title: Lrrc10 Adult 1

city: Madison

first: Matt

last: Brody

state: WI

address: 1300 University Ave.

institute: UW-Madison

hyb_protocol: Agilent Two-Color Microarray-Based Gene Expression Analysis 17hrs 65 deg celcius Surehyb chamber

scan_protocol: Agilent Technologies Scanner G2505B US22502567 5um 16bit

data_processing: Agilent Feature extraction versions 9..5 for background subtraction - localbackground and normalization Linear LOWESS, Goodspots were designated as those features with both channels r and g where controltype=0, issaturated=0,isfeatnonunifol=0,isfeatpopnol=0,iswellabovebg=1 in 80% of arrays

source_name: Lrrc10 KO heart_2 months

label_protocol: Total RNA was amplified and labeled according to manufactures instructions. Agilent Two-Color Microarray-Based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS

growth_protocol: Ad lib feeding and drinking.  12hours light:12hours dark.

extract_protocol: Polytron 10 seconds  and processed with an Qiagen Rneasy Mini kit

treatment_protocol: Sacrificed and dissected at two months of age and placed in Trizol, flash frozen and stored at -80C.

tag: genotype

value: two months

value: heart

source_name: Heart reference pool, pooled heart RNA from two wildtype (Lrrc10+/+) mice.


title: Cord_Placebo_M_318

status: Public on Mar 15 2012

type: genomic

city: Cambridge

first: Julien

last: Bauer

state: Cambridgeshire

address: Tennis court road

country: United Kingdom

institute: Cambridge University

description: From the same individual as infant peripheral blood 541

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v2011.1

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: Gentra Puregene (Qiagen)

treatment_protocol: Consenting, non-pregnant women aged 17-45 resident in West Kiang, Gambia were randomised to receive daily supplementation with either UNIMMAP [daily dose; Vitamin A (800 RE), Vitamin D (200 IU), Vitamin E (10 mg), Vitamin C (70 mg),Vitamin B1(1.4 mg), Vitamin B2 (1.4 mg), Niacin (18 mg), Vitamin B6 (1.9 mg), Vitamin B12 (2.6 mg), Folic acid (400 μg), Iron (30 mg), Zinc (15 mg), Copper (2 mg), Selenium (65 μg) and Iodine (150 μg)] or placebo.  Once pregnancy was confirmed by positive pregnancy test at mean gestational age 9.5 weeks women ceased supplementation, and all women received a standard antenatal preparation of iron (60 mg) and folate (250 μg).  Women were excluded from this analysis if they were enrolled for less than 14 days before last menstrual period, or if they apparently consumed less than 70% of allocated tablets.  The trial was approved by the MRC / Gambian Government Ethics Committee, and the current study was also approved by the MRC Laboratories Fajara Scientific Co-ordinating Committee (L2007.77, 21/9/07) and the Gambian Government Ethics Committee (25/10/07).

tag: tissue

value: Umbilical cord blood

tag: treatment

value: Placebo

tag: gender

value: male

tag: month of conception (estimated)


title: Adult male Shelf replicate 3

type: RNA

city: Urbana

first: Kirstin

last: Replogle

state: IL

address: 1206 W Gregory Drive

country: USA

institute: University of Illinois

hyb_protocol: Samples were suspended in SlideHyb#1 (Ambion), applied to slides in Corning Hybridization Chambers, and incubated O/N at 42C. After hybridization, the slides were washed sequentially in 1X SSC, 0.2% SDS; 0.1X SSC, 0.2% SDS; and 0.1X SSC for 5 minutes each, and spun dry.

scan_protocol: Scanned on an Axon GenePix 4000B scanner Images were quantified using Axon GenePix 6.0.

data_processing: no data processing (providing only raw data)

molecule: total RNA

organism: Taeniopygia guttata

source_name: universal SoNG reference

label_protocol: 1 µg of aRNA was primed with 3 µl of 100 µM random hexamer primers at 70C for 10 min, then reversed transcribed at 42C for 16 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM dATP, dCTP, dGTP, 60µM dTTP and 40µM aa-dUTP; RNA was hydrolyzed in the presence of NaOH and EDTA and samples were cleaned up on a spin column. Finally, Cy3 and Cy5 dye esters (GE Healthcare) were coupled to aa-dUTP residues in NaCO3 buffer for 2 hrs at room temp, then neutralized and cleaned on spin columns.

extract_protocol: Experimental samples: Total RNA was extracted using Absolutely RNA Microprep kit (Stratagene). 200ng total RNA was double-amplified using MessageAmp II aRNA kit (Ambion). Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Brain regions HVC and Shelf were laser-capture microdissected from brain sections of adult male zebra finches.

tag: brain region

value: Telencephalon

value: Male and female

tag: age

value: Adult

source_name: Shelf

value: Shelf

value: Male


title: Comparative experiment (#3-2) of wild type vs ntrBC mutant

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

hyb_protocol: The hybridization mixtures containing the two labeled cDNA samples to be compared were applied to microarray slides that had been covered with Lifterslips (Erie Scientific Company, Portsmouth, NH). The slides were assembled with hybridization chambers (Corning, Corning, NY) and submerged in a 65ºC water bath for 14-16 h of hybridization.

scan_protocol: After hybridization, the slides were washed and scanned with a scanner from PerkinElmer or Agilent.

data_processing: Images (Cy3 and Cy5) were captured as TIFF files and were analyzed with the image processing software ImaGene version 5.6 (BioDiscovery, Inc., El Segundo, CA).

organism: Rhodopseudomonas palustris

source_name: ntrBC mutant (Cy3)

label_protocol: Fluorescently labeled cDNA was prepared by direct incorporation of either Cy3-dCTP or Cy5-dCTP during a first-strand reverse transcription reaction.

extract_protocol: Rhodopseudomonas palustris cells were disrupted by bead beating and RNA was purified with the RNeasy Mini kit (Qiagen) including DNase treatment on the column.

tag: genotype/variation

value: ntrBC mutant cells

tag: growth

value: NF with succinate and yeast extract

source_name: wild type (Cy5)

value: wild-type cells


title: 116V

city: rochester

first: keyi

last: liu

address: 1425 portland ave

institute: Rochester General Research Institute

description:
3 technical replicates: V1_H001, V1_H002, V1_H003
30,968 highly sensitive 60-mer sense-strand polynucleotide human genome probes and 1082 experimental control probes are spotted onto the array in a highly consistent manner.

hyb_protocol: 10 μg Cy5-labeled aRNA was hybridized to Human OneArray glass slide containing 30,968 human genome probes and 1,082 experimental control probes according to the manufacturer's standard protocols (PhalanxBio, CA, USA). The Human OneArray slide was prehybridized for 2 h at 42C with OneArray Pre-hybridization buffer and then hybridized for 16 h at 42C with OneArray hybridization buffer. The slides were then washed according to the manufacturer’s instruction (PhalanxBio Inc, CA, USA).

scan_protocol: The arrays were scanned at 5 μm resolution using a Molecular Dynamics Axon 4100A scanner. Raw intensity signals for each microarray were captured and computed using the GenePixPro™ Software. Raw data formats were stored in TIFF images and GPR data files.

data_processing: The data from all microarrays in each experimental set was then analyzed using Omicsoft Array Studio software; control and missing features were removed, and the remaining signals were quantile normalized. Testing was performed by combining technical replicates and performing statistical analyses using Rosetta Resolver’s proprietary modeling techniques.

source_name: PBMCs

label_protocol: 10 µg of total RNA was amplified with the Amino Allyl MessageAmp II aRNA Amplification Kit (Cat. No. 1753) (Applied Biosystems) according to the instructions. The aRNA product was subsequently conjugated with Cy5™ NHS ester (GEH Lifesciences). RNA was purified and fragmented using Ambion’s RNA Fragmentation Reagents.

growth_protocol: Blood was collected from children with acute otitis media caused by Nontypeable Haemophilus influenzae and their pre-infection healthy stage.

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by the Ficoll gradient and total RNA was extracted from PBMCs using the QIAamp RNA blood Mini Kit (Qiagen, Maryland, USA) according to manufacturer’s instructions.

value: blood

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: patient

tag: infection stage

value: pre-infection


title: Lrrc10 Adult 3

organism: Mus musculus

tag: strain


title: Comparative experiment (#3-1) of wild type vs ntrBC mutant


title: Cord_Placebo_M_278


title: Lrrc10 Adult 2


title: Adult male Shelf replicate 2


title: Adult male Shelf replicate 6


title: Adult male HVC replicate 5

source_name: HVC

value: HVC


title: Adult male Shelf replicate 4


title: Adult male Shelf replicate 1


title: Adult male HVC replicate 1


title: Cord_Placebo_M_170

description: From the same individual as infant peripheral blood 498


title: Adult male HVC replicate 2


title: AL of adult silence control replicate 6

source_name: Silence control

extract_protocol: Experimental samples: Total RNA was extracted using RNAqueous Mini kit (Ambion) and DNase treated with TURBO DNase (Ambion), and cleaned on a spin column. 500ng total RNA was amplified using Agilent's Low RNA input linear amplification kit. Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Adult male zebra finches (Taeniopygia guttata) were acoutically isolated in playback chambers overnight. The next day (day1), one group of birds heard 30 minutes of a novel song (e.g. SongA), sacrificed and tissue collected and flash frozen. Silence control birds were taken at the equivalent time of day1 as novel song birds, but heard no song playback. The birds hearing familiar song were isolated as the others, but on the first day heard 180 min of SongA, remained in the chambers a second night, and heard 30 min of SongA again the following day (day2).

value: AL (auditory lobule)

tag: song playback experience

value: Silence control

value: adult


title: AL of adult male familiar song replicate 6

source_name: Familiar song

value: Trained 180 min with song on day1, heard 30 min of same song on day2


title: AL of adult novel song replicate 6

source_name: Novel song

value: 30 min of novel song

value: male


title: Adult male HVC replicate 3

value: Telencephalon

value: Male and female


title: Comparative experiment (#1-2) of wild type vs ntrBC mutant

source_name: wild type (Cy3)

source_name: ntrBC mutant (Cy5)


title: Comparative experiment (#2-1) of wild type vs ntrBC mutant


title: Adult male Shelf replicate 5

value: Adult

value: Shelf


title: Cord_Placebo_M_147

value: Umbilical cord blood

value: Placebo


title: AL of adult silence control replicate 5

value: male and female

value: Male


title: AL of adult novel song replicate 5


title: Cord_Placebo_M_138


title: Comparative experiment (#1-1) of wild type vs ntrBC mutant

value: wild-type cells

value: NF with succinate and yeast extract

value: ntrBC mutant cells


title: Cord_Placebo_M_41


title: AL of adult male familiar song replicate 5

value: AL (auditory lobule)


title: AL of adult silence control replicate 4

value: Silence control


title: Cord_Placebo_M_156


title: Cord_Placebo_M_9


title: B43, Liver, CCl4, 2000mg/kg, 3d CCl2000_3d_9

city: Boston

first: Zhenqiang

last: Su

state: MA

address: 22 Thomson Place

department: IP & Science

institute: Thomson Reuters

description: Gene expression after classical hepatotoxicants exposure

hyb_protocol: Cy3-labeled cRNA (1650 ng) from each sample was hybridized to an Agilent Rat Genome 4x44K Microarray following the manufacturer’s protocol.

scan_protocol: The hybridized array was then washed and scanned and data was extracted from the scanned image using Feature Extraction version 10.7 (Agilent Technologies).

organism: Rattus norvegicus

source_name: B43, Liver, CCl4, 2000mg/kg, 3d

label_protocol: Two hundred nanograms of total RNA was converted into labeled cRNA with nucleotides coupled to fluorescent dye Cy3 using the Low Input Quick Amp Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol. cRNA yield and quality were checked with the Agilent Bioanalyzer.

extract_protocol: Total RNA was isolated from approximately 30 mg of liver using Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s protocol. Total RNA concentrations were quantitated on a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE).  The purity and quality of extracted RNA were evaluated using the RNA Nano Chips and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA samples with RNA integrity numbers (RINs) greater than 8.0 were used for microarray analysis.

treatment_protocol: Six to seven week-old male Sprague-Dawley rats, provided by the US Food and Drug Administration National Center for Toxicological Research (NCTR) breeding colonies, were used for the study. After a seven day acclimation period, rats were assigned to experimental groups by weight averaging and housed individually in polycarbonate cages using hardwood chip bedding.  During the study, room temperatures remained within 19 – 23°C, and fluorescent lighting was provided on a 12 h on, 12 h off cycle.  Filtered tap water was provided ad libitum and NIH-41 irradiated diet was provided ad libitum except during designated periods of fasting. APAP, CCl4 were administered as a single dose via oral gavage.  For APAP, rats were fasted overnight for at least 12 hours prior to dosing, with feed given back to the animals 4 hours after dosing.  The CCl4 rats were administered feed ad libitum.

