title: NOD MZ B cells, biological replicate 1

city: Concord

first: Pablo

last: Silveira

state: NSW

address: Gate 3 Hospital Rd, Concord Hospital

institute: ANZAC Research Institute

description: Gene expression data from splenic NOD MZ B cells

hyb_protocol: 10ug of fragmented and biotin-labeled cRNA was hybridised for 16h at 45C on Affymetrix Mouse Genome 4.30 2.0 Arrays. Washing and staining performed as per manufacturer's instruction on Affymetrix Fludics Station 450 instrument.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 laser confocal slide scanner (Affymetrix).

data_processing: Analysis of data was performed using GeneSpring 12.0 software (Agilent).  Samples were preprocessed with RMA. All samples were normalised on a per gene basis to the median of total samples.

source_name: Splenic NOD MZ B cells

label_protocol: Following reverse transcription with an Oligo(dT)-T7 primer (Affymetrix, Santa Clara, Ca), double stranded stranded cRNA was synthesized with the GeneChip® Two-cycle Target Labeling and Control Kit (Affymetrix, Santa Clara, Ca).  In an in vitro (IVT) reaction with T7 RNA polymerase, the cRNA was linearly amplified and labeled with biotinylated nucleotides (Affymetrix).

extract_protocol: Trizol extraction of total RNA from sorted cells was performed according to the manufacturer's instructions and quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA).

tag: gender

value: female

tag: strain

value: NOD/ShiLtJ (NOD)

value: 7 weeks

value: splenic B cells

tag: subset

value: MZ


title: NOD MZ B cells, biological replicate 2

status: Public on May 16 2013

type: RNA

country: Australia

label: biotin

molecule: total RNA

organism: Mus musculus

tag: age

tag: tissue


title: NOD T2MZ B cells, biological replicate 2

description: Gene expression data from splenic NOD T2MZ B cells

source_name: Splenic NOD T2MZ B cells


title: Blood_BMS_MVL436-1

city: Quebec

first: Frederic

last: Guenard

address: 2440, Hochelage blvd

country: Canada

institute: Laval University

hyb_protocol: See Illumina protocols

scan_protocol: See Illumina protocols

data_processing: Lumi algorithm was used for expression data correction and normalization (RMA background adjustment; log base 2 variance stabilization; quantile normalization). A probe had to show a detection p-value ≤ 0.05 in at least 25% of samples of a group to be considered as detected.

organism: Homo sapiens

source_name: whole blood from offspring born before maternal bariatric surgery

label_protocol: See Illumina protocols

growth_protocol: Blood samples were collected after an over-night fast from an antecubital vein

extract_protocol: PAXgene™ Blood RNA Kit (Qiagen)

treatment_protocol: Born before (BMS) or after (AMS) maternal bariatric surgery

tag: status

value: BMS

tag: Sex

value: Female

value: Whole blood


title: tumor_A2B5-_05

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

country: USA

institute: University of Rochester

description:
CGCLG_062108_HG-U133_Plus_2_AF28492_1
low grade tumor

hyb_protocol: Standard Affymetrix protocol for U133 Plus 2.0 Arrays

data_processing: Affymetrix .cel raw data files were normalized using RMA. All data processing was performed using R and the Bioconductor package.

source_name: tumor, astrocytoma low grade, A2B5- sort

label_protocol: Nugen Ovation biotin labeling system using the standard protocol

growth_protocol: Adult human white matter and cortex tissues from epileptic patients and glioma tissue were dissociated using papain. Glial progenitor cells derived from adult human brain and glioma were cultured in DMEM/F12/N2 media supplemented with bFGF, EGF, and PDGF-AA (20ng/ml) in cell suspension plates.

extract_protocol: Total RNA was extracted using RNeasy (Qiagen) and amplified using 3 -biased ribo-SPIA (NuGen Ovation), according to the manufacturer's instructions.

treatment_protocol: Glioma and non-neoplastic A2B5+ GPCs were isolated using magnetic-beads (MACS) or fluorescent-activated (FACS) cell sorting followed by confirmation of the purity of the separated cell populations. CD11b+ microglia were isolated from adult human non-neoplastic tissue using a similar procedure. . The purity of sorted CD11b+ microglia was verified using RCA-lectin staining (Vector Labs). Acutely isolated cells were frozen for RNA extraction

value: tumor

tag: pathology

value: astrocytoma

tag: sort population

tag: cell type

tag: tumor grade (who)

value: II


title: Blood_BMS_MVL428-1


title: tumor_A2B5+_10

description:
CGCLG_120808_HG-U133_Plus_2_AF28979_1
high grade tumor

scan_protocol: Standard Affymetrix protocol for U133 Plus 2.0 Arrays

source_name: tumor, anaplastic astrocytoma high grade, A2B5+ sort

value: anaplastic astrocytoma

value: III


title: Blood_BMS_5958091030_R03C02

type: genomic

hyb_protocol: standard illumina protocol

scan_protocol: standard illumina protocol

data_processing:
The GenomeStudio® software version 2011.1 (Illumina Inc.) and the Methylation Module were used. Beta values were estimated and data correction (background subtraction and normalization) was applied using internal control probe pairs. CpG sites with a detection p-value > 0.05 were removed from analysis.
SIGNAL A IS UNMETHYLATED AND SIGNAL B IS METHYLATED

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Whole blood

label_protocol: standard illumina protocol

extract_protocol: Genomic DNA was isolated from buffy coat using the GenElute™ Blood Genomic DNA kit (Sigma, St Louis, MO, USA)


title: Blood_BMS_5958091030_R04C02


title: Blood_BMS_5958091030_R02C02


title: Blood_BMS_5958091029_R05C02


title: NOD T2MZ B cells, biological replicate 1


title: Blood_BMS_5958091030_R01C02

value: Male


title: Blood_AMS_5958091029_R06C01

value: AMS


title: Blood_AMS_5958091028_R06C01


title: Blood_AMS_MVL426-1

source_name: whole blood from offspring born after maternal bariatric surgery


title: tumor_A2B5+_05

description:
CGCLG_062108_HG-U133_Plus_2_AF28491_1
low grade tumor

source_name: tumor, astrocytoma low grade, A2B5+ sort


title: tumor_A2B5+_06

description:
CGCLG_062108_HG-U133_Plus_2_AF28494_1
high grade tumor

source_name: tumor, glioblastoma small cell high grade, A2B5+ sort

value: glioblastoma, small cell

value: IV


title: Blood_BMS_MVL424-1


title: Blood_BMS_MVL425-1


title: tumor_A2B5+_08

description:
CGCLG_120808_HG-U133_Plus_2_AF28968_1
high grade tumor

source_name: tumor, glioblastoma high grade, A2B5+ sort

value: glioblastoma


title: NOD T3 B cells, biological replicate 2

description: Gene expression data from splenic NOD T3 B cells

source_name: Splenic NOD T3 B cells

value: female

value: NOD/ShiLtJ (NOD)


title: NOD FO B cells, biological replicate 1

description: Gene expression data from splenic NOD FO B cells

source_name: Splenic NOD FO B cells

value: 7 weeks

value: splenic B cells

value: FO


title: tumor_A2B5+_09

description:
CGCLG_120808_HG-U133_Plus_2_AF28976_1_2
high grade tumor


title: Blood_AMS_5958091028_R03C02

value: Female


title: Blood_BMS_MVL421-1

value: BMS

value: Whole blood


title: Blood_AMS_5958091028_R01C02


title: Blood_BMS_5958031032_R06C01


title: NOD FO B cells, biological replicate 2


title: NOD T2FO B cells, biological replicate 2

description: Gene expression data from splenic NOD T2FO B cells

source_name: Splenic NOD T2FO B cells


title: NOD T3 B cells, biological replicate 1


title: tumor_A2B5+_03

description:
CGCLG_062108_HG-U133_Plus_2_AF28487_1
high grade tumor

value: tumor


title: Blood_AMS_5958091028_R04C02


title: Blood_AMS_MVL419-1


title: tumor_A2B5+_04

description:
CGCLG_062108_HG-U133_Plus_2_AF28489_1
low grade tumor

source_name: tumor, oligoastrocytoma low grade, A2B5+ sort

value: oligoastrocytoma

value: II


title: NOD T2FO B cells, biological replicate 1


title: Blood_AMS_MVL418-1


title: Blood_BMS_MVL417-1


title: Blood_AMS_MVL422-1


title: NOD T1 B cells, biological replicate 2

description: Gene expression data from splenic NOD T1 B cells

source_name: Splenic NOD T1 B cells


title: Blood_AMS_5958031032_R04C02


title: tumor_A2B5+_01

description:
CGCLG_062108_HG-U133_Plus_2_AF28482_1
low grade tumor

source_name: tumor, oligodendroglioma low grade, A2B5+ sort

value: oligodendroglioma


title: Blood_AMS_5958091028_R02C02

value: Male


title: tumor_A2B5+_02

description:
CGCLG_062108_HG-U133_Plus_2_AF28484_1
low grade tumor

value: astrocytoma


title: Blood_BMS_MVL416-1


title: CTX_unsorted_04

description:
FJS324_Goldman_U133Plus_2
normal

source_name: cortex, unsorted

value: cortex

value: epilepsy

value: unsorted

value: non-tumor


title: Blood_AMS_MVL414-1

value: AMS


title: Blood_BMS_5958031032_R01C02


title: Blood_BMS_5958031032_R02C02


title: Blood_AMS_MVL411-1


title: B6 MZ B cells, biological replicate 1

description: Gene expression data from splenic B6 MZ B cells

source_name: Splenic B6 MZ B cells

value: female

value: 7 weeks

value: MZ


title: CTX_unsorted_02

description:
FJS267_Goldman_U133Plus_2
normal


title: NOD T1 B cells, biological replicate 1

value: NOD/ShiLtJ (NOD)

