilent Two-color GE Hyb/Wash Protocol, incubated at 65 deg C for 17 hours at 10 rpm

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 um resolution.  Primary scan at 100% laser power, and secondary scan at 10% power

data_processing: Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization.

organism: Mus musculus

label_protocol: Agilent Two-Color Low RNA input Linear Amplification Kit, with purification using the Qiagen Rneasy mini kit.

growth_protocol: embryonic development timed with noon on the day a copulation plug identified in female mouse designated a e0.5

extract_protocol: 5 tissue pieces pooled for each sample and total RNA purified using Qiagen Rneasy micro kit.

treatment_protocol: Embryos harvested in ice cold PBS at 3pm on e10.5,  heart AVC tissue samples micro-dissected and placed in RLT buffer then frozen at -80C until all samples collected.

tag: age

value: heart AVC

tag: background strain

tag: genotype variation

value: wild type control

value: Tbx3 mutant


title: non-smoker 392M

city: Prague 2

first: Hana

last: Bruchova

address: U nemocnice 1

department: Molecular Genetics

country: Czech Republic

institute: Institute of Hematology and Transfusion

hyb_protocol: 750 ng of biotinylated cRNA was hybridized to the array for 17 hours according to the manufacturer manual. Final staining was performed with streptavidin conjugated to Cy-3 fluorescent dye.

scan_protocol: Arrays were scanned using BeadArray Reader (Illumina), and bead level data were extracted by BeadStudio Software (Illumina).

data_processing: Bead summary data were imported into the R statistical environment (www.r-project.org) and normalized by the quantile method in the Lumi package. Only probes that reached detection P-value < 0.01 in all samples were used for further analyses. Differentially expressed genes were analysed in the Limma package. A linear model was fitted for each gene given a series of arrays using the lmFit function. Using the Benjamini and Hochberg method, P-values were corrected for multiple testing. The M, PL, and D groups were normalized separately.

label: biotin

source_name: maternal peripheral blood, non-smoker

label_protocol: Biotinylated cRNA was prepared from 200 ng of total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion). In vitro transcription (IVT) was performed at 37°C for 14 hours.

extract_protocol: Peripheral blood was sampled and processed using the LeukoLOCK™ Total RNA Isolation System (Ambion, Austin, TX, USA) according to the manufacturer manual. The system employs filter-based leukocyte-depletion technology to isolate leukocytes from whole blood and RNAlater™ (Ambion) to stabilize the cells on the filter. By removal of red blood cells, the RNA purified from captured leukocytes is inherently depleted of globin mRNA, which improves sample quality for expression profiling and other applications. Integrity of the total RNAs was assayed by the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), and only samples with RNA integrity number (RIN) above 7.0 were used for gene expression profiling.

value: maternal peripheral blood

tag: smoking status

value: non-smoker

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

value: vaginal

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: non-smoker 388M

tag: tissue


title: MGH_Liver_pool vs MGH_Liver_74

tag: reference

tag: ID


title: smoker 384M

source_name: maternal peripheral blood, smoker

value: smoker


title: CpG ODN 3

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

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

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

tag: cell line

tag: treatment


title: d2-Cya

city: Sinjuku-ku

first: Masami

last: Tanaka

state: Tokyo

address: Sinjuku 6-1-1

country: Japan

institute: Tokyo Medical University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4121F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Images was scanned with Agilent scanner at 5µm resolution

data_processing: The scanned images was analyzed automatically in Agilent feature extraction 9.5.3 (Agilent) using default protocol (GE1-v5_95_Feb07). No interarray normalization method was employed.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 3T3-L1 preadipocytes (American Type Culture Collection, Manassas, VA) were grown to confluence in DMEM media (Sigma Aldrich, Tokyo, Japan) with 10% calf serum and penicillin (100 U/ml)/streptomycin (100 ug/ml). Adipogenesis was induced using an adipogenesis assay kit (Chemicon International, Temecula, CA). On day 0, cells were induced with initiation media (10 ug/ml insulin, 1µM dexamethasone and 0.5 uM IBMX in DMEM media supplemented with 10% fetal calf serum. On day 3, initiation media was replaced with progression media (10 µg/ml insulin in DMEM media supplemented with 10% fetal calf serum). On day 6, progression media was replaced with maintenance media (DMEM supplemented with 10% fetal calf serum). From day 6, cells were kept in maintenance media with new maintenance media being replaced by every two days. Cells are incubated at 37°C with 5% CO2 at all time.

extract_protocol: Total RNA was extracted by using ISOGEN  (Nippon gene) according to manufacturer’s instruction.

treatment_protocol: 3T3-L1 were treated for 6 days (from day0 to day6) with additives.

tag: cell type

value: adipocyte

tag: additive

value: Cyanidin


title: CpG ODN 1


title: d2-Del

value: Delphinidin


title: non-smoker 389M

tag: smoking status

tag: age (years)

tag: maternal bmi


title: non-smoker 383M

tag: parity

tag: gestational age (weeks)

tag: mode of delivery


title: Saline 3

source_name: IGROV-1 cells treated with ascitic fluid from saline-treated mice

value: saline


title: non-smoker 381M

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)


title: d2-BB

value: Bilberry extract


title: Saline 2


title: non-smoker 379M

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: wt_SD_55min_3

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: Gene expression data from wt yeast cells shifted to minimal media (no aa) for 55 min

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.

data_processing: Array intensities were processed using the RMA algorithm in R/bioconductor. We processed the microarrays using only the probes for cerevisiae to avoid normalization artifacts.

organism: Saccharomyces cerevisiae

source_name: wt yeast cells shifted to minimal media (no aa) for 55 min, replicate 3

label_protocol: Biotinylated cRNA were prepared according to the Ambion MessageAmp III protocol from 300 ng total RNA (MessageAmp III Amplification kit Manual, 2007, Ambion).

growth_protocol: Cultures were innoculated to an initial OD600 of 0.05 from fresh overnights and grown at 30C in YPD+CSM to an OD as indicated.

extract_protocol: Total RNA was extracted using the hot acid phenol method.

treatment_protocol: Cells growing in exponential phase in YPD+CSM were pelleted by centrifugation and resuspended in minimal media without amino acids. 50 ml aliquots were harvested at the indicated time by filtration.

tag: time

tag: media

value: SD

tag: genotype

value: wt


title: wt_SD_55min_1

source_name: wt yeast cells shifted to minimal media (no aa) for 55 min, replicate 1


title: wt_SD_55min_2

source_name: wt yeast cells shifted to minimal media (no aa) for 55 min, replicate 2


title: MGH_Liver_pool vs MGH_Liver_73

tag: reference

tag: tissue

tag: ID


title: Saline 1

tag: cell line

tag: treatment


title: MGH_Liver_pool vs MGH_Liver_72


title: MGH_Liver_pool vs MGH_Liver_71


title: MGH_Liver_pool vs MGH_Liver_69


title: MGH_Liver_pool vs MGH_Liver_70


title: smoker 377M

tag: smoking status

tag: age (years)

tag: maternal bmi

tag: parity


title: wt_SD_35min_2

description: Gene expression data from wt yeast cells shifted to minimal media (no aa) for 35 min

source_name: wt yeast cells shifted to minimal media (no aa) for 35 min, replicate 2


title: wt_SD_35min_3

source_name: wt yeast cells shifted to minimal media (no aa) for 35 min, replicate 3


title: smoker 374M

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: newborn weight (g)


title: wt_SD_15min_3

description: Gene expression data from wt yeast cells shifted to minimal media (no aa) for 15 min

source_name: wt yeast cells shifted to minimal media (no aa) for 15 min, replicate 3


title: MGH_Liver_pool vs MGH_Liver_68


title: non-smoker 372M

tag: apgar score (5s)

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: wt_SD_15min_2

source_name: wt yeast cells shifted to minimal media (no aa) for 15 min, replicate 2

tag: time

tag: media

tag: genotype


title: Temporal Cortex_Old_F3

city: Montpellier

first: Gina

last: DEVAU

address: Place Eugene Bataillon

department: Universite de Montpellier CC105

country: France

institute: Inserm U1198-UM-EPHE

description: Microcebus murinus were divided in 3 groups: the first group included 6 young adults (4 females and 2 males), the second included 10 healthy old animals (7 females and 3 males) and the third one was composed by 2 "AD-like" old females. Since Microcebus murinus microarrays do not exist, we decided to use Affymetrix human genome chips (HG U133 plus 2), since studies have illustrated the feasibility of detecting non-human primate brain transcripts using human genome chips.

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

label: Biotin

organism: Microcebus murinus

source_name: Temporal cortex from old Microcebus murinus, female (3)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 µg total RNA.

extract_protocol: Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.

tag: gender

value: female

tag: tissue

value: temporal cortex

tag: age category

value: old


title: non-smoker 368M

tag: smoking status

tag: age (years)


title: Temporal Cortex_Young A_F2

source_name: Temporal cortex from young adult Microcebus murinus, female (2)

value: young


title: Temporal Cortex_Old_F1

source_name: Temporal cortex from old Microcebus murinus, female (1)


title: Temporal Cortex_Old_F2

source_name: Temporal cortex from old Microcebus murinus, female (2)


title: MGH_Liver_pool vs MGH_Liver_67

tag: reference

value: liver

tag: ID


title: wt_YPD_0min_3

description: Gene expression data from wt yeast cells in rich media

source_name: wt yeast cells in rich media, replicate 3

value: YPD


title: smoker 356M

value: maternal peripheral blood

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery


title: non-smoker 371M

value: non-smoker

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)

tag: maternal blood cotinine (ng/ml)


title: Temporal Cortex_Young A_F3

source_name: Temporal cortex from young adult Microcebus murinus, female (3)


title: MGH_Liver_pool vs MGH_Liver_66

source_name: liver


title: wt_SD_15min_1

source_name: wt yeast cells shifted to minimal media (no aa) for 15 min, replicate 1

tag: time

tag: media


title: wt_YPD_0min_2

source_name: wt yeast cells in rich media, replicate 2

tag: genotype


title: MGH_Liver_pool vs MGH_Liver_64

tag: tissue


title: non-smoker 378M

source_name: maternal peripheral blood, non-smoker

value: vaginal

tag: cord blood cotinine (ng/ml)

tag: individual


title: smoker 369M

source_name: maternal peripheral blood, smoker

tag: smoking status

value: smoker

tag: age (years)


