title: LPSX1 Xenograft passage 2

description: Xenograft tumor of LPSX1 at passage 2

source_name: LPSX1 Xenograft passage 2

value: de-differentiated

value: Mus musculus


title: HFHC-4wk-R04

status: Public on Dec 19 2012

type: RNA

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip mouse genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were normalized using the Robust Multichip Average methods (RMA)

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Liver, 4 weeks feeding

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

extract_protocol: Liver total RNA was extracted from frozen tissue using TriPure Isolation Reagent (Roche Applied Science, Indianapolis, IN, USA), following the instruction of the manufacturer.

tag: gender

value: male

tag: strain

tag: diet

value: HFHC

tag: time point


title: HFHC-4wk-R03


title: LNCaP-2

city: Cleveland

first: Angela

last: Ting

state: Ohio

address: 9500 Euclid Ave/NE50

department: Genomic Medicine

country: USA

institute: Cleveland Clinic

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was quantile normalized and analyzed using the Illumina GenomeStudio v2009.1.

organism: Homo sapiens

source_name: cultured prostate carcinoma cell line

growth_protocol: All cell lines were cultured in media recommended by the distributors at 37oC, 5% CO2.

extract_protocol: Total RNA was extracted with Trizol reagent, followed by DNase I treatment.  RNA quality and concentration was measure using the nanodrop spectrophtometer.

tag: origin

value: ATCC

tag: cell line

value: LNCaP


title: LPSX3_com_2

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description: LPSX3 xenograft tumor after combination (rapamycin & sorafenib) treatment, biological replicate 2

hyb_protocol: Following Agilent SurePrint Human GE 8x60 microarray protocol

scan_protocol: Arrays were scanned with Agilent DNA Microarray Scanner.   Numerical results were extracted with Feature Extraction software version 10.7.1 using 028004_D_F_20110708 grid, GE1_107_Sep09 protocol and GE1_QCMT_Sep09 metric set

data_processing: Text files from Agilent Feature Extraction software were processed and normalized by Agi4x44PreProcess package (version 1.14.0)  downloaded from Bioconductor.  In brief, the signal was adjusted by background correction, and the normalized by quantile method.  Probes were fitered out if their signals were abcent (i.e. not above the background) in more than 75% of samples.

source_name: LPSX3, combo treated

label_protocol: Using Agilent LowInput Quick Amp One Color Labeling Kit (Agilent Technologies) and protocol

extract_protocol: Roche's MagNA Pure Compact Nucleic Acid Purification System was used for automated RNA isolation.

tag: tissue type

value: xenograft

tag: cell type

value: liposarcoma

tag: tumor histology

tag: host organism


title: Microdissected Male control 2

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

hyb_protocol: 1.4 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul  containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x GEx HI-RPM Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent S.mansoni 44k oligoneucleotide microarray for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 024207_D_F_20090609) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Schistosoma mansoni

source_name: Adult S. mansoni microdissected male control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 20ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from LMM samples using RNAqueous®-Micro kits (Ambion) using the manufacturer’s protocol for LMM samples

tag: Sex

tag: tissue

value: whole worm


title: Microdissected Male control 1


title: HFHC-2d-R10

source_name: Liver, 2 days feeding


title: HFHC-2d-R12


title: HFHC-2d-R11


title: HFHC-4wk-R02


title: DU 145-2

description: replicate 2

label_protocol: Standard Illumina hybridization protocol


title: LPSX3_veh_3

description: LPSX3 xenograft tumor after vehicle treatment, biological replicate 3

source_name: LPSX3, vehicle treated


title: RWPE-1-2

description: replicate 2

source_name: cultured HPV-tranformed normal prostate epithelial cells

value: RWPE


title: LPSX3_veh_2

description: LPSX3 xenograft tumor after vehicle treatment, biological replicate 2


title: PrEC-2

description: replicate 2

source_name: cultured normal prostate epithelial cells

value: Lonza

value: PrEC


title: LPSX1_com_3

description: LPSX1 xenograft tumor after combination (rapamycin & sorafenib) treatment, biological replicate 3

source_name: LPSX1, combo treated


title: LPSX1_com_2

description: LPSX1 xenograft tumor after combination (rapamycin & sorafenib) treatment, biological replicate 2


title: HFHC-4wk-R01


title: LPSX3_com_1

description: LPSX3 xenograft tumor after combination (rapamycin & sorafenib) treatment, biological replicate 1


title: DU 145-1

description: replicate 1


title: Microdissected Oesophageal gland 1

source_name: Adult S. mansoni male oesophagus

value: oesophageal gland


title: HFHC-2d-R09


title: HFHC-2d-R08


title: LPSX3_veh_1

description: LPSX3 xenograft tumor after vehicle treatment, biological replicate 1


title: APL bone marrow

type: genomic

city: Seoul

first: Eul-Ju

last: Seo

address: 88, Olympic-ro, 43-gil, Songpa-gu

department: Laboratory Medicine

country: South Korea

institute: Asan Medical Center

description: A 59-year-old male was diagnosed with variant acute promyelocytic leukemia. This case had a novel RARA rearrangement.

hyb_protocol: Hybridization was performed using the Agilent Human Genome Microarray Kit 244K in a hybridization oven set to 65°C for 40 hours.

scan_protocol: The slide was scanned on an Agilent high-resolution C scanner. Image was quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: APL patient bone marrow

label_protocol: Patient DNA and reference DNA were labeled with Agilent Genomic labeling kit PLUS as recommended by the manufacture.

extract_protocol: Genomic DNA was extracted using Qiagen kit according to the manufacturer's instructions. Reference DNA was purchased from Promega.

tag: disease state

value: variant acute promyelocytic leukemia

value: bone marrow

tag: age

tag: genotype

value: RARA rearrangement

source_name: Promega pooled male PB

value: peripheral blood

tag: sample type

value: Promega reference


title: RWPE-1-1

description: replicate 1


title: LNCaP-1

description: replicate 1


title: PrEC-3

description: replicate 3


title: LPSX1_com_1

description: LPSX1 xenograft tumor after combination (rapamycin & sorafenib) treatment, biological replicate 1

value: de-differentiated

value: Mus musculus


title: HFHC-2d-R07

value: male

value: HFHC


title: HFHC-2d-R04


title: Microdissected Oesophageal gland 2


title: 293T + hairpin vector, biological rep3

city: New York

first: Roy

middle: Louis

last: Maute

state: NY

address: 1130 St. Nicholas Ave., ICRC 507

department: Institute for Cancer Genetics

institute: Columbia University

description: Gene expression from 293T transiently transfected with vector encoding for artificially constructed CU1276 hairpin

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized to Affymetrix U133p2 arrays according to manufacturer's indications