value: splenic B cells


title: Blood_BMS_MVL410-1

value: BMS

value: Female

value: Whole blood


title: tumor_A2B5+_07

description:
CGCLG_062108_HG-U133_Plus_2_AF28497_1
high grade tumor

value: tumor

value: glioblastoma

value: IV


title: Blood_BMS_MVL413-1


title: CTX_unsorted_03

description:
FJS318_Goldman_U133Plus_2
normal


title: Blood_AMS_5958031032_R03C02


title: B6 T2MZ B cells, biological replicate 2

description: Gene expression data from splenic B6 T2MZ B cells

source_name: Splenic B6 T2MZ B cells


title: B6 MZ B cells, biological replicate 2


title: Blood_AMS_5765301054_R06C01


title: B6 FO B cells, biological replicate 2

description: Gene expression data from splenic B6 FO B cells

source_name: Splenic B6 FO B cells

value: FO


title: CTX_unsorted_01

description:
FJS198_Goldman_U133Plus_2
normal

value: cortex


title: B6 T2MZ B cells, biological replicate 1


title: Blood_AMS_5765301054_R05C02


title: CTX_A2B5+_05

description:
FJS325_Goldman_U133Plus_2
normal

source_name: cortex, glial progenitor cell, A2B5+ sort

value: epilepsy

value: glial progenitor cell


title: Blood_AMS_5765301054_R03C01


title: Blood_BMS_5765301054_R04C02


title: Blood_BMS_MVL407-1

source_name: whole blood from offspring born before maternal bariatric surgery


title: B6 FO B cells, biological replicate 1


title: CTX_A2B5+_02

description:
FJS265_Goldman_U133Plus_2
normal

value: non-tumor


title: CTX_A2B5+_01

description:
FJS196_Goldman_U133Plus_2
normal


title: Blood_AMS_MVL402-1

value: AMS


title: Blood_AMS_MVL405-1

value: Male


title: Blood_AMS_5765301054_R04C01

source_name: Whole blood


title: Blood_BMS_MVL404-1


title: B6 T2FO B cells, biological replicate 2

description: Gene expression data from splenic B6 T2FO B cells

source_name: Splenic B6 T2FO B cells

value: female

value: 7 weeks


title: B6 T3 B cells, biological replicate 1

description: Gene expression data from splenic B6 T3 B cells

source_name: Splenic B6 T3 B cells


title: B6 T3 B cells, biological replicate 2


title: Blood_BMS_MVL401-1


title: Blood_AMS_MVL399-1

source_name: whole blood from offspring born after maternal bariatric surgery


title: Blood_BMS_5765301054_R01C01


title: Blood_BMS_5765301040_R06C02


title: Blood_BMS_5765301054_R02C01


title: B6 T2FO B cells, biological replicate 1


title: Blood_AMS_MVL408-1


title: Blood_AMS_5765301054_R02C02


title: Blood_AMS_MVL398-1


title: Blood_AMS_5765301054_R01C02


title: Blood_BMS_MVL397-1


title: U10

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Hybridization buffer: Supply by Genisphere 3DNA kits.  Slide blocking: 3x SSC, 0.1% SDS, 0.1 mg/mL BSA. Prehybridization for 30 min at 50°C.  wash procedure:  1x 10 min with 2x SSC, 0.2% SDS at 60oC;   1x 10 min with 2x SSC, at room temperature;  1x 10 min with 0.2x SSC at room temperature;  spin-dried at 250 x g for 3 min.  first step Hybridization: overnight (16 h), 25 µl, at 60 °C;  second step Hybridization: 2 h, 25 µl, at 60 °C.  hybridization instruments: 10-slide hybridization chamber (Genetix)

scan_protocol: Axon GenePix4000A  GenePix Pro 4.1 software (Axon Instrument, Inc.)  Expected spot diameter: 140 Micrometer.  PixelSize = 10

data_processing: Normalization strategy : total array   Normalization algorithm : Lowess (local weighted regression), available http://www.stat.berkeley.edu/users/terry/zarray/Html/soft.html

label_protocol: 2 µg of total RNA (Genisphere 3DNA-Random Primer)  Genisphere 3DNA-Random Primer Submicro Expression Array Detection Kit (category # W300130/W300140);.

growth_protocol: ulcerative and polypoid CRC

extract_protocol: Cells were grown at 37oC in RPMI1640 medium or DMEM supplemented with 10% FCS and 1% antibiotics.  Cell were trypsinized from culture dish. Cell pellets were harvested and washed with PBS and subjected to RNA extraction.  Total RNA was extracted from the RR cells with TRIzol reagent (Gibco BRL) following the manufacturer’s instructions. The concentration, purity, and amount of total RNA were determined by ultraviolet spectrometry.

treatment_protocol: Therapeutic surgery

tag: race

value: Han Chinese

value: ulcerative colorectal cancer

source_name: normal mucosa_U10

value: normal mucosa


title: U19

source_name: normal mucosa_U19


title: Blood_AMS_5765301040_R06C01

value: Female


title: U11

source_name: normal mucosa_U11


title: B6 T1 B cells, biological replicate 1

description: Gene expression data from splenic B6 T1 B cells

source_name: Splenic B6 T1 B cells

value: splenic B cells


title: Blood_BMS_MVL396-1

value: BMS

value: Whole blood


title: B6 T1 B cells, biological replicate 2


title: F187_Swg_37 hr_rep1

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

description: F187_Swg_37 hr_rep1

hyb_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing: Statistical analysis was done with JMP Genomics 4.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the Loess normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

organism: Acetivibrio thermocellus ATCC 27405

source_name: Clostridium thermocellum 27405 growth on switchgrass

growth_protocol: Batch fermentations were conducted in approximately 5 L of MTC medium in 7.5 L BioFlo110 biopreactors (New Brunswick Scientific, Edison, NJ) fitted with agitation, pH and temperature probes and controls as described previously (Yang et al., 2008).

extract_protocol: Cells were harvested by centrifugation and resuspended in Trizol reagent (Life Technologies, CA).  The suspension was transferred to a 2.0 mL screw top tube containing 800 mg of ashed glass beads.  Trizol was added to make up any remaining volume in the tube and then each tube was disrupted for three 20 second bead beating treatments at 6,500 rpm in a Precellys 24 high-throughput tissue homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France).  Chloroform was added and mixed with the sample, and then separated by centrifugation.  The aqueous layer was collected in fresh tubes and a 1:1 volume of 75% ethanol was added.  After mixing, the sample was applied to an RNeasy column (Qiagen, CA) and processed following the manufacturer’s instructions including an on column DNA digestion.  Total cellular RNA was quantified with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DE) and RNA quality was assessed with Agilent Bioanalyzer (Agilent, CA).  The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

treatment_protocol: Clostridium thermocellum was grown in batch fermentations with populus or switchgrass.  Total RNA was recovered at 12 and 37 hours for comparison.

tag: batch fermentations with

value: switchgrass

tag: time (hours)


title: F187_Swg_12 hr_rep1

description: F187_Swg_12 hr_rep1

scan_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: CTX_A2B5+_03

description:
FJS319_Goldman_U133Plus_2
normal


title: Blood_AMS_MVL394-1


title: F188_Pop_12 hr rep1

description: F188_Pop_12 hr rep1

source_name: Clostridium thermocellum 27405 growth on Populus

label_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

value: Populus


title: U08

source_name: normal mucosa_U08


title: Blood_AMS_MVL393-1


title: Blood_BMS_5765301040_R05C02


title: Blood_AMS_5765301040_R03C01


title: Blood_BMS_MVL392-1


title: F186_Swg_37 hr_rep1

description: F186_Swg_37 hr_rep1


title: F188_Pop_37 hr rep1

description: F188_Pop_37 hr rep1


title: Blood_BMS_5765301040_R02C02


title: Blood_BMS_5765301040_R04C01


title: Blood_AMS_5765301040_R05C01


title: U23

source_name: normal mucosa_U23


title: Blood_AMS_5765301040_R03C02


title: F185_Pop_37 hr rep1

description: F185_Pop_37 hr rep1


title: Blood_BMS_MVL385-1


title: Blood_BMS_5765301032_R05C01


title: Iron-limited 2, day 3

city: New Brunswick

first: Kim

last: Thamatrakoln

state: New Jersey

address: 71 Dudley Road

institute: Rutgers University

description: Gene expression in iron-limited cultures in late exponential phase

hyb_protocol: Hybridization was performed for 40 h, rotating at a speed of 10 rpm in a 65 degree C oven; Hybridized slide was washed using a commerical kit from Agilent Technologies

scan_protocol: Slide was scanned using an Agilent A2565BA microarray scanner

data_processing: Scanned images were anlayzed and normalized signal intensities obtained by normalizng the median signal intensity to 1.

organism: Thalassiosira pseudonana

source_name: Cells were grown in replete media, then washed and resuspended in iron-free media; cells were harvested on day 3

label_protocol: Amplified cDNA was fragmented and biotin-labeled with FL-Ovation cDNA Fluorescent Module (NuGEN) according to manufacturer's instructions

growth_protocol: All cultures were maintained at 18 degree C on a 14:10 light:dark cycle with constant bubbling, growth irradiance was approximately 100 umol photons/m2/s, replete media was f/2; iron-free media was f/2 without iron added

extract_protocol: Total RNA was extracted using Trizol according to manufacturer's protocol

treatment_protocol: Exponentially growing replete cultures were collected by filtration, washed in iron-free media, and resuspended in either replete or iron-free media

tag: nutrient condition

value: Iron-limited

tag: growth stage

value: late exponential


title: U29

source_name: normal mucosa_U29


title: P30

source_name: polypoid CRC_P30

value: polypoid colorectal cancer

source_name: normal mucosa_P30


title: P31

source_name: polypoid CRC_P31

source_name: normal mucosa_P31


title: Blood_BMS_MVL391-1

source_name: whole blood from offspring born before maternal bariatric surgery


title: U24

source_name: normal mucosa_U24


title: Blood_BMS_5765301032_R06C02

source_name: Whole blood


title: Blood_BMS_5765301032_R06C01


title: Blood_AMS_MVL386-1

source_name: whole blood from offspring born after maternal bariatric surgery


title: Blood_BMS_MVL388-1


title: Blood_BMS_MVL384-1


title: U09

source_name: normal mucosa_U09


title: Iron-limited 2, day 5

description: Gene expression in iron-limited cultures in stationary phase

source_name: Cells were grown in replete media, then washed and resuspended in iron-free media; cells were harvested on day 5

value: stationary


title: Blood_BMS_5765301040_R01C02


title: Iron-limited 1, day 5


title: Blood_AMS_5765301032_R04C02

value: AMS


title: P20

source_name: polypoid CRC_P20

source_name: normal mucosa_P20


title: P21

source_name: polypoid CRC_P21

source_name: normal mucosa_P21


title: P13

source_name: polypoid CRC_P13

source_name: normal mucosa_P13


title: Blood_AMS_MVL382-1


title: Blood_AMS_MVL380-1

value: Male


title: Iron-limited 1, day 3

source_name: Cells were grown in replete media, then washed and resuspended in iron-free media; cells were harvested on day 3