value: CCl4, 2000mg/kg

tag: time

value: liver

value: six to seven week

value: Sprague-Dawley


title: B44, Liver, CCl4, 2000mg/kg, 3d CCl2000_3d_9

data_processing: The hybridized array was then washed and scanned and data was extracted from the scanned image using Feature Extraction version 10.7 (Agilent Technologies).

source_name: B44, Liver, CCl4, 2000mg/kg, 3d

value: male


title: Cord_Placebo_M_16


title: B41, Liver, CCl4, 2000mg/kg, 3d CCl2000_3d_9

source_name: B41, Liver, CCl4, 2000mg/kg, 3d


title: AL of adult male familiar song replicate 4

value: Trained 180 min with song on day1, heard 30 min of same song on day2

value: adult

value: Telencephalon

value: Male and female


title: AL of adult novel song replicate 4

value: 30 min of novel song


title: AL of adult silence control replicate 3

value: male and female


title: AL of adult novel song replicate 3

value: Male


title: AL of adult male familiar song replicate 3


title: B42, Liver, CCl4, 2000mg/kg, 3d CCl2000_3d_9

source_name: B42, Liver, CCl4, 2000mg/kg, 3d


title: AL of adult silence control replicate 2


title: AL of adult male familiar song replicate 2


title: Cord_UNIMMAP_F_412

description: From the same individual as infant peripheral blood 517

value: Umbilical cord blood

value: UNIMMAP (micronutrient supplemented)

value: female


title: B45, Liver, CCl4, 2000mg/kg, 3d CCl2000_3d_9

source_name: B45, Liver, CCl4, 2000mg/kg, 3d


title: AL of adult novel song replicate 2

value: AL (auditory lobule)


title: Cord_UNIMMAP_F_401


title: AL of adult silence control replicate 1

value: Silence control


title: B40, Liver, CCl4, 50mg/kg, 3d CCl50_3d_8

source_name: B40, Liver, CCl4, 50mg/kg, 3d

value: CCl4, 50mg/kg


title: AL of adult male familiar song replicate 1

source_name: universal SoNG reference


title: AL of adult novel song replicate 1


title: B39, Liver, CCl4, 50mg/kg, 3d CCl50_3d_8

source_name: B39, Liver, CCl4, 50mg/kg, 3d

value: liver


title: B38, Liver, CCl4, 50mg/kg, 3d CCl50_3d_8

source_name: B38, Liver, CCl4, 50mg/kg, 3d

value: six to seven week


title: Cord_UNIMMAP_F_334

description: From the same individual as infant peripheral blood 546


title: B36, Liver, CCl4, 50mg/kg, 3d CCl50_3d_8

source_name: B36, Liver, CCl4, 50mg/kg, 3d

value: Sprague-Dawley


title: Cord_UNIMMAP_F_281


title: B35, Liver, control, 3d Cntl_3d_7

source_name: B35, Liver, control, 3d

value: control

value: male


title: Cord_UNIMMAP_F_291

description: From the same individual as infant peripheral blood 601


title: Cord_UNIMMAP_F_151


title: B37, Liver, CCl4, 50mg/kg, 3d CCl50_3d_8

source_name: B37, Liver, CCl4, 50mg/kg, 3d


title: Cord_UNIMMAP_F_272

description: From the same individual as infant peripheral blood 522


title: HeLa JADE1L over-expression control 2

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description: HeLa S3 transduced with a control retrovirus

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw bead studio data were processed using R and the BioConductor package lumi. Data were log2 transformed and quantile normalized using subsequently the lumiT and lumiN functions.

label: biotin

source_name: cervical adenocarcinoma

growth_protocol: HeLa S3 cells were grown on 150mm plastic dishes at 37C, 5% CO2 to an approximate confluence of 90%

extract_protocol: Total cellular RNA was extracted with Trizol (Invitrogen) and purified using Macherey-Nagel NucleoSpin RNA II kit.

treatment_protocol: For JADE1 over-expression, HeLa S3 were infected with a retrovirus encoding FLAG-JADE1, and stable clones expressing the FLAG protein were isolated. For HBO1 knock-down, HeLa S3 cells were transiently transfected with siRNA directed against HBO1 using Invitrogen Oligofectamine as per manufacturer's protocol.

tag: cell line

value: HeLa

value: JADE1 control


title: B34, Liver, control, 3d Cntl_3d_7

source_name: B34, Liver, control, 3d


title: HeLa JADE1L over-expression control 1

label_protocol: Standard Illumina hybridization protocol


title: B32, Liver, control, 3d Cntl_3d_7

source_name: B32, Liver, control, 3d


title: B33, Liver, control, 3d Cntl_3d_7

source_name: B33, Liver, control, 3d


title: B30, Liver, CCl4, 2000mg/kg, 24h CCl2000_24h_6

source_name: B30, Liver, CCl4, 2000mg/kg, 24h

value: CCl4, 2000mg/kg


title: Cord_UNIMMAP_M_22


title: Cord_UNIMMAP_F_142


title: Cord_UNIMMAP_F_146


title: Cord_Placebo_F_607

value: Placebo


title: HeLa JADE1L over-expression 1

description: HeLa S3 transduced with retrovirus encoding FLAG-JADE1

value: JADE1 over-expression


title: Cord_Placebo_F_444


title: B31, Liver, control, 3d Cntl_3d_7

source_name: B31, Liver, control, 3d


title: Cord_UNIMMAP_F_8

description: From the same individual as infant peripheral blood 589


title: B29, Liver, CCl4, 2000mg/kg, 24h CCl2000_24h_6

source_name: B29, Liver, CCl4, 2000mg/kg, 24h


title: Cord_Placebo_F_437

description: From the same individual as infant peripheral blood 558


title: adipose tissue  at Wk2 AZT 004-2

city: Dublin

first: Claudette

last: Satchell

address: Belfield

country: Ireland

institute: University College Dublin

description:
adipose tissue  at Wk2
Gene expression data from dipose tissue after 2 weeks AZT drug exposure

hyb_protocol: Following fragmentation, 25ng/µL of ssDNA was hybridized for 17hr at 45oC on GeneChip® Human ST 1.0 Arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with dChip 2010.01 using Affymetrix default analysis settings and global scaling as normalization method. Mean fold change ≥ 1.2 and mean P≤ 0.05 of signal intensity required for significant change in gene expression.

source_name: adipose tissue after 2 weeks AZT drug exposure

label_protocol: Biotinylated single-stranded DNA (ssDNA) was prepared according to the  Affymetrix protocol from 5.5 µg ssDNA (Genechip®Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2009, Affymetrix).

growth_protocol: Subjects were exposed to 2 weeks of either d4T (40 mg twice daily) and lamivudine (150 mg twice daily) or AZT (300 mg twice daily) and lamivudine (150 mg twice daily).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturers instructions.

treatment_protocol: Subcutaneous fat biopsies were collected from the flank region, split into 300mg aliquots and stored in 1mL trizol and stored at -70 oC.

value: adipose tissue

tag: drug exposure

value: 2 weeks AZT (300 mg twice daily) and lamivudine (150 mg twice daily)


title: HeLa JADE1L over-expression 2


title: adipose tissue  at Wk0 AZT 005-0

description:
adipose tissue  at Wk0
Gene expression data from adipose tissue before AZT drug exposure

source_name: adipose tissue before AZT drug exposure


title: B27, Liver, CCl4, 2000mg/kg, 24h CCl2000_24h_6

source_name: B27, Liver, CCl4, 2000mg/kg, 24h


title: adipose tissue  at Wk2 AZT 005-2


title: Cord_Placebo_F_422

description: From the same individual as infant peripheral blood 597

value: Umbilical cord blood


title: adipose tissue  at Wk2 AZT 002-2


title: adipose tissue  at Wk0 AZT 004-0


title: adipose tissue  at Wk0 AZT 002-0


title: adipose tissue  at Wk0 AZT 003-0


title: Cord_Placebo_F_435

value: female


title: B28, Liver, CCl4, 2000mg/kg, 24h CCl2000_24h_6

source_name: B28, Liver, CCl4, 2000mg/kg, 24h


title: B26, Liver, CCl4, 2000mg/kg, 24h CCl2000_24h_6

source_name: B26, Liver, CCl4, 2000mg/kg, 24h


title: adipose tissue  at Wk2 AZT 003-2


title: Cord_Placebo_F_386


title: B24, Liver, CCl4, 50mg/kg, 24h CCl50_24h_5

source_name: B24, Liver, CCl4, 50mg/kg, 24h


title: adipose tissue  at Wk2 d4T 005-2

description:
adipose tissue  at Wk2
Gene expression data from adipose tissue after 2 weeks d4T drug exposure

value: 2 weeks d4T (40 mg twice daily) and lamivudine (150 mg twice daily)


title: adipose tissue  at Wk0 AZT 001-0


title: Cord_Placebo_F_328

description: From the same individual as infant peripheral blood 585


title: adipose tissue  at Wk2 d4T 004-2

source_name: adipose tissue after 2 weeks d4T drug exposure


title: adipose tissue  at Wk0 d4T 005-0

description:
adipose tissue  at Wk0
Gene expession data from adipose tissue before d4T drug exposure

source_name: adipose tissue before d4T drug exposure


title: B23, Liver, CCl4, 50mg/kg, 24h CCl50_24h_5

source_name: B23, Liver, CCl4, 50mg/kg, 24h


title: Cord_Placebo_F_290

description: From the same individual as infant peripheral blood 543


title: adipose tissue  at Wk0 d4T 004-0


title: adipose tissue  at Wk2 AZT 001-2


title: Cord_Placebo_F_324


title: adipose tissue  at Wk0 d4T 003-0


title: adipose tissue  at Wk2 d4T 003-2


title: B22, Liver, CCl4, 50mg/kg, 24h CCl50_24h_5

source_name: B22, Liver, CCl4, 50mg/kg, 24h


title: Cord_Placebo_F_288


title: adipose tissue  at Wk2 d4T 002-2


title: adipose tissue  at Wk2 d4T 001-2


title: adipose tissue  at Wk0 d4T 001-0


title: adipose tissue  at Wk0 d4T 002-0


title: B20, Liver, control, 24h Cntl_24h_4

source_name: B20, Liver, control, 24h


title: B25, Liver, CCl4, 50mg/kg, 24h CCl50_24h_5

source_name: B25, Liver, CCl4, 50mg/kg, 24h


title: B19, Liver, control, 24h Cntl_24h_4

source_name: B19, Liver, control, 24h


title: Cord_Placebo_F_271


title: U-87MG-PK7 set 3

first: Felicia

last: Ng

address: Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road

institute: Cambridge Institute for Medical Research

description:
AFGE1068-10.CEL
Gene expression data from parkin-expressing U-87MG

hyb_protocol: The targets were hybridized to the GeneChip® Human Gene 1.0 ST Array according to the manufacturer hybridization protocol which constituted 28,000 gene-level probe sets.

scan_protocol: 300ng of total RNA were used for the experiments and the arrays were washed and stained using the FS450_0007 fluidics protocol and scanned using an Affymetrix 3000 7G scanner. The scanned images were inspected for hybridization efficiency and CEL files generated from GCOS (GeneChip Operating Software) were imported into Expression Console (EC) 1.1 software for array QC.

data_processing: The data was processed using Bioconductor packages in the R statistical software.  RMA normalization was applied and p-values were generated by comparing against the detection above background probes. Probe sets with DABG p-value >0.01 in all samples was removed.

label_protocol: After the quality of the RNA was ascertained, the GeneChip® WT cDNA Synthesis and Amplification Kit (Affymetrix, USA) was used to generate the first and second cycle cDNA synthesis and the cRNA synthesis through in vitro transcription amplification. After the second cycle cDNA synthesis and cRNA hydrolysis step, the GeneChip® WT Terminal Labeling Kit was used for the fragmentation and terminal labeling of the cDNA to generate targets compatible with the GeneChip arrays.

growth_protocol: The cells were similarly seeded at a concentration of 500,000 cells in 10ml of culture medium in 10-cm tissue culture plate and incubated at 37oC in a 5.0% CO2 incubator for 24 hours.

extract_protocol: Total RNA from the various U-87MG parkin expressing and vector control cells were extracted using the RNeasy Mini Kit (Qiagen, USA). The concentration and quality of the total RNA extracted was assessed by the NanoDrop ND-1000 machine (Thermo Scientific, USA) and the Bioanalyzer (Agilent, USA).