title: MGH_Liver_pool vs MGH_Liver_65

tag: reference

tag: ID


title: non-smoker 355M

tag: maternal bmi

tag: parity


title: Temporal Cortex_Old_M3

source_name: Temporal cortex from old Microcebus murinus,male (3)

tag: gender

value: male

tag: age category


title: MGH_Liver_pool vs MGH_Liver_63


title: Temporal Cortex_AD_F1

source_name: Temporal cortex from old Microcebus murinus, "AD-like", female (1)


title: wt_YPD_0min_1

source_name: wt yeast cells in rich media, replicate 1


title: MGH_Liver_pool vs MGH_Liver_62


title: Temporal Cortex_Old_F4

source_name: Temporal cortex from old Microcebus murinus, female (4)


title: Temporal Cortex_Young A_F4

source_name: Temporal cortex from young adult Microcebus murinus, female (4)


title: non-smoker 354M

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: newborn weight (g)


title: Scc2-D730V_SD_55min_2

description: Gene expression data from Scc2-D730V mutant yeast cells shifted to minimal media (no aa) for 55 min

source_name: Scc2-D730V mutant yeast cells shifted to minimal media (no aa) for 55 min, replicate 2

tag: time

tag: media


title: non-smoker 352M

tag: tissue

tag: apgar score (5s)

tag: maternal blood cotinine (ng/ml)


title: non-smoker 353M

tag: smoking status

tag: cord blood cotinine (ng/ml)

tag: individual


title: Scc2-D730V_SD_55min_3

source_name: Scc2-D730V mutant yeast cells shifted to minimal media (no aa) for 55 min, replicate 3

tag: genotype


title: MGH_Liver_pool vs MGH_Liver_61

tag: reference

tag: ID


title: Scc2-D730V_SD_35min_3

description: Gene expression data from Scc2-D730V mutant yeast cells shifted to minimal media (no aa) for 35 min

source_name: Scc2-D730V mutant yeast cells shifted to minimal media (no aa) for 35 min, replicate 3


title: Scc2-D730V_SD_55min_1

source_name: Scc2-D730V mutant yeast cells shifted to minimal media (no aa) for 55 min, replicate 1


title: Temporal Cortex_Young A_M1

source_name: Temporal cortex from young adult Microcebus murinus, male (1)

tag: gender


title: smoker 351M

tag: age (years)

tag: maternal bmi

tag: parity


title: MGH_Liver_pool vs MGH_Liver_60


title: smoker 350M

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)


title: Scc2-D730V_SD_35min_2

source_name: Scc2-D730V mutant yeast cells shifted to minimal media (no aa) for 35 min, replicate 2

tag: time

tag: media


title: non-smoker 347M

tag: tissue

tag: newborn weight (g)

tag: apgar score (5s)


title: MGH_Liver_pool vs MGH_Liver_59


title: Temporal Cortex_Old_M2

source_name: Temporal cortex from old Microcebus murinus,male (2)

tag: age category


title: MGH_Liver_pool vs MGH_Liver_58

source_name: liver


title: smoker 349M

tag: smoking status

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: Temporal Cortex_AD_F2

source_name: Temporal cortex from old Microcebus murinus, "AD-like", female (2)

tag: gender


title: MGH_Liver_pool vs MGH_Liver_56

tag: reference

tag: ID


title: Scc2-D730V_SD_35min_1

source_name: Scc2-D730V mutant yeast cells shifted to minimal media (no aa) for 35 min, replicate 1

tag: genotype


title: smoker 344M

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)


title: Temporal Cortex_Old_F7

source_name: Temporal cortex from old Microcebus murinus, female (7)


title: Temporal Cortex_Old_M1

source_name: Temporal cortex from old Microcebus murinus,male (1)


title: MGH_Liver_pool vs MGH_Liver_55


title: MGH_Liver_pool vs MGH_Liver_57


title: Temporal Cortex_Young A_M2

source_name: Temporal cortex from young adult Microcebus murinus, male (2)


title: Scc2-D730V_SD_15min_3

description: Gene expression data from Scc2-D730V mutant yeast cells shifted to minimal media (no aa) for 15 min

source_name: Scc2-D730V mutant yeast cells shifted to minimal media (no aa) for 15 min, replicate 3

tag: time

tag: media


title: Scc2-D730V_SD_15min_2

source_name: Scc2-D730V mutant yeast cells shifted to minimal media (no aa) for 15 min, replicate 2


title: Temporal Cortex_Young A_F1

source_name: Temporal cortex from young adult Microcebus murinus, female (1)

tag: tissue


title: Scc2-D730V_SD_15min_1

source_name: Scc2-D730V mutant yeast cells shifted to minimal media (no aa) for 15 min, replicate 1


title: Scc2-D730V_YPD_0min_3

description: Gene expression data fromScc2-D730V mutant yeast cells in rich media

source_name: Scc2-D730V mutant yeast cells in rich media, replicate 3


title: smoker 342M

source_name: maternal peripheral blood, smoker

tag: mode of delivery

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)


title: Scc2-D730V_YPD_0min_2

source_name: Scc2-D730V mutant yeast cells in rich media, replicate 2


title: non-smoker 343M

source_name: maternal peripheral blood, non-smoker

tag: smoking status

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)


title: Temporal Cortex_Old_F6

source_name: Temporal cortex from old Microcebus murinus, female (6)

tag: gender

tag: age category


title: MGH_Liver_pool vs MGH_Liver_54

tag: reference

tag: ID


title: Scc2-D730V_YPD_0min_1

source_name: Scc2-D730V mutant yeast cells in rich media, replicate 1

tag: genotype


title: Temporal Cortex_Old_F5

source_name: Temporal cortex from old Microcebus murinus, female (5)


title: MGH_Liver_pool vs MGH_Liver_53

source_name: liver


title: 924C - mAdbID:63799

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 63799

hyb_protocol: Affymetrix Hybridization Protocol Other: Following fragmentation, 15 micrograms of cRNA was hybridized for 16 hours at 45C on arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affy Scanning Protocol Other: Scanning was performed by the Affymetrix 3000 Scanner.

data_processing:
MAS 5.0 Data Processing Protocol
Calculation Method: The data were analyzed with Microarray Suite version 5.0 (MA S 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
Sample RNA Extraction Protocol
Other: Total RNA was extracted using the FastTrack kit from Invitrogen.

tag: disease state

value: Mantle Cell Lymphoma (MCL)

tag: individual


title: MGH_Liver_pool vs MGH_Liver_51


title: non-smoker 340M

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)


title: Eco1-W216G_SD_55min_3

description: Gene expression data from Eco1-W216G mutant yeast cells shifted to minimal media (no aa) for 55 min

source_name: Eco1-W216G mutant yeast cells shifted to minimal media (no aa) for 55 min, replicate 3

tag: time

tag: media


title: MGH_Liver_pool vs MGH_Liver_50

tag: tissue


title: 1028C - mAdbID:64162

description: mAdb experiment ID: 64162


title: 936C - mAdbID:63801

description: mAdb experiment ID: 63801


title: non-smoker 339M

tag: smoking status

tag: mode of delivery

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)


title: 933C - mAdbID:64161

description: mAdb experiment ID: 64161


title: MGH_Liver_pool vs MGH_Liver_48

tag: reference


title: wt_SD_35min_1

source_name: wt yeast cells shifted to minimal media (no aa) for 35 min, replicate 1


title: non-smoker 336M

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)


title: non-smoker 338M


title: 918C - mAdbID:63798

description: mAdb experiment ID: 63798

tag: disease state


title: smoker 337M

tag: individual


title: MGH_Liver_pool vs MGH_Liver_49

tag: ID


title: Eco1-W216G_SD_35min_3

description: Gene expression data from Eco1-W216G mutant yeast cells shifted to minimal media (no aa) for 35 min

source_name: Eco1-W216G mutant yeast cells shifted to minimal media (no aa) for 35 min, replicate 3

tag: genotype


title: Eco1-W216G_SD_55min_2

source_name: Eco1-W216G mutant yeast cells shifted to minimal media (no aa) for 55 min, replicate 2


title: Eco1-W216G_SD_55min_1

source_name: Eco1-W216G mutant yeast cells shifted to minimal media (no aa) for 55 min, replicate 1


title: non-smoker 335M

tag: age (years)

tag: maternal bmi

tag: parity


title: 939C - mAdbID:63797

description: mAdb experiment ID: 63797


title: MGH_Liver_pool vs MGH_Liver_46


title: non-smoker 334M

tag: gestational age (weeks)


title: Eco1-W216G_SD_35min_1

source_name: Eco1-W216G mutant yeast cells shifted to minimal media (no aa) for 35 min, replicate 1

tag: time

tag: media


title: Eco1-W216G_SD_15min_3

description: Gene expression data from Eco1-W216G mutant yeast cells shifted to minimal media (no aa) for 15 min

source_name: Eco1-W216G mutant yeast cells shifted to minimal media (no aa) for 15 min, replicate 3


title: non-smoker 332M

tag: tissue

tag: smoking status

tag: mode of delivery


title: Eco1-W216G_SD_15min_2

source_name: Eco1-W216G mutant yeast cells shifted to minimal media (no aa) for 15 min, replicate 2


title: Eco1-W216G_SD_35min_2

source_name: Eco1-W216G mutant yeast cells shifted to minimal media (no aa) for 35 min, replicate 2


title: 981C - mAdbID:63793

description: mAdb experiment ID: 63793


title: MGH_Liver_pool vs MGH_Liver_47


title: 1012C - mAdbID:63790

description: mAdb experiment ID: 63790


title: Eco1-W216G_SD_15min_1

source_name: Eco1-W216G mutant yeast cells shifted to minimal media (no aa) for 15 min, replicate 1


title: non-smoker 330M

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)


title: non-smoker 329M

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)


title: 956C - mAdbID:63792

description: mAdb experiment ID: 63792

tag: disease state

tag: individual


title: MGH_Liver_pool vs MGH_Liver_45

tag: reference

tag: ID


title: MGH_Liver_pool vs MGH_Liver_42


title: 1166 - mAdbID:62895

description: mAdb experiment ID: 62895


title: 991C - mAdbID:63794

description: mAdb experiment ID: 63794


title: 1176 - mAdbID:62897

description: mAdb experiment ID: 62897


title: non-smoker 331M

tag: age (years)

tag: maternal bmi


title: MGH_Liver_pool vs MGH_Liver_43


title: MGH_Liver_pool vs MGH_Liver_44


title: MGH_Liver_pool vs MGH_Liver_41


title: MGH_Liver_pool vs MGH_Liver_40


title: Eco1-W216G_YPD_0min_2

description: Gene expression data from Eco1-W216G mutant yeast cells in rich media

source_name: Eco1-W216G mutant yeast cells in rich media, replicate 2

tag: genotype


title: Eco1-W216G_YPD_0min_3

source_name: Eco1-W216G mutant yeast cells in rich media, replicate 3

tag: time


title: Eco1-W216G_YPD_0min_1

source_name: Eco1-W216G mutant yeast cells in rich media, replicate 1

tag: media


title: Yeast_20.9%oxygen_transient79h_rep2

city: VTT

first: Eija

last: Rintala

country: Finland

institute: VTT Technical Research Centre of Finland

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 79 hours sample from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 20.9 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

hyb_protocol: Hybridisation was done at +45°C overnight (16 h) according to GeneChip Expression Analysis Technical Manual (Affymetrix). GeneChip Fluidics Station 450 was used to wash and stain the arrays. GeneChip Scanner 3000 with AutoLoader was used to scan the arrays.