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: 293T + hairpin vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 293T were grown in 10cm plates with DMEM supplemented with 10% FBS and 1% penicillin/streptomycin according to standart tissue culture protocol

extract_protocol: Cells were collected in cold PBS 48 hours post-transfection, and pellets were lysed with Trizol reagent; RNA was purified according to manufacturers indications

treatment_protocol: Cells were transiently transfected with plasmids using the PEI reagent, as described in EHRHARDT ET AL, SIGNAL TRANSDUCTION 2006; 6: 179-84

value: Human embryonic kidney


title: Male C57Bl6J mice-control WC-840

city: Columbus

first: kalpana

last: ghoshal

state: OH

address: 420 W. 12th Avenue

department: Molecular and Cellular Biochemistry

institute: The Ohio State University

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), BioArray Eukaryotic Hybridization Controls (Enzo Life Sciences), heated at 65oC for 5 minutes, 99oC for 5 minutes, 45oC for 5 minutes centrifuged at maximum speed for 5 minutes, hybridized for 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using GCOS version 1.4.0.036

data_processing:
RMA expression value derived from Expression Console software; core-exon analysis
Data were processed using Affymetrix Expression Console software. Robust Multichip Average (RMA) method was used to do background correction, quantile normalization, and expression level summarization.

source_name: Male C57Bl6J mice-control

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: 6 week old male mice were fed Lieber DeCarli’s liquid alcoholic diet purchased from BioServe. To start with mice were fed 2.06% alcoholic diet for 3 days, 4.18% alcoholic diet for next 4 days followed by 6.2% alcoholic diet for additional 5 weeks.  Control mice were pair-fed calorie-matched liquid diet containing maltose and dextrin for 6 weeks. 6.2% alcohol containing diet constitutes 35% of total calorie.

extract_protocol: Total RNA was isolated from the liver using miRVana kit (Ambion).

value: liver

value: no-alcohol


title: 293T + hairpin vector, biological rep4


title: HFHC-2d-R06


title: 293T + hairpin vector, biological rep2


title: 293T + tRNA vector, biological rep4

description: Gene expression from 293T transiently transfected with vector encoding for human chr1.tRNA68-Gly(GCC) tRNA, which is cleaved to form mature CU1276

source_name: 293T + tRNA vector


title: LPSX1_veh_2

description: LPSX1 xenograft tumor after vehicle treatment, biological replicate 2

source_name: LPSX1, vehicle treated

value: xenograft

value: liposarcoma


title: Male C57Bl6J mice-control WC-834


title: Male C57Bl6J mice-Alcohol WA-836

source_name: Male C57Bl6J mice-Alcohol

value: alcohol


title: HFHC-2d-R03


title: HFHC-2d-R05


title: 293T + hairpin vector, biological rep1


title: TUMOR, MANTLE CELL LYMPHOMA  ID6 [Affy_NSP]

city: Barcelona

first: Sílvia

last: Beà

state: Barcelona

address: Rossello, 153

department: HematoPathology

country: Spain

institute: Hospital Clinic

description: Tumor, nsp array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Image data were analysed
Primary data description: Data files were generated using the Affymetrix gene chip operating (GCOS) and gene chip genotyping analysis (GTYPE) software suites. GTYPE version 4.1 was used for the analysis of signal intensity and to determine genotype calls. Since no matched normal DNA was available, unpaired analysis using an independent reference set was performed. The complete data set was analyzed as combined subarrays (500K) by visual inspection using CNAT 4.0 (Affymetrix) and the copy number analyzer for gene chip (CNAG) v3.0 and by an algorithm described by Lenz and coworkers

label: Biotin

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID6

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from genomic DNA.

extract_protocol: Genomic DNA was extracted from frozen tissue of MCL prior to treatment using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.

tag: patient identifier

tag: source type

value: tumor genomic DNA from MCL patient

tag: translocation status of ccnd2

value: neg

tag: transl

tag: age/gender

tag: ln involvement

value: LN

tag: extranodal

value: BM

tag: ldh

value: Normal

tag: Stage

value: IV

tag: ipi

tag: therapy

value: C

tag: response

value: PR

tag: os (+ indicates alive)


title: Male C57Bl6J mice-Alcohol WA-833

tag: strain

tag: tissue

tag: diet


title: TUMOR, MANTLE CELL LYMPHOMA  ID5 [Affy_NSP]

description: Tumor, nsp array

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID5

tag: gender

value: CHOP


title: HFHC-2d-R02

value: male

tag: time point


title: TUMOR, MANTLE CELL LYMPHOMA  ID4 [Affy_NSP]

description: Tumor, nsp array

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID4

tag: patient identifier

tag: source type

value: LN (multiple)

value: PB, BM, Spleen

value: High

value: COP+FCR


title: TUMOR, MANTLE CELL LYMPHOMA  ID3 [Affy_NSP]

description: Tumor, nsp array

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID3

tag: translocation status of ccnd2

tag: transl


title: TUMOR, MANTLE CELL LYMPHOMA  ID1 [Affy_NSP]

description: Tumor, nsp array

source_name: TUMOR, MANTLE CELL LYMPHOMA  ID1

value: female

tag: age/gender

tag: ln involvement

value: LN (inguinal)

value: Intestine

value: IIIA

value: CR


title: Male C57Bl6J mice-control WC-824

value: liver

value: no-alcohol


title: HPHC-2d-R08

source_name: Liver, 2 days feeding

value: HPHC


title: colon heme repl3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization, washing and scanning of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).

source_name: colon of mouse, after 14 days on a Westernized high fat (heme) diet, replicate 3

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: C57BL/6J mice were purchased from Harlan (Horst, the Netherlands), and housed in a light and temperature-controlled animal facility of Wageningen University (12:12 h light/dark cycle, 20±2 °C). Mice had free access to feed and water.

extract_protocol: Total RNA was prepared from colonic scrapings using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Male control and heme-fed mice were maintained on a high fat-low calcium diet (with or without heme) for 2 weeks. After 2 weeks diet intervention all mice were sacrificed and colons were taken out. Mesenteric fat was removed. Colons were cut open longitudinally, washed in PBS, and epithelial cells were scraped off.