value: parkin


title: B21, Liver, CCl4, 50mg/kg, 24h CCl50_24h_5

description: Gene expression after classical hepatotoxicants exposure

source_name: B21, Liver, CCl4, 50mg/kg, 24h

value: CCl4, 50mg/kg


title: U-87MG-PK25 set 2

description:
AFGE1068-8.CEL
Gene expression data from parkin-expressing U-87MG


title: Cord_Placebo_F_284


title: U-87MG-PK7 set 2

description:
AFGE1068-6.CEL
Gene expression data from parkin-expressing U-87MG


title: Cord_Placebo_F_144

description: From the same individual as infant peripheral blood 559


title: U-87MG-PK19 set 3

description:
AFGE1068-11.CEL
Gene expression data from parkin-expressing U-87MG


title: B16, Liver, control, 24h Cntl_24h_4

source_name: B16, Liver, control, 24h

value: liver


title: B17, Liver, control, 24h Cntl_24h_4

source_name: B17, Liver, control, 24h

value: six to seven week


title: Cord_Placebo_F_165


title: U-87MG-PK19 set 2

description:
AFGE1068-7.CEL
Gene expression data from parkin-expressing U-87MG


title: U-87MG-PK7 set 1

description:
AFGE1068-2.CEL
Gene expression data from parkin-expressing U-87MG


title: U-87MG-PK25 set 1

description:
AFGE1068-4.CEL
Gene expression data from parkin-expressing U-87MG


title: U-87MG-PK25 set 3

description:
AFGE1068-12.CEL
Gene expression data from parkin-expressing U-87MG


title: U-87MG-PK19 set 1

description:
AFGE1068-3.CEL
Gene expression data from parkin-expressing U-87MG


title: B18, Liver, control, 24h Cntl_24h_4

source_name: B18, Liver, control, 24h

value: Sprague-Dawley


title: Cord_Placebo_F_10

description: From the same individual as infant peripheral blood 583


title: Cord_Placebo_F_33


title: U-87MG-V22 set 6

description:
AFGE1068-9.CEL
Gene expression data from U-87MG

value: vector


title: Cord_Placebo_F_7


title: B15, Liver, CCl4, 2000mg/kg, 6h CCl2000_6h_3

source_name: B15, Liver, CCl4, 2000mg/kg, 6h

value: male


title: U-87MG-V22 set 3

description:
AFG1081-9.CEL
Gene expression data from U-87MG


title: B14, Liver, CCl4, 2000mg/kg, 6h CCl2000_6h_3

source_name: B14, Liver, CCl4, 2000mg/kg, 6h


title: Cord_Placebo_F_29


title: U-87MG-V22 set 4

description:
AFGE1068-1.CEL
Gene expression data from U-87MG


title: B12, Liver, CCl4, 2000mg/kg, 6h CCl2000_6h_3

source_name: B12, Liver, CCl4, 2000mg/kg, 6h


title: U-87MG-V17 set 3

description:
AFG1081-8.CEL
Gene expression data from U-87MG


title: U-87MG-V22 set 5

description:
AFGE1068-5.CEL
Gene expression data from U-87MG


title: U-87MG-V8 set 3

description:
AFG1081-7.CEL
Gene expression data from U-87MG


title: NAcc_No-GRov_19

city: ann arbor

first: Qiang

last: Wei

state: MI

address: 205 zina pitcher pl

department: MBNI

institute: University of Michigan

description:
Gene expression data from the nucleus accumbens
NACC_19.CEL

hyb_protocol: 15 ug of biotinylated aRNA was hybridized to Affymetrix Mouse Genome 430_2.0 GeneChip.Arrays were hybridized for 18 h at 45°C, washed, and stained on an Affymetrix fluidics station using the standard EukGEWS2v4_450 protocol.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner.

data_processing: GeneChip signal intensity data were interpreted by use of a custom chip description file (filename Mouse4302_Mm_REFSEQ_v13). This file is available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/refseq.asp. CEL intensity files from the Affymetrix GeneChip arrays were normalized by the robust multi-array average (RMA) algorithm.

source_name: Nucleus Accumbens

label_protocol: Biotin labeling (PerkinElmer)

growth_protocol: Undisturbed mice in the morning.

extract_protocol: PicoPure RNA isolation kit. RNA samples were then subjected to two rounds of amplication (RiboAmp OA RNA kit).

treatment_protocol: Male adult mouse brain. Brains were cryostat-sectioned in the coronal place at 12 µm. Laser capture microdissection was performed with an AutoPix instrument.

value: control (No-GRov)

value: Nucleus Accumbens

tag: developmental stage (of tissue collection)

value: adult


title: U-87MG-V22 set 2

description:
AFG1081-6.CEL
Gene expression data from U-87MG


title: B13, Liver, CCl4, 2000mg/kg, 6h CCl2000_6h_3

description: Gene expression after classical hepatotoxicants exposure

source_name: B13, Liver, CCl4, 2000mg/kg, 6h

value: CCl4, 2000mg/kg

tag: tissue


title: U-87MG-V22 set 1

description:
AFG1081-3.CEL
Gene expression data from U-87MG

tag: treatment


title: B11, Liver, CCl4, 2000mg/kg, 6h CCl2000_6h_3

source_name: B11, Liver, CCl4, 2000mg/kg, 6h

tag: gender


title: U-87MG-V8 set 2

description:
AFG1081-4.CEL
Gene expression data from U-87MG


title: NAcc_No-GRov_17

description:
Gene expression data from the nucleus accumbens
NACC_17.CEL


title: NAcc_No-GRov_18

description:
Gene expression data from the nucleus accumbens
NACC_18.CEL


title: U-87MG-V17 set 2

description:
AFG1081-5.CEL
Gene expression data from U-87MG


title: B09, Liver, CCl4, 50mg/kg, 6h CCl50_6h_2

source_name: B09, Liver, CCl4, 50mg/kg, 6h


title: U-87MG-V17 set 1

description:
AFG1081-2.CEL
Gene expression data from U-87MG


title: U-87MG-V8 set 1

description:
AFG1081-1.CEL
Gene expression data from U-87MG


title: NAcc_No-GRov_16

description:
Gene expression data from the nucleus accumbens
NACC_16.CEL


title: B10, Liver, CCl4, 50mg/kg, 6h CCl50_6h_2

source_name: B10, Liver, CCl4, 50mg/kg, 6h


title: B08, Liver, CCl4, 50mg/kg, 6h CCl50_6h_2

source_name: B08, Liver, CCl4, 50mg/kg, 6h


title: Prol_12h-_repA

city: Napoli

first: Mario

last: Lauria

address: via P. Castellino 111

country: Italy

institute: TIGEM

data_processing: The raw array data was generated by Illumina's GenomeStudio and processed by the Bioconductor package Lumi using quantile normalization.

source_name: control, 12h

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion) for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. DNAse treatment was performed according to Qiagen kit instructions.

treatment_protocol: Primary murine NSCs were isolated from E13.5 Id1L/L;Id2L/L;Id3-/-;Rosa-Cre-ER mouse telencephalon and cultured in the presence of FGF-2 and EGF (20 ng/ml each). For Id gene deletion, cells cultured on laminin-coated dishes in the presence of FGF-2 and EGF were treated with 250 nM 4-OHT dissolved in 100% ethanol or vehicle.

tag: agent

value: control vehicle

tag: time point

value: Neural Stem Cell

value: Id-cTKO-Rosa-Cre-ER

value: 129/Svj;C57Bl/6 hybrid


title: B07, Liver, CCl4, 50mg/kg, 6h CCl50_6h_2

source_name: B07, Liver, CCl4, 50mg/kg, 6h

tag: age


title: Prol_12h-_repC

tag: genotype/variation


title: Prol_12h-_repB


title: NAcc_No-GRov_14

description:
Gene expression data from the nucleus accumbens
NACC_14.CEL


title: NAcc_No-GRov_15

description:
Gene expression data from the nucleus accumbens
NACC_15.CEL


title: Prol_12h+_repC

source_name: OHT treated, 12h


title: B06, Liver, CCl4, 50mg/kg, 6h CCl50_6h_2

source_name: B06, Liver, CCl4, 50mg/kg, 6h


title: NAcc_Lifetime GRov_13

description:
Gene expression data from the nucleus accumbens
NACC_13.CEL

value: glucocorticoid receptor overexpression (GRov)

tag: development period of grov

value: lifetime


title: Prol_6h-_repB

source_name: control, 6h

tag: cell type


title: Prol_12h+_repA


title: Prol_12h+_repB


title: Prol_6h-_repA


title: Prol_6h-_repC


title: B03, Liver, control, 6h Cntl_6h_1

source_name: B03, Liver, control, 6h

value: control


title: Prol_6h+_repA

source_name: OHT treated, 6h


title: NAcc_Lifetime GRov_11

description:
Gene expression data from the nucleus accumbens
NACC_11.CEL


title: B02, Liver, control, 6h Cntl_6h_1

source_name: B02, Liver, control, 6h


title: B04, Liver, control, 6h Cntl_6h_1

source_name: B04, Liver, control, 6h


title: NAcc_Lifetime GRov_12

description:
Gene expression data from the nucleus accumbens
NACC_12.CEL


title: Prol_6h+_repC


title: Prol_6h+_repB


title: B01, Liver, control, 6h Cntl_6h_1

source_name: B01, Liver, control, 6h


title: Prol_D4-_repC

source_name: control, 96h


title: Prol_D6-_repC

source_name: control, 144h


title: Prol_48h+_repC

source_name: OHT treated, 48h


title: A51, Liver, APAP, 1250mg/kg, 7d APAP1250_7d_10

source_name: A51, Liver, APAP, 1250mg/kg, 7d

value: APAP, 1250mg/kg


title: NAcc_Lifetime GRov_10

description:
Gene expression data from the nucleus accumbens
NACC_10.CEL

source_name: Nucleus Accumbens


title: NAcc_Lifetime GRov_9

description:
Gene expression data from the nucleus accumbens
NACC_9.CEL


title: A52, Liver, APAP, 1250mg/kg, 7d APAP1250_7d_10

source_name: A52, Liver, APAP, 1250mg/kg, 7d

value: liver


title: NAcc_Lifetime GRov_8

description:
Gene expression data from the nucleus accumbens
NACC_8.CEL


title: Prol_D4+_repC

source_name: OHT treated, 96h


title: Prol_48h-_repC

source_name: control, 48h


title: NAcc_Earlylife GRov_6

description:
Gene expression data from the nucleus accumbens
NACC_6.CEL

value: early life


title: NAcc_Lifetime GRov_7

description:
Gene expression data from the nucleus accumbens
NACC_7.CEL


title: Prol_24h+_repC

source_name: OHT treated, 24h


title: Prol_18h-_repC

source_name: control, 18h


title: Prol_24h-_repC

source_name: control, 24h


title: Prol_D6+_repC

source_name: OHT treated, 144h


title: Prol_D6-_repA


title: A50, Liver, APAP, 1250mg/kg, 7d APAP1250_7d_10

description: Gene expression after classical hepatotoxicants exposure

source_name: A50, Liver, APAP, 1250mg/kg, 7d

value: six to seven week

value: Sprague-Dawley


title: A49, Liver, APAP, 1250mg/kg, 7d APAP1250_7d_10

source_name: A49, Liver, APAP, 1250mg/kg, 7d

value: male


title: Prol_D6+_repA


title: Prol_D4-_repB


title: Prol_18h+_repC

source_name: OHT treated, 18h


title: A48, Liver, APAP, 1250mg/kg, 7d APAP1250_7d_10

source_name: A48, Liver, APAP, 1250mg/kg, 7d


title: Prol_D4-_repA


title: NAcc_Earlylife GRov_3

description:
Gene expression data from the nucleus accumbens
NACC_3.CEL


title: NAcc_Earlylife GRov_2

description:
Gene expression data from the nucleus accumbens
NACC_2.CEL


title: A46, Liver, APAP, 1250mg/kg, 7d APAP1250_7d_10

source_name: A46, Liver, APAP, 1250mg/kg, 7d


title: Prol_D4+_repA


title: Prol_48h-_repA


title: NAcc_Earlylife GRov_5

description:
Gene expression data from the nucleus accumbens
NACC_5.CEL


title: Dentate_No-GRov_18

description:
Gene expression data from hippocampal dentate gyrus
DENTATE18.CEL

source_name: Dentate Gyrus

value: control (No-GRov)