scan_protocol: GeneChip Scanner 3000 with AutoLoader

data_processing:
RMA normalised using R/Bioconductor (rma package), version 2.5.1.
The control probes and S.pombe probes were removed from the data before RMA normalisation. Thus the RMA processed data, reported in the Sample table, does not include control and S.pombe probes. The raw data of the removed probes is present in the raw data (.CEL) files.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 20.9% to 0% oxygen, timepoint 79h.

label_protocol: Approximately 2 µg of total RNA was processed to produce biotinylated cRNA targets using Affymetrix One-Cycle Target prep protocol.

growth_protocol: Cells were grown in 0.8–1 L of medium in B. Braun Biotech International (Sartorius AG, Germany) Biostat CT (2.5 Lworking volume) bioreactors. Cultures were inoculated to aninitial OD600 nm of c. 0.5, and maintained as batch culturesfor 6–9 h, after which continuous medium feed was started while the cells were still growing exponentially. Chemostatcultures were maintained at D= 0.10 /h, pH 5.0, and30C, with 1.5 volume gas [volume culture]/min (vvm).For cultures that received 20.9% O2 in the gas stream, O2was replaced with the equivalent volume of N2, so that totalgas flow was kept constant for all experiments. Steady-state samples were taken after the cultures had beenin constant conditions for a minimum of four residence times (six generations). Steady states were assessed over fourto nine residence times (six to 13 generations) for constantbiomass production, carbon dioxide evolution and oxygenuptake rates (CER and OUR), alkali utilization, and extracellularmetabolites, as well as constant intracellular metabolites and gene transcription. Cultures that were fed 20.9% O2 were subject tooscillations. To prevent these, c. 5% of the total cellconcentration in the bioreactor was added to the culture ascells in mid-exponential to late exponential phase at thetime when continuous medium feed was started (Zamamiri et al., 2001).

extract_protocol: 10 ml of cell culture was centrifuged for 5 min, 3500 rpm, +4C, cells were frozen in liquid nitrogen and stored at -80C. Total RNA was extracted using QIAGEN RNeasy Mini Kit (QIAGEN, Inc., Valencia, CA) according to the manufacturers instructions with the following modification to the cell lysis step. 5-20 mg dry mass of cells were suspended in 400µl of cold (+4°C) disruption buffer (20mM Tris-HCl, pH 7.4, 100 mM KCl, 2 mM MgCl2,  2 mM DTT). 400µl of phenol-chlorophorm (50:50), 5µl 20% SDS and 400 µl glass beads (0.5 mm diameter; Biospec Products) was added. The cells were disrupted with Fastprep machine (Q-Biogene), 2 x 20s, at speed 6. After centrifugation (14000 rpm, 15 min, +4°C), supernatant was used for total RNA extraction. RNA quality was checked with Agilent bioanalyzer (Agilent Technologies).

tag: protocol

value: transition from 20.9% to 0% oxygen


title: non-smoker 327M

source_name: maternal peripheral blood, non-smoker

tag: tissue

tag: smoking status

tag: parity

tag: gestational age (weeks)


title: MGH_Liver_pool vs MGH_Liver_39


title: Yeast_20.9%oxygen_transient24h_rep2

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 24 hours sample from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 20.9 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 20.9% to 0% oxygen, timepoint 24h.


title: Yeast_20.9%oxygen_transient8h_rep2

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 8 hours sample from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 20.9 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 20.9% to 0% oxygen, timepoint 8h.


title: 975 - mAdbID:62886

description: mAdb experiment ID: 62886


title: MGH_Liver_pool vs MGH_Liver_38

description: Gene expression data from Human livers, biopsies taken during RY gastric bypass surgery. All individuals were compared to a common pool created from equal portions of RNA.

source_name: liver


title: non-smoker 320M

tag: mode of delivery

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)


title: smoker 324M

source_name: maternal peripheral blood, smoker

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: 1091 - mAdbID:62893

description: mAdb experiment ID: 62893

tag: disease state


title: 980 - mAdbID:62889

description: mAdb experiment ID: 62889


title: 979 - mAdbID:62888

description: mAdb experiment ID: 62888


title: 1114 - mAdbID:62894

description: mAdb experiment ID: 62894


title: non-smoker 317M

tag: age (years)

tag: maternal bmi


title: non-smoker 318M


title: MGH_Liver_pool vs MGH_Liver_35

tag: reference

tag: ID


title: MGH_Liver_pool vs MGH_Liver_37


title: MGH_Liver_pool vs MGH_Liver_52


title: MGH_Liver_pool vs MGH_Liver_34


title: MGH_Liver_pool vs MGH_Liver_36


title: non-smoker 316M


title: MGH_Liver_pool vs MGH_Liver_33


title: Yeast_20.9%oxygen_transient0h_rep2

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 0 hours sample (steady state) from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 20.9 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 20.9% to 0% oxygen, timepoint 0h.

tag: protocol

tag: time


title: smoker 328M

tag: tissue

tag: smoking status


title: 974 - mAdbID:62884

description: mAdb experiment ID: 62884


title: smoker 313M

tag: parity

tag: gestational age (weeks)


title: non-smoker 311M

tag: mode of delivery

tag: placental weight (g)


title: 959 - mAdbID:62876

description: mAdb experiment ID: 62876


title: MGH_Liver_pool vs MGH_Liver_26


title: MGH_Liver_pool vs MGH_Liver_30


title: Yeast_20.9%oxygen_transient8h_rep1


title: 963 - mAdbID:62877

description: mAdb experiment ID: 62877


title: MGH_Liver_pool vs MGH_Liver_29


title: MGH_Liver_pool vs MGH_Liver_32


title: Yeast_20.9%oxygen_transient79h_rep1


title: Yeast_20.9%oxygen_transient3h_rep1

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 3 hours sample from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 20.9 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 20.9% to 0% oxygen, timepoint 3h.


title: non-smoker 314M

tag: newborn weight (g)

tag: apgar score (5s)


title: 958 - mAdbID:62875

description: mAdb experiment ID: 62875


title: MGH_Liver_pool vs MGH_Liver_31


title: smoker 312M

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)


title: 965 - mAdbID:62882

description: mAdb experiment ID: 62882

tag: disease state

tag: individual


title: 982 - mAdbID:62891

description: mAdb experiment ID: 62891


title: Yeast_20.9%oxygen_transient24h_rep1


title: 954 - mAdbID:62873

description: mAdb experiment ID: 62873


title: 972 - mAdbID:62883

description: mAdb experiment ID: 62883


title: smoker 322M

tag: age (years)

tag: maternal bmi


title: non-smoker 315M


title: Yeast_20.9%oxygen_transient0.2h_rep2

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 0.2 hours sample from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 20.9 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 20.9% to 0% oxygen, timepoint 0.2h.


title: non-smoker 306M


title: Yeast_20.9%oxygen_transient1h_rep2

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 1 hours sample from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 20.9 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 20.9% to 0% oxygen, timepoint 1h.


title: Yeast_20.9%oxygen_transient1h_rep1


title: Yeast_20.9%oxygen_transient3h_rep2


title: 957 - mAdbID:62874

description: mAdb experiment ID: 62874


title: Yeast_20.9%oxygen_transient0h_rep1


title: MGH_Liver_pool vs MGH_Liver_28

tag: reference

tag: ID


title: Yeast_20.9%oxygen_transient0.2h_rep1

tag: protocol

tag: time


title: MGH_Liver_pool vs MGH_Liver_27

tag: tissue


title: MGH_Liver_pool vs MGH_Liver_23


title: Yeast_1%oxygen_transient72h_rep2

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 72 hours sample from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 1 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 1% to 0% oxygen, timepoint 72hh.

value: transition from 1% to 0% oxygen


title: MGH_Liver_pool vs MGH_Liver_25


title: MGH_Liver_pool vs MGH_Liver_24


title: 944 - mAdbID:62864

description: mAdb experiment ID: 62864


title: 953 - mAdbID:62872

description: mAdb experiment ID: 62872


title: non-smoker 308M

tag: smoking status

tag: parity


title: 962 - mAdbID:62871

description: mAdb experiment ID: 62871


title: MGH_Liver_pool vs MGH_Liver_22


title: smoker 303M

tag: gestational age (weeks)

tag: mode of delivery


title: non-smoker 307M

tag: placental weight (g)

tag: newborn weight (g)


title: non-smoker 302M

tag: apgar score (5s)

tag: maternal blood cotinine (ng/ml)


title: Yeast_1%oxygen_transient24h_rep2

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 24 hours sample from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 1 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 1% to 0% oxygen, timepoint 24h.


title: non-smoker 305M

tag: cord blood cotinine (ng/ml)


title: 942 - mAdbID:62862

description: mAdb experiment ID: 62862

tag: disease state

tag: individual


title: Yeast_1%oxygen_transient8h_rep2

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 8 hours sample from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 1 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 1% to 0% oxygen, timepoint 8h.


title: Yeast_1%oxygen_transient1h_rep2

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 1 hours sample from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 1 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 1% to 0% oxygen, timepoint 1h.