tag: backgroud

tag: age

value: 11 weeks

value: colon

value: Westernized high fat (heme) diet


title: 293T + tRNA vector, biological rep2

tag: cell line

tag: cell type

value: Human embryonic kidney


title: PrEC-1

description: replicate 1

source_name: cultured normal prostate epithelial cells

tag: origin

value: Lonza

value: PrEC


title: Male C57Bl6J mice-control WC-820


title: Male C57Bl6J mice-Alcohol WA-817

value: alcohol


title: Male C57Bl6J mice-Alcohol WA-811


title: 293T + tRNA vector, biological rep1


title: LPSX1_veh_3

description: LPSX1 xenograft tumor after vehicle treatment, biological replicate 3

tag: tissue type

value: xenograft

value: liposarcoma

tag: tumor histology

value: de-differentiated

tag: host organism

value: Mus musculus


title: HFHC-2d-R01

value: male

tag: strain

tag: diet

value: HFHC


title: 293T + empty vector, biological rep3

description: Gene expression from 293T transiently transfected with empty control vector

source_name: 293T + empty vector


title: colon heme repl1

source_name: colon of mouse, after 14 days on a Westernized high fat (heme) diet, replicate 1

tag: gender

tag: tissue


title: colon control repl4

source_name: colon of mouse, after 14 days on a Westernized high fat (control) diet, replicate 4

value: Westernized high fat (control) diet


title: 293T + empty vector, biological rep4


title: colon heme repl2

source_name: colon of mouse, after 14 days on a Westernized high fat (heme) diet, replicate 2


title: colon control repl2

source_name: colon of mouse, after 14 days on a Westernized high fat (control) diet, replicate 2


title: T123

status: Public on Dec 18 2012

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Gene expression data of original tumor tissue of pancreatic ductal adenocarcinoma patient

hyb_protocol: Purified fragmented biotinylated cRNA and hybridization controls (Affymetrix) were mixed, hybridized on Affymetrix HG U133 Plus 2.0 arrays, and subsequently stained and washed in the GeneChip fluidics station 450 (Affymetrix).

scan_protocol: To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).

data_processing: To decide whether a signal was significantly above background, the MAS 5.0 algorithm was applied to calculate probe set detection calls. Robust Multichip Average (RMA) was applied to probe sets that had a present detection call in at least 4 out of 6 CCD samples. Using limma, the average expression value for each experimental condition was estimated. Based on these estimates, the contrasts CTC vs. T, CTC vs. P, CTC vs. G, T vs. P, T vs. G, and P vs. G were estimated. For each contrast it was tested whether it was significantly different from 0 using a moderated t-statistic (implemented in limma).

label_protocol: Per sample, ideally an amount of 5-10 ng of total RNA spiked with four bacterial RNA transcripts (Affymetrix) was converted and amplified to double stranded cDNA in a 2-cycle cDNA reverse transcription reaction. Subsequently the sample was converted to antisense cRNA and labeled with biotin through an in vitro transcription reaction according to the manufacturer’s protocol (Affymetrix).

extract_protocol: RNA was isolated using a protocol combining Trizol/chloroform extraction, followed by column chromatography with the RNeasy Mini kit (Qiagen).

tag: patient code

value: Male

tag: tumor grade

tag: t-stage

tag: n-stage

tag: ajcc classif. (2002)


title: P123

description: Gene expression data of non-tumor pancreatic control tissue of pancreatic ductal adenocarcinoma patient


title: P138


title: CTC123

description: Gene expression data of circulating tumor cells of pancreatic ductal adenocarcinoma patient


title: P91

value: Female


title: G123

description: Gene expression data of haematological cells of pancreatic ductal adenocarcinoma patient


title: 293T + empty vector, biological rep2


title: G91


title: G138


title: CTC91


title: colon control repl1

source_name: colon of mouse, after 14 days on a Westernized high fat (control) diet, replicate 1

tag: backgroud


title: CTC138

tag: age


title: T91


title: colon control repl3

source_name: colon of mouse, after 14 days on a Westernized high fat (control) diet, replicate 3


title: CTC105


title: G104


title: T138


title: 293T + empty vector, biological rep1

tag: cell line


title: P105


title: G105


title: P104


title: T104


title: CTC117


title: CTC104


title: G117


title: P117


title: T117


title: Leaf_Cont_30h_rep2

city: Nijmegen

first: Tom

last: Tytgat

address: Heyendaalseweg 135

department: Ecogenomics

institute: Radboud University Nijmegen

data_processing: Scanned microarray images were quantified using ImaGene® 7.0 software (BioDiscovery, El Segundo, CA, USA), and transcript abundance is expressed as the spot mean intensity minus the mean of the local background intensity. Data were median normalised.

organism: Brassica oleracea

source_name: Leaf tissue_control treatment_30 h

growth_protocol: Plants were grown in sterilized plain river sand, in a 16:8 (L/D) light regime at 21°C (day) and 16°C (night). Three times a week, they were provided with sufficient with half-strength Hoagland solution with a doubled P-content to maintain the water percentage in the pots at 14% w/w.

extract_protocol: Total RNA was prepared with Trizol® Reagent (Invitrogen, California, USA) and further purified on RNeasy Mini Spin Columns (Qiagen GmbH, Hilden, Germany).

treatment_protocol: Thirty three days after the seedlings were transferred to pots the plants had on average 9 true leaves, and were treated with 500 µg jasmonic acid in 0.1% triton in water applied on two fully expanded leafs or injected into the soil surrounding the root system. Control plants received equal amounts of acidic 0.1% triton in water on both organs. Similarly, jasmonic acid treated plants received equal amounts of acid 0.1% triton in water on the untreated organs.

tag: treated with

tag: treatment group

value: Control

tag: tissue harvested

value: leaf

tag: time point


title: T105


title: Leaf_Leaf JA_30h_rep2

description: Leaf_Leaf JA_30h_rep2

source_name: Leaf tissue_leaf jasmonic acid treatment_30 h

value: 500 µg jasmonic acid in 0.1% triton in water

value: Leaf jasmonic acid

tag: treated tissue

value: two fully expanded leaves


title: Leaf_Cont_30h_rep3

value: equal amounts of acidic 0.1% triton in water


title: Leaf_Leaf JA_30h_rep1

description: Leaf_Leaf JA_30h_rep1


title: Leaf_Root JA_30h_rep1

description: Leaf_Root JA_30h_rep1

source_name: Leaf tissue_root jasmonic acid treatment_30 h

value: Root jasmonic acid

value: root (soil surrounding the root system)


title: Leaf_Leaf JA_30h_rep3

description: Leaf_Leaf JA_30h_rep3


title: Leaf_Root JA_30h_rep3

description: Leaf_Root JA_30h_rep3


title: Leaf_Cont_30h_rep1


title: WT-4

city: new haven

first: yong

last: deng

state: CT Connecticut

address: 300 george st room 749

department: cardiology

institute: Yale School of Medicine

description: replicate 4

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

source_name: HUVEC

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

growth_protocol: EBM-2 (Lonza), 37 degree, 5% CO2

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

treatment_protocol: infected with lentivirus and selected with 0.5 ug/ml puromycin for a week.