value: Hippocampal Dentate Gyrus


title: Prol_24h-_repB


title: Prol_48h+_repB


title: A47, Liver, APAP, 1250mg/kg, 7d APAP1250_7d_10

source_name: A47, Liver, APAP, 1250mg/kg, 7d


title: Prol_24h-_repA


title: Prol_48h-_repB


title: NAcc_Earlylife GRov_1

description:
Gene expression data from the nucleus accumbens
NACC_1.CEL

value: Nucleus Accumbens

value: adult


title: Prol_24h+_repA


title: Prol_48h+_repA

source_name: OHT treated, 48h


title: Prol_D4+_repB


title: Dentate_No-GRov_19

description:
Gene expression data from hippocampal dentate gyrus
DENTATE19.CEL


title: A45, Liver, control, 7d Cntl_7d_9

source_name: A45, Liver, control, 7d


title: Dentate_No-GRov_17

description:
Gene expression data from hippocampal dentate gyrus
DENTATE17.CEL


title: Dentate_No-GRov_16

description:
Gene expression data from hippocampal dentate gyrus
DENTATE16.CEL


title: Prol_24h+_repB


title: A42, Liver, control, 7d Cntl_7d_9

source_name: A42, Liver, control, 7d


title: A43, Liver, control, 7d Cntl_7d_9

source_name: A43, Liver, control, 7d


title: Prol_18h-_repB

value: control vehicle


title: Prol_18h+_repB

value: Neural Stem Cell


title: NAcc_Earlylife GRov_4

description:
Gene expression data from the nucleus accumbens
NACC_4.CEL

source_name: Nucleus Accumbens


title: Prol_18h+_repA

value: Id-cTKO-Rosa-Cre-ER


title: Prol_18h-_repA

value: 129/Svj;C57Bl/6 hybrid


title: A41, Liver, APAP, 1250mg/kg, 3d APAP1250_3d_8

source_name: A41, Liver, APAP, 1250mg/kg, 3d


title: Dentate_No-GRov_15

description:
Gene expression data from hippocampal dentate gyrus
DENTATE15.CEL


title: Dentate_No-GRov_14

description:
Gene expression data from hippocampal dentate gyrus
DENTATE14.CEL


title: Dentate_Lifetime GRov_12

description:
Gene expression data from hippocampal dentate gyrus
DENTATE12.CEL

value: glucocorticoid receptor overexpression (GRov)


title: A39, Liver, APAP, 1250mg/kg, 3d APAP1250_3d_8

source_name: A39, Liver, APAP, 1250mg/kg, 3d


title: Dentate_Lifetime GRov_11

description:
Gene expression data from hippocampal dentate gyrus
DENTATE11.CEL

value: lifetime


title: Old liver 4 hr (Jan 2010)

city: Baton Rouge

first: Jeffrey

last: Gimble

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

hyb_protocol: MouseWG-6 v2 Beadchip (Illumina Sentrix Beadchip Array #11278593) were hybridized for 18 hrs at 58 degrees C with 1.5 micrograms of labeled cRNA.

scan_protocol: Data was scanned using an Illumina BeadArray Reader (Illumina, Inc., San Diego, CA)

data_processing:
Metrics files from the bead scanner were checked to ensure that all samples fluoresced at comparable levels before importing samples into BeadStudio (Framework version 3.1.1.0) Gene Expression module v.3.2. Reference, hybridization control, stringency and negative control genes were checked for proper chip detection. Two datasets were created and exported for downstream analysis. Each contained the average signal for each transcript and the detection p-value. Both data sets had background subtracted from the transcript signals. One data set was quantile normalized and the other was not normalized.
We have applied Benjamini-Hochberg procedure (Benjamini 1995) (p<0.05) for FDR control in analysis of differential expression between age cohorts. Since we interpret and discuss differential genes in the context of their molecular function and gene interaction neighborhood we apply FDR to adjust the discovery of statistically significant biological pathways.

label: Biotin

source_name: 24 month old n = 3

label_protocol: The Illumina TotalPrep RNA Amplification Kit (Applied Biosystems Inc., Foster City, CA, Catalog #AMIL1791) was used to create labeled cRNA from 750ng of input total RNA according to the manufacturer’s protocol.

growth_protocol: Male C57BL/6 mice were aged for periods of 5 or 24 months under 12 hr light: 12 hr dark conditions with ad libitum access to a chow diet.

extract_protocol: Total RNA was extracted using TriReagent (MRC, Cincinnati OH) in accordance with the manufacturer’s recommendations.

treatment_protocol: Five days prior to the experiment, animals were housed in a controlled dim (red) light setting with ad libitum chow food access. Groups of n = 3 mice from each age group were harvested at 3 hr intervals over a 24 hr period for tissues (brown fat, inguinal fat, liver). Tissues were flash frozen in liquid nitrogen at the time of harvest and frozen at -80 degrees C until processed.

tag: time of euthanasia

value: 4 hr


title: A40, Liver, APAP, 1250mg/kg, 3d APAP1250_3d_8

source_name: A40, Liver, APAP, 1250mg/kg, 3d

value: APAP, 1250mg/kg


title: A37, Liver, APAP, 1250mg/kg, 3d APAP1250_3d_8

source_name: A37, Liver, APAP, 1250mg/kg, 3d

value: liver


title: Dentate_Lifetime GRov_10

description:
Gene expression data from hippocampal dentate gyrus
DENTATE10.CEL


title: Old liver 0 hr (Jan 2010)

value: 0 hr


title: Old liver 16 hr (Jan 2010)

value: 16 hr


title: Old liver 12 hr (Jan 2010)

value: 12 hr


title: Young liver 8 hr (Jan 2010)

source_name: 5 month old n = 3

value: male

value: 8 hr


title: Old liver 8 hr (Jan 2010)


title: Old liver 20hr (Jan 2010)

value: 20 hr


title: Young liver 20 hr (Jan 2010)


title: Young liver 12 hr (Jan 2010)


title: A38, Liver, APAP, 1250mg/kg, 3d APAP1250_3d_8

source_name: A38, Liver, APAP, 1250mg/kg, 3d

value: six to seven week

value: Sprague-Dawley


title: Dentate_Lifetime GRov_9

description:
Gene expression data from hippocampal dentate gyrus
DENTATE9.CEL

value: Hippocampal Dentate Gyrus

value: adult


title: Young liver 16 hr (Jan 2010)


title: Dentate_Lifetime GRov_8

description:
Gene expression data from hippocampal dentate gyrus
DENTATE8.CEL


title: A35, Liver, APAP, 1250mg/kg, 3d APAP1250_3d_8

description: Gene expression after classical hepatotoxicants exposure

source_name: A35, Liver, APAP, 1250mg/kg, 3d


title: A36, Liver, APAP, 1250mg/kg, 3d APAP1250_3d_8

source_name: A36, Liver, APAP, 1250mg/kg, 3d


title: Young liver 0 hr (Jan 2010)


title: Young liver 4 hr (Jan 2010)


title: Old brown fat 20hr (Jan 2010)

value: brown fat


title: Dentate_Lifetime GRov_7

description:
Gene expression data from hippocampal dentate gyrus
DENTATE7.CEL


title: Old brown fat 16 hr (Jan 2010)


title: Old brown fat 12 hr (Jan 2010)


title: Dentate_Earlylife GRov_6

description:
Gene expression data from hippocampal dentate gyrus
DENTATE6.CEL

value: early life


title: Dentate_Earlylife GRov_5

description:
Gene expression data from hippocampal dentate gyrus
DENTATE5.CEL

value: glucocorticoid receptor overexpression (GRov)


title: Calibration experiment (#2-1) of wild type and ntrBC mutant

source_name: wild type and ntrBC mutant (Cy3)

tag: sample type

value: mixed RNA from wild-type and ntrBC mutant cells

tag: growth

value: NF with succinate and yeast extract

source_name: wild type and ntrBC mutant (Cy5)


title: Old brown fat 8 hr (Jan 2010)

tag: strain


title: Old brown fat 4 hr (Jan 2010)

value: 4 hr


title: Young brownl fat 20 hr (Jan 2010)


title: Old brown fat 0 hr (Jan 2010)


title: Calibration experiment (#1-2) of wild type and ntrBC mutant


title: Young brown fat 16 hr (Jan 2010)


title: Dentate_Earlylife GRov_3

description:
Gene expression data from hippocampal dentate gyrus
DENTATE3.CEL

source_name: Dentate Gyrus


title: Young brown fat 12 hr (Jan 2010)


title: Young brown fat 8 hr (Jan 2010)


title: Calibration experiment (#2-2) of wild type and ntrBC mutant


title: Calibration experiment (#1-1) of wild type and ntrBC mutant


title: Young brown fat 0 hr (Jan 2010)


title: Dentate_Earlylife GRov_2

description:
Gene expression data from hippocampal dentate gyrus
DENTATE2.CEL


title: Comparative experiment (#3-1) of wild type vs nifA mutant

source_name: wild type (Cy3)

value: wild-type cells

source_name: nifA mutant (Cy5)

value: nifA mutant cells


title: Comparative experiment (#3-2) of wild type vs nifA mutant


title: Young brown fat 4 hr (Jan 2010)


title: Old Inguinal fat 20hr (Jan 2010)

value: inguinal fat


title: Old Inguinal fat 8 hr (Jan 2010)


title: Old Inguinal fat 16 hr (Jan 2010)

value: 16 hr


title: Dentate_Earlylife GRov_1

description:
Gene expression data from hippocampal dentate gyrus
DENTATE1.CEL

value: male


title: Old Inguinal fat 4 hr (Jan 2010)


title: Comparative experiment (#2-1) of wild type vs nifA mutant

source_name: nifA mutant (Cy3)

source_name: wild type (Cy5)


title: Comparative experiment (#2-2) of wild type vs nifA mutant


title: Dentate_Earlylife GRov_4

description:
Gene expression data from hippocampal dentate gyrus
DENTATE4.CEL


title: Old Inguinal fat 12 hr (Jan 2010)

value: 12 hr


title: Young Inguinal fat 16 hr (Jan 2010)


title: Calibration experiment (#2-2) of wild type and nifA mutant

source_name: wild type and nifA mutant (Cy3)

value: mixed RNA from wild-type and nifA mutant cells

source_name: wild type and nifA mutant (Cy5)


title: Young Inguinal fat 4 hr (Jan 2010)


title: Calibration experiment (#1-2) of wild type and nifA mutant


title: Old Inguinal fat 0 hr (Jan 2010)

value: 0 hr


title: Old liver 20hr (Nov 2009)

value: liver

value: 20 hr


title: Young Inguinal fat 20 hr (Jan 2010)


title: Young Inguinal fat 12 hr (Jan 2010)


title: Old liver 12 hr (Nov 2009)


title: A33, Liver, control, 3d Cntl_3d_7

source_name: A33, Liver, control, 3d

value: control

tag: time

value: six to seven week

value: Sprague-Dawley


title: Old liver 16 hr (Nov 2009)

source_name: 24 month old n = 3


title: Calibration experiment (#2-1) of wild type and nifA mutant


title: A32, Liver, control, 3d Cntl_3d_7

source_name: A32, Liver, control, 3d


title: Young Inguinal fat 8 hr (Jan 2010)

value: 8 hr


title: Young Inguinal fat 0 hr (Jan 2010)


title: A34, Liver, control, 3d Cntl_3d_7

source_name: A34, Liver, control, 3d


title: Old liver 8 hr (Nov 2009)


title: Old liver 0 hr (Nov 2009)


title: A31, Liver, control, 3d Cntl_3d_7

source_name: A31, Liver, control, 3d


title: Calibration experiment (#1-1) of wild type and nifA mutant


title: Young liver 20 hr (Nov 2009)

source_name: 5 month old n = 3


title: Young liver 16 hr (Nov 2009)


title: Old liver 4 hr (Nov 2009)


title: Young liver 8 hr (Nov 2009)


title: A30, Liver, APAP, 1250mg/kg, 24h APAP1250_24h_6

source_name: A30, Liver, APAP, 1250mg/kg, 24h

value: APAP, 1250mg/kg


title: A28, Liver, APAP, 1250mg/kg, 24h APAP1250_24h_6

source_name: A28, Liver, APAP, 1250mg/kg, 24h


title: A44, Liver, control, 7d Cntl_7d_9

source_name: A44, Liver, control, 7d


title: Young liver 4 hr (Nov 2009)


title: A26, Liver, APAP, 1250mg/kg, 24h APAP1250_24h_6

source_name: A26, Liver, APAP, 1250mg/kg, 24h


title: Young liver 12 hr (Nov 2009)


title: Old brown fat 12 hr (Nov 2009)

value: brown fat


title: Old brown fat 16 hr (Nov 2009)


title: A29, Liver, APAP, 1250mg/kg, 24h APAP1250_24h_6

source_name: A29, Liver, APAP, 1250mg/kg, 24h


title: Young liver 0 hr (Nov 2009)


title: A24, Liver, APAP, 1250mg/kg, 24h APAP1250_24h_6

source_name: A24, Liver, APAP, 1250mg/kg, 24h


title: A25, Liver, APAP, 1250mg/kg, 24h APAP1250_24h_6

source_name: A25, Liver, APAP, 1250mg/kg, 24h


title: Old brown fat 8 hr (Nov 2009)


title: A23, Liver, APAP, 100mg/kg, 24h APAP100_24h_5

source_name: A23, Liver, APAP, 100mg/kg, 24h

value: APAP, 100mg/kg


title: A27, Liver, APAP, 1250mg/kg, 24h APAP1250_24h_6

source_name: A27, Liver, APAP, 1250mg/kg, 24h


title: A22, Liver, APAP, 100mg/kg, 24h APAP100_24h_5

source_name: A22, Liver, APAP, 100mg/kg, 24h


title: experiment 46, PGC-1alpha transduced

city: Barcelona

first: Sergi

last: Beltran

address: Baldiri Reixac 10

department: Serveis Cientificotècnics

country: Spain

institute: Universitat de Barcelona

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Illumina BeadScan software.