title: Yeast_1%oxygen_transient3h_rep2

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 3 hours sample from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 1 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 1% to 0% oxygen, timepoint 3h.


title: leaf 30%Inhibition rep4 [Soy]

city: Oak Ridge

first: David

middle: J

last: Weston

state: TN

department: Environmental Sciences Division

institute: David Weston

description: Gene expression data from the first fully expanded leaf of Glycine max 'Williams 82' at 30% inhibition from optimum

hyb_protocol: Following fragmentation, cRNA was hybridized to the GeneChip Soybean array according to standard protocols (#PM702232; www.affymetrix.com).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 according to standard protocol (#PM702232; www.affymetrix.com).

data_processing: Signal values were determined using GeneChip MAS5.0 algorithm.

organism: Glycine max

source_name: Glycine max leaf, 30% inhibition

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

growth_protocol: Soybean (Glycine max cv.Williams 82), were grown in pots containing Fafard 3B soil.  Plants were grown in a Conviron BDW80 walk-in growth chamber under the following growth conditions: 22 °C, 60% relative humidity, a 10 h photoperiod, and 350 μmol m-2s-1 light intensity. Plants were watered as needed and fertilized weekly using 125 ppm N of Jack's Professional

extract_protocol: Total RNA was isolated from 100 mg of tissue using an RNeasy® Mini Kit (Qiagen Inc., CA) according to the manufacturer’s instructions.  An on-column DNase 1 treatment (Sigma-Aldrich) was used during RNA extraction to remove any potential genomic DNA contamination.

treatment_protocol: Fully expanded leaf samples from 4 randomly collected plants per species were harvested at 4 physiological states as determined from prior gas exchange measurements (growth temperature - baseline, photosynthetic optimum, 20% inhibition of optimum and 30% inhibition of optimum). The temperature response curves were created by increasing temperature step-wise (2 °C per 10 mins) from 22 to 42 °C to the desired physiological state and waiting 20-30 mins for photosynthesis to stabilize before sampling. Each curve took 3-4 h to complete.

value: leaf, first fully expanded

tag: line

value: Williams 82

tag: treatment

value: Photosynthesis at 30% inhibition from optimum


title: 943 - mAdbID:62863

description: mAdb experiment ID: 62863


title: MGH_Liver_pool vs MGH_Liver_21

tag: reference

tag: ID


title: Yeast_1%oxygen_transient0h_rep2

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 0 hours sample (steady state) from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 1 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 1% to 0% oxygen, timepoint 0h.

tag: protocol

tag: time


title: 940 - mAdbID:62860

description: mAdb experiment ID: 62860


title: 941 - mAdbID:62861

description: mAdb experiment ID: 62861


title: 938 - mAdbID:62859

description: mAdb experiment ID: 62859


title: MGH_Liver_pool vs MGH_Liver_20

tag: tissue


title: MGH_Liver_pool vs MGH_Liver_19


title: Yeast_1%oxygen_transient72hh_rep1


title: Yeast_1%oxygen_transient0.2h_rep2

description:
Study description: S. cerevisiae CEN.PK113-1A (MATa, URA3, HIS3, LEU2, TRP1, MAL2-8c, SUC2) grown in Verduyn mimimal medium with 10 g/L glucose as carbon source, and supplemented with 10 mg/L ergosterol and 420 mg/L Tween 80, in Biostat CT  bioreactor. Sample from steady state with 1% oxygen, transient timepoint 0h
This sample: This sample: 0.2 hours sample from a time-series experiment. Glucose-limited chemostat, starting oxygen provision 1 %. After steady state was achieved, oxygen feed was switched to nitrogen for anaerobic conditions.

source_name: Saccharomyces cerevisiae cells, glucose-limited chemostat, transient from 1% to 0% oxygen, timepoint 0.2h.


title: MGH_Liver_pool vs MGH_Liver_18


title: MGH_Liver_pool vs MGH_Liver_16


title: leaf 30%Inhibition rep3 [Soy]


title: leaf 30%Inhibition rep1 [Soy]


title: Yeast_1%oxygen_transient24h_rep1


title: 937 - mAdbID:62858

description: mAdb experiment ID: 62858


title: 881 - mAdbID:62857

description: mAdb experiment ID: 62857


title: 1133 - mAdbID:62839

description: mAdb experiment ID: 62839


title: MGH_Liver_pool vs MGH_Liver_15


title: leaf 20%Inhibition rep4 [Soy]

description: Gene expression data from the first fully expanded leaf of Glycine max 'Williams 82' at 20% inhibition from optimum

source_name: Glycine max leaf, 20% inhibition

value: Photosynthesis at 20% inhibition from optimum


title: leaf 20%Inhibition rep2 [Soy]


title: 1194 - mAdbID:62833

description: mAdb experiment ID: 62833


title: leaf 20%Inhibition rep3 [Soy]


title: MGH_Liver_pool vs MGH_Liver_14


title: Yeast_1%oxygen_transient8h_rep1


title: MGH_Liver_pool vs MGH_Liver_17


title: leaf 30%Inhibition rep2 [Soy]


title: Yeast_1%oxygen_transient3h_rep1


title: MGH_Liver_pool vs MGH_Liver_13


title: leaf 20%Inhibition rep1 [Soy]


title: Yeast_1%oxygen_transient1h_rep1


title: Yeast_1%oxygen_transient0.2h_rep1


title: 1180 - mAdbID:62832

description: mAdb experiment ID: 62832


title: leaf optimum rep4 [Soy]

description: Gene expression data from the first fully expanded leaf of Glycine max 'Williams 82' at optimum temperature

source_name: Glycine max leaf, optimum

value: Photosynthesis at optimum temperature


title: MGH_Liver_pool vs MGH_Liver_12


title: 1172 - mAdbID:62829

description: mAdb experiment ID: 62829


title: leaf optimum rep3 [Soy]


title: leaf optimum rep2 [Soy]


title: MGH_Liver_pool vs MGH_Liver_10


title: MGH_Liver_pool vs MGH_Liver_11


title: Yeast_1%oxygen_transient0h_rep1


title: 1171 - mAdbID:62828

description: mAdb experiment ID: 62828


title: 1178 - mAdbID:62830

description: mAdb experiment ID: 62830


title: leaf baseline rep4 [Soy]

description: Gene expression data from the first fully expanded leaf of Glycine max 'Williams 82' at growth temperature

source_name: Glycine max leaf, baseline

value: Photosynthesis at growth temperature


title: 1111 - mAdbID:62817

description: mAdb experiment ID: 62817


title: MGH_Liver_pool vs MGH_Liver_9

source_name: liver


title: leaf optimum rep1 [Soy]


title: 1169 - mAdbID:62827

description: mAdb experiment ID: 62827


title: 1118 - mAdbID:62820

description: mAdb experiment ID: 62820


title: 1179 - mAdbID:62831

description: mAdb experiment ID: 62831


title: MGH_Liver_pool vs MGH_Liver_8


title: leaf baseline rep3 [Soy]


title: 1117 - mAdbID:62819

description: mAdb experiment ID: 62819


title: CarpADNg-2 with array type poplar from Affymetrix

type: genomic

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

description: The project aims to identify genes of interest for water deficit acclimation in poplar. We look for genes and gene expression networks related to drought stress in two hybrid cultivars, differing in their drought tolerance in field. Affymetrix poplar genome array was designed on several Populus species. In order to deal with comparative approaches, we checked the convenience of the array by hybridizing genomic DNA of the two hybrid cultivars (Populus deltoides × Populus nigra, namely ‘cv Carpaccio’ and ‘cv Soligo’). This point is important as transcript sequence might have diverged in the two genomes (Fossati et al, 2005), which could lead to absence of hybridization without physiological meaning.

hyb_protocol: labelled extract quantity: 20ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

molecule: genomic DNA

organism: Populus x canadensis

label_protocol: labelling Biotin indirect, amplification=no, DNA  .

growth_protocol: aerial - Growth conditions (Media/hygrometry/Temperature/Light): Plants were grown in 10-liter pots filled with peat/sand mix (50/50 v/v amended with 1g/l CaMg(CO2)3 and fertilised with Nutricote T100 (13-13-13-2, N-P-K-Mg + trace elements)). In the greenhouse, temperature oscillated with outside irradiance but kept in the range 15-26 °C, and air humidity during day oscillated in the range 50-75%. Irradiance depended on outside and varied in the range 300-850 µmol m-1 s-1 (cloudy-sunny), and was over750 µmol m-1 s-1 most of the experience. During the 3 days preceding harvest, mean day temperature was 25°C, humidity was 65% and light was 850 µmol m-1 s-1.

treatment_protocol: no treatment

tag: harvest date

value: leaf

tag: cultivar

value: Carpacio


title: DBA_104_R_HD

city: Knoxville

first: Rachel

last: Lynch

address: 2640 Morgan Circle Drive, 51f McCord Hall

department: Life Sciences

institute: University of Tennessee

description: Pool of equal amounts of RNA from 2 individuals from same sex/strain

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was normalized using Variance Stabilizing Transformation (VST) followed by Robust Spline Normalization (RSN) using the lumi package in Bioconductor.

source_name: DBA/2J Mouse spleen control High Dose

label_protocol: Ambion Illumina TotalPrep RNA Amplification Kit (Ambion Catalog # IL1791)

extract_protocol: Spleens were stabilized in RNAlater and total RNA was extracted using RNeasy Mini Kits (Qiagen, Valencia, CA), and RNA concentration and quality was assessed using the Experion RNA StdSens Chips on the Experion system (Bio-Rad, Hercules, CA).

treatment_protocol: Mice were exposed to low dose (10cGy at 9cGy/hour from a 137Cs source) or high dose (1Gy at 6Gy/min from a 60Co) whole body gamma radiation.