tag: cell type

value: HUVEC

tag: treatment

value: RAF1 WT


title: WT-2

description: replicate 2


title: S259A-1

description: replicate 1

value: RAF1 S259A


title: S259A-3

description: replicate 3


title: control-4

description: replicate 4

value: empty lentiviral vector pLVX-IRES-puro


title: Leaf_Root JA_30h_rep2

description: Leaf_Root JA_30h_rep2


title: WT-3

description: replicate 3


title: Leaf_Leaf JA_18h_rep2

description: Leaf_Leaf JA_18h_rep2

source_name: Leaf tissue_leaf jasmonic acid treatment_18 h


title: Leaf_Leaf JA_18h_rep1

description: Leaf_Leaf JA_18h_rep1


title: colon heme repl4

source_name: colon of mouse, after 14 days on a Westernized high fat (heme) diet, replicate 4

tag: gender

value: male

value: 11 weeks

value: colon

tag: diet

value: Westernized high fat (heme) diet


title: WT-1

description: replicate 1


title: 293T + tRNA vector, biological rep3

source_name: 293T + tRNA vector

value: Human embryonic kidney


title: 20151_DAC 100_635258

city: StLouis

first: Nobish

last: Varghese

state: MO

address: 4444 Forest Park Ave.

institute: Washington University in St.Louis

hyb_protocol: Labeled targets were hybridized to Human Exon 1.0 ST arrays (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using Affymetrix GeneArray scanner GS 3000.

data_processing:
Raw data were processed with the RMA algorithm in Affymetrix Expression ConsoleTM version1.1 (Affymetrix Inc., USA). Full exons were included in the analysis.
Meta-probeset file: HuEx-1_0-st-v1.r2.dt1.mm9.full.mps

source_name: Bone marrow culture, DAC

label_protocol: Amplified cDNA was biotin labeled using the EncoreTM Biotin Module (NuGen Technologies, San Carlos, CA) according to the manufacturer's instructions.

extract_protocol: Total cellular RNA was purified using Trizol reagent, quantified using UV spectroscopy (Nanodrop Technologies, Wilmington,DE) and qualitatively assessed using an Experian Bioanalyzer (Hercules,CA). Amplified cDNA was prepared from 20ng of total RNA using the whole transcript WT-Ovation TM RNA Amplification System.

treatment_protocol: Samples were cultured for 7 days, the last 3 days of which included 100 nM decitabine (DAC), 100 nm cytarabine (AraC), or DMSO vehicle (mock).

tag: disease status

value: acute myeloid leukemia (AML)

tag: tissue

value: bone marrow

tag: cultured

value: yes

value: decitabine (DAC)

tag: treatment dosage

tag: treatment duration

value: 3 days

tag: aml sample identifier


title: Leaf_Root JA_18h_rep2

description: Leaf_Root JA_18h_rep2

source_name: Leaf tissue_root jasmonic acid treatment_18 h

value: 500 µg jasmonic acid in 0.1% triton in water

value: leaf


title: Leaf_Root JA_18h_rep3

description: Leaf_Root JA_18h_rep3

value: Root jasmonic acid

value: root (soil surrounding the root system)


title: Leaf_Root JA_18h_rep1

description: Leaf_Root JA_18h_rep1


title: Leaf_Leaf JA_6h_rep2

description: Leaf_Leaf JA_6h_rep2

source_name: Leaf tissue_leaf jasmonic acid treatment_6 h

value: Leaf jasmonic acid

value: two fully expanded leaves

value: 6 h


title: Leaf_Cont_18h_rep1

source_name: Leaf tissue_control treatment_18 h

value: equal amounts of acidic 0.1% triton in water

value: Control


title: Leaf_Cont_18h_rep2


title: Leaf_Cont_18h_rep3


title: control-3

description: replicate 3

value: HUVEC

value: empty lentiviral vector pLVX-IRES-puro


title: S259A-2

description: replicate 2

value: RAF1 S259A


title: 20145_AraC_418499

source_name: Bone marrow culture, AraC

value: acute myeloid leukemia (AML)

value: cytarabine (AraC)


title: 20149_Mock_635258

source_name: Bone marrow culture, mock

value: bone marrow

value: yes

value: DMSO vehicle (mock)


title: control-2

description: replicate 2


title: 20150_AraC_635258

value: 3 days


title: 20148_Unc_635258

source_name: Bone marrow, uncultured (day 0)

value: no


title: Leaf_Leaf JA_6h_rep3

description: Leaf_Leaf JA_6h_rep3

value: 500 µg jasmonic acid in 0.1% triton in water

value: leaf


title: S259A-4

description: replicate 4


title: LPSX1_veh_1

description: LPSX1 xenograft tumor after vehicle treatment, biological replicate 1

source_name: LPSX1, vehicle treated

tag: tissue type

value: xenograft

value: liposarcoma

tag: tumor histology

value: de-differentiated

tag: host organism

value: Mus musculus


title: Leaf_Root JA_6h_rep3

description: Leaf_Root JA_6h_rep3

source_name: Leaf tissue_root jasmonic acid treatment_6 h

tag: treated with

tag: treatment group

value: Root jasmonic acid

value: root (soil surrounding the root system)

value: 6 h


title: Leaf_Leaf JA_6h_rep1

description: Leaf_Leaf JA_6h_rep1

value: Leaf jasmonic acid

value: two fully expanded leaves

tag: tissue harvested

tag: time point


title: Leaf_Cont_6h_rep3

source_name: Leaf tissue_control treatment_6 h

value: equal amounts of acidic 0.1% triton in water

value: Control


title: control-1

description: replicate 1

tag: cell type

value: HUVEC

value: empty lentiviral vector pLVX-IRES-puro


title: Root_Leaf JA_30h_rep3

description: Root_Leaf JA_30h_rep3

source_name: Root tissue_leaf jasmonic acid treatment_30 h

tag: treated tissue

value: root


title: Leaf_Cont_6h_rep1


title: Leaf_Leaf JA_18h_rep3

description: Leaf_Leaf JA_18h_rep3


title: control 7

city: Heidelberg

first: Benjamin

last: Meder

state: Baden-Württemberg

address: Im Neuenheimer Feld 350

department: Internal Medicine III

country: Germany

institute: University Heidelberg

hyb_protocol: The procedure followed the manufacturers standard workflow, starting with the bisulfite treatment of the sample DNA leading to a conversion of unmethylated cytosins to uracil, while 5-methylcytosines remain unchanged. After amplification and fragmentation of the bisulfite-converted DNA, they were hybridized to the Infinium BeadChips

scan_protocol: standard Illumina protocol

data_processing: BeadStudio

label: C-Bio and A-DNP

source_name: Heart biopsy left ventricle control

label_protocol: standard Illumina protocol

extract_protocol: Biopsy specimens were obtained from the apical part of the free left ventricular wall (LV) from DCM patients or cardiac transplant patients (controls) undergoing cardiac catheterization using a standardized protocol. Biopsies were washed with NaCl (0.9%) and immediately transferred and stored in liquid nitrogen until DNA extracted.