data_processing: Raw data was extracted, background corrected and summarized using BeadStudio data analysis software. Statistical analysis was carried out with Bioconductor. The lumi package was used to apply log2 transformation followed by quantile normalization to the BeadStudio summarized data. Then, a paired t-test  was conducted with Limma to select differentially expressed genes between the PGC-1alpha-overexpressers and controls. Only those genes with a p value smaller than 0.025 and a fold change greater than 1.5 were selected.

source_name: primary cultured skeletal muscle, PGC-1alpha transduced

label_protocol: Biotinylated cRNA were prepared using the Illumina Amplification kit (Ambion).

growth_protocol: Cells were grown at 37ºC and 5% CO2 conditions.

extract_protocol: RNA was extracted with the QIAGEN Rneasy kit, treated with DNase, and homogenized with a Polytron. Quality of samples were monitored with an Agilent 2100 Bioanalyzer.

treatment_protocol: Differentiated cultured muscle cells were transduced with adenoviruses containing PGC-1alpha or GFP.

value: paravertebral muscles biopsies

tag: transfection

value: adenovirus containing PGC-1aplha

tag: experiment


title: experiment 44, PGC-1alpha transduced


title: experiment 44, GFP transduced

source_name: primary cultured skeletal muscle, control

value: adenovirus containing GFP


title: Old brown fat 4 hr (Nov 2009)

source_name: 24 month old n = 3

value: 4 hr


title: Old brown fat 0 hr (Nov 2009)

value: male


title: experiment 46, GFP transduced


title: Young brownl fat 20 hr (Nov 2009)


title: experiment 24, GFP transduced


title: Young brown fat 16 hr (Nov 2009)

value: 16 hr


title: B6 Blu ES cells

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module,2.5 ug of cDNA were hybridized into the GeneChipHybridization Oven 640 for 18 hr at 45C on Gene 1.0 ST Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing:
The data were analyzed with the Affymetrix GeneChip Command Console. Microarray expression data and were processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software using Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).
RMA-EXON-CORE-DABG-SIGNAL

source_name: Mouse embryonic stem cells

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system from 500pg-50 ng total RNA.

growth_protocol: iPS clones were generated from fibroblasts obtained from wildtype B6 mouse (C57Bl/6 mice) embryonic fibroblasts (MEFs). Briefly, 3x105 fibroblasts were seeded on 6 well plates and allowed to grow overnight. The next day, the cells were transduced with the OSK lentivirus at an MOI of 1-5. The cells were incubated with virus for 48 hours, trypsinized, and transferred to a 100-mm dish without a feeder MEF layer. Cells were grown for 2-3 weeks with daily media changes. After 17-26 days individual colonies were picked and expanded on MEF feeder layers.

extract_protocol: All 10 iPS clones were assessed for ES cell-like morphology and stained for alkaline phosphatase according to the manufacturer‟s instructions (Millipore)

value: B6 Blu ES cells


title: A21, Liver, APAP, 100mg/kg, 24h APAP100_24h_5

source_name: A21, Liver, APAP, 100mg/kg, 24h


title: experiment 24, PGC-1alpha transduced


title: MPSVII MEFs_replicate2

source_name: wildtype B6 mouse embryonic fibroblasts

value: MPSVII MEFs


title: MPSVII MEFs_replicate1


title: A20, Liver, APAP, 100mg/kg, 24h APAP100_24h_5

source_name: A20, Liver, APAP, 100mg/kg, 24h

value: liver


title: Old brown fat 20hr (Nov 2009)

value: 20 hr


title: A19, Liver, APAP, 100mg/kg, 24h APAP100_24h_5

source_name: A19, Liver, APAP, 100mg/kg, 24h


title: Young brown fat 4 hr (Nov 2009)

source_name: 5 month old n = 3


title: Young brown fat 12 hr (Nov 2009)

value: 12 hr


title: A16, Liver, control, 24h Cntl_24h_4

source_name: A16, Liver, control, 24h

value: control

value: six to seven week


title: Young brown fat 8 hr (Nov 2009)

value: 8 hr


title: MPSVII ES cells_replicate1

value: MPSVII ES cells


title: MPSVII iPS#5_replicate1

value: MPSVII iPS#5


title: MPSVII iPS#6_replicate1

value: MPSVII iPS#6


title: A18, Liver, control, 24h Cntl_24h_4

source_name: A18, Liver, control, 24h

value: Sprague-Dawley


title: MPSVII ES cells_replicate2


title: Old Inguinal fat 16 hr (Nov 2009)

value: inguinal fat


title: A17, Liver, control, 24h Cntl_24h_4

source_name: A17, Liver, control, 24h


title: Young brown fat 0 hr (Nov 2009)

value: brown fat

value: 0 hr


title: Old Inguinal fat 20hr (Nov 2009)

value: male


title: MPSVII iPS#6_replicate2


title: A12, Liver, APAP, 1250mg/kg, 6h APAP1250_6h_3

source_name: A12, Liver, APAP, 1250mg/kg, 6h

value: APAP, 1250mg/kg


title: A15, Liver, control, 24h Cntl_24h_4

source_name: A15, Liver, control, 24h


title: Old Inguinal fat 4 hr (Nov 2009)

value: 4 hr


title: Old Inguinal fat 8 hr (Nov 2009)


title: MPSVII iPS#2_replicate1

value: MPSVII iPS#2


title: MPSVII iPS#5_replicate2


title: A14, Liver, APAP, 1250mg/kg, 6h APAP1250_6h_3

source_name: A14, Liver, APAP, 1250mg/kg, 6h

value: liver


title: MPSVII iPS#1_replicate1

value: MPSVII iPS#1


title: Old Inguinal fat 12 hr (Nov 2009)

value: 12 hr


title: A13, Liver, APAP, 1250mg/kg, 6h APAP1250_6h_3

source_name: A13, Liver, APAP, 1250mg/kg, 6h


title: MPSVII iPS#1_replicate2


title: A11, Liver, APAP, 1250mg/kg, 6h APAP1250_6h_3

source_name: A11, Liver, APAP, 1250mg/kg, 6h


title: Young Inguinal fat 20 hr (Nov 2009)

value: 20 hr


title: Old Inguinal fat 0 hr (Nov 2009)


title: A07, Liver, APAP, 100mg/kg, 6h APAP100_6h_2

source_name: A07, Liver, APAP, 100mg/kg, 6h

value: APAP, 100mg/kg

value: six to seven week


title: A10, Liver, APAP, 1250mg/kg, 6h APAP1250_6h_3

source_name: A10, Liver, APAP, 1250mg/kg, 6h


title: A08, Liver, APAP, 100mg/kg, 6h APAP100_6h_2

source_name: A08, Liver, APAP, 100mg/kg, 6h


title: A09, Liver, APAP, 100mg/kg, 6h APAP100_6h_2

source_name: A09, Liver, APAP, 100mg/kg, 6h


title: A06, Liver, APAP, 100mg/kg, 6h APAP100_6h_2

source_name: A06, Liver, APAP, 100mg/kg, 6h


title: Young Inguinal fat 12 hr (Nov 2009)


title: Young Inguinal fat 16 hr (Nov 2009)

value: 16 hr


title: Mississippi_CD30_cell_transcriptome_array3

city: College Station

first: Huaijun

last: Zhou

state: TX

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

description: Four arrays are included in one slide

hyb_protocol: A 825 ng of labeled cRNA with specificity over 8 were used for the hybridization reaction using the in situ hybridization kit plus (Agilent Technologies). A 100 ul hybridization solution was loaded on each of array in Agilent 4x44K microarrays. Arrays were incubated at 65 ℃ for 17h in Agilent’s microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol.

scan_protocol: Slides were scanned at 5-μm resolution using GenePix Personal 4100A (Molecular Devices Corporation, Sunnyvale, CA) and were saved as TIFF images. Auto Photomultiplier tube (PMT) were selected and adjusted to get the ratio of the overall intensities between the two channels (Cy3 and Cy5) was 0.9~1.1. The intensities of the spots on each image were quantified by Genepix pro 6.0 software (Molecular Devices Corporation, Downingtown, PA), and data were saved as .txt files for further analyses.

data_processing: The signal intensity of each gene was globally normalized using LOWESS by R program (Yang et al, 2002).

organism: Gallus gallus

source_name: CD30(hi)(positive) cells - rep3

label_protocol: A 300 ng of aliquot of total RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The synthesized cDNA was transcribed into cRNA labeled with one of two cyanine-labeled nucleotides (Perkin Elmer, Wellesley, MA). Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity measured with ND-100 spectrophotometer (NanoDrop Technologies).

growth_protocol: The CD30(hi) cells were sorted using monoclonal antibody (mAb) AV37 using magnetic activated cell sorting (Militenyi Biotech) and the purity of sort was analyzed by flow cytometry.

extract_protocol: RNA was isolated from four replicates of 10^6 CD30(hi) lymphocytes using the TRI Reagent® (Applied Biosystems). The quality of purified RNA was analyzed using the Agilent 2100 Bioanalyzer (Agilent Technologies) and RNA was quantified using the GeneSpec I spectrophotometer.

treatment_protocol: MD lymphomas were isolated from white leghorn chickens infected with MDV GA/22 strain using the standard techniques.

tag: disease

value: marek’s disease (md) lymphomas

value: CD30(hi)(positive) cells

source_name: CD30(lo)(negative) cells - rep3

growth_protocol: The CD30(lo) cells were sorted using monoclonal antibody (mAb) AV37 using magnetic activated cell sorting (Militenyi Biotech) and the purity of sort was analyzed by flow cytometry.

extract_protocol: RNA was isolated from four replicates of 10^6 CD30(lo) lymphocytes using the TRI Reagent® (Applied Biosystems). The quality of purified RNA was analyzed using the Agilent 2100 Bioanalyzer (Agilent Technologies) and RNA was quantified using the GeneSpec I spectrophotometer.

value: CD30(lo)(negative) cells


title: Young Inguinal fat 8 hr (Nov 2009)

tag: tissue

value: inguinal fat

value: 8 hr


title: Young Inguinal fat 0 hr (Nov 2009)

value: 0 hr


title: Mississippi_CD30_cell_transcriptome_array4

description: Four arrays are included in one slide

source_name: CD30(lo)(negative) cells - rep4

source_name: CD30(hi)(positive) cells - rep4


title: Young Inguinal fat 4 hr (Nov 2009)

source_name: 5 month old n = 3

value: male


title: Mississippi_CD30_cell_transcriptome_array1

description: Four arrays are included in one slide

source_name: CD30(hi)(positive) cells - rep1

source_name: CD30(lo)(negative) cells - rep1


title: biological replicate #9

city: Hsinchu

first: Yu-Ting

last: Chen

address: No.101, Sec. 2, Guang-Fu Rd.

department: Institute of Molecular and Cellular Biology

country: Taiwan

institute: National Tsing Hua University, Taiwan

hyb_protocol: Pre-hybridized with 1% BSA 5x SSC and 0.1% SDS at  42 °C for 1hr. Subsequently washed with 0.1x SSC two times vigorously for 5 min at 25 °C. Then washed in ddH2O for 30 sec at 25 °C, and rinsed with isopropanol prior to drying and hybridizing. The array was hybridized with Cy-3 and Cy-5 labeled aRNA (+ 20µg of poly A and yeast tRNA) in Corning Microarray Hybridization Chamber (No.2551, Corning). The hybridization was reacted at 65˚C water bath for 16 hours. Array then washed in 2x SSC (+ 0.03 % SDS) at 65 °C for 2min.  Sub-washed in 2x SSC, 1x SSC, 0.2x SSC and 0.1x SSC, each at 25 °C for 2min prior to drying and scanning.

scan_protocol: The slide were scanned using Axon GenePix 4000B scanner (Axon Instruments, Inc., Union City, CA); Genepix software was used to pick up the spot.