tag: strain

value: High Dose(1 Gy Irradatiation)

tag: sex

value: Male

value: spleen


title: DBA_420_R_LD

source_name: DBA/2J Mouse spleen control Low Dose

value: Low Dose(10 cGy Irradatiation)


title: DBA_102_R_HD


title: CarpADNg-1 with array type poplar from Affymetrix


title: DBA_416_R_LD


title: SolADNg-2 with array type poplar from Affymetrix

value: Soligo


title: leaf baseline rep2 [Soy]


title: SolADNg-1 with array type poplar from Affymetrix


title: leaf baseline rep1 [Soy]


title: 1126 - mAdbID:62823

description: mAdb experiment ID: 62823


title: 1029 - mAdbID:62814

description: mAdb experiment ID: 62814


title: 1092 - mAdbID:62816

description: mAdb experiment ID: 62816


title: 1ug/ml DMSO control, biological rep 3

city: Glasgow

first: Steven

middle: Thomas

last: Laing

address: 464 Bearsden Road

department: Veterinary Medicine

country: United Kingdom

institute: University of Glasgow

description: Gene expression data from adult C. elegans exposed to 1.5% v/v DMSO for 4 hrs

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChips were washed and stained according to manufacturer supplied protocols.

scan_protocol: GeneChips were scanned using an Affymetrix GCS3000 scanner

data_processing: The data were analyzed with R and Bioconductor packages (e.g. limma) using RMA as the normalization method.

organism: Caenorhabditis elegans

source_name: Adult C. elegans exposed to 0.01% v/v DMSO for 4 hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: Synchronised DA1316 L1 (approx. 10000 per experimental condition) were grown on standard NGM plates at 20oC for 53 hrs

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

treatment_protocol: 53 hr DA1316 cultures were transferred to 100 ng/ml or 1 µg/ml IVM NGM plates (diluted from 10mg/ml IVM in DMSO stock) or DMSO control plates for four hours, then were harvested by washing with M9 buffer.

value: whole nematode

tag: genotype

tag: culture method

value: NGM plates with OP50 bacterial lawn

tag: age

value: 53hrs from L1 (20oC)

tag: drug exposure

value: 0.01% v/v DMSO for 4 hrs


title: DBA_427_C

source_name: DBA/2J Mouse spleen control

value: Control


title: MGH_Liver_pool vs MGH_Liver_4

description: Gene expression data from Human livers, biopsies taken during RY gastric bypass surgery. All individuals were compared to a common pool created from equal portions of RNA.

value: liver


title: 1115 - mAdbID:62818

description: mAdb experiment ID: 62818

tag: disease state

value: Mantle Cell Lymphoma (MCL)


title: MGH_Liver_pool vs MGH_Liver_3


title: 989 - mAdbID:62813

description: mAdb experiment ID: 62813

tag: individual


title: M1094 SNP Hybe

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 280 Galvin Life Science

department: Biological Sciences

institute: University of Notre Dame

hyb_protocol: Used NimbleGen's standard CGH hybridization protocol (http://www.nimblegen.com/products/lit/lit.html) with the following modification: used 1x Denhardt's Solution in place of sample tracking control

scan_protocol: Arrays were scanned at 2um on a NimbleGen MS200 scanner with autogain per manufacturer's instructions (http://www.nimblegen.com/products/lit/lit.html)

data_processing:
Arrays were processed using NimbleScan v2.5 per manufacturer's instructions (http://www.nimblegen.com/products/lit/lit.html)
The .bases files were created from scanned images using NimbleGen’s NimbleScan software (Analysis -> Reports -> Sequencing Bases ). These files contain the same information as NimbleGen .pair files but the probes have been collated by SNP locus. Due to this enhanced organization and readability, we use the .bases file instead of the .pair file as our raw data. We do not attempt to normalize between samples or across an entire image within one sample and directly use these intensity values in our secondary analysis, so no processed data is provided.

organism: Plasmodium falciparum

source_name: M1094 DNA

label_protocol: Used NimbleGen's standard labeling protocol (http://www.nimblegen.com/products/lit/lit.html) with the following modification: used a custom 65% AT random nonamer mix from TriLink Biotechnologies

extract_protocol: Phenol-chloroform extraction (Moll et al. 2008. Methods in Malaria Research. MR4/ATCC.)


title: M1069 SNP Hybe

source_name: M1069 DNA


title: MGH_Liver_pool vs MGH_Liver_5


title: M1176 SNP Hybe

source_name: M1176 DNA


title: DBA_103_R_HD


title: DBA_101_R_HD


title: M1321 WGA SNP Hybe

source_name: M1321 WGA DNA


title: 1ug/ml DMSO control, biological rep 4


title: DBA_426_C


title: DBA_428_C


title: 1072 - mAdbID:62815

description: mAdb experiment ID: 62815


title: MGH_Liver_pool vs MGH_Liver_7


title: 1ug/ml DMSO control, biological rep 5


title: MGH_Liver_pool vs MGH_Liver_6


title: DBA_417_R_LD


title: MGH_Liver_pool vs MGH_Liver_1


title: M1111 WGA SNP Hybe 2

source_name: M1111 WGA DNA


title: M1064 WGA SNP Hybe 2

source_name: M1064 WGA DNA


title: SC05 SNP Hybe 2

source_name: SC05 DNA


title: SC05 SNP Hybe 1


title: 7C126 SNP Hybe 2

source_name: 7C126 DNA


title: 1ug/ml ivermectin exposure, biological rep 5

source_name: Adult C. elegans exposed to 1 μg/ml IVM and 0.01% v/v DMSO for 4 hrs

value: 1 μg/ml IVM and 0.01% v/v DMSO (excipient) for 4 hrs


title: 1ug/ml DMSO control, biological rep 1


title: 983 - mAdbID:62810

description: mAdb experiment ID: 62810


title: 7C126 SNP Hybe 1


title: 1ug/ml DMSO control, biological rep 2


title: Dd2 SNP Hybe 3

source_name: Dd2 DNA


title: DBA_425_C


title: B61388_R_LD

source_name: C57BL/6J Mouse spleen control Low Dose


title: B6_1384_R_LD


title: 1ug/ml ivermectin exposure, biological rep 2


title: 931 - mAdbID:62809

description: mAdb experiment ID: 62809


title: 922 - mAdbID:62799

description: mAdb experiment ID: 62799


title: 987 - mAdbID:62811

description: mAdb experiment ID: 62811


title: 1ug/ml ivermectin exposure, biological rep 4


title: B6_1385_R_LD


title: 1ug/ml ivermectin exposure, biological rep 3


title: 1ug/ml ivermectin exposure, biological rep 1


title: Dd2 SNP Hybe 2


title: B6_1383_R_LD


title: 928 - mAdbID:62808

description: mAdb experiment ID: 62808


title: 100ng/ml DMSO control, biological rep 5

description: Gene expression data from adult C. elegans exposed to 300 µg/ml ABZ and 1.5% v/v DMSO for 4 hrs

source_name: Adult C. elegans exposed to 0.001% v/v DMSO for 4 hrs

value: 0.001% v/v DMSO for 4 hrs


title: Dd2 SNP Hybe 1


title: B6_1455_R_HD

source_name: C57BL/6J Mouse spleen control High Dose


title: 100ng/ml DMSO control, biological rep 4


title: MGH_Liver_pool vs MGH_Liver_2

source_name: liver


title: 921 - mAdbID:62798

description: mAdb experiment ID: 62798


title: 920 - mAdbID:62797

description: mAdb experiment ID: 62797


title: B6_1449_R_HD


title: B6_1450_R_HD


title: 916 - mAdbID:62795

description: mAdb experiment ID: 62795


title: HB3 SNP Hybe 5

source_name: HB3 DNA


title: HB3 SNP Hybe 4


title: HB3 SNP Hybe 6


title: HB3 SNP Hybe 3


title: B6_1458_R_HD


title: 100ng/ml DMSO control, biological rep 2


title: 868 - mAdbID:62793

description: mAdb experiment ID: 62793


title: B6_1409_C

source_name: C57BL/6J Mouse spleen control


title: B6_1408_C


title: HB3 SNP Hybe 2


title: 100ng/ml ivermectin exposure, biological rep 4

source_name: Adult C. elegans exposed to 100 ng/ml IVM and 0.001% v/v DMSO for 4 hrs

value: 100 ng/ml IVM and 0.001% v/v DMSO (excipient) for 4 hrs


title: 100ng/ml ivermectin exposure, biological rep 5


title: 100ng/ml DMSO control, biological rep 3


title: B6_1401_C


title: 3D7 SNP Hybe 14

source_name: 3D7 DNA


title: 3D7 SNP Hybe 15


title: B6_1403_C


title: 741 - mAdbID:62792

description: mAdb experiment ID: 62792


title: 3.27 350

city: Sutton

first: Anguraj

last: Sadanandam

state: Surrey

address: 15 Cotswold Road

department: Molecular Pathology

institute: Institute of Cancer Research (ICR), London

description: Human pancreatic ductal adenocarcinoma cell line sample

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed using Bioconductor and normalized using RMA using R package.

source_name: Human pancreatic cancer cell line sample

extract_protocol: Extracted using a propriatary method by Response Genetics Inc. (www.responsegenetics.com/)

tag: cell line


title: 100ng/ml ivermectin exposure, biological rep 2


title: Tu8988T 298


title: 100ng/ml ivermectin exposure, biological rep 3


title: 100ng/ml DMSO control, biological rep 1


title: 3D7 SNP Hybe 13


title: CFPac1 347


title: Skin_fibroblasts_0.6_uM_rotenone_3_hours_subject_JS05

first: Andrea

middle: B

last: Maier

address: postbox 9600

country: Netherlands

institute: LUMC

description: Gene expression after 3 hours rotenone treatment

hyb_protocol: Labelled cRNA was purified using an RNeasy Mini Kit (Qiagen Ltd, Crawley, UK) and 2μg was hybridised to Agilent human whole genome Oligo Arrays (G4112F) using reagents supplied in the Agilent Hybridisation Kit (One-Color Microarray-Based Gene Expression Analysis Protocol). Microarray slides were hybridised for 17 h at 65 ºC and subsequently washed in acetonitrile for 1 min followed by 30s in Agilent Stabilisation and Drying Solution.

scan_protocol: Scanning of the slides was performed with the Agilent G2565BA Microarray Scanner System. The Agilent G2567AA Feature Extraction Software (v.9.1) was used to extract data and check the quality.

data_processing:
The Agilent G2567AA Feature Extraction Software (v.9.1) was used to extract data and check the quality. The data was background corrected by Normexp+offset, quantile normalised and log transformed:
# normalise
# background correction - normexp + offset method
dat2<- backgroundCorrect(ddaux,"normexp",offset=50)
# quantile
dat2<-normalizeBetweenArrays(dat2$R,method="quantile")
# ln
dat2<-log(dat2)