value: apical left ventricular biopsies

tag: disease state

value: control


title: Root_Leaf JA_30h_rep2

description: Root_Leaf JA_30h_rep2

value: 500 µg jasmonic acid in 0.1% triton in water


title: control 8


title: control 5


title: 20147_Unc_418499

value: acute myeloid leukemia (AML)

value: bone marrow

value: no

tag: treatment


title: Root_Leaf JA_30h_rep1

description: Root_Leaf JA_30h_rep1


title: Root_Root JA_30h_rep3

description: Root_Root JA_30h_rep3

source_name: Root tissue_root jasmonic acid treatment_30 h


title: 20140_DAC 100_387919

tag: disease status

value: yes

value: decitabine (DAC)

value: 3 days


title: 20138_Mock_387919

tag: tissue

value: DMSO vehicle (mock)


title: 20139_AraC_387919

tag: cultured

value: cytarabine (AraC)


title: 20141_Mock_412761


title: Root_Root JA_30h_rep1

description: Root_Root JA_30h_rep1

value: Root jasmonic acid

value: root (soil surrounding the root system)


title: control 4


title: Root_Cont_30h_rep2

source_name: Root tissue_control treatment_30 h

value: equal amounts of acidic 0.1% triton in water

value: Control


title: Root_Cont_30h_rep1


title: 20143_DAC 100_412761

tag: treatment dosage


title: control 3


title: Root_Root JA_30h_rep2

description: Root_Root JA_30h_rep2


title: control 1


title: 20142_AraC_412761

tag: treatment duration


title: Root_Cont_30h_rep3


title: control 2


title: Root_Leaf JA_18h_rep2

description: Root_Leaf JA_18h_rep2

source_name: Root tissue_leaf jasmonic acid treatment_18 h

value: Leaf jasmonic acid

value: two fully expanded leaves


title: 20133_Unc_329614

tag: aml sample identifier


title: Root_Leaf JA_18h_rep3

description: Root_Leaf JA_18h_rep3

value: root


title: 20137_Unc_387919


title: 20134_Mock_329614


title: Leaf_Root JA_6h_rep2

description: Leaf_Root JA_6h_rep2

value: leaf

value: 6 h


title: Root_Leaf JA_18h_rep1

description: Root_Leaf JA_18h_rep1

value: 500 µg jasmonic acid in 0.1% triton in water


title: 20136_DAC 100_329614

value: acute myeloid leukemia (AML)

value: bone marrow


title: Root_Root JA_18h_rep3

description: Root_Root JA_18h_rep3

source_name: Root tissue_root jasmonic acid treatment_18 h


title: Root_Root JA_18h_rep1

description: Root_Root JA_18h_rep1


title: DCM 7

source_name: Heart biopsy left ventricle DCM

value: apical left ventricular biopsies

value: idiopathic dilated cardiomyopathy


title: Root_Root JA_18h_rep2

description: Root_Root JA_18h_rep2


title: 20132_DAC 100_319955

source_name: Bone marrow culture, DAC

value: yes

value: decitabine (DAC)

value: 3 days


title: DCM 9


title: Root_Cont_18h_rep3

source_name: Root tissue_control treatment_18 h


title: DCM 8


title: DCM 6


title: Root_Leaf JA_6h_rep3

description: Root_Leaf JA_6h_rep3

source_name: Root tissue_leaf jasmonic acid treatment_6 h


title: Root_Leaf JA_6h_rep2

description: Root_Leaf JA_6h_rep2


title: Root_Cont_18h_rep1


title: Leaf_Root JA_6h_rep1

description: Leaf_Root JA_6h_rep1

value: Root jasmonic acid


title: 20131_AraC_319955

value: cytarabine (AraC)


title: 20130_Mock_319955

value: DMSO vehicle (mock)


title: Leaf_Cont_6h_rep2

value: equal amounts of acidic 0.1% triton in water

value: Control


title: Root_Leaf JA_6h_rep1

description: Root_Leaf JA_6h_rep1

value: Leaf jasmonic acid

value: two fully expanded leaves


title: control 6

value: control


title: DCM 5


title: Root_Root JA_6h_rep3

description: Root_Root JA_6h_rep3

source_name: Root tissue_root jasmonic acid treatment_6 h

value: root (soil surrounding the root system)

value: root

value: 6 h


title: DCM 3


title: DCM 4


title: Root_Cont_6h_rep3

source_name: Root tissue_control treatment_6 h


title: Root_Root JA_6h_rep1

description: Root_Root JA_6h_rep1

value: 500 µg jasmonic acid in 0.1% triton in water


title: Root_Cont_6h_rep2


title: 20127_DAC 100_296361

value: acute myeloid leukemia (AML)

value: bone marrow


title: Root_Root JA_6h_rep2

description: Root_Root JA_6h_rep2


title: DCM 2

value: apical left ventricular biopsies

value: idiopathic dilated cardiomyopathy


title: Root_Cont_6h_rep1


title: 128min_GLC

city: Gothenburg

first: Abraham

last: Ericsson

address: Medicinaregatan 9C

department: Cell and Molecular Biology

country: Sweden

institute: Gothenburg University

description: each sample represents multiple biological and scan replicates

hyb_protocol: Hybridization was performed at 42°C for 12–18 h.     RNA from dormant spores was used as reference RNA for all microarrays.

scan_protocol: The slides were scanned on a GenePix 4000B scanner and quantized using the software GenePix Pro 4.0 resulting in data for 13056 spots, two spots represented one gene.

data_processing: Normalization was performed by a correction for dye-bias and intensity dependent trends. The normalization method was chosen by fitting a robust line (loess line) on the M-values and then corrected each value according to the value of the line. Statistical data analysis was carried out to obtain significantly different gene expression by using a moderated t-test analysis in R and Limma package (Smyth et al, 2005). Empirical Bayesian statistics were used to moderate the standard errors within each gene and Benjamini-Hochberg method (Benjamini et al, 1995) was applied for correction of multiple testing.

organism: Saccharomyces cerevisiae

source_name: Spore germination on 2% glucose medium at 128 min

label_protocol: Labeled cDNA was cleaned (microcon YM-30 columns, Milipore), combined, vacuum-dried, and resuspended in 80 µl of DIGeasy hybridization buffer (Roche Diagnostics).

extract_protocol: Total RNA was isolated. 16 µg of total RNA were primed with 3 µg of random hexamer (Invitrogen) and 3 µg of anchored oligo(dT) 20 primer (ABgene) and labeled in a reverse transcription reaction with Cy3-dUTP or Cy5-dUTP (Amersham Pharmacia Biotech) in a volume of 30 µl, according to standard protocols (http://cmgm.stanford.edu/pbrown).

tag: strain

value: Spores of Y55 strain background

source_name: dormant spores, prior to addition of germinant


title: 32min_GLC

source_name: Spore germination on 2% glucose medium at 32 min


title: 48min_GLC

source_name: Spore germination on 2% glucose medium at 48 min


title: 20126_AraC_296361

source_name: Bone marrow culture, AraC

value: yes

value: 3 days


title: 20125_Mock_296361

source_name: Bone marrow culture, mock

value: DMSO vehicle (mock)


title: 20124_DAC 100_255421

value: decitabine (DAC)


title: 8min_GLC

source_name: Spore germination on 2% glucose medium at 8 min


title: 16min_GLC

source_name: Spore germination on 2% glucose medium at 16 min


title: 64min_GLC

source_name: Spore germination on 2% glucose medium at 64 min


title: DCM 1


title: 96min_GLC

source_name: Spore germination on 2% glucose medium at 96 min


title: 4min_GLC

source_name: Spore germination on 2% glucose medium at 4 min


title: 20128_Unc_296361

source_name: Bone marrow, uncultured (day 0)

value: no


title: 128min_YPD

source_name: Spore germination on YPD medium at 128 min


title: 96min_YPD

source_name: Spore germination on YPD medium at 96 min


title: 20123_AraC_255421

value: cytarabine (AraC)


title: 0min_GLC

source_name: Spore germination on 2% glucose medium at 0 min


title: 20122_Mock_255421


title: UPN 989176, 3 day Mock treatment, array plate number 7

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChips using the standard Illumina protocol.