data_processing: Lowess normalization was used to remove intensity-based variation across channels. The following linear model was then fitted for each of the spot on DNA microarrays: y ijkl = strain i + dye j + array k + ε ijkl, where strain i stands for the ith strain for i=1, 2, dye j stands for the jth dye effect for j=1,2, array k stands for the overall array effect and is a random effect, and ε ijkl is the residual term for random variation that is not caught by the above model. y ijkl is the intensity we want to model. The genes with significant strain effects are selected using False Discovery Rate (FDR)=0.05, which is equivalent to p-value ≤ 0.0148. The analysis was carried out with JMP Genomics (SAS Institute Inc., Cary, NC) and the R package qvalue

organism: Candida albicans

source_name: Mid log-phase rhb1 mutant cultured in SD medium at 30˚C

label_protocol: cDNA synthesis, aRNA synthesis and Cy-dye coupling was carried out by using Amino Allyl MessageAmp™ II aRNA Amplification Kit (AM1753, Ambion) following by manufacturer’s manual. Briefly, the first strand of cDNA was then prepared from total RNA using ArrayScript™ reverse transcriptase. After processing, DNA polymerase and RNase H was further used for second strand cDNA synthesis. In vitro transcription by using T7 RNA polymerase and purified cDNA as the template, the amino allyl UTP (aaUTP) incorporated aRNA (amino allyl-modified aRNA) was synthesized. aRNA was purified and performed Cy5  (Amersham Cy5 Mono-Reactive Dye Pack, PA25001, GE Healthcare) or Cy3 (Amersham Cy3 Mono-Reactive Dye Pack, PA23001, GE Healthcare) dye coupling. Cy dye coupled aRNA is purified by ultrafiltration using RNeasy® MinElute™ Cleanup kit (QIAGEN).

growth_protocol: Wild type (SC5314) and rhb1∆/rhb1∆ (CCT-D1) Candida albicans strains were subcultured in 40 mL of fresh SD (synthetic defined) medium (250mL flask) for 5.5 hours at 30˚C and 220rpm to reach O.D. 600 nm approximately at 4.0.

extract_protocol: Total RNA was extracted by RNeasy® kit (74106, QIAGNE, Valencia, CA) following by manufacturer’s manual. Extracted total RNA was subsequently treated with Turbo DNA-free™ DNase (Ambion, Austin, TX) for 1 h at 37˚C to degrade residual DNA. The quality and quantity of total RNA are determined using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) or agarose gel electrophoresis and ND-1000 spectrophotometer (NanoDrop Technologies).

treatment_protocol: The cell was removed to 50 mL conical tubes and centrifuged (3,220 g, 4˚C) to discard the supernatant completely; the cell was stored at -80˚C prior to RNA extraction.

tag: genotype

source_name: Mid log-phase wild type cultured in SD medium at 30˚C

value: wild type


title: MPSVII iPS#2_replicate2

source_name: wildtype B6 mouse embryonic fibroblasts


title: biological replicate #6


title: biological replicate #7


title: A05, Liver, APAP, 100mg/kg, 6h APAP100_6h_2

source_name: A05, Liver, APAP, 100mg/kg, 6h

tag: treatment

tag: gender

value: Sprague-Dawley


title: A04, Liver, control, 6h Cntl_6h_1

source_name: A04, Liver, control, 6h

value: control


title: biological replicate #4


title: 1 month Math1-Cre;SmoM2 medulloblastoma

city: San Francisco

first: Xi

last: Huang

state: CA

address: 1550 4th Street, Room RH-481

institute: University of California, San Francisco

description: Gene expression data from medulloblastoma

scan_protocol: Standard protocols for Affymetrix GeneChip 3000 7G laser confocal slide scanner

data_processing:
Standard protocols for Affymetrix GeneChip Mouse Gene 1.0 ST array using Affymetrix Expression Console software
affymetrix-algorithm-name = rma-gene-default

source_name: mouse medulloblastoma

growth_protocol: Medulloblastomas spontaneously develop in the PtchLacZ/+ and Math1-Cre;SmoM2 mice.

extract_protocol: Medulloblastoma tumor tissues and the control wild-type cerebellum were quickly removed from the skull of euthanized mice, and directly processed for total RNA extraction using RNeasy mini kit (Qiagen)

value: mixed genetic background involving C57BL/6 and C3H strains

value: 1 months

value: medulloblastoma


title: A01, Liver, control, 6h Cntl_6h_1

source_name: A01, Liver, control, 6h

value: liver


title: A03, Liver, control, 6h Cntl_6h_1

source_name: A03, Liver, control, 6h


title: biological replicate #3


title: biological replicate #10


title: A02, Liver, control, 6h Cntl_6h_1

source_name: A02, Liver, control, 6h


title: biological replicate #2


title: Pollen at Pb, biological rep1

city: Chengdu

first: Sheng-hua

last: Wang

state: Sichuan

address: No.24 South Section 1, Yihuan Road

department: College of Life Science

country: China

institute: Sichuan University

description: Gene expression data from  bicellular pollen stage.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree celsius on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using script EukGE-WS2v4.

scan_protocol: GeneChips were scanned using the Gene array Scanner3000 7G.

data_processing: All data were normalized using Robust Multiarray Averaging (RMA) method by AffylmGUI. The dChip software be used to analysis each microarray group for detection call, and each probe set was assigned a P (present) or A (absent) using Model-Based Expression Indexes (MBEI) algorithm.

organism: Oryza sativa Indica Group

source_name: Rice male gametophyte in bicellular pollen stage

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

growth_protocol: Rice grown under natural field conditions.

extract_protocol: Extraction of total RNA was performed using the RNeasy Plant Kit (Qiagen), according to the manufacturer's instructions

treatment_protocol: Tissue samples were collected at sunny noon on June-July. Collected biological samples were frozen in liquid nitrogen and kept -80C until RNA extraction.

value: Male gametophyte

tag: variety

value: Guichao No.2

value: bicellular pollen stage


title: Pollen at Pc, biological rep1

description: Gene expression data from  tricellular pollen stage.

source_name: Rice male gametophyte in ticellular pollen stage

tag: age

value: tricellular pollen stage


title: 5 month PtchLacZ/+ medulloblastoma

hyb_protocol: Standard protocols for Affymetrix GeneChip Mouse Gene 1.0 ST array

tag: genotype/variation

value: PtchLacZ/+

value: 5 months


title: biological replicate #8


title: SQ4

city: Utrecht

first: Jantine

middle: Wilhelmina Paula Maria

last: van Baal

address: Heidelberglaan 100

department: Gastroenterology and Hepatology

country: Netherlands

institute: University Medical Center Utrecht

hyb_protocol: Hybridization was performed by Exiqon according to manufacturer protocol

scan_protocol: Scanning was performed by Exiqon according to manufacturer protocol

data_processing: Data processing was performed by Exiqon according to manufacturer protocol; in brief normalization included background subtraction and normalization with global Lowess (Locally Weighter Scatterplot Smoothing) regression algorithm. This within-slide normalization was performed to minimize differences between the colors in an intensity-dependent manner. The criterion for deciding that a miRNA had failed on a particular array was the observation that 3 or more of the 4 replicated measures of this miRNA had a signal that was below background. In addition, Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide were excluded. Replicated measurements of the same miRNA from each slide were averaged to per-chip median values and then used to obtain geometric means and standard deviations for each miRNA.

source_name: normal squamous esophagus biopsy

label_protocol: Labeling was performed by Exiqon, according to manufacturer protocol; in brief 2 ug of total RNA was labeled using the miRCURY Hy3/Hy5 labeling kit according to Exiqon protocol (Vedbaek, Denmark)

extract_protocol: Total RNA was extracted from biopsy samples using miRNeasy Minikit (Qiagen) according to manufacturer protocol

treatment_protocol: none, fresh biopsy material

value: esophagus

tag: tumor stage

tag: Stage

source_name: common reference

tag: reference

value: common reference (mixture of all esophageal adenocarcinoma, Barrett's esophagus and normal squamous esophagus samples used)


title: 2 month wild-type cerebellum

description: Gene expression data from cerebellum

source_name: adult mouse whole cerebellum

label_protocol: Standard protocols for Affymetrix GeneChip Mouse Gene 1.0 ST array

value: wild-type

value: 2 months

value: cerebellum


title: Mississippi_CD30_cell_transcriptome_array2

description: Four arrays are included in one slide

source_name: CD30(lo)(negative) cells - rep2

value: marek’s disease (md) lymphomas

tag: cell type

value: CD30(lo)(negative) cells

source_name: CD30(hi)(positive) cells - rep2

value: CD30(hi)(positive) cells


title: biological replicate #5

value: wild type


title: SQ3

value: male


title: Pollen at Pc, biological rep2


title: SQ2


title: 2 month Math1-Cre;SmoM2 medulloblastoma

value: mixed genetic background involving C57BL/6 and C3H strains

value: medulloblastoma


title: Pollen at Pb, biological rep2

value: Male gametophyte

value: Guichao No.2


title: biological replicate #1


title: Pollen at Pa, biological rep1

description: Gene expression data from uninucleate microspores stage.

source_name: Rice male gametophyte in uninucleate microspores stage

value: uninucleate microspores stage


title: SQ1


title: qseC grown OD1 DMEM

city: Dallas

first: Jacqueline

middle: Wanjiku

last: Njoroge

address: 5323 Harry Hines Blvd

institute: UTSW medical center

hyb_protocol: standard Affymetrix procotocl

scan_protocol: standard Affymetrix procotocl

data_processing: GCOS v1.4

organism: Escherichia coli O157:H7

source_name: qseC mutant grown in DMEM to OD1.0

label_protocol: standard Affymetrix procotocl

growth_protocol: All strains grown in DMEM

extract_protocol: Ambion RiboPure RNA isolation protocol

value: qseC


title: qseC grown OD1 DMEM with epinephrine

source_name: qseC mutant grown in DMEM with epinephrine to OD1.0

value: epinephrine


title: WT vs nhr-80-/- (replicate 4)

first: Pranali

middle: Prasad

last: Pathare

address: 1100 Fairview Ave. N

department: Basic Sciences

institute: FHCRC

hyb_protocol: Wash at 42C for 5 cycles in 2XSSC and 3 cycles in 0.1XSSC using an automated Gene Tac Hybridization Station

scan_protocol: Scanned on a GenePix 4000B scanner

data_processing: Array data was pre-processed through a custom-built application used to filter data based on criteria associated with spot-level signal quality (e.g., signal-to-noise, lower bound intensity threshold, spot dimension).  Each array was background subtracted and ratio values were log2 transformed.  Intra-array normalization was performed using a loess algorithm to correct for intensity-dependent ratio biasing.

organism: Caenorhabditis elegans

label_protocol: Cy5- and Cy3-labeled cDNA targets were generated from 30 ug of total RNA using a reverse transcription, amino-allyl based protocol

extract_protocol: Total RNA extracted using Tri-Reagent kit following manufacturer's instructions

source_name: WT

value: WT


title: WT vs nhr-80-/- (replicate 3)


title: WT vs nhr-80-/- (replicate 1)


title: qseE grown OD1 DMEM with epinephrine

source_name: qseE mutant grown in DMEM with epinephrine to OD1.0

value: qseE


title: BE2

source_name: Barrett's esophagus biopsy

value: esophagus

value: metaplasia

value: common reference (mixture of all esophageal adenocarcinoma, Barrett's esophagus and normal squamous esophagus samples used)


title: BE4


title: WT vs nhr-80-/- (replicate 2)


title: WT vs nhr-66-/- (replicate 3)


title: Pollen at Pa, biological rep2


title: qseE grown OD1 DMEM

source_name: qseE mutant grown in DMEM to OD1.0


title: BE1


title: BE3


title: wt grown OD1 DMEM with epinephrine

source_name: wt grown in DMEM with epinephrine to OD1.0

value: wt


title: WT vs nhr-66-/- (replicate 1)


title: EAC4

source_name: esophageal adenocarcinoma biopsy


title: EAC3


title: wt grown OD1 DMEM

source_name: wt grown in DMEM to OD1.0


title: qseC-qseE grown OD1 DMEM with epinephrine

source_name: qseCqseE mutant grown in DMEM with epinephrine to OD1.1

value: qseC-qseE


title: WT vs nhr-49-/- (replicate 1)


title: WT vs nhr-66-/- (replicate 2)


title: EAC1


title: qseC-qseE grown OD1 DMEM

source_name: qseCqseE mutant grown in DMEM to OD1.0


title: Rhodopseudomonas palustris cells NF with succinate and yeast extract #2

first: Yasuhiro

last: Oda

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

institute: University of Washington

description: A high-density oligonucleotide microarray (Affymetrix GeneChip) was custom designed and manufactured by Affymetrix based on the sequences of ORFs and intergenic regions. cDNA synthesis, fragmentation, labeling, hybridization, and processing of custom designed Rhodopseudomonas palustris GeneChips were carried out as recommended by the manufacturer. Experiments were performed in duplicate with independently prepared samples.

hyb_protocol: As recommended by the manufacturer (Affymetrix)

data_processing: The Affymetrix GeneChip Operating Software Version 1.4 was used for initial data acquisition and processing.

label: Biotinylated GeneChip reagent

source_name: Rhodopseudomonas palustris

extract_protocol: Rhodopseudomonas palustris cells were disrupted by bead beating and RNA was purified with the RNeasy Mini kit (Qiagen) including DNase treatment on the column.

tag: growth

value: NF with succinate and yeast extract


title: WT vs nhr-49-/- (replicate 2)


title: Rhodopseudomonas palustris cells grown on PM with succinate #1

scan_protocol: As recommended by the manufacturer (Affymetrix)

tag: strain

value: PM with succinate


title: Rhodopseudomonas palustris cells NF with succinate and yeast extract #1

label_protocol: As recommended by the manufacturer (Affymetrix)


title: EAC2

value: male

source_name: common reference


title: Mouse Embryonic Fibroblasts KO3 vs WT3

city: Madrid

first: Silvia

last: Remeseiro

state: Madrid

address: Calle Melchor Fernandez Almagro 3

institute: Spanish National Cancer Research Centre (CNIO)

description: Biological replicate 3 of 3. Primary Mouse Embryonic Fibroblasts, untreated.