title: F186_Swg_12 hr_rep1

description: F186_Swg_12 hr_rep1

source_name: Clostridium thermocellum 27405 growth on switchgrass


title: Blood_AMS_MVL376-1


title: Blood_AMS_MVL381-1


title: Replete 1, day 5

description: Gene expression in replete cultures in stationary phase

source_name: Cells grown in replete media, harvested on day 5

value: Replete


title: Replete 2, day 3

description: Gene expression in replete cultures in late exponential phase

source_name: Cells grown in replete media, harvested on day 3


title: P15

source_name: polypoid CRC_P15

source_name: normal mucosa_P15


title: Blood_BMS_MVL372-1

source_name: whole blood from offspring born before maternal bariatric surgery


title: Blood_BMS_5765301032_R04C01

source_name: Whole blood


title: P12

source_name: polypoid CRC_P12

source_name: normal mucosa_P12


title: Blood_BMS_5765301032_R03C02


title: Blood_AMS_5765301032_R03C01


title: P16

source_name: polypoid CRC_P16

source_name: normal mucosa_P16


title: Replete 2, day 5


title: Blood_AMS_5765301032_R02C01


title: Blood_BMS_5765301032_R01C02


title: Replete 1, day 3


title: CNE-1-empty vector

status: Public on May 15 2013

city: Suzhou

first: Li

last: Wei

state: Jiangsu

address: 199# ren’ai road

department: Medical College of Soochow University

country: China

institute: soochow university

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Control

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

value: Human nasopharyngeal carcinoma (NPC)


title: CNE-1-miRNA-608-G

description: replicate 1

source_name: miRNA-608 rs4919510G phenotype


title: CNE-1-miRNA-608-C

description: replicate 1

source_name: miRNA-608 rs4919510C phenotype


title: PTEN KO 3

city: Athens

first: Xuanyang

last: Li

state: GA

address: 315 Riverbend Rd

department: Biochemistry&Molecular Biology

institute: University of Georgia

description: Gene expression data from 5-week-old prostate

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 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 with AltAnalyze using the RMA algorithm Affymetrix default analysis settings.

source_name: Pten Knockout prostates at 5 weeks of age

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: Mice were genotyped  and housed in standard mouse room conditions (Jackson Laboratory)

extract_protocol: RNA extraction was performed according to the standard protocol of RNeasy kit (QIAGEN Inc.).

treatment_protocol: Dorsal, lateral, ventral and anterior prostate lobes were dissected and immersed immediately in RNALater(QIAGEN Inc.). All the lobes of an individual mouse were pooled and homogenized using a Kinematica PT 2100 homogenizer.

value: prostate

tag: genotype

value: PB-Cre+ Pten f/f

value: 5 weeks


title: WT 3

source_name: Wildtype prostates at 5 weeks of age

value: Wildtype


title: PTEN KO 2


title: PTEN EXT KO 1

source_name: Pten and Ext1 Knockout prostates at 5 weeks of age

value: PB-Cre+ Pten f/f Ext1 f/f


title: Blood_AMS_5765301016_R05C02

value: Female


title: Blood_BMS_5765301016_R06C01

value: BMS


title: PTEN EXT KO 3


title: Blood_BMS_5765301032_R01C01


title: PTEN KO 1


title: Blood_AMS_5765301016_R03C01


title: Blood_AMS_5765301016_R02C02


title: F185_Pop_12 hr rep1

description: F185_Pop_12 hr rep1

source_name: Clostridium thermocellum 27405 growth on Populus


title: WT 1


title: Usp22 depleted replicate 1

city: Philadelphia

middle: B

last: McMahon

state: PA

department: Cancer Biology

institute: Thomas Jefferson University

hyb_protocol: Affymetrix gene chips, Mouse gene 1.0 ST array (Affymetrix, Santa Clara, CA), were hybridized with fragmented and biotin-labeled target (2.5 mg) in 110 μl of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h. Arrays were then washed and stained using Gene chip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG and anti-streptavidin biotinylated antibody.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software

data_processing: Background correction and normalization were done using Iterative Plier 16 with GeneSpring V12.0 software (Agilent, Palo Alto, CA, USA). 1.5-fold (p-value<0.12) differentially expressed gene list was generated. The differentially expressed gene list was loaded into Ingenuity Pathway Analysis (IPA) 8.0 software (http://www.ingenuity.com) to perform biological network and functional analyses.

source_name: 2i/LIF maintained Usp-22 depleted Embryonic Stem Cell

label_protocol: cDNAs were fragmented and chemically labeled with biotin to generate biotinylated ST-cDNA using FL-Ovation cDNA biotin module V2 (NuGen Technologies, Inc.).

growth_protocol: Mouse ESCs were maintained in feeder-free conditions on gelatin-coated plates in 20% defined FBS-DMEM supplemented with 1% L-glutamine, 1% HEPES, 1% NEAA, 0.001% beta-merceptoethanol, and fresh LIF. The MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CH99021 (3 μM), together known as 2i, were added fresh along with LIF.

extract_protocol: mRNA was harvested using Trizol reagent and cleaned up using Rneasy column from Qiagen

treatment_protocol: E14 mESCs were infected with lentivirus containing shRNA targeting Usp22 or control (Luc).  RNA was extracted from both samples and subjected to expression analysis by affymetrix array.

tag: treatment

value: Usp22 depletion


title: Usp22 depleted replicate 2


title: PYR48_3

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

description:
PYR48
Biological rep3.
Gene expression in zebrafish embryo at 48 hpf.

hyb_protocol: Equal amounts of Cy3- and Cy5-labeled samples were mixed, fragmented, and hybridized to Agilent Zebrafish V2 array chips.

scan_protocol: Agilent Technologies Scanner G2505C 3um 20bit.

data_processing: Raw intensity data were processed by Agilent Feature Extraction software using Lowess normalization.

organism: Danio rerio

source_name: Zebrafish embryos exposed to pyrene until 48 hpf

label_protocol: cDNA was synthesized from 1.2 μg of total RNA from each sample and labeled with Cy3 (experimental samples) or Cy5 (pooled control sample) according to the Agilent protocol with minor modifications.

extract_protocol: Embryos were homogenized in TriReagent (Molecular Research Center, Cincinnati, OH) at 24 and 48 hpf for RNA isolation. Total RNA was isolated with phenol-chloroform extraction, and RNA was quantified and quality confirmed with a NanoDrop ND-1000 UV-Vis spectrophotometer and Agilent Bioanalyzer 2100.

treatment_protocol: 1,2-benzanthracene (99%), dibenzothiophene (>99%), and pyrene (99%) were purchased from Sigma-Aldrich and dissolved in DMSO (J.T. Baker) at 25 mM, 50 mM and 50 mM concentrations, respectively. Embryos were cleaned, developmentally staged, and batch-exposed in glass vials at 6 hours post fertilization (hpf) with chorions intact to PAHs or vehicle control with 1% final DMSO concentration in E2 embryo medium (Kimmel, 1995). Exposures were conducted on a rocker and protected from light until experimental time points (24 or 48 hpf). Microarray exposures were conducted with 40 embryos per vial in 4 ml solution. Four independent biological replicates were prepared for each treatment.

tag: strain

value: wild type

value: whole embryo

value: pyrene (PYR)

tag: time

value: 48 hpf

source_name: Pool of zebrafish embryos exposed to DMSO control until 24 and 48 hpf

value: DMSO

value: 24 and 48 hpf combined

tag: sample type

value: reference


title: PYR48_2

description:
PYR48
Biological rep2.
Gene expression in zebrafish embryo at 48 hpf.

tag: tissue


title: control replicate 2

source_name: 2i/LIF maintained Embryonic Stem Cell

value: control


title: WT 2

tag: age


title: PYR48_4

description:
PYR48
Biological rep4.
Gene expression in zebrafish embryo at 48 hpf.


title: PYR24_3

description:
PYR24
Biological rep3.
Gene expression in zebrafish embryo at 24 hpf.

source_name: Zebrafish embryos exposed to pyrene until 24 hpf

value: 24 hpf


title: DMSO48_4

description:
DMSO48
Biological rep4.
Gene expression in zebrafish embryo at 48 hpf.

source_name: Zebrafish embryos exposed to DMSO control until 48 hpf


title: DMSO24_4

description:
DMSO24
Biological rep4.
Gene expression in zebrafish embryo at 24 hpf.

source_name: Zebrafish embryos exposed to DMSO control until 24 hpf


title: PYR24_1

description:
PYR24
Biological rep1.
Gene expression in zebrafish embryo at 24 hpf.


title: DMSO48_2

description:
DMSO48
Biological rep2.
Gene expression in zebrafish embryo at 48 hpf.


title: PYR24_4

description:
PYR24
Biological rep4.
Gene expression in zebrafish embryo at 24 hpf.


title: PYR24_2

description:
PYR24
Biological rep2.
Gene expression in zebrafish embryo at 24 hpf.


title: PYR48_1

description:
PYR48
Biological rep1.
Gene expression in zebrafish embryo at 48 hpf.


title: DMSO48_1

description:
DMSO48
Biological rep1.
Gene expression in zebrafish embryo at 48 hpf.


title: DMSO48_3

description:
DMSO48
Biological rep3.
Gene expression in zebrafish embryo at 48 hpf.


title: Blood_BMS_5765301016_R04C02

source_name: Whole blood

tag: status

tag: Sex


title: DMSO24_2

description:
DMSO24
Biological rep2.
Gene expression in zebrafish embryo at 24 hpf.


title: DBT48_3

description:
DBT48
Biological rep3.
Gene expression in zebrafish embryo at 48 hpf.

source_name: Zebrafish embryos exposed to dibenzothiophene until 48 hpf

value: dibenzothiophene (DBT)


title: DBT48_4

description:
DBT48
Biological rep4.
Gene expression in zebrafish embryo at 48 hpf.


title: DMSO24_3

description:
DMSO24
Biological rep3.
Gene expression in zebrafish embryo at 24 hpf.


title: DMSO24_1

description:
DMSO24
Biological rep1.
Gene expression in zebrafish embryo at 24 hpf.


title: PTEN EXT KO 2

description: Gene expression data from 5-week-old prostate

value: prostate


title: control replicate 1


title: DBT48_2

description:
DBT48
Biological rep2.
Gene expression in zebrafish embryo at 48 hpf.


title: DBT24_2

description:
DBT24
Biological rep2.
Gene expression in zebrafish embryo at 24 hpf.

source_name: Zebrafish embryos exposed to dibenzothiophene until 24 hpf


title: DBT24_3

description:
DBT24
Biological rep3.
Gene expression in zebrafish embryo at 24 hpf.


title: Naive tumor-specific CD4+ T cells, biological rep1

city: Oslo

first: Alexandre

last: Corthay

address: Rikshospitalet

department: Department of Biosciences

country: Norway

institute: University of Oslo

description: Non activated (from naive mice)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneChip Operating Software 1.3 (Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: mouse tumor-specific CD4+ T cells, non activated

growth_protocol: in vivo activated T cells.