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 hours, subject JS05

label_protocol: 300ng  mRNA was mixed with an appropriate amount of One-Color RNA Spike-In RNA and converted into labelled cRNA (One-Color Low RNA Input Linear Amplification Kit PLUS).

growth_protocol: Three-mm (Leiden 85-plus Study) were taken from the sun unexposed medial side of the upper arm. Fibroblasts were grown in D-MEM:F-12 (1:1) medium supplemented with 10% fetal calf serum (FCS), 1 mM MEM sodium pyruvate, 10 mM HEPES, 2 mM glutamax I, and antibiotics (100 Units/mL penicillin, 100 μg/mL streptomycin, and 0.25–2.5 μg/mL amphotericin B), all obtained from Gibco, Breda, the Netherlands. Different FCS batches were used for fibroblasts from the Leiden 85-plus Study (Gibco, batch no. 40G4932F) and for fibroblasts from the LLS (Bodinco, Alkmaar, the Netherlands, batch no. 162229). This medium will be referred to as standard medium. Fibroblasts were incubated at 37oC with 5% CO2 and 100% humidity. All cultures that are used in the present study were grown under predefined, highly standardized conditions as published earlier {Maier, 2007 118 /id} and frozen at low passage. Trypsin (Sigma, St Louis, MO, USA) was used to split fibroblasts using a 1:4 ratio each time they reached 80-100% confluence.

extract_protocol: Total mRNA was isolated using the RNeasy Mini Kit (Qiagen Ltd, Crawley, UK)

treatment_protocol: To chronically stress fibroblast strains, medium was supplemented for 3 hours and 3 days with 0.6 μM rotenone (Sigma, St Louis, MO, USA), known to induce an increase in the intracellular production of ROS at the mitochondrial level

value: human skin fibroblasts

tag: gender

value: female

tag: young/old

value: young

tag: batch


title: 988 - mAdbID:62812

description: mAdb experiment ID: 62812


title: Panc1 403.6


title: 100ng/ml ivermectin exposure, biological rep 1


title: 3D7 SNP Hybe 12


title: Capan1 393


title: Skin_fibroblasts_0.6_uM_rotenone_3_days_subject_JS05

description: Gene expression after 3 days rotenone treatment

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 days, subject JS05


title: 3D7 SNP Hybe 11


title: 3D7 SNP Hybe 10


title: Tu8902 406


title: 3D7 SNP Hybe 9


title: 3D7 SNP Hybe 8


title: HPAC 295

value: HPAC


title: Skin_fibroblasts_0.6_uM_rotenone_3_hours_subject_JS30

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 hours, subject JS30

value: male


title: gun4-1, rep3

city: Berlin

first: Bernhard

last: Grimm

state: Berlin

address: Philippstr. 13, building 12

department: Institute of Biology

country: Germany

institute: Humboldt University Berlin

description: Gene expression data from Arabidopsis thliana seedlings

hyb_protocol: Following fragmentation, 12.5 µg of cRNA were hybridized for 16 hr at 45C on GeneChip ATH1 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridisation was performed at KFB Regensburg, Germany.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000. Scaning was performed at KFB Regensburg, Germany.

data_processing: The data were analyzed with Affymetrix GeneChip Command Console and Expression Console Software. Primary data presented here were analysed at KFB Regensburg, Germany.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana gun4-1 mutant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3'IVT Kit, Affymetrix 2008). Labeling was performed at KFB Regensburg, Germany.

growth_protocol: Surface sterilised seedlings were plated on solid MS medium and etiolated for 3 days in darkness at 23°C. Subsequently, plates were illuminated for 6 hours at araound 100 µmol photons m2 s-1.

extract_protocol: Extraction of total RNA was performed using InviTrap® Spin Plant RNA Mini Kit (Invitek, Germany) according to the manufacturer's instructions.

treatment_protocol: One set of seedlings was treated with 10 µM gabaculin. Gabaculin was supplied with the medium.

tag: genotype/variation

tag: agent

value: seedling

value: 3 days, 6 hours


title: Skin_fibroblasts_0.6_uM_rotenone_3_days_subject_S534

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 days, subject S534

tag: tissue

value: old


title: Skin_fibroblasts_0.6_uM_rotenone_3_hours_subject_S534

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 hours, subject S534


title: 3D7 SNP Hybe 7


title: Col-0 gabaculin treated, rep2

source_name: Arabidopsis thaliana gabaculin treated

value: wild type

value: 10 µM gabaculin


title: Capan2 174


title: 3D7 SNP Hybe 6


title: Col-0 gabaculin treated, rep3


title: gun4-1, rep2


title: gun4-1, rep1


title: 2.13 389


title: Skin_fibroblasts_non-treated_3_days_subject_JS30

description: Gene expression non-stressed

source_name: Skin fibroblasts, non-treated, 3 days, subject JS30


title: Skin_fibroblasts_0.6_uM_rotenone_3_days_subject_JS30

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 days, subject JS30


title: Skin_fibroblasts_non-treated_3_days_subject_JS05

description: Gene expression non-stressed

source_name: Skin fibroblasts, non-treated, 3 days, subject JS05


title: Skin_fibroblasts_non-treated_3_days_subject_S591

description: Gene expression non-stressed

source_name: Skin fibroblasts, non-treated, 3 days, subject S591


title: 3D7 SNP Hybe 5


title: Skin_fibroblasts_non-treated_3_days_subject_S534

description: Gene expression non-stressed

source_name: Skin fibroblasts, non-treated, 3 days, subject S534


title: SW1990 232


title: HPAF_II 335


title: wild type Col-0, rep3

source_name: Arabidopsis thaliana Col-0


title: Tu8988S 309


title: wild type Col-0, rep2


title: Mpanc96 323


title: Skin_fibroblasts_0.6_uM_rotenone_3_hours_subject_S591

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 hours, subject S591


title: 6.03 289


title: 3D7 SNP Hybe 3


title: 3D7 SNP Hybe 2


title: Col-0 gabaculin treated, rep1


title: 3D7 SNP Hybe 1


title: Colo357 478


title: 3D7 SNP Hybe 4


title: wild type Col-0, rep1


title: Skin_fibroblasts_0.6_uM_rotenone_3_days_subject_S591

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 days, subject S591


title: 10.05 309


title: Dan_G 311


title: Suit2 233


title: Skin_fibroblasts_non-treated_3_days_subject_JS10

description: Gene expression non-stressed

source_name: Skin fibroblasts, non-treated, 3 days, subject JS10


title: Skin_fibroblasts_0.6_uM_rotenone_3_days_subject_JS10

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 days, subject JS10


title: Skin_fibroblasts_non-treated_3_days_subject_S569

description: Gene expression non-stressed

source_name: Skin fibroblasts, non-treated, 3 days, subject S569


title: HupT3 183

source_name: Human pancreatic cancer cell line sample


title: Skin_fibroblasts_0.6_uM_rotenone_3_hours_subject_JS10

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 hours, subject JS10


title: Miapaca2 332


title: Skin_fibroblasts_0.6_uM_rotenone_3_hours_subject_S569

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 hours, subject S569


title: Skin_fibroblasts_0.6_uM_rotenone_3_hours_subject_JS20

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 hours, subject JS20


title: Microdissected PDA tumor sample (AGR06.1130)

description: Microdissected patient pancreatic ductal adenocarcinoma sample

value: ductal adenocarcinoma tumor


title: Skin_fibroblasts_0.6_uM_rotenone_3_days_subject_S386

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 days, subject S386


title: Microdissected PDA tumor sample (AGR08.475)

source_name: Microdissected patient pancreatic ductal adenocarcinoma sample


title: Skin_fibroblasts_0.6_uM_rotenone_3_days_subject_S569

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 days, subject S569


title: Microdissected PDA tumor sample ( AGR08.477)


title: Skin_fibroblasts_non-treated_3_days_subject_JS20

description: Gene expression non-stressed

source_name: Skin fibroblasts, non-treated, 3 days, subject JS20


title: Skin_fibroblasts_0.6_uM_rotenone_3_days_subject_JS20

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 days, subject JS20


title: Skin_fibroblasts_0.6_uM_rotenone_3_hours_subject_JS15

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 hours, subject JS15


title: Skin_fibroblasts_non-treated_3_days_subject_S386

description: Gene expression non-stressed

source_name: Skin fibroblasts, non-treated, 3 days, subject S386


title: Microdissected PDA tumor sample (AGR06.0929)


title: Microdissected PDA tumor sample (AGR07.1320)


title: Microdissected PDA tumor sample (AGR06.1121)


title: Skin_fibroblasts_0.6_uM_rotenone_3_hours_subject_S386

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 hours, subject S386


title: M1064 WGA vs. M1316 WGA CGH Hybe

data_processing: Arrays were processed using NimbleScan v2.5 per manufacturer's instructions (http://www.nimblegen.com/products/lit/lit.html)

source_name: M1064 WGA DNA

source_name: M1316 WGA DNA


title: Skin_fibroblasts_non-treated_3_days_subject_JS15

description: Gene expression non-stressed

source_name: Skin fibroblasts, non-treated, 3 days, subject JS15


title: Skin_fibroblasts_0.6_uM_rotenone_3_days_subject_JS15

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 days, subject JS15


title: Skin_fibroblasts_0.6_uM_rotenone_3_hours_subject_S175

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 hours, subject S175


title: SC05 vs. 3D7 CGH Hybe 1

source_name: SC05 DNA

source_name: 3D7 DNA


title: Microdissected PDA tumor sample (AGR06.1127)


title: SC05 vs. 3D7 CGH Hybe 2


title: Microdissected PDA tumor sample (AGR06.1126)


title: Microdissected PDA tumor sample (AGR08.469)


title: HB3 vs. 3D7 CGH Hybe 6

source_name: HB3 DNA


title: Skin_fibroblasts_0.6_uM_rotenone_3_days_subject_S175

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 days, subject S175


title: Skin_fibroblasts_non-treated_3_days_subject_S175

description: Gene expression non-stressed

source_name: Skin fibroblasts, non-treated, 3 days, subject S175


title: Microdissected PDA tumor sample (AGR06.0931)

source_name: Microdissected patient pancreatic ductal adenocarcinoma sample


title: Microdissected PDA tumor sample (AGR06.1119)


title: Microdissected PDA tumor sample (AGR06.1128)


title: Microdissected PDA tumor sample (AGR06.1125)


title: Microdissected PDA tumor sample (AGR06.1124)


title: HB3 vs. 3D7 CGH Hybe 5


title: Skin_fibroblasts_0.6_uM_rotenone_3_hours_subject_JS14

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 hours, subject JS14


title: Skin_fibroblasts_0.6_uM_rotenone_3_hours_subject_S030

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 hours, subject S030


title: HB3 vs. 3D7 CGH Hybe 2


title: STAT1-/-Fib/IRF1 rep2

city: New York

first: Charles

last: Rice

state: NY

address: 1230 York Ave

department: Virology and Infectious Disease

institute: The Rockefeller University

description: replicate 2

data_processing: The raw data was extracted using Illumina BeadStudio software without normalization. For normalization in GeneSpring, the threshold raw signal was set to 1.0 and the global normalization algorithm (percentile shift) was used with a percentile target of 75. This normalized data was used for statistical analysis, in which our IRF1-expressing cell lines were compared to control. There were 3 biological replicates for each condition. We used student's unpaired t-test to identify genes that had were significantly (p<0.05) changed in expression levels. We then selected a cutoff of 3.0 fold (upregulated) and presented the absolute fold change for this subset of genes in our publication.