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 825 ng. Volume: 100 uL. Temperature (C): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2565C DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 10.7).

data_processing: Data were preprocessed using Bioconductor's limma package. Background correction was performed usign normexp. Data were normalized using whithin-array lowess and between array quantile normalization.

source_name: WT Mouse Embryonic Fibroblasts

label_protocol: Amount of nucleic acid labeled: 1µg. Amplification: by RNA polymerases. Commercial Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit by following manufacturer instructions. Agilent manual G4140-90050 Ver. 5.7 March 2008.

growth_protocol: MEFs were grown in DMEM supplemented with 10% FBS

extract_protocol: Total RNA was isolated with Qiagen RNeasy kit according to manufacturer's conditions

treatment_protocol: Untreated

tag: embryo stage

source_name: SA1-KO Mouse Embryonic Fibroblasts


title: Rhodopseudomonas palustris cells grown on PM with succinate #2

city: Seattle


title: CD46+/STAT1-KO hippo - Untreated-E

status: Public on Mar 14 2012

city: Philadelphia

first: Michael

last: Slifker

state: PA

address: 333 Cottman Ave.

institute: Fox Chase Cancer Center

description: Gene expression in untreated STAT1-KO mouse neurons

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

scan_protocol: Scanned on an Agilent G2565B scanner with default settings

data_processing: Microarray images were processed using Agilent Feature Extraction software (version 9.5). Data were background corrected using normexp (offset=25), followed by quantile normalization. Control probes, probes lacking Entrez ID, and probes with intensity close to background across all arrays were removed.

source_name: CD46+/STAT1-KO hippo - Untreated-E

label_protocol: 500 ng total RNA was amplified and labeled using the Low RNA input linear amplification kit (Agilent). Labeled cRNA targets were hybridized onto Agilent 4×44k mouse whole genome arrays. Microarray images were processed using Agilent Feature Extraction software (version 9.5).

growth_protocol: Primary hippocampal neurons were prepared from embryonic (E15-16) mice as previously described {Banker and Goslin, 1991, Rall, et al, 1997). Neurons were plated on 15mm glass coverslips or in 12-well plates coated with poly-L-lysine (Sigma) at a density of 2.5x105 cells/well.  Neurons were incubated at 37°C in a humidified incubator with 5% CO2 for 5d prior to IFNγ treatment or infection to allow for full differentiation.

extract_protocol: RNA was purified from whole cell lysates using the RNeasy Mini kit (Qiagen), and contaminating DNA was removed using an RNase-Free DNase set.

treatment_protocol: Five days post-plating, primary hippocampal neurons from NSE-CD46+ mice and NSE-CD46+/STAT1-KO mice were treated with murine IFNγ (BD Transduction Labs), diluted in B27-free Neurobasal Media, added to the cultures (100 U/ml final concentration) and incubated for the indicated times prior to collection.

tag: time (h)

value: primary hippocampal neuron

value: untreated

tag: genetic background


title: Mouse Embryonic Fibroblasts KO2 vs WT2

description: Biological replicate 2 of 3. Primary Mouse Embryonic Fibroblasts, untreated.


title: CD46+/STAT1-KO hippo - IFNg-24h-E

description: Gene expression at 24h after treatment with IFNg in STAT1-KO mouse neurons

source_name: CD46+/STAT1-KO hippo - IFNg-24h-E

value: IFNg


title: CD46+/STAT1-KO hippo - IFNg-24h-B

source_name: CD46+/STAT1-KO hippo - IFNg-24h-B


title: CD46+/STAT1-KO hippo - IFNg-6h-D

description: Gene expression at 6h after treatment with IFNg in STAT1-KO mouse neurons

source_name: CD46+/STAT1-KO hippo - IFNg-6h-D


title: Mouse Embryonic Fibroblasts KO1 vs WT1

description: Biological replicate 1 of 3. Primary Mouse Embryonic Fibroblasts, untreated.


title: CD46+/STAT1-KO hippo - IFNg-3h-B

description: Gene expression at 3h after treatment with IFNg in STAT1-KO mouse neurons

source_name: CD46+/STAT1-KO hippo - IFNg-3h-B


title: CD46+/STAT1-KO hippo - IFNg-3h-A

source_name: CD46+/STAT1-KO hippo - IFNg-3h-A


title: CD46+/STAT1-KO hippo - IFNg-6h-E

source_name: CD46+/STAT1-KO hippo - IFNg-6h-E


title: CD46+ hippo - IFNg-24h-D

description: Gene expression at 24h after treatment with IFNg in WT mouse neurons

source_name: CD46+ hippo - IFNg-24h-D


title: CD46+/STAT1-KO hippo - IFNg-24h-A

source_name: CD46+/STAT1-KO hippo - IFNg-24h-A


title: CD46+/STAT1-KO hippo - Untreated-D

source_name: CD46+/STAT1-KO hippo - Untreated-D


title: CD46+/STAT1-KO hippo - Untreated-C

source_name: CD46+/STAT1-KO hippo - Untreated-C


title: CD46+ hippo - IFNg-24h-E

source_name: CD46+ hippo - IFNg-24h-E


title: CD46+ hippo - IFNg-6h-D

description: Gene expression at 6h after treatment with IFNg in WT mouse neurons

source_name: CD46+ hippo - IFNg-6h-D


title: CD46+ hippo - IFNg-3h-C

description: Gene expression at 3h after treatment with IFNg in WT mouse neurons

source_name: CD46+ hippo - IFNg-3h-C


title: CD46+ hippo - IFNg-6h-A

source_name: CD46+ hippo - IFNg-6h-A


title: CD46+ hippo - IFNg-6h-E

source_name: CD46+ hippo - IFNg-6h-E


title: CD46+ hippo - IFNg-24h-A

source_name: CD46+ hippo - IFNg-24h-A


title: CD46+/STAT1-KO hippo - IFNg-3h-C

source_name: CD46+/STAT1-KO hippo - IFNg-3h-C


title: CD46+ hippo - Untreated-C

description: Gene expression in untreated WT mouse neurons

source_name: CD46+ hippo - Untreated-C


title: CD46+ hippo - Untreated-D

source_name: CD46+ hippo - Untreated-D


title: CD46+ hippo - Untreated-A

source_name: CD46+ hippo - Untreated-A


title: CD46+ hippo - IFNg-3h-D

source_name: CD46+ hippo - IFNg-3h-D


title: CD46+ hippo - IFNg-3h-B

source_name: CD46+ hippo - IFNg-3h-B


title: FV-P6 35C rep1

city: Chestnut Hill

first: Marc-Jan

last: Gubbels

address: 140 Commonwealth Avenue

department: Biology

institute: Boston College

description: FV-P6 at 35C

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Probe intensities were measured with the Affymetrix GeneChip Scanner 3000 7G and were processed into image analysis (.CEL) files with either GeneChip Operating Software or Expression Console Software (Affymetrix). CEL files were processed together with Robust Multi-array Average (RMA).

organism: Toxoplasma gondii

source_name: FV-P6 35C rep1

label_protocol: standard Affymetrix protocol

growth_protocol: Parasites were grown in confluent HFF monolayers.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) including β-mercaptoethanol and DNase I treatment according to the manufacturer’s instructions. RNA quality was determined using the Agilent Bioanalyzer 2100

treatment_protocol: Parasites were allowed to invade confluent HFF monolayers for 2 hrs at 35C before the medium was aspirated and the cells washed twice with PBS. Fresh Ed1 medium was added and flasks were left for an additional 16 hrs at 35C before flasks were either left at 35C or placed at 40C and incubated for 24 hrs to induce phenotypic arrest. Parasites were harvested by scraping off the monolayer, needle passing through a 27G needle, and filtration through a 3 µm polycarbonate filter.


title: FV-P6 35C rep2

description: FV-P6 at 35C

source_name: FV-P6 35C rep2


title: FV-P6 40C rep1

description: FV-P6 at 40C

source_name: FV-P6 40C rep1


title: Leukemia Dnmtfl/+ Cre+, biological replicate 1

city: Boston

first: Jennifer

last: Trowbridge

address: 44 Binney St., Mayer 652

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from bulk leukemia cells from Dnmt1fl/+ Mx-Cre+ leukemias, experimental sample, biological replicate 1

hyb_protocol: cRNA were hybridized overnight at 45oC on Affymetrix GeneChip Mouse Genome 430A 2.0 Arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with dChip using the default normalization method.

source_name: Dnmt1fl/+ Mx-Cre+ leukemic spleen bulk cells

label_protocol: Purified single-stranded cRNA (5ug) was fragmented and biotin labeled with the FL-Ovation cDNA Biotin Module V2 (NuGEN) according to the manufacturer's instructions

growth_protocol: The Dnmt1fl/fl Mx-Cre mouse strain was maintained on a C57BL/6 background. All mice were used between 8-12 weeks of age. Each biological replicate (control & experimental samples) were obtained from littermates.

extract_protocol: Total RNA was extracted from cell pellets using the Rneasy Micro Kit (Qiagen), was reverse transcribed and amplified using the WT-Ovation Pico RNA Amplification System (NuGEN Technologies). Single-stranded cRNA amplification products were purified with QIAquick PCR purification kit (Qiagen).

treatment_protocol: Leukemic mice were administered 7 injections of poly(I)-poly(C) (Sigma) at 25ug/kg every other day.

value: Dnmt1fl/+ Mx-Cre

tag: background strain

value: Spleen


title: FV-P6 40C rep2

description: FV-P6 at 40C

source_name: FV-P6 40C rep2


title: Pseudo-diploid Y661HCactin 40C

description: Pseudodiploid Y661HCactin at 40C

source_name: Pseudodiploid Y661HCactin 40C

value: Pseudodiploid Y661HCactin


title: FV-P6 + cosmid TOXOA93 35C rep2

description: FV-P6 + cosmid TOXOA93 at 35C

source_name: FV-P6 + cosmid TOXOA93 35C rep2

value: FV-P6 + cosmid TOXOA93


title: Leukemia Dnmtfl/fl, biological replicate 2

description: Gene expression data from bulk leukemia cells from Dnmt1fl/fl leukemias, control sample, biological replicate 2

source_name: Dnmt1fl/fl leukemic spleen bulk cells

tag: tissue


title: LGMP Dnmtfl/fl, biological replicate 1

description: Gene expression data from sorted L-GMPs (Lineage-IL-7Ra-c-Kit+Sca-1-FcgR+CD34+) from Dnmt1fl/fl leukemias, control sample, biological replicate 1

source_name: Dnmt1fl/fl leukemic spleen Lineage-IL-7Ra-c-Kit+Sca-1-FcgR+CD34+

tag: cell surface antigens


title: LGMP Dnmtfl/fl, biological replicate 2

description: Gene expression data from sorted L-GMPs (Lineage-IL-7Ra-c-Kit+Sca-1-FcgR+CD34+) from Dnmt1fl/fl leukemias, control sample, biological replicate 2


title: LGMP Dnmtfl/+ Cre+, biological replicate 1

description: Gene expression data from sorted L-GMPs (Lineage-IL-7Ra-c-Kit+Sca-1-FcgR+CD34+) from Dnmt1fl/+ Mx-Cre+ leukemias, experimental sample, biological replicate 1

source_name: Dnmt1fl/+ Mx-Cre+ leukemic spleen Lineage-IL-7Ra-c-Kit+Sca-1-FcgR+CD34+