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

treatment_protocol: TCR-transgenic mice were challenged s.c. with MOPC315 myeloma cells.

value: tumor-specific CD4+ T cells

tag: cell type

tag: background strain

value: Balb/c

value: adult (7-12 weeks)


title: DBT24_4

description:
DBT24
Biological rep4.
Gene expression in zebrafish embryo at 24 hpf.


title: Naive tumor-specific CD4+ T cells, biological rep2

description: Non activated (from naive mice)

value: mouse tumor-specific CD4+ T cells, non activated


title: DBT48_1

description:
DBT48
Biological rep1.
Gene expression in zebrafish embryo at 48 hpf.


title: DBT24_1

description:
DBT24
Biological rep1.
Gene expression in zebrafish embryo at 24 hpf.


title: Activated tumor-specific CD4+ T cells, biological rep3

description: Day +8 in vivo activated

source_name: mouse tumor-specific CD4+ T cells, activated


title: Activated tumor-specific CD4+ T cells, biological rep1

description: Day +8 in vivo activated

value: mouse tumor-specific CD4+ T cells, activated


title: BAA48_4

description:
BAA48
Biological rep4.
Gene expression in zebrafish embryo at 48 hpf.

source_name: Zebrafish embryos exposed to benzanthracene until 48 hpf

value: benzanthracene (BAA)


title: red5-2

city: Tsukuba

first: Tomoyasu

last: Sugiyama

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: This sample is of S.pombe carrying red5-2 mutation.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Schizosaccharomyces pombe

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

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 26˚C.

extract_protocol: Total RNA was extracted using mirVana miRNA isolation kit (Applied Biosystems) according manufacturer's instructions.

treatment_protocol: Culture temperature was shifted to 37˚C, and then S. Pombe cells were cultured for 4 hours.


title: BAA48_3

description:
BAA48
Biological rep3.
Gene expression in zebrafish embryo at 48 hpf.

value: wild type


title: BAA48_2

description:
BAA48
Biological rep2.
Gene expression in zebrafish embryo at 48 hpf.

value: whole embryo


title: BAA48_1

description:
BAA48
Biological rep1.
Gene expression in zebrafish embryo at 48 hpf.


title: WT 2

city: Munich

first: Jacek

last: Puchałka

address: Lindwurmstrasse 2a

department: University Children's Hospital

country: Germany

institute: Munich University Hospital

description: Samples of P.putida KT2440 WT taken in steady state from a continuous carbon-limited culture grown on mineral medium with 10 Mm glucose as sole carbon end energy source. Second technical relicate.

hyb_protocol: The labelled and fragmented cDNA was hybridized to high-density oligonucleotide microarrays of Nimble ExpressTM arrays (Roche, Switserland)/ hybridisation and washing of the microarrays were performed on a Genechip® Node system (Hybridisation tempearture 49°C/ Hybrdisation oven 640/Fluidics Station 450/ Affymetrix, Santa Clara, CA, USA) following the supplier´s instructions

scan_protocol: High resolution Gene Chip® Scanner 3000 7G System with autoloader (Affymetrix, Santa Clara, CA, USA).

data_processing: Bioconductor microarray analysis suite/ Raw data were normalized and the expression values computed, with the GC-RMA algorithm using default parameters. The Rank products algorithm was used to identify differentially expressed genes in pairwise comparisons between two conditions.

organism: Pseudomonas putida KT2440

source_name: P. putida KT2440 WT grown in continuous culture with 10mM glucose

label_protocol: cDNA was generated from mRNA by using the Affymetrix Poly-A RNA control Kit and random priming (Affymetrix, USA)/ 0.8-1.2 µg of cDNA was fragmented with 0.1 U DNaseI (Pharmacia Biotech, Sweden) per µg DNA at 37ºC for 10 min/ The fragments were labelled with biotinylated GeneChip® DNA labeling reagent (Affymetrix, USA)

growth_protocol: contnuous culture, 10 mM glucose, E-2 mineral medium, with or without the presence of 5 mM benzoate

extract_protocol: Qiagen® RNeasy Mini Purification Kit and QIAGEN® RNase-Free DNase Set (Qiagen, The Netherlands)/ 10 µg of the bacterial RNA was purified from ribosomal RNA by the Ambion® MICROBExpress Bacterial mRNA Purification

treatment_protocol: Samples of 1 ml were taken from the cultures and immediately cooled by adding 1 ml of very cold methanol (-80 ºC)/ The samples were quickly centrifuged at 16,873 × g at 4°C for 50 s, after which the supernatant was discarded/ 1 ml RNA later ® (Ambion, USA) was added to stabilize and protect the RNA in the cells/ The tubes were vortexed for 1 second and incubated at 4°C for 1-2 h, after which the cells were harvested by centrifugation (16,873 × g, 4 °C, 1 min)/ The cell pellet was dried for 5 min, frozen in liquid nitrogen, and stored at -80 ºC.

tag: genotype/variation

value: wildtype


title: WT+ben 2

description: Samples of P.putida KT2440 WT taken in steady state from a continuous carbon-limited culture grown on mineral medium with 10mM glucose and 5 M benzoate as sole carbon end energy source. Second technical relicate.

source_name: P. putida KT2440 WT grown in continuous culture with 10mM glucose + 5mM benzoate


title: JD1+ben 1

description: Samples of P.putida KT2440 JD1 taken in steady state from a continuous carbon-limited culture grown on mineral medium with 10mM glucose and 5 M benzoate as sole carbon end energy source. First technical relicate.

organism: Pseudomonas putida

source_name: P. putida KT2440 JD1 grown in continuous culture with 10mM glucose + 5mM benzoate

value: mutant in catR gene


title: JD1 2

description: Samples of P.putida KT2440 JD1 taken in steady state from a continuous carbon-limited culture grown on mineral medium with 10 Mm glucose as sole carbon end energy source. Second technical relicate.

source_name: P. putida KT2440 JD1 grown in continuous culture with 10mM glucose


title: BAA24_1

description:
BAA24
Biological rep1.
Gene expression in zebrafish embryo at 24 hpf.

source_name: Zebrafish embryos exposed to benzanthracene until 24 hpf

value: DMSO


title: wild-type

description: This sample is of wild-type S.pombe.

value: wild-type


title: BAA24_2

description:
BAA24
Biological rep2.
Gene expression in zebrafish embryo at 24 hpf.

value: 24 and 48 hpf combined

value: reference


title: WT+ben 1

description: Samples of P.putida KT2440 WT taken in steady state from a continuous carbon-limited culture grown on mineral medium with 10mM glucose and 5 M benzoate as sole carbon end energy source. First technical relicate.


title: JD1 1

description: Samples of P.putida KT2440 JD1 taken in steady state from a continuous carbon-limited culture grown on mineral medium with 10 Mm glucose as sole carbon end energy source. First technical relicate.


title: BAA24_3

description:
BAA24
Biological rep3.
Gene expression in zebrafish embryo at 24 hpf.

value: 24 hpf


title: BAA24_4

description:
BAA24
Biological rep4.
Gene expression in zebrafish embryo at 24 hpf.


title: C10-437

city: Fort Detrick

first: Meskerem

last: Jibitu

address: 568 Doughten Drive

department: Integrative Systems Biology

institute: US Army Center for Environmental Health Research

description: 1_5 Controls

hyb_protocol: The samples were hybridized to Agilent 4 x 44k slides (platform number: 14868) and left for 16 h at 55˚C.  Reference and sample RNAs were tagged with Cy-3 and Cy-5 dyes with a series of washes.  We left the slides for overnight hybridizations and performed series of subsequent washings

scan_protocol: We scanned the slides using an Agilent DNA microarray scanner and extracted the features (Feature Extraction software v. 10.7, Agilent, CA).

data_processing:
We used GeneSpring v. 10.1 (Agilent Technologies, Inc., CA) to carry out the preliminary data filtration and statistical analysis.  Each chip was subjected to intra-chip normalization using the locally weighted scatter-plot smoothing method (LOWESS) (Berger et al., 2004).  We identified the genes differently expressed between the hemibrains of mice fed by FD vs. SD based on ±1.5 fold change cut-off with FDR < 0.05.
Based on 1.5 +_ fold change cut off

source_name: pooled Hemi brain  mouse tissue cell line

label_protocol: individually labeled 200-2000 ng purified RNA was labeled by Biotin and the reference RNA (Agilent, CA) by Fluorescein

growth_protocol: C57BL/6J male mice were purchased from Jackson Laboratory (Bar Harbor, ME) at the age of 3 weeks, single-housed and introduced to either SD or FD.  Mice had free access to their respective diets and standard lab-supplied liquids for next 5 months (~ 20 weeks) till the euthanasia

extract_protocol: On the day of nucleic acid isolation, we weighed organs before thawing and added the appropriate amount of TrizolTM (Invitrogen, NY). RNA and DNA were isolated from the TrizolTM sample as per the manufacturer’s guideline.  For the sake of consistency we always used the left hemibrans for this study.  Briefly, we homogenized the hemibrain in Tissue Lyzer (Qiagen, MD), phase separated from the organic phase after vigorous agitation, and collected the aqueous phase.  Serial alcohol-based precipitations and washings were performed on the aqueous phase to obtain RNA.  We quantified and qualified the isolated nucleic acids using the Agilent BioAnalyzer as reported earlier

treatment_protocol: We euthanized mice by cervical dislocation and removed the brains from the skulls.  The hemibrains were collected by a trained person with more than forty years experience in this particular job, who was kept blinded from the animal identities during the dissection period.  We snapped freeze the dissected brain parts saved in the individually labeled tubes and transferred them to the freezer at the end of the day.  The entire process starting with the brain removal from the skull to the snap-freeze of the last brain region took less than 20 minutes and described elsewhere in detail

value: Hemi brain

tag: diet

value: standard lab diet (SD)

source_name: C57BL/6j mice  consume Omega 3 enriched dietary supplements up to 5 month of age

value: 5 months

value: n-3 PUFA enriched diet (FD)


title: C10-435

description: 1_4 Controls


title: Activated tumor-specific CD4+ T cells, biological rep2

description: Day +8 in vivo activated

value: tumor-specific CD4+ T cells

value: Balb/c

value: adult (7-12 weeks)


title: JD1+ben 2

description: Samples of P.putida KT2440 JD1 taken in steady state from a continuous carbon-limited culture grown on mineral medium with 10mM glucose and 5 M benzoate as sole carbon end energy source. Second technical relicate.