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

data_processing: BeadStudio software v3.2.

label: Cy5 and Cy3

source_name: Bone marrow biopsy, mock

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified using the Qiagen QIAamp DNA Mini Kit according to standard instructions.

tag: fab

tag: molecular classification

value: normal karyotype

tag: gender

value: female

tag: age

value: 76 years

value: mock

tag: array plate number


title: 20114_Mock_100232


title: 20120_DAC 100_237983

source_name: Bone marrow culture, DAC


title: 20115_AraC_100232


title: 20118_Mock_237983


title: UPN 989176, 3 day DAC treatment, array plate number 7

source_name: Bone marrow biopsy, DAC


title: 20073_AraC_721214


title: 64min_YPD

source_name: Spore germination on YPD medium at 64 min

source_name: dormant spores, prior to addition of germinant


title: 20121_Unc_255421


title: 48min_YPD

source_name: Spore germination on YPD medium at 48 min


title: 20116_DAC 100_100232


title: 20119_AraC_237983

source_name: Bone marrow culture, AraC


title: 20113_Unc_100232


title: 32min_YPD

source_name: Spore germination on YPD medium at 32 min


title: UPN 989176, 3 day AraC treatment, array plate number 7

source_name: Bone marrow biopsy, AraC


title: UPN 869922, 3 day Mock treatment, array plate number 9

value: 56 years


title: 20129_Unc_319955


title: UPN 989176, 3 day Mock treatment, array plate number 3


title: 20072_Mock_721214

source_name: Bone marrow culture, mock


title: 16min_YPD

source_name: Spore germination on YPD medium at 16 min


title: UPN 989176, 3 day AraC treatment, array plate number 3


title: 4min_YPD

source_name: Spore germination on YPD medium at 4 min


title: 20071_DAC 100_737451


title: 20117_Unc_237983


title: 20052_Unc_989176


title: UPN 869922, 3 day DAC treatment, array plate number 10


title: UPN 869922, 3 day DAC treatment, array plate number 9


title: 20051_DAC 100_989176


title: 20050_Mock_989176


title: UPN 831711, 3 day Mock treatment, array plate number 10

value: 57 years


title: UPN 869922, 3 day AraC treatment, array plate number 10

value: acute myeloid leukemia (AML)


title: UPN 869922, 3 day AraC treatment, array plate number 9

value: bone marrow


title: 8min_YPD

source_name: Spore germination on YPD medium at 8 min


title: UPN 831711, 3 day DAC treatment, array plate number 9


title: UPN 775109, 3 day Mock treatment, array plate number 9

value: MLL translocation, poor risk

value: male

value: 45 years


title: UPN 869922, 3 day Mock treatment, array plate number 10


title: UPN 831711, 3 day AraC treatment, array plate number 9


title: UPN 775109, 3 day Mock treatment, array plate number 10


title: 20049_DAC 100_869922

value: yes


title: UPN 831711, 3 day DAC treatment, array plate number 10


title: 20048_AraC_869922

value: 3 days


title: UPN 831711, 3 day AraC treatment, array plate number 10


title: 0min_YPD

source_name: Spore germination on YPD medium at 0 min

value: Spores of Y55 strain background


title: 20046_Unc_869922

source_name: Bone marrow, uncultured (day 0)


title: UPN 775109, 3 day DAC treatment, array plate number 9

value: decitabine (DAC)


title: Mouse_pancreatic_bTC1, control, 24H (rep 3)

city: Catania

first: Michele

last: Purrello

email: purrello@unict.it, dbarbaga@unict.it

address: Via S. Sofia, 87

country: Italy

institute: University of Catania

description: Control

data_processing:
Matrix non-normalized worksheet reports non-normalized Ct values as obtained through RQ Manager v. 1.2 (Applied Biosystems), starting from .sds files.
The normalization and all the data analysis were performed trough Real-Time Statminer© software (www.integromics.com) (Integromics, Granada, Spain). Multiple reference genes were used to normalise data: Genorm (integrated into Real-Time Statminer©) and DataAssist™ (Lifetechnologies™) software allowed to choose the best ones.
Target gene signals normalized to housekeeping genes; Data are reported as DCt = (Ct_Target − Ct_HKG)] and 2^-DCt
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports as test/control (e.g., Cytokines treated/Control cells or bTC1 Control/aTC1 Control) ratios.

label: FAM

source_name: Mouse pancreatic insulinoma cell line bTC1, Control, 24H

label_protocol: PCR assays were performed using TaqMan® Rodent miRNA A+B Cards Set v2.0. Specifically RNA for HT miRNA expression profiling was reverse transcribed into cDNA of 519 mouse-specific and 68 rat-specific miRNAs through Megaplex™ RT Rodent Primer Pool sets, and preamplified through Megaplex™ PreAmp Rodent Primer Pool sets (Lifetechnologies™). Resulting cDNAs were loaded onto TaqMan Low Density miR Arrays (TLDA) cards, according to manufacturer’s instructions.

extract_protocol: Total RNA was extracted with Trizol (Lifetechnologies™, Foster-City, CA, USA), according to manufacturer's instructions.