title: Leukemia Dnmtfl/+ Cre+, biological replicate 2

description: Gene expression data from bulk leukemia cells from Dnmt1fl/+ Mx-Cre+ leukemias, experimental sample, biological replicate 2


title: Leukemia Dnmtfl/fl, biological replicate 1

description: Gene expression data from bulk leukemia cells from Dnmt1fl/fl leukemias, control sample, biological replicate 1


title: FV-P6 + cosmid TOXOA93 40C rep2

description: FV-P6 + cosmid TOXOA93 at 40C

source_name: FV-P6 + cosmid TOXOA93 40C rep2

tag: genotype

tag: treatment


title: untreated vs treated 48h time point-rep2

city: Bloemfontein

first: Carolina

middle: Henrietta

last: Pohl-Albertyn

state: Free State

address: Swot Road, University of the Free State, 205 Nelson Mandela Drive

department: Microbial Biochemical and Food Biotechnology

country: South Africa

institute: University of the Free State

hyb_protocol: Oligomer based spotted microarrays for the C. albicans genome, spotted in triplicate on epoxy slides, was purchesed from the Washington University School of Medicine, Genome Sequencing Centre, USA (http://genome.wustl.edu/services/microarray/candida_albicans). Probes were prepared by combining selected Cy3 and Cy5 labelled samples, which were then dried in a vacuum desiccator, and resuspended in 50 µl hybridisation buffer [35% (v/v) formamide, 5x saline sodium citrate, 0.1% (w/v) sodium dodecyl sulfate, 0.1 mg/mL salmon sperm, deionised water].  Probes were denatured at 95°C for 2 min. The glass slide was initially incubated in pretreatment solution (5X SSC; 0.1% SDS; 10% bovine serum albumin) without probe at 60°C for 20 min.  Thereafter, the slide was placed in a HybUP hybridisation chamber (NB Engineering, Pretoria, South Africa) with the denatured probe solution at 42°C for 16 h.  After hybridisation, slides were washed for 4 min at 42°C with 1 X SSC/0.2% SDS, 0.1 X SSC/0.2% SDS (twice) followed by three washes in 0.1 X SSC for 1 min at room temperature.  Slides were rinsed with distilled water, and dried by centrifugation (2000Xg for 15 sec).

scan_protocol: The slides were dried by centrifugation and scanned with a GenePix 4000B laser scanner (Axon Instruments Inc., Foster City, CA, USA). Separate images were acquired for each fluorophore at a resolution of 10 μm per pixel.

data_processing: Scanned images (tiff images) were imported into GenePix Pro 5.1 (Axon Instruments), and fluorescence intensity in both red (Cy5) and green (Cy3) channels for each spot was quantified. Grids were predefined and manually adjusted to ensure optimal spot recognition, and spots with dust or locally high background were flagged as bad.  Fluorescence data from a total of 18 slides were imported into limma in the R computing environment where data was background subtracted using the limma normexp function, and normalised (within array global loess normalisation and between array aquantile normalisation). Individual linear models were based on the comparison between treated and untreated samples for each time point. The FDR function (Benjamini-Hochberg method) in limma was used to correct for false positives, and genes were classified as differentially expressed if they showed a P-value ≤ 0.05 and a fold change ≥ 1.5.

source_name: untreated C. albicans 48h biofilms

label_protocol: 15µg/22µL of total RNA of each sample was divided into two fractions (technical replicate) and primed with random nonamer primer together with 20 X aa-dNTP (Ambion) and 5 x 1st strand buffer (250 mM Tris-HCl, pH 8.3 at room temperature; 375 mM KCl; 15 mM MgCl2) and reversed transcribed in the presence of SuperScript® III Reverse Transcriptase, (Invitrogen) overnight at 42°C. The cDNA was then labelled at room temperature for 2 h with Cy3 or Cy5 dye (CY Dye Post Labelling reactive Dye Pack, GE Healthcare, UK) (dissolved in DMSO, stored at -80 °C), depending on the technical replicate.

growth_protocol: Candida albicans biofilms were grown for 8, 24 and 48h at 37°C in cell culture plates in the absence (Control) and presence of 500µM arachidonic acid.

extract_protocol: Total RNA extraction and purification were done with an RNeasy Mini Kit (Qiagen) with an on-column DNase (RNase-Free DNase Set, Qiagen) digestion according to the manufactures instructions.

treatment_protocol: The C. albicans biofilms were treated with 500µM arachidonic acid in cell culture plates, and incubated for 8, 24 and 48h at 37°C. The control biofilms were not treated.

tag: time

source_name: Treated C. albicans 48h biofilms

value: Arachidonic acid


title: untreated vs treated 48h time point-rep2 swap


title: Pseudo-diploid Y661HCactin 35C

description: Pseudodiploid Y661HCactin at 35C

source_name: Pseudodiploid Y661HCactin 35C


title: untreated vs treated 8h time point-rep3

source_name: untreated C. albicans 8h biofilms

value: 8 h

source_name: Treated C. albicans 8h biofilms


title: untreated vs treated 24h time point-rep2 swap

source_name: untreated C. albicans 24h biofilms

source_name: Treated C. albicans 24h biofilms


title: untreated vs treated 48h time point-rep3 swap


title: untreated vs treated 48h time point-rep3


title: untreated vs treated 24h time point-rep3


title: LGMP Dnmtfl/+ Cre+, biological replicate 2

description: Gene expression data from sorted L-GMPs (Lineage-IL-7Ra-c-Kit+Sca-1-FcgR+CD34+) from Dnmt1fl/+ Mx-Cre+ leukemias, experimental sample, biological replicate 2


title: untreated vs treated 8h time point-rep3 swap


title: untreated vs treated 24h time point-rep3 swap


title: untreated vs treated 24h time point-rep2


title: untreated vs treated 48h time point-rep1


title: untreated vs treated 8h time point-rep2


title: untreated vs treated 24h time point-rep1


title: untreated vs treated 8h time point-rep2 swap


title: untreated vs treated 48h time point-rep1 swap


title: Fish 12

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned GenePix 4100A at a resolution of 5 microns

data_processing: GenePix Pro 6.0 was used for spot to grid alignment, feature extraction and quantification. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Skeletal muscle

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: Fish reared in sea water cages was slaughtered at average body weight 3.5 kg

extract_protocol: RNA was isolated using the iPrep™ TRIzol® Plus kit (Invitrogen), and purified with RNeasy mini kit (QIAGEN)

value: skeletal muscle

tag: fillet firmness

source_name: Mixture of all samples

tag: sample type

value: reference


title: untreated vs treated 8h time point-rep1


title: untreated vs treated 24h time point-rep1 swap


title: Fish 16


title: Fish 7


title: untreated vs treated 8h time point-rep1 swap


title: Fish 15


title: Fish 13


title: Fish 10


title: Fish 14


title: Fish 9


title: Fish 6


title: Fish 3


title: Fish 11


title: Fish 2


title: Fish 8


title: Fish 1


title: BMM_F2D_131_F

city: Cleveland

first: Jeff

last: Hsu

state: OH

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

institute: Cleveland Clinic Lerner Research Institute

description: Bone marrow was flushed with DMEM and cells were grown for 10-14 days in Bone marrow macrophages complete media

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized.

source_name: Bone marrow derived macrophages from female DBA/2J x AKR/J F2 mice

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: gender

value: female

value: bone marrow derived macrophages (BMM)


title: Fish 4


title: BMM_F2A_120_F


title: BMM_F2A_118_F


title: BMM_F2D_130_F


title: BMM_F2D_129_F


title: BMM_F2A_119_F


title: BMM_F2A_115_F


title: BMM_F2D_128_F


title: BMM_F2A_116_F


title: Fish 5


title: BMM_F2A_113_F


title: BMM_F2A_110_F


title: BMM_F2D_126_F


title: BMM_F2A_112_F


title: BMM_F2A_107_F


title: BMM_F2A_117_F


title: BMM_F2A_109_F


title: BMM_F2A_114_F


title: BMM_F2D_122_F


title: BMM_F2D_120_F


title: BMM_F2D_119_F


title: BMM_F2D_116_F


title: BMM_F2D_117_F


title: BMM_F2D_118_F


title: BMM_F2D_125_F


title: BMM_F2A_106_F


title: BMM_F2A_108_F


title: Mouse 16 MA10 Array

first: Floyd

last: Dukes

address: 3615 Civic Center Boulevard

institute: University of Pennsylvania

description:
MC-S_16_MA10
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.

hyb_protocol: Hybridization was in 2.5 ml Micro-Hyb (Research Genetics) at 42oC for 18 h.

scan_protocol: Scanned at 50-μm resolution on a Storm PhosphorImager, and visualized using ImageQuant (Molecular Dynamics).

data_processing: Local background median was subtracted from signal median as background-corrected signal. Background-corrected signals were divided by their median on the array as the normalized expression values.

source_name: Mouse lung, flaxseed diet and radiation

label_protocol: RNA target was labeled with 33P (3,000–5,000 Ci/mM) using reverse transcriptase.

extract_protocol: Acid guanidinium-thiocyanate phenol-chloroform extraction.

treatment_protocol: C57BL/6 black mice were fed a 10% flaxseed diet for 21 days and/or given 13.5Gy radiation and sacrificed 48hrs post radiation.

value: lung

value: 3 weeks 10% flaxseed diet + 13.5Gy radiation


title: BMM_F2D_113_F


title: BMM_F2A_102_F


title: Mouse 19 MA10 Array

description:
MC-S_19_MA10
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: BMM_F2A_105_F


title: Mouse 14 MA10 Array

description:
MC-S_14_MA10
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.

source_name: Mouse lung, radiation

value: 13.5Gy radiation


title: Mouse 17 MA10 Array

description:
MC-S_17_MA10
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: Mouse 18 MA10 Array

description:
MC-S_18_MA10
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: BMM_F2A_111_F


title: BMM_F2A_101_F


title: BMM_F2D_111_F


title: Mouse 13 MA10 Array

description:
MC-S_13_MA10
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: BMM_F2D_115_F


title: BMM_F2D_112_F


title: BMM_F2D_107_F


title: BMM_F2D_109_F


title: Mouse 15 MA10 Array

description:
MC-S_15_MA10
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: BMM_F2D_114_F


title: BMM_F2D_103_F


title: BMM_F2D_110_F


title: BMM_F2D_106_F


title: Mouse 12 MA10 Array

description:
MC-S_12_MA10
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: BMM_F2D_104_F


title: BMM_F2D_101_F


title: BMM_F2D_108_F


title: BMM_F2D_105_F


title: BMM_F2A_104_F


title: BMM_F2D_102_F


title: Mouse 08 MA10 Array

description:
MC-S_08_MA10
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.

source_name: Mouse lung, flaxseed diet

value: 3 weeks 10% flaxseed diet


title: Mouse 07 MA10 Array

description:
MC-S_07_MA10
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.


title: Mouse 11 MA10 Array

description:
MC-S_11_MA10
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: Mouse 01 MA10 Array

description:
MC-S_01_MA10
C57BL/6 black mouse.

source_name: Mouse lung, untreated


title: Mouse 03 MA10 Array

description:
MC-S_03_MA10
C57BL/6 black mouse.


title: Mouse 02 MA10 Array

description:
MC-S_02_MA10
C57BL/6 black mouse.


title: Mouse 10 MA10 Array

description:
MC-S_10_MA10
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.


title: Mouse 04 MA10 Array

description:
MC-S_04_MA10
C57BL/6 black mouse.


title: BMM_F2A_151_F


title: Mouse 20 MA07 Array

description:
MC-S_20_MA07
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: Mouse 09 MA10 Array

description:
MC-S_09_MA10
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.


title: BMM_F2A_146_F


title: BMM_F2A_144_F


title: Mouse 05 MA10 Array

description:
MC-S_05_MA10
C57BL/6 black mouse.


title: BMM_F2A_148_F


title: Mouse 19 MA07 Array

description:
MC-S_19_MA07
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: BMM_F2A_149_F


title: Mouse 18 MA07 Array

description:
MC-S_18_MA07
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days, then given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: BMM_F2A_141_F

description: Bone marrow was flushed with DMEM and cells were grown for 10-14 days in Bone marrow macrophages complete media


title: BMM_F2A_142_F


title: Mouse 06 MA10 Array

description:
MC-S_06_MA10
C57BL/6 black mouse fed a 10% flaxseed diet for 21 days.


title: BMM_F2A_139_F


title: BMM_F2A_147_F


title: Mouse 14 MA07 Array

description:
MC-S_14_MA07
C57BL/6 black mouse given 13.5Gy radiation and sacrificed 48hrs post radiation.


title: BMM_F2A_143_F