title: WT 1

description: Samples of P.putida KT2440 WT taken in steady state from a continuous carbon-limited culture grown on mineral medium with 10 Mm glucose as sole carbon end energy source. First technical relicate.


title: C10-424

description: 1_1 Controls


title: ColdShock_K326_lea_24h_afternoon_r3

city: Neuchatel

first: Sam

last: Ansari

state: Neuchatel

address: Quai Jeanrenaud 5

department: Research & Development

country: Switzerland

institute: Philip Morris Products SA

description: QC Passed

hyb_protocol: Frozen samples (-80 Celsius) packed in dry ice were sent to DNA-Vision (Charleroi, Belgium). Total RNA isolation using a Trizol(R) method (Invitrogen 155596-018), microarray hybridization and quality checked by Agilent 2100 Bioanalyzer were executed at DNA-Vision and.  Affymetrix hybridizations were performed using Affymetrix kits with catalog numbers 900652 and 900454; probe labeling was checked as suggested by the manufacturer.

scan_protocol: Standard Affymetrix scanning procedure

data_processing:
An in-house QC pipeline was developed to assess the quality of the gene-expression data. In addition to the standard quality metrics suggested by Affymetrix, an in-house QC metrics including probe-level models, Normalized Unscaled Standard Error (NUSE) and Relative Log Expression (RLE) plots, and the analysis of DABG results were used. The QC pipeline involves a combination of Affymetrix Power Tools (APT) and Bioconductor packages, for which the Tobacco Exon Array (TobArray520623F) cdf environment was created.
As the exon array design had no mismatch probes, summarization was performed using Robust Multiarray Average (RMA) method. A total of 272,472 probesets expression values were generated, and DABG P-values were computed to assess the significance of the signal obtained for each probeset. This involved the background probes that are spread over the chip. Those random probes have a varying GC content. Once the expression values were available, differential gene analysis was performed using moderated t-statistics in linear model LIMMA. In addition, gene sets were defined by first annotating probesets by homology to Arabidopsis thaliana genes and using Arabidopsis thaliana gene sets, and mean-rank gene-set enrichment analysis was performed.

organism: Nicotiana tabacum

source_name: Leaves

label_protocol: Standard Affymetrix labeling procedure using biotin

growth_protocol: Tobacco seeds ofK326 varieties were germinated in floating trays and grown 6 weeks.

extract_protocol: Approximately 100 ug of plant tissue was placed in a 1.5 ml Eppendorf tube (1/3 in volume), and snap frozen in liquid nitrogen. RNA extraction was performed by two methods: Trizol(R) for microarray analysis and Qiagen RNeasy Plant mini kit for semi-quantitative RT-PCR.   In case of RNA extraction for microarray experiment, 400 ul of Trizol(R) reagent (Invitrogen) was added to the frozen plant tissue and the sample was ground to homogeneity before an additional 600 ul of Trizol(R) was added. Samples were vortexed for 15 sec, then incubated at for 5 min room temperature. 200 ul of chloroform was added and the tubes were gently mixed before centrifugation (12,000 x g) at a temperature of 4 Celsius for 15 min. The aqueous phase was transferred to an Eppendorf tube containing 500 ul of isopropyl alcohol. After 15 min incubation on ice, RNA was pelleted by centrifugation at a temperature of 4 Celsius for 10 min. The RNA pellet was finally washed with 1 ml of 70% ethanol, and centrifuged for five minutes a 7,500 x g. After air-drying, RNA was resuspended in 50 ul of nucleotide-free H2O. RNA concentration was analyzed by measuring optical density (OD) at 260 nm. RNA quality control was determined by OD260/OD280 and using Agilent 2100 Bioanalyzer before cDNA preparation.

treatment_protocol: Leaves were quickly chilled for 10 minutes in a blast chiller at a temperature included between 0 Celsius and 5 Celsius, monitored to avoid frost. After fast chilling, the samples were incubated at the same temperature for 5 hours or 24 hours before to be frozen in liquid nitrogen. Two harvesting times, one in the morning (7:30am) and one in the afternoon (1:00pm)

value: Induced Stress

tag: stress

value: ColdShock

tag: harvest time

value: afternoon

tag: pos-harvest time

tag: developmental stage

value: four leaves visible

tag: provider

value: DNAVision


title: C10-416

description: 1_2 Controls


title: C10-415

description: 1_1 Controls


title: Patient 143N

city: Tainan

first: Yi-Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

institute: National Cheng Kung University

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1120 experimental control probes).

hyb_protocol: HOA v4.2 arrays (Phalanx Biotech Group, Taiwan) were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 10 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 33 PMT 460; 532nm power 33, PMT 460) and quantify the fluoresence intensity.

data_processing: All signal intensities was combined together and processed background subtraction by Microsoft Excel 9.0 software. Keep those probes that flags of GenePix have to be equal to 0 and the signal/noise ratio should be more than 5 for further Quantile normalization developed from Matlab 7.3.

source_name: primary normal lung tissue

label_protocol: 5 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion). Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

extract_protocol: Total RNA was prepared from tumors and normal lung tissues using TRIzol reagent (Invitrogen), and cleaned up RNA with RNeasy mini kit (Qiagen) and RNase-free DNase set (Qiagen).

value: primary normal lung tissue

tag: sex

value: Male

value: 81 years


title: Patient 148N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1121 experimental control probes).

value: 78 years


title: Patient 152N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1122 experimental control probes).

value: 79 years


title: ColdShock_K326_lea_24h_afternoon_r1

description: QC Passed


title: C10-417

description: 1_3 Controls

tag: strain

value: Hemi brain


title: C10-423

description: 1_4 Controls

value: standard lab diet (SD)


title: C10-434

description: 1_3 Controls

value: 5 months


title: Patient 176N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1123 experimental control probes).

value: 50 years


title: Patient 139N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1119 experimental control probes).

value: 67 years


title: C10-425

description: 1_2 Controls

value: n-3 PUFA enriched diet (FD)


title: ColdShock_K326_lea_24h_afternoon_r2

description: QC Passed


title: W1_Daweizi pig

city: Beijing

first: Huimin

last: Kang

state: Beijing

address: Beijing

institute: China Agriculture University

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Standard NimbleGen protocol.

data_processing:
Spatial correction and Lowess data normalization, segmentation were performed using the DEVA 1.2 software (Roche-NimbleGen).
Two criteria, i.e., mean log2 ratio ≥ |0.5| and at least 5 consecutive probes0.5 log2 shift and 5 neighboring probes, were used to filter CNVs.

organism: Sus scrofa

source_name: [test] ear tissue

label_protocol: Test DNA and reference DNA samples were independently labeled with either Cy3 or Cy5 dyes.

extract_protocol: Genomic DNA for each  individuals was extracted from the ear tissue using Qiagen DNeasy Tissue kit (Qiagen, Germany).

tag: breed

value: Daweizi

tag: gender

value: female

source_name: [reference] ear tissue

value: Duroc


title: Patient 124N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1117 experimental control probes).

tag: tissue

value: 75 years


title: C10-413

description: 1_ 4 Controls

source_name: pooled Hemi brain mouse tissue cell line

tag: age


title: Patient 129N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1118 experimental control probes).

value: 77 years


title: Z2_Tibetan pig

value: Tibetan


title: ColdShock_K326_lea_24h_morning_r2

description: QC Passed

value: Induced Stress

value: ColdShock

value: morning

value: four leaves visible

value: DNAVision


title: ColdShock_K326_lea_24h_morning_r3

description: QC Passed


title: Patient 114N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1116 experimental control probes).

value: primary normal lung tissue

value: Male


title: Patient 104N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1115 experimental control probes).

value: 69 years


title: Patient 103N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1114 experimental control probes).

value: 62 years


title: ColdShock_K326_lea_5h_afternoon_r3

description: QC Passed

value: afternoon


title: MS7_Meishan pig

value: Meishan


title: ColdShock_K326_lea_5h_afternoon_r2

description: QC Passed


title: Patient 94N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1112 experimental control probes).

value: 58 years


title: DN5_Diannan small-ear pig

value: Diannan small-ear

value: female


title: Z5_Tibetan pig

value: Duroc


title: M2_Min pig

value: Min


title: DN1_Diannan small-ear pig

value: male


title: Y2_Yorkshire

value: Yorkshire


title: Patient 85N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1111 experimental control probes).

value: 66 years


title: ColdShock_K326_lea_24h_morning_r1

description: QC Passed

value: Induced Stress

value: ColdShock

value: morning


title: ColdShock_K326_lea_5h_morning_r2

description: QC Passed

value: four leaves visible

value: DNAVision


title: Patient 75N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1110 experimental control probes).

value: primary normal lung tissue

value: Male

value: 74 years


title: Patient 42N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1107 experimental control probes).

value: 73 years


title: A1_wild pig

value: wild


title: ColdShock_K326_lea_5h_morning_r1

description: QC Passed


title: Patient 44N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1108 experimental control probes).

value: 60 years


title: Patient 34N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1105 experimental control probes).

value: 65 years


title: Patient 48N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1109 experimental control probes).

value: 78 years


title: ColdShock_K326_lea_5h_morning_r3

description: QC Passed


title: Patient 26N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1104 experimental control probes).


title: Patient 41N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1106 experimental control probes).


title: R2_Rongchang pig

value: Rongchang

value: Duroc

value: female


title: Patient 100N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1113 experimental control probes).

value: 71 years


title: ColdShock_K326_lea_0h_afternoon_r2

description: QC Passed

value: Induced Stress

value: afternoon


title: MS8_Meishan pig

value: Meishan


title: C3_Landrace

value: Landrace


title: ColdShock_K326_lea_0h_afternoon_r1

description: QC Passed

value: ColdShock

value: four leaves visible

value: DNAVision


title: ColdShock_K326_lea_0h_morning_r3

description: QC Passed

value: morning


title: ColdShock_K326_lea_0h_afternoon_r3

description: QC Passed


title: B73_lowP_1

city: Erlangen

first: Urte

last: Schluter

address: Staudtstr. 5

department: Biology

institute: FA University Erlangen

hyb_protocol: After fragmentation, an aliquot of 1.65 µg of Cy3-labeled cRNA were hybridisied for 17h at 65°C on Mais_array (Agilent-025271). Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5).