treatment_protocol: αTC1-6 and βTC1 cells (passages 20-40) were seeded the day before treatment in 60 mm dishes at a density of 4.5 x 10e5 cells. Control cells were grown without any treatment; test cells were treated with a cocktail of inflammatory cytokines containing IL1b 50 IU/ml; IFNg 1000 IU/ml; TNFa 1000 IU/ml

value: Pancreatic beta cell

tag: activation agent

value: Control

tag: time

tag: cell line

value: control


title: UPN 775109, 3 day DAC treatment, array plate number 10


title: Mouse_pancreatic_bTC1, control, 24H (rep 2)

description: Control

tag: cell type


title: 20047_Mock_869922

tag: treatment

value: DMSO vehicle (mock)


title: UPN 775109, 3 day AraC treatment, array plate number 10

tag: disease status

value: cytarabine (AraC)


title: UPN 831711, 3 day Mock treatment, array plate number 9

value: normal karyotype

value: female

tag: tissue

value: mock


title: UPN 737451, 3 day Mock treatment, array plate number 3

value: acute myeloid leukemia (AML)

value: 21 years


title: UPN 737451, 3 day DAC treatment, array plate number 7

value: bone marrow


title: Mouse_pancreatic_aTC1-6, cytokines, 48H (rep 3)

description: Test

source_name: Mouse pancreatic glucagonoma cell line aTC1-6, Cytokines, 48H

value: Pancreatic alpha cell

value: Cytokines

value: IL1b 50 IU/ml; IFNg 1000 IU/ml; TNFa 1000 IU/ml


title: UPN 737451, 3 day Mock treatment, array plate number 7

source_name: Bone marrow biopsy, mock


title: Mouse_pancreatic_aTC1-6, cytokines, 48H (rep 1)

description: Test


title: Mouse_pancreatic_aTC1-6, cytokines, 48H (rep 2)

description: Test


title: 20044_DAC 100_831711

source_name: Bone marrow culture, DAC

tag: cultured

value: yes

value: 3 days


title: 20043_AraC_831711

tag: treatment dosage


title: UPN 737451, 3 day AraC treatment, array plate number 7


title: UPN 721214, 3 day Mock treatment, array plate number 7

value: unknown

value: 41 years


title: UPN 775109, 3 day AraC treatment, array plate number 9

value: MLL translocation, poor risk

value: male

value: 45 years


title: UPN 737451, 3 day DAC treatment, array plate number 3

source_name: Bone marrow biopsy, DAC

value: decitabine (DAC)


title: UPN 721214, 3 day DAC treatment, array plate number 3


title: UPN 721214, 3 day Mock treatment, array plate number 3


title: UPN 721214, 3 day DAC treatment, array plate number 7


title: Mouse_pancreatic_bTC1, control, 24H (rep 1)

description: Control

value: Pancreatic beta cell

value: Control

value: control


title: Mouse_pancreatic_aTC1-6, control, 48H (rep 3)

description: Control

source_name: Mouse pancreatic glucagonoma cell line aTC1-6, Control, 48H


title: UPN 737451, 3 day AraC treatment, array plate number 3

value: acute myeloid leukemia (AML)

value: normal karyotype

value: female

value: cytarabine (AraC)


title: H841

city: Frederick

first: Jigui

last: Shan

address: 430 Miller Dr

institute: NCI-Frederick

description: CSC treatment

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
Fold Change worksheet reports test/control (i.e., CSC treatment/ DMSO control) ratios.

label: SYBR Green

source_name: Lung cancer cells

label_protocol: PCR assays were performed using specific primers for mature miRNAs (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions.

growth_protocol: All lung cancer lines were obtained from American Type Culture Collection (ATCC).  NCI-SB-EsC2 (EsC2) was established in our lab; OE-33 was purchased from Sigma.  All cancer lines were maintained in RPMI media supplemented with 10% FCS, 10 mM of glutamic acid, and 1% penicillin/streptomycin (normal media). Primary normal human small airway epithelial cells (SAEC) were obtained from Lonza, Inc., and cultured per vendor instructions.  Immortalized human bronchial epithelial cells (HBEC) were generously provided by John D. Minna (U-T Southwestern, Dallas, TX), and cultured as described (64).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: Cigarette smoke condensates (CSC) derived from Kentucky Reference 3R4F research blend cigarettes (University of Kentucky) were prepared as described (64), and resuspended at a concentration of 10 mg tar/ml in DMSO as stock concentration.  For smoke exposure experiments, cells were cultured in 10-cm dishes in appropriate normal media (NM) with DMSO or NM with CSC (0.02mg/ml).  Medium was changed daily with the addition of fresh CSC or DMSO control.

value: CSC treatment


title: UPN 721214, 3 day AraC treatment, array plate number 7

value: bone marrow


title: Mouse_pancreatic_aTC1-6, control, 48H (rep 1)

description: Control

value: Pancreatic alpha cell


title: UPN 632729, 3 day Mock treatment, array plate number 9

value: 75 years

value: mock


title: Mouse_pancreatic_aTC1-6, cytokines, 24H (rep 3)

description: Test

source_name: Mouse pancreatic glucagonoma cell line aTC1-6, Cytokines, 24H

value: Cytokines

value: IL1b 50 IU/ml; IFNg 1000 IU/ml; TNFa 1000 IU/ml


title: UPN 721214, 3 day AraC treatment, array plate number 3

value: unknown

value: 41 years


title: Mouse_pancreatic_aTC1-6, control, 48H (rep 2)

description: Control


title: 20036_AraC_737451

source_name: Bone marrow culture, AraC

value: yes

tag: treatment duration

value: 3 days


title: UPN 989176, 3 day DAC treatment, array plate number 3

value: 76 years

value: decitabine (DAC)

tag: aml sample identifier


title: 20035_Mock_737451

value: acute myeloid leukemia (AML)

value: DMSO vehicle (mock)


title: Calu-6

description: CSC treatment


title: 20034_Unc_737451

value: no


title: 20040_DAC 100_775109


title: Calu-6+CSC

description: Control

value: Control


title: UPN 632729, 3 day Mock treatment, array plate number 10

value: normal karyotype

value: male


title: 20038_Mock_775109

value: bone marrow


title: HBEC

description: CSC treatment

source_name: Normal respiratory epithelia

value: HBEC

value: CSC treatment


title: UPN 632729, 3 day DAC treatment, array plate number 9

value: 75 years


title: Mouse_pancreatic_aTC1-6, cytokines, 24H (rep 1)

description: Test

value: Pancreatic alpha cell

value: Cytokines

value: IL1b 50 IU/ml; IFNg 1000 IU/ml; TNFa 1000 IU/ml


title: 20033_DAC 100_721214

value: yes


title: UPN 632729, 3 day DAC treatment, array plate number 10


title: 20045_Unc_831711


title: HBEC+CSC

description: Control


title: Mouse_pancreatic_aTC1-6, control, 24H (rep 2)

description: Control

source_name: Mouse pancreatic glucagonoma cell line aTC1-6, Control, 24H

value: control


title: Mouse_pancreatic_aTC1-6, control, 24H (rep 3)

description: Control


title: 20039_AraC_775109

value: cytarabine (AraC)

value: 3 days


title: SAEC

description: CSC treatment

value: SAEC


title: 20030_Unc_721214

value: acute myeloid leukemia (AML)


title: H841+CSC

description: Control


title: SAEC+CSC

description: Control


title: Mouse_pancreatic_aTC1-6, control, 24H (rep 1)

description: Control


title: UPN 632729, 3 day AraC treatment, array plate number 9

source_name: Bone marrow biopsy, AraC


title: 20028_AraC_632729


title: 20041_Unc_775109

value: no


title: 20029_DAC 100_632729

value: decitabine (DAC)


title: JON [reps 1 and 2]

status: Public on Dec 17 2012

city: cankiri

first: mine

last: turktas

address: ballica campus

country: Turkey

institute: cankiri karatekin university

description:
Leaf
Samples 9,10

hyb_protocol: Hybridization was performed by following standard NimbleGen operating protocol.

scan_protocol: Scaning was performed by following standard NimbleGen operating protocol.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185).

organism: Olea europaea

source_name: Olea europaea cv. Ayvalik

label_protocol: Labeling was performed by following standard NimbleGen operating protocol.

extract_protocol: Leaves and fruits were collected, and transferred directly into liquid nitrogen. The total RNA extractions were performed using the RNeasy Plant Mini Kit (Qiagen, Germany).

tag: variety

value: Ayvalık

value: Leaf

tag: tissue status

value: juvenile

tag: year

value: on-year


title: NON-1

description:
Leaf
Sample 11

value: mature


title: Spleen BALB/c F1_irradiated male 6_tech_rep1_rep2

city: Leicester

first: Yuri

middle: E

last: Dubrova

address: University Road

department: Genetics

country: United Kingdom

institute: University of Leicester

description:
two technical replicas used to generate the data for this sample
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

hyb_protocol: Hybridization was performed using the NimbleGen Hybridization System 4 following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed using GenePix Axon 4200 AL scanner, following their standard operating protocol.

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

source_name: BALB/c F1_irradiated male 6 Spleen

label_protocol: Labeling was performe using the NimbleGen One-Color DNA Labeling Kit.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: 1 Gy of acute X-rays delivered at 0.5 Gy/min (250 kV constant potential, HLV 1.5 mm Cu, Pantak industrial X-ray machine, Connecticut, USA).

tag: strain

value: BALB/c

value: Offspring of irradiated male, 1Gy acute X-rays

value: Spleen


title: RF [reps 1 and 2]

description:
Fruit
Samples 3/4

value: Fruit

value: ripe


title: 20027_Mock_632729

source_name: Bone marrow culture, mock

value: bone marrow

value: yes

value: DMSO vehicle (mock)


title: DS1-iPS 6

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

institute: Australian Institute for Bioengineering and Nanotechnology

description:
5991413017_L
Down's Syndrome;induced pluripotent stem cell;CCL54 C18;rep6

hyb_protocol: For microarray experiments cDNA was synthesized using the TotalPrep RNA Amplification Kit (Illumina) and cDNA was hybridized to Illumina HT12 v4 BeadChip microarrays according to manufacturer's instructions.

scan_protocol: Bead array (Standard Illumina protocol).

data_processing: For each probe, raw signal intensity was calculated using GenomeStudio software (Illumina). Normalization and statistical analysis of microarray data were performed in R using the Bioconductor packages Lumi and Limma.

source_name: DS fibroblast-derived iPSC

label_protocol: Samples were labelled using Illumina TotalPrep RNA Amplification Kit, following manufacturer's instructions.

growth_protocol: Human ES cells and iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEFs) in DMEM/F12 culture medium supplemented with 20% KnockOut serum replacement (KOSR), 0.1 mM non-essential amino acids, 1 mM L-glutamine, 0.1 mM ß-mercaptoethanol and 100 ng/mL human bFGF (all from Invitrogen). Feeder-free culture on Matrigel (BD Biosciences) with conditioned medium was carried out in the presence of 100 ng/ml human bFGF. Human male CRL2429 and female CRL1502 fibroblasts, and male DS CCL-54 fibroblasts (ATCC) were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS), 0.1 mM non-essential amino acids and 2.0 mM Glutamax (all from Invitrogen).

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini RNA extraction kit (Qiagen) according to the manufacturer's protocols.

treatment_protocol: The oriP/EBNA1-based pCEP4 episomal vectors pEP4EO2SCK2MEN2L (7.3 μg) (Addgene plasmid 20924) and pEP4EO2SET2K (3.2 μg) (Addgene plasmid 20927) were transfected into 106 human fibroblasts using nucleofection (NHDF - VPD-1001 with U020 program, Amaxa). After 2 days of culture in fibroblast medium, 50,000 fibroblasts were seeded onto MEF feeder plates and adapted to KOSR medium containing 100 ng ml b-FGF over a course of 3 days. The cultures were next supplemented with 20 mg/ml pifithrin-α and cultured for 3-4 weeks (first week with unconditioned KOSR + 100 ng/ml b-FGF and week 2-4 with MEF conditioned KOSR + 100 ng/ml b-FGF (Invitrogen)) under low oxygen (2%) conditions with daily medium changes. Subsequently 20 colonies of each line were manually picked and cultured on fresh MEF feeder plates for 4 weeks before bulk expansion by Collagenase IV (Gibco) passaging. Ultimately two iPSC clones from each fibroblast donor that conformed to the criteria of iPS cells were established.

value: induced pluripotent stem cell

tag: disease state

value: Down's Syndrome

tag: gender

value: male

tag: passage

tag: clone


title: NOFF [reps 1 and 2]

description:
Leaf
Samples 7,8

value: off-year


title: UF [reps 1 and 2]

description:
Fruit
Samples 1/2

value: Ayvalık

value: unripe


title: 20042_Mock_831711

value: acute myeloid leukemia (AML)

value: 3 days


title: DS1-iPS 5

description:
5991413017_K
Down's Syndrome;induced pluripotent stem cell;CCL54 C18;rep5

tag: cell line


title: DS2-iPS 6

description:
5991413017_I
Down's Syndrome;induced pluripotent stem cell;CCL54 C11;rep6

tag: cell type


title: Spleen BALB/c F1_irradiated male 3_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 3 Spleen

tag: treatment


title: Mouse_pancreatic_aTC1-6, cytokines, 24H (rep 2)

description: Test

value: Pancreatic alpha cell

tag: activation agent

value: Cytokines

tag: time

value: IL1b 50 IU/ml; IFNg 1000 IU/ml; TNFa 1000 IU/ml


title: UPN 410324, 3 day Mock treatment, array plate number 3

tag: disease status

tag: fab

tag: molecular classification

value: MLL translocation, poor risk

tag: age

value: 60 years

tag: tissue

value: mock

tag: array plate number


title: DS2-iPS 5

description:
5991413017_H
Down's Syndrome;induced pluripotent stem cell;CCL54 C11;rep5


title: Spleen BALB/c F1_irradiated male 5_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 5 Spleen

value: BALB/c

value: Offspring of irradiated male, 1Gy acute X-rays

value: Spleen


title: UPN 632729, 3 day AraC treatment, array plate number 10

value: normal karyotype

value: 75 years

value: bone marrow

value: cytarabine (AraC)

tag: aml sample identifier


title: DS1-