source_name: skin fibroblasts

extract_protocol: Extraction of total cellular RNA was carried out with Qiagen Rneasy Kit according to manufactuer's recommendations.

tag: cell type

value: skin fibroblasts

value: Stat -/-

tag: transfection


title: Skin_fibroblasts_non-treated_3_days_subject_JS14

description: Gene expression non-stressed

source_name: Skin fibroblasts, non-treated, 3 days, subject JS14


title: Dd2 vs. 3D7 CGH Hybe 4

source_name: Dd2 DNA

tag: strain


title: HB3 vs. 3D7 CGH Hybe 1


title: Microdissected PDA tumor sample (AGR06.0932)


title: Microdissected PDA tumor sample (AGR06.1129)


title: Dd2 vs. 3D7 CGH Hybe 2


title: STAT1-/-Fib/IRF1 rep3

description: replicate 3


title: Skin_fibroblasts_0.6_uM_rotenone_3_days_subject_S030

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 days, subject S030


title: HB3 vs. 3D7 CGH Hybe 3


title: Skin_fibroblasts_0.6_uM_rotenone_3_days_subject_JS14

source_name: Skin fibroblasts, 0.6 uM rotenone, 3 days, subject JS14


title: Skin_fibroblasts_non-treated_3_days_subject_S030

description: Gene expression non-stressed

source_name: Skin fibroblasts, non-treated, 3 days, subject S030


title: Microdissected PDA tumor sample (AGR06.0933)


title: Microdissected PDA tumor sample (AGR06.0930)


title: STAT1-/-Fib/Fluc rep3

description: replicate 3

value: luciferase


title: Microdissected PDA tumor sample (AGR06.1120)


title: Gene expression in A549 cells treated with control siRNA

city: Sendai

first: Hozumi

last: Motohashi

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

department: Center for Radioisotope Science

institute: Tohoku University Graduate School of Medicine

description: Gene expression at 24 hours after transfection

hyb_protocol: 750 ng of Cy3-labeled cRNA was fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: Agilent Feature Extraction Software

source_name: human lung cancer cell line, A549 cells, treated with netagive control siRNA (DS scrambled negative control siRNA)

label_protocol: 500 ng of Total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

growth_protocol: A549 cells were maintained in RPMI1640 medium supplemented with 20% FBS.

extract_protocol: Total RNA was extracted from A549 cells using Isogen (Nippon Gene). RNA was further purified using an RNeasy Mini Kit (Qiagen).

treatment_protocol: The siRNAs were introduced into A549 cells by electroporation using the MP-100 MicroPorator (Digital Bio Technology).

tag: treatment

value: Control


title: Gene expression in NRF2-knockdown A549 cells (no.2)

source_name: human lung cancer cell line, A549 cells, treated with NRF2 siRNA (HSS107129)

value: NRF2 KD-2


title: Huh-7/IRF1 rep1

description: replicate 1

source_name: hepatoma cells

value: hepatoma cells


title: Gene expression in NRF2-knockdown A549 cells (no.1)

source_name: human lung cancer cell line, A549 cells, treated with NRF2 siRNA (HSS107128)

value: NRF2 KD-1


title: STAT1-/-Fib/Fluc rep2

description: replicate 2

tag: genotype


title: Huh-7/Fluc rep2

description: replicate 2


title: Huh-7/IRF1 rep2

description: replicate 2


title: Microdissected PDA tumor sample (AGR08.472)


title: Huh-7/Fluc rep3

description: replicate 3


title: Microdissected PDA tumor sample (AGR08.480)


title: 10d seedlings harboring empty vector treated with CHX, rep2

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

description: Total RNA from 10d whole seedlings expressing 35S:VP16-GR (empty vector) treated with 10mM CHX for 6hrs was isolated to use for control. Replicate 2 of 5.

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. All signals were divided by median value of all probe sets.

source_name: 10d whole seedlings harboring empty vector treated with 10mM CHX for 6hrs

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

growth_protocol: Seedlings were grown in MS agar medium in 16 hrs light at 23 centigrade degree.

extract_protocol: Total RNA was extracted using Nucleospin RNA Plant System (Macherey-Nagel) following instruction.

treatment_protocol: Ten-day-old seedlings grown on a medium were soaked with sterilized water containing 10 µM cycloheximide (CHX), a protein synthesis inhibitor, for 2 hours. After removal of the solution, the seedlings were soaked with sterilized water containing CHX and with or without 10 µM DEX for 4 hours.

value: whole seedlings

value: 10 day old

value: 35S:VP16-GR:NOS homozygous, single insertion

value: 10mM cycloheximide (CHX) 6hrs


title: Microdissected PDA tumor sample (AGR06.1118)


title: Microdissected PDA tumor sample (AGR07.1324)


title: Gene expression in NRF2-knockdown A549 cells (no.3)

source_name: human lung cancer cell line, A549 cells, treated with NRF2 siRNA (HSS107130)

value: NRF2 KD-3


title: Microdissected PDA tumor sample (AGR07.1325)


title: Microdissected PDA tumor sample (AGR07.1322)


title: Huh-7/IRF1 rep3

description: replicate 3


title: Microdissected PDA tumor sample (AGR07.1326)


title: E38T8-cy5 vs. E42T5-cy3 (combined vs. combined)

city: Albuquerque

middle: A

last: Belinsky

state: NM

address: 2425 Ridgecrest Dr SE

department: Lung Cancer Program

institute: Lovelace Respiratory Research Institute

description: comparison of Combined therapy treated tumor from E38 to combined therapy treated tumor from E42

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: fold_change.txt: bioconductor package limma was used for background correction and Lowess normalization, VALUE = default Agilent Feature Extraction software normalized values

source_name: Calu6 tumor, Combined therapy

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label.

growth_protocol: Calu6 cells were instilled into lungs and grown orthotopically in lungs of nude rats.

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

value: Calu6 tumor from lung

tag: source

value: AZA + MS-275

source_name: Calu6 tumor, combined therapy


title: E38T3-cy5 vs. E34T1-cy3 (combined vs. combined)

description: comparison of Combined therapy treated tumor from E38 to combined therapy treated tumor from E34


title: Dd2 vs. 3D7 CGH Hybe 1

source_name: 3D7 DNA


title: Microdissected PDA tumor sample (AGR08.479)

source_name: Microdissected patient pancreatic ductal adenocarcinoma sample


title: D42T5-cy5 vs. E38T3-cy3 (aza vs. combined)

description: comparison of Aza treated tumor from D42 to combined therapy treated tumor from E38

source_name: Calu6 tumor, Aza treatment

value: AZA


title: E34T1-cy5 vs. E38T8-cy3 (combined vs. combined)

description: comparison of Combined therapy treated tumor from E34 to combined therapy treated tumor from E38


title: Affy_Human Dermal Lymphatic Endothelial Cells Donor 2

city: Zurich

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities across microarrays were normalized using the quantile normalization (www.bioconductor.org).

label: ENZO biotin labeled

source_name: Neonatal human foreskin

label_protocol: Approximately 10 micrograms of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Isolate total cellular RNA with 1 ml of the Trizol reagent (Invitrogen) after washing one 80-90 % confluent 10 cm culture dish with PBS. Homogenize the sample using a cell scraper and add 0.2 ml of chloroform in a 1.5 ml tube. Shake the sample vigorously for 15 seconds and allow standing for 5 minutes. Centrifuge the resulting mixture at 12,000 x g for 15 minutes at 4 degree Celsius. Transfer the aqueous phase to a fresh tube and add 0.5 ml of iso-propanol and mix. Allow the sample to stand for 5 minutes at room temperature and centrifuge at 12,000 x g for 10 minutes at 4 degrees Celsius. Remove the supernatant and wash the RNA pellet by adding 1 ml of 75% ethanol. Vortex the sample and then centrifuge at 12,000 x g for 5 minutes at 4 degrees Celsius. Remove the ethanol and briefly dry the RNA pellet for 5 minutes and add 50 micro-liter of RNAase/DNAase free water and mix by repeated pipetting until RNA pellet is fully dissolved.

tag: CD45-/CD34-/CD31+ Human Lymphatic Endothelial Cell (LEC)


title: E42T5-cy5 vs. Pool-cy3 (combined vs. untreated)

description: comparison of Combined therapy treated tumor from E42 to pooled untreated tumors

source_name: pooled untreated Calu6 tumors from 4 animals

value: Pool

value: untreated


title: D38T2-cy5 vs. D42T12-cy3 (aza vs. aza)

description: comparison of Aza treated tumor from D38 to Aza treated tumor from D42


title: Affy_Human Dermal Blood Vascular Endothelial Cells Donor 2

tag: CD45-/CD34+ Human Blood Vascular Endothelial Cell (BVEC)


title: D38T4-cy5 vs. D42T5-cy3 (aza vs. aza)

description: comparison of  Aza treated tumor from D38 to Aza treated tumor from D42


title: Affy_Human Dermal Lymphatic Endothelial Cells Donor 1


title: Huh-7/Fluc rep1

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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


title: D42T12-cy5 vs. D38T4-cy3 (aza vs. aza)

description: comparison of Aza treated tumor from D42 to Aza treated tumor from D38


title: STAT1-/-Fib/IRF1 rep1

description: replicate 1

source_name: skin fibroblasts

value: skin fibroblasts


title: Pool-cy5 vs. D38T2-cy3 (untreated vs. aza)

description: comparison of pooled untreated tumors to tumor T2 from 5-aza treated animal

source_name: Calu6  tumor , Aza treatment


title: Affy_Human Dermal Blood Vascular Endothelial Cells Donor 1


title: Transcriptome alteration during immortalization (BEAS2B / NHBE)

status: Public on Mar 31 2011

first: Phillip

last: Dennis

address: 37 Convent Dr.

department: MOB, CCR

institute: NCI

description:
Analysis used NHBE RNA as a control for comparison to immortalized BEAS2B RNA.