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565B Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software version 11.7.1 (Agilent) using default parameters (protocol GE-v5_95_Feb07). The processed signals were log2 transformed and normalised to the 75th percentile followed by median base line correction using the Agilent GeneSpring GX 11.0 software. Normalisation was done across all samples.

organism: Zea mays

source_name: lamina sixth leaf, low phosphorus

label_protocol: Cy3-labeled cRNA were prepared according to the Agilent protocol from 500ng total RNA (One-Color Microarray-based gene expression analysis v.5.5).

growth_protocol: For all experiments, B73 seeds were incubated on wet filter paper for three days, and uniform seedlings were transferred into pots of 1.5L volume containing nutrient-poor peat soil (Basissubstrat 2, Klasmann & Deilmann, Germany). Fertilization started at day seven of the experiment with modified Hoagland solutions. The low temperature experiment was performed in two Snijders climate chambers (IMAGO F3000, Snijders Scientific) at 14h days with 28°C and 80% humidity, followed by 10h of night at 20°C and 50% humidity. Light intensity on soil level was ca. 600µmol m-2 s-1, and ca. 800µmol m-2 s-1 at the position of the highest leaves. All seedlings were allowed to establish in the pots under control conditions. The nutrient deficiency experiments (N, P) were performed in a CLF climate chamber (PlantMaster PGR 3045, CLF Plant Climatics GmbH, Germany) with a diurnal rhythm of 14h light (ca. 200 µmol m-2 s-1 at level of the soil surface and ca. 650 µmol m-2 s-1 just under the light source which was adjusted according to plant height to give maximal possible irradiance) at 28°C and 80% humidity, and 10h night at 20°C and 50% humidity.

extract_protocol: RNA was extracted from four biological replicates per treatment after the method described by Logemann et al. (1987) using 100mg of frozen leaf material. The isolated RNA was purified with the RNeasy purification kit according to the manufacturer's instructions (Qiagen, Germany). The quality was checked with the Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit.

treatment_protocol: Control and low temperature treated plants were supplied with full-strength Hoagland solution (15mM KNO3, 5mM CaCl2, 2mM MgSO4, 2mg/L Fe, 0.5mM KH2PO4, 50µM H3BO4, 10µM MnCl2, 1µM ZnSO4, 0.3µM CuSO4, 0.5µM Na2MoO4). For low N treatment, the nitrate content was reduced to 0.15mM KNO3, for low P treatment the phosphate content of the nutrient solution was 0.1mM KH2PO4. For low temperature treatment, conditions in one chamber were switched to night temperatures of 4°C at day seven after germination while all other settings were kept constant.

tag: maize inbred line

value: lamina sixth leaf

tag: treatment

value: phosphate supply reduced to 0.1mM KH2PO4

tag: plant age

value: day 30 after germination


title: B73_lowP_4


title: ColdShock_K326_lea_0h_morning_r2

description: QC Passed


title: Patient 148T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1100 experimental control probes).

source_name: primary lung tumor

value: primary lung tumor

tag: histology

value: AD

tag: stage

value: IV

value: Male


title: Patient 25N

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1103 experimental control probes).

value: primary normal lung tissue

value: 73 years


title: ColdShock_K326_lea_0h_morning_r1

description: QC Passed

value: Induced Stress


title: Patient 143T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1099 experimental control probes).

value: SQ

value: IB

value: 81 years


title: ColdShock_K326_lea_5h_afternoon_r1

description: QC Passed

value: ColdShock

value: afternoon


title: Patient 152T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1101 experimental control probes).

value: IA

value: 79 years


title: B73_controlP_3

source_name: lamina sixth leaf, control nutrient solution

value: lamina sixth leaf

value: control Hoagland solution


title: Patient 129T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1097 experimental control probes).

value: 77 years


title: B73_controlP_2

value: day 30 after germination


title: Patient 114T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1095 experimental control probes).

value: primary lung tumor

value: 67 years


title: B73_controlP_4


title: B73_lowN_3

source_name: lamina sixth leaf, low nitrogen

value: nitrate supply reduced to 0.15mM KNO3


title: B73_lowN_4


title: Patient 124T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1096 experimental control probes).

value: IIB

value: Male

value: 75 years


title: B73_lowN_1


title: B73_controlN_4


title: CFR / CFS

city: Paris

last: Pawlik

address: 28 rue du Dr. Roux

country: France

institute: Institut Pasteur

description: data table include data for 6 replicates (merge dye-swap)

hyb_protocol: The hybridization procedure has been done according to the manufacturer (Agilent)

scan_protocol: Fluorescent signals were acquired with a Genepix 4200AL microarray scanner (Axon Instruments) with 5 microns per pixel resolution. The PMT gain for the 635 and 532nm wavelengths were automatically set with control yellow hybridizations (sample hybridized versus itself). The quantification of the signal for each spot was performed with the image analysis GenePix Pro 6.0 software (Axon Instruments)

data_processing: All the data generated by the scan were imported into the statistical data analysis system R. The data were globally normalized using the Lowess regression approach. Data were then converted to relative ratio of fold activation changes. Differential analysis was conducted using the varmixt package and the VM method. To ensure the robustness of the results, the resulting raw P values were adjusted according to the Benjamini and Yekutieli method and a cutoff of significance was set to 0.05.

organism: Mycobacteroides abscessus

source_name: CFR

label_protocol: Labeled cDNA obtained by using the SuperScript Indirect cDNA Labeling System (Invitrogen)

growth_protocol: Strains were grown aerobically in Middlebrook 7H9-OADC media supplemented with 0.05% Tween 80 at 37°C

extract_protocol: Total RNA was extracted from cultures harvested during the exponential phase of growth (OD at 600nm between 0.7 and 0.8). A Trizol RNA isolation protocol (Invitrogen) was used with mechanical lysis via rapid agitation in the presence of 0.1 mm zirconium/glass beads in a Mini-Bead-Beater. The RNA samples were then treated with DNase (TURBO DNA-freeTM Kit, Ambion). The RNA concentrations were measured with a Nanodrop ND-1000 spectrophotometer. The RNA integrity/quality was monitored with a Bioanalyzer RNA nano assay.

value: CF

tag: variant

value: Rough

source_name: CFS

value: Smooth


title: Patient 104T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1094 experimental control probes).

value: AD

value: 69 years


title: B73_lowN_2


title: 19977-ATR / 19977-ATS


title: Patient 100T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1092 experimental control probes).

value: SQ

value: IB

value: 71 years


title: B73_controlP_1

value: lamina sixth leaf

value: control Hoagland solution


title: B73_controlN_3

value: day 30 after germination


title: PN6_testes_father_8T2R

city: Montreal

first: Jennifer

last: Maselli

state: Quebec

address: 3655 Prom Sir William Osler

institute: McGill University

description: Gene Expression

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

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software v10.7 (Agilent)

organism: Rattus norvegicus

source_name: PN6 testes from 8T2R

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Rneasy Micro kit with on-column DNase digestion (Qiagen)

value: Brown Norway male X Sprague Dawley female cross

value: Testis

value: male

value: Postnatal day 6


title: B73_controlN_2


title: PN6_testes_father_7T2R

description: Gene Expression

source_name: PN6 testes from 7T2R


title: Patient 94T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1091 experimental control probes).

value: primary lung tumor

value: IV

value: Male

value: 58 years


title: Patient 85T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1090 experimental control probes).

value: 66 years


title: Patient 75T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1089 experimental control probes).

value: AD

value: 74 years


title: B73_lowT_4

source_name: lamina fifth leaf, low temperature

value: lamina fifth leaf

value: low temperature (day 28°C/night 4°C)

value: day 20 after germination


title: human dermal fibroblast-fetal origin, biological repC

city: Beaverton

first: Shoukhrat

last: Mitalipov

address: 505 N.W. 185th Avenue

institute: Oregon National Primate Research Center

description:
human skin
gender: female,embryo: skin derived fibroblast culture
Gene expression profile of HDF-f is  parental human skin fibroblast for hESO-NT1 in biological replicate C.

hyb_protocol: Labeled target is fragmented at 95o C in Fragmentation Buffer (Affymetrix). The GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix) is used to complete the hybridization, wash, and staining processes for GeneChip arrays following the target preparation steps. The fragmented material is combined with biotinylated hybridization control oligomer B2 and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  8.8 μg of sample target is hybridized with the GeneChip Primeview Human array (Affymetrix) for 18 hours at 45°C, 45 rpm in an Affymetrix Hybridization Oven 645. The arrays are washed and stained on the Fluidics Station 450 (Affymetrix) in a multi-step process: stringent wash, staining with streptavidin-phycoerythrin, signal amplification with biotinylated anti-streptavidin antibody, and a final staining step. The distribution of fluorescent material on the processed array is determined using the GeneChip Scanner 3000 with the 7G upgrade (Affymetrix) and AGCC version 3.2 software (Affymetrix), yielding cell fluorescence intensity (.cel files). Image inspection is performed manually immediately following each scan.

scan_protocol: The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with AGCC version 3.2 software (Affymetrix), arrays are normalized in Expression Console using default Affymetrix parameters for 3’ IVT Expression Robust Multichip Analyis (RMA).  Sixteen values are examined to assess overall assay performance: corner, PM mean, probeset mean (all), Probeset stdev, MAD residual mean (All), MAD residual stdev  RLE mean (All), RLE stdev, Actin Ave signal, Actin 3’/5’ ratio, GAPDH Ave signal, GAPDH 3’/5’ ratio, and total Signal for probe sets for BioB, BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged.

data_processing: The processed image files (.CEL) were normalized across arrays using the robust multichip average (RMA) algorithm and log-transformed (base 2).After normalization, GeneSifter microarray expression analysis software was used to analyze the resultant data.

label: Biotin

source_name: HDF-f is fetal skin fibroblast culture from ScienCell Research Laboratories.

label_protocol: Microarray assays were performed in the the OHSU Gene Profiling Shared Resource. Messenger RNA is amplified and labeled from 200 ng of total RNA using the Affymetrix GeneChip 3’IVT Express Kit. In this protocol mRNA is converted to double-stranded cDNA using an oligo-dT primer linked to a T7 RNA polymerase binding site sequence and then amplified and labeled  in an in vitro transcription reaction to produce biotinylated cRNA (target). Following removal of free nucleotides, target yield is measured by UV260 absorbance.

growth_protocol: All humanESCs were grown at 37oC, 3% CO2, 5%O2 and 92% N2 upon mitotically inactivated mouse embryonic fibroblast (MEF) feeder cells in DMEM/F12 medium (Invitrogen) with 0.1 mM nonessential amino acids, 1 mM l-glutamine, 0.1 mM β-mercaptoethanol, 5 ng/ml basic fibroblast growth factor, 10µM ROCK inhibitor (Sigma), 10% fetal bovine serum and 10% knockout serum replacement (KSR; Invitrogen). Medium was changed daily and ESC colonies were split every 5-7 days by manual disaggregation and replating collected cells onto dishes with fresh feeder layers.

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions, and total RNA obtained by Trizol extraction was further purified using RNeasy spin columns (Qiagen) following manufacturer instructions.

treatment_protocol:
hESO-NT1 was established from human cloned blastocyst generated by SCNT of huam skin fibroblasts (HDF-f) at the Oregon National Primate Reearch Center. RNA were isolated from only nice undifferentiated colonies.
hESO-7 was established from human blastocyst generated by regular IVF using oocytes from identical donor for hESO-NT1 at the Oregon National Primate Reearch Center. RNA were isolated from only nice undifferentiated colonies.
A primary culture of female fetal skin fibroblasts (HDF-f) was obtained from ScienCell Research Laboratories and were cultured in  DMEM/F12 supplemented with 100 IU ml-1 penicillin, 100 μg ml-1 streptomycin (Invitrogen) and 10% FBS. RNA were isolated when cells reached confluency in 75 cm3 cell culture flasks.

value: female

tag: cell line

value: HDF-f


title: Patient 176T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1102 experimental control probes).

value: 50 years


title: B73_controlN_1

value: lamina sixth leaf

value: control Hoagland solution

value: day 30 after germination


title: PN6_testes_father_6T1R

description: Gene Expression

source_name: PN6 testes from 6T1R

value: Brown Norway male X Sprague Dawley female cross

value: Testis

value: male

value: Postnatal day 6


title: B73_lowP_3

value: phosphate supply reduced to 0.1mM KH2PO4


title: B73_lowT_3


title: B73_lowT_2


title: PN6_testes_father_4T1R

description: Gene Expression

source_name: PN6 testes from 4T1R


title: 19977-IPR / 19977-IPS

value: Rough

value: Smooth


title: Clonhuman Embryonic Stem cells in Oregon-7, biological repC

description:
ICM of human blastocyst derived by IVF
gender: female,embryo: Blastocyst, cell type: cloned embryonic stem cell
Gene expression profile of hESO-7 is IVF derived control in biological replicate C.

source_name: hESO-7 is embryonic stem cells which dereived from IVF blastocyst.


title: Patient 44T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1087 experimental control probes).

value: primary lung tumor

value: AD

value: IV

value: Male

value: 60 years


title: human dermal fibroblast-fetal origin, biological repA

description:
human skin
gender: female,embryo: skin derived fibroblast culture
Gene expression profile of HDF-f is  parental human skin fibroblast for hESO-NT1 in biological replicate A.

value: female

value: HDF-f


title: B73_lowT_1

value: lamina fifth leaf

value: low temperature (day 28°C/night 4°C)

value: day 20 after germination


title: human dermal fibroblast-fetal origin, biological repB

description:
human skin
gender: female,embryo: skin derived fibroblast culture
Gene expression profile of HDF-f is  parental human skin fibroblast for hESO-NT1 in biological replicate B.


title: Patient 48T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1088 experimental control probes).

value: IIIA

value: 78 years


title: Patient 42T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1086 experimental control probes).

value: 73 years


title: PN6_testes_father_6C1R

description: Gene Expression

source_name: PN6 testes from 6C1R

value: Brown Norway male X Sprague Dawley female cross

value: Testis

value: male

value: Postnatal day 6


title: human Embryonic Stem cells in Oregon-derived by NT,biological rep C

description:
ICM of human blastocyst derived by SCNT
gender: female,embryo: Blastocyst, cell type: cloned embryonic stem cell
Gene expression profile of hESO-NT1 is rhesus cloned ES in biological replicate C.

source_name: hESO-NT1 is embryonic stem cells which dereived from human SCNT blastocyst.


title: Patient 41T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1085 experimental control probes).

value: primary lung tumor

value: SQ

value: 74 years


title: B73_controlT_4

source_name: lamina fifth leaf, control temperature

value: control temperature (day 28°C/night 20°C)


title: human Embryonic Stem cells in Oregon-derived by NT,biological rep B

description:
ICM of human blastocyst derived by SCNT
gender: female,embryo: Blastocyst, cell type: cloned embryonic stem cell
Gene expression profile of hESO-NT1 is rhesus cloned ES in biological replicate B.


title: Patient 34T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1084 experimental control probes).

value: Male

value: 65 years


title: Clonhuman Embryonic Stem cells in Oregon-7, biological repB

description:
ICM of human blastocyst derived by IVF
gender: female,embryo: Blastocyst, cell type: cloned embryonic stem cell
Gene expression profile of hESO-7 is IVF derived control in biological replicate B.

value: female


title: B73_controlT_3

value: lamina fifth leaf


title: B73_controlT_2


title: PN6_testes_father_2C2R

description: Gene Expression

source_name: PN6 testes from 2C2R


title: Patient 26T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1083 experimental control probes).

value: AD

value: IB


title: PN6_testes_father_3C1R

description: Gene Expression

source_name: PN6 testes from 3C1R


title: human Embryonic Stem cells in Oregon-derived by NT,biological rep A

description:
ICM of human blastocyst derived by SCNT
gender: female,embryo: Blastocyst, cell type: cloned embryonic stem cell
Gene expression profile of hESO-NT1 is rhesus cloned ES in biological replicate A.


title: PN6_testes_father_5C1R

description: Gene Expression

source_name: PN6 testes from 5C1R


title: B73_controlT_1

value: day 20 after germination


title: PN6_testes_father_2T1R

description: Gene Expression

source_name: PN6 testes from 2T1R


title: Clonhuman Embryonic Stem cells in Oregon-7, biological repA

description:
ICM of human blastocyst derived by IVF
gender: female,embryo: Blastocyst, cell type: cloned embryonic stem cell
Gene expression profile of hESO-7 is IVF derived control in biological replicate A.


title: PN6_testes_father_4C1R

description: Gene Expression

source_name: PN6 testes from 4C1R


title: Patient 25T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1082 experimental control probes).

source_name: primary lung tumor

value: IIB


title: B73_lowP_2

source_name: lamina sixth leaf, low phosphorus

value: lamina sixth leaf

value: phosphate supply reduced to 0.1mM KH2PO4

value: day 30 after germination


title: Patient 139T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1098 experimental control probes).

value: IIIB

value: 67 years


title: Low GSK Rep 2

status: Public on May 14 2013

first: Robert

middle: L

last: Tanguay

department: EMT

description: 24 hpf zebrafish embryo exposed to Low GSK Rep 2

hyb_protocol: Hybridization was performed by Nimblegen processing center (Reykjavik, Iceland) following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Nimblegen processing center (Reykjavik, Iceland) following their standard operating protocol. See www.nimblegen.com.

source_name: 24 hpf Danio rerio, static waterborne exposed 8-24 hpf, 0.1 µM GSK

label_protocol: Labeling was performed by Nimblegen processing center (Reykjavik, Iceland) following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Embryos were incubated in fish water until 8 hpf, then exposed to vehicle control or chemical until 24 hpf, at 28 degrees Celcius

extract_protocol: total RNA was isolated using RNAzol protocol

treatment_protocol: Embryos were static waterborne exposed individually in 96-well microtiter plates (parafilm sealed and covered with foil) to either 0.1% DMSO control, 0.1 uM E2, or 0.1 uM GSK4716

tag: developmental state

value: 24 hpf

value: whole embryo

value: 0.1 µM GSK


title: Low GSK Rep 3

description: 24 hpf zebrafish embryo exposed to Low GSK Rep 3


title: rectal_primary_MO_32

city: Seoul

first: Jungsoo

middle: Ieden

last: Gim

state: Gwanak gu

address: Gwanak ro 1

country: South Korea

institute: Seoul National University

hyb_protocol: The labaled cDNA was hybridized to Affymetrix Human Gene 1.0ST arrays

scan_protocol: Scan was performed using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: All raw data were preprocessed using R program. CEL files were loaded and processed by background correction and normalized by robust multi-array average (RMA) algorithm (Irizarry et al., 2003) using R package. Resulting expressions are in log2-transformed intensity.

source_name: primary cancer cell

label_protocol: The RNA was amplified and labelled according to the Affymetrix GeneChip Whole Trasncript (WT) Sense Target Labelling protocol

tag: chemoradiation therapy response

value: MO

tag: Sex

value: male

tag: tumor stage (uicc-7th)

tag: description (operation)

value: LAR


title: gabazine 3

city: Barcelona

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

country: Spain

institute: CNAG,Centro Nacional de Análisis Genómico

description: treated (gabazine) cultures

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix GeneChip Rat Genome 230 2.0 Array (GPL1355). Washing and staining were performed after hybridization under Affymetrix fluidics station protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Low level analysis was performed using an Robust Multi-array Average (RMA) algorithm directly on the scanned images, using the R statistical software with Bioconductor packages as normalization method.

source_name: rat organotypic hippocampal cultures

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

extract_protocol: The total RNA for the microarray samples and the time-course samples was extracted using the TRIzol reagent (Sigma, Milano, Italy) according to the manufacturer’s instructions followed by a DNase I (Invitrogen, Carlsbad, California, USA) treatment to remove any genomic DNA contamination. The total RNA was further purified using RNeasy Mini Kit Column (Qiagen, Valencia, CA)

treatment_protocol: Gabazine was purchased from Tocris (Bristol, UK). Gabazine treatment (GabT) for microarray samples consisted in treating the cultures for 90 min with 20 µM of gabazine

value: gabazine

value: organotypic hippocampal cultures


title: Low GSK Rep 1

description: 24 hpf zebrafish embryo exposed to Low GSK Rep 1


title: rectal_primary_MO_29

value: I


title: rectal_primary_MO_31

value: female

value: ULAR


title: rectal_primary_TO_17

value: TO


title: control 2

description: untreated (control) cultures

value: control


title: control 3

description: untreated (control) cultures


title: rectal_primary_MO_25

value: IIIA


title: rectal_primary_MI_9

value: MI


title: rectal_primary_MO_30


title: rectal_primary_MO_28

value: IIIB

value: ISR


title: gabazine 1

description: treated (gabazine) cultures


title: rectal_primary_TO_15


title: rectal_primary_MO_27

value: IIA


title: rectal_primary_MO_24


title: rectal_primary_TO_16

value: lll


title: rectal_primary_MI_6


title: rectal_primary_TO_13

value: ELAR


title: gabazine 2

description: treated (gabazine) cultures


title: rectal_primary_MO_26

value: MO


title: rectal_primary_MI_8

value: male

value: IV


title: rectal_primary_TO_14


title: rectal_primary_NT_11

value: NT

value: ISR, colonic pouch, ileostomy, Rt PLND


title: control 1

description: untreated (control) cultures

value: organotypic hippocampal cultures


title: rectal_primary_MI_7

value: LAR


title: Patient 103T

description: Hybridization targets were prepared from total RNA and hybridized according to standard protocol using Phalanx Human OneArray chip (32,050 total features: 30968 human genome probes and 1093 experimental control probes).

value: primary lung tumor

value: SQ

tag: sex

value: Male

value: 62 years


title: rectal_primary_MI_4

value: MI

value: ISR, coloanal, ileostomy


title: rectal_primary_MI_5

value: I

value: ISR, Coloanal, ileostomy


title: rectal_primary_NT_10

value: ISR, colonic pouch, Ileostomy


title: rectal_primary_TO_12

value: TO


title: rectal_primary_MO_22

value: MO

value: LAR, ileostomy


title: rectal_primary_TO_8

value: male

value: TEM


title: rectal_primary_MO_21

value: IIA

value: L-LAR, Rt PLND, ileostomy


title: rectal_primary_TO_11

value: LAR


title: rectal_primary_TO_10

value: R-LAR, ileostomy


title: rectal_primary_MO_23

value: female


title: rectal_primary_TO_7


title: rectal_primary_MO_20


title: rectal_primary_TO_6

value: IVA


title: rectal_primary_NT_8

value: NT

value: ISR, colonic pouch, ileostomy


title: rectal_primary_NT_5

value: APR,TAH,LSO,S6 segmentectomy


title: rectal_primary_MO_19

value: IIIB


title: rectal_primary_MO_18


title: rectal_primary_MO_17

value: IIIC


title: rectal_primary_MO_16

value: ULAR


title: rectal_primary_NT_4

value: I


title: rectal_primary_TO_9

value: TO

value: ISR, coloanal, ileostomy


title: rectal_primary_MO_14

value: MO

value: male


title: rectal_primary_NT_9

value: IIA


title: rectal_primary_MO_13


title: rectal_primary_NT_3

value: IIIA


title: rectal_primary_NT_6


title: rectal_primary_MO_11

value: LAR


title: rectal_primary_MO_15


title: rectal_primary_TO_5


title: rectal_primary_MO_12


title: rectal_primary_MI_3

value: MI

value: APR


title: rectal_primary_MO_10


title: rectal_primary_TO_4


title: rectal_primary_MO_6

value: female

value: LAR, ileostomy


title: siRNA FoxE1 vs siRNA scramble 1 Replicate3

city: Madrid

first: Pilar

last: Santisteban

address: Arturo Duperier 4

department: Physiopathology of Endocrine and Nervous System

institute: Instituto Investigaciones Biomédicas Alberto Sols

description:
Biological replicate 3 of 4
siRNA FoxE1 vs siRNA scramble 3

hyb_protocol: Microarray: Rat Gene Expression G3 8x60K (Agilent microarray design ID 028279 , P/N G4853A ) Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 10.7).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. R and Bioconductor software (v.2.5), Limma (v.3.2.3) was used.

source_name: siRNA FoxE1

label_protocol:
Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010. Amplification: by RNA polymerases.
Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores.
Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).

growth_protocol: PCCl3 thyroid cells were grown were grown in Coon's modified Ham's F-12 medium supplemented with 5% donor calf serum and a six-hormone mixture [1 nM TSH, 10  g/ml insulin, 10 ng/ml somatostatin, 5  g/ml transferrin, 10 nM hydrocortisone, and 10 ng/ml glycyl-L-histidyl-L-lysine acetate]

extract_protocol: To isolate total RNA we used TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s recommended protocol.

treatment_protocol: PCCl3 cells were transfected with 25nM of siFoxE1 (Rat FoxE1 ON-TARGET plus SMART pool) using DharmaFECT 1 Transfection Reagent and following the manufacturer’s protocol (Dharmacon, Denver, USA).

tag: cell type

value: thyroid cells

tag: genotype/variation

value: FoxE1 silenced

source_name: siRNA scramble

treatment_protocol: PCCl3 cells were transfected with 25nM of scramble (Non-targeting ON-TARGET plus Pool) using DharmaFECT 1 Transfection Reagent and following the manufacturer’s protocol (Dharmacon, Denver, USA).

value: siRNA scramble control


title: siRNA FoxE1 vs siRNA scramble Dye Swap

description:
Pool of biological replicates
siRNA FoxE1 vs siRNA scramble DS


title: rectal_primary_NT_1

value: NT


title: rectal_primary_MO_8


title: rectal_primary_MI_2

value: LAR, TAH


title: siRNA FoxE1 vs siRNA scramble 1 Replicate1

description:
Biological replicate 1 of 4
siRNA FoxE1 vs siRNA scramble 1


title: rectal_primary_MO_2

value: I

value: ULAR


title: rectal_primary_NT_7


title: rectal_primary_NT_2

value: Hartmann's procedure


title: rectal_primary_MO_9

value: MO


title: siRNA FoxE1 vs siRNA scramble 1 Replicate4

description:
Biological replicate 4 of 4
siRNA FoxE1 vs siRNA scramble 4


title: rectal_primary_TO_2

value: TO

value: male


title: rectal_primary_TO_1


title: rectal_primary_MO_1

value: IIIB


title: rectal_primary_MO_5

value: IIA

value: LAR


title: rectal_primary_MI_1

value: MI


title: rectal_primary_MO_3

value: female


title: siRNA FoxE1 vs WT 1 Replicate 3

description:
Biological replicate 3 of 4
siRNA FoxE1 vs WT 3

source_name: Wild Type

treatment_protocol: PCCl3 cells were untreated

value: wild type


title: siRNA FoxE1 vs WT Dye swap

description:
Pool of biological replicates
siRNA FoxE1 vs WT DS

value: thyroid cells


title: siRNA FoxE1 vs WT 1 Replicate 1

description:
Biological replicate 1 of 4
siRNA FoxE1 vs WT 1

value: FoxE1 silenced


title: rectal_primary_MO_4


title: siRNA FoxE1 vs WT 1 Replicate 4

description:
Biological replicate 4 of 4
siRNA FoxE1 vs WT 4


title: rectal_primary_MO_7


title: siRNA FoxE1 vs siRNA scramble 1 Replicate2

description:
Biological replicate 2 of 4
siRNA FoxE1 vs siRNA scramble 2

value: siRNA scramble control


title: Hippocampus, Tg2576-APPSwe mice, 12 month-old, with low Abeta plaque load-rep2

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

institute: ETH Zurich

description: Gene expression data of hippocampi isolated from 12 month-old untreated Tg2576 (APPSwe-transgenic) AD mice with low Abeta plaque load

hyb_protocol: For hybridization, 15 µg of fragmented, biotin-labeled cRNA were incubated with the chip (Mouse Genome MG430 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual.

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

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 600.

source_name: Hippocampi isolated from 12 month-old Tg2576 APPSwe-transgenic mice with low Abeta plaque load

label_protocol: Biotin-labeled cRNA was prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual; Rev.3).

growth_protocol: The study was performed with 18 month-old Tg2576 (APPSwe-transgenic) AD mice treated for six months without or with the brain-penetrating ACE inhibitor, captopril. Mice had free access to food and water, and were fed a standard rodent chow. The treatment group of Tg2576 mice received the centrally active ACE inhibitor, captopril (20 mg/kg/day supplied in drinking water) for 6 months. The control group of Tg2576 mice received drinking water without captopril. At an age of 18 months, hippocampi were isolated from Tg2576 mice treated without or with captopril for six months. As an additional control group, hippocampi were isolated from 12 month-old untreated Tg2576 mice with low Abeta plaque load, reflecting the time point when treatment with captopril was initiated.

extract_protocol: Total hippocampal RNA was isolated with the RNeasy Mini kit according to the manufacturer`s instructions (Qiagen).

treatment_protocol: The study was performed with hippocampi isolated from three groups of mice, i.e. (i) untreated 18 month-old Tg2576 (APPSwe-transgenic) AD mice with high Abeta plaque load (APP-18 mo), (ii) 18 month-old Tg2576 (APPSwe-transgenic) AD mice treated for 6 months with the brain-penetrating ACE inhibitor, captopril (20mg/kg/day in drinking water; APP-18mo-ACEI), and (iii) untreated 12 month-old Tg2576 (APPSwe-transgenic) AD mice with low Abeta plaque load (APP-12mo).

tag: strain

tag: tissue

value: Hippocampi

value: 12 months old

tag: genotype/variations

value: Tg2576 APPSwe-transgenic mice


title: rectal_primary_TO_3

tag: age

value: ULAR


title: siRNA FoxE1 vs WT 1 Replicate 2

description:
Biological replicate 2 of 4
siRNA FoxE1 vs WT 2


title: MOER experimental 2

city: Dublin 2

first: Harry

middle: Myles

last: Harvey

address: York Street

country: Ireland

institute: Royal COllege of Surgeons in Ireland

description: Gene expression data from MOER mouse livers treated with PPT

hyb_protocol: Microarray facility at the UC-Irvine.

scan_protocol: Microarray facility at the UC-Irvine.

data_processing:
CyberT program was used by the UC-Irvine array facility to identify differences from the various treatments
The array data was analyzed using the bayesian / Cyber-T algorithm. Genes with a bayes p-value of < 0.001, a posterior probability of differential expression (PPDE) > 0.99 and a minimum 2-fold change in expression were considered differentially expressed.

source_name: Liver, PPT (100microgram for 3 days)

label_protocol: Microarray facility at the UC-Irvine.

growth_protocol: Wild type, ERalpha KO, and membrane ERalpha only mice were ovariectomized, recovered for 1 week, then injected with an ERalpha agonist, PPT 100 micrograms each day for 3 days. The mice were then sacrificed and the livers removed for obtaining RNA

extract_protocol: Snap frozen dissected whole liver was ground to a fine powder and total RNA was extracted and used for qRT-PCR analysis and Affymetrix DNA microarray analysis. cDNA was synthesized using approximately 500ng RNA and Oligo dT primers with the Improm-II reverse transcription system (Promega) for qRT-PCR or converted to cRNA for microarray.  The RNA from three animals was pooled for each treatment type and each mouse type for microarray analysis, the study repeated a second time. For each pooled sample, mouse DNA microarray using the Affymetrix mouse gene 1.0ST chip was run at the Microarray facility at the UC-Irvine. The array data was analyzed using the Cyber T program at a confidence interval of 99.99% and a minimum of a two-fold change was considered significant. The software David (33) was used to determine mRNA targets changed only following PPT treatment in both wild type and MOER mice and not in ERKO.

treatment_protocol: As described immediately above

value: Liver

value: MOER


title: MOER experimental 1