This Sample represents two dye-swap hybridizations.

hyb_protocol: Purified Cy3/Cy5-labelled probes were combined and hybridized in the presence of 2x Denhart's solution, 3.2x saline sodium citrate (SSC), and 0.5% sodium dodecyl sulfate (SDS) in a humidified chamber at 65°C overnight. Prior to scanning (Agilent Technologies, Foster City, CA), slides were successively washed at 22°C in 0.5xSSC/0.1% SDS for 2 min, 0.5xSSC/0.01% SDS for 2 min, and 0.06xSSC for 2 min.

scan_protocol: A laser confocal scanner (Agilent Technologies, Palo Alto, CA) was used to measure the fluorescence intensities at the target locations on the array using the DEARRAY software (www.scanalytics.com). Image analyses were performed with the IPLab software (Fairfax, VA).

data_processing: After background subtraction, average intensities at each clone in the test hybridization were divided by the average intensity of the corresponding clone in the control hybridization. The ratios were normalized on the basis of the distribution of ratios of all targets on the array and for the expression analysis on the basis of 88 housekeeping genes, which were spotted 4 times onto the array. Low-quality measurements (i.e. copy number data with mean reference intensity less than 100 fluorescent units, and expression data with both test and reference intensity less than 100 fluorescent units and/or with spot size less than 50 units) were excluded from the analysis and were treated as missing values. The reference cell (NHBE) was included in the every individual hybridization to allow for normalization of each clone’s expression relative to the reference for each cell line (BEAS-2B, NNK-BEAS-2B or H157). A self-to-self hybridization with dye reversal was performed to exclude preferential differences in probe labeling. Every sample was labeled with Cy5 and Cy3 and hybridized twice. The two fluorescent images (red and green channels) obtained from the scanner constituted the intensity raw data from which differential gene expression ratio and quality control values were calculated. All data were entered into a relational database, using the FileMaker Pro 5 software (Santa Clara, CA). Genes were identified as differentially regulated only if corrected red/green hybridization signals differed by at least two-fold.

source_name: SV40-immortalized human bronchial epithelial cells

label_protocol: Fluorescently labeled cDNA were synthesized from 100 mg RNA by oligo(dT)-primed reverse transcription in the presence of Cy3- or Cy5-dUTP (Amersham Bisciences, Piscataway, NJ).

growth_protocol: NHBE, BEAS2B, NNK-BEAS2B and H157 cells were incubated at 37 °C in 5% CO2.  When cultures reached 90% confluence, cells were harvested and frozen at –80°C prior to RNA and protein isolation. NHBE cells were obtained from Cambrex Bio Science Walkersville, Inc. (Walkersville, MD), and were cultured using Bronchial Epithelial Medium (BEGM) containing 2 µl/ml bovine pituitary extract, 5 µg/ml insulin, 0.5 µg/ml hydrocortisone, 0.5 ng/ml human epidermal growth factor, 0.5 µl/ml epinephrine, 10 µg/ml transferrin, 0.1 ng/ml retinoic acid, 6.5 ng/ml triiodothyronine, 50 µg/ml gentamycin and 50 ng/ml amphotericin-B. The BEAS2B and NNK-BEAS2B cells were maintained with LHC-8 (Biofluids, MD) with 100 units/ml penicillin and 100 µg/ml streptomycin (GIBCO-BRL, Gaithersburg, MD). The H157 lung squamous cell carcinoma cell line was provided by H. Oie and Dr. F. Kaye at the National Cancer Institute/Naval Medical Oncology (Bethesda, MD), and were maintained in RPMI 1640 medium with 10% fetal bovine serum with 100 units/ml penicillin and 100 µg/ml streptomycin.

extract_protocol: RNA was isolated using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). Briefly, 1 ml of TRIzol reagent was used per 10 cm^2 flask to lyse cells by rapid up and down pipetting, subsequently incubated at room temperature for 5 min, and then mixed with 2/10 volume chloroform by vigorous shaking for 15 sec. Phase separation was achieved by placing the samples at room temperature for 3 min, then centrifuging 3,500rpm at 4°C for 15 min. The RNA from the top aqueous layer was removed to another 50ml tube, slowly mixed with an equal volume 70% ethanol, and then transferred to an RNeasy column (Qiagen, Inc., Valencia, CA) for purification. RNA was eluted from the column with RNase-free water, concentrated to >7mg/ml by centrifugation on a MicroCon YM-30 filter (Millipore, Billerica, MA), and quantified using a UV/visible spectrophotometer Ultrospec3000 (Amersham Biosciences, Piscataway, NJ). The integrity of the total RNA was verified by denaturing gel electrophoresis.

source_name: Normal human bronchial epithelial cells (NHBE)

value: NHBE

value: primary normal human bronchial epithelial cells


title: Fz4Fz8 DKO M2

status: Public on Mar 23 2011

city: Baltimore

first: Xin

last: Ye

address: 725 N Wolfe Street, PCTB 805

institute: Johns Hopkins School of Medicine

description: Gene expression data from whole kidneys at E13.5

hyb_protocol: Hybridization performed by Johns Hopkins Microarray Core Facility with their standard protocol. Samples were hybridized to Affymetrix MOE430.2 array

scan_protocol: Scanning were performed by Johns Hopkins Microarray Core Facility with their standard protocol

data_processing: Raw data was processed in R2.9.1 using the affy and rma packages from the Bioconductor Project (www.bioconductor.org).

source_name: E13.5 Fz4-/-Fz8-/- embryonic kidneys sample 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

extract_protocol: Trizol and RNeasy according to manufacturer's instructions

value: hybrid between C57BL/6, 129X1/SvJ and 129S1/Sv

value: whole kidney

tag: developmental stage


title: Transcriptome alteration during malignancy (H157 / NHBE)

description:
Analysis used NHBE RNA as a control for comparison to malignant lung cancer cells RNA.

This Sample represents two dye-swap hybridizations.

source_name: Non-small cell lung cancer cells

value: non-small cell lung cancer cells


title: Fz4Fz8 DKO C2

source_name: E13.5 Fz4+/+Fz8-/- embryonic kidneys sample 2


title: Transcriptome alteration during transformation (NNK-BEAS2B / NHBE)

description:
Analysis used NHBE RNA as a control for comparison to transformed NNK-BEAS2B RNA.

This Sample represents two dye-swap hybridizations.

source_name: NNK-transformed human bronchial epithelial cells


title: STAT1-/-Fib/Fluc rep1

description: replicate 1

value: Stat -/-

value: luciferase


title: Fz4Fz8 DKO M3

source_name: E13.5 Fz4-/-Fz8-/- embryonic kidneys sample 3


title: kidney_double-transgenic_rat_male_rep7

status: Public on Jan 25 2011

city: Allschwil

first: Axel

last: Klenk

address: Hegenheimermattweg 91

department: Research Informatics

institute: Idorsia Pharmaceuticals Ltd.

description: no additional information

hyb_protocol: a pool of 825 ng of Cy3 labeled aRNA (examined sample) and 825 ng of Cy5 labeled aRNA rat reference (Stratagene, Agilent, Austin TX, USA) were hybridized using the Agilent Hybridization kit (Agilent, Austin TX, USA) according to the manufacturer's instructions. Hybridization was performed for 17 hours and washed according to Agilent's instructions.

scan_protocol: Scanned on an Agilent G2505B scanner using Agilent scan control (version 7.0) Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: BioConductor package vsn was used for background subtraction, variance-stabilizing normalization and glog transformation

organism: Rattus norvegicus

source_name: kidney, double-transgenic_rat, male

label_protocol: 1 µg of totRNA were labeled using the low RNA Input Linear Amplification Kit PLUS (Agilent, Austin TX, USA) following the manufacturer's instructions.

growth_protocol: Three-week old dTGR and SD were purchased from RCC (Füllinsdorf, Switzerland) and were sacrified at seven weeks.

extract_protocol: total RNA extracted  using RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's instructions

value: kidney

value: male

tag: age

value: 7 weeks

source_name: Stratagene Reference

tag: reference

value: Pool of 14 rat cell types


title: kidney_sprague-dawley_male_rep1

description: no additional information

source_name: kidney, sprague-dawley, male

value: sprague-dawley

tag: gender


title: ExVivoHybridomacell_4hr_0ug/ml_rep1

status: Public on Feb 17 2011

city: Nanjing

first: Pu

middle: Yan

last: Chen

address: No. 1, Weigang

country: China

institute: Nanjing Agriculture University

description: Gene expression after 4hr in 0ug/ml BSP-II-treated hybridoma cell

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >20.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome microarrays (G2505B) for 17 hours at 65℃ 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℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The resulting text files extracted from Agilent Feature Extraction Software (version 10.5.1.1) were imported into the Agilent GeneSpring GX software (version 11.0) for further analysis. The microarray data sets were normalized in GeneSpring GX using the Agilent FE one-color scenario (mainly median normalization)

source_name: Hybridoma cell, 4hr, 0ug/ml, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA usingQuick 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 the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Hybridoma cells were cultured with RPMI 1640 supplemented with 20% heat-inactivated fetal bovine serum (Invitrogen) at 37℃ with 5% CO2.

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Hybridoma cell was treated by BSP-II with RPMI 1640 medium supplemented with 20% heat-inactivated fetal bovine serum. The cultures were incubated for 4 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: condition

value: 4hr in 0ug/ml BSP-II

value: Hybridoma cell


title: kidney_sprague-dawley_male_rep8

description: no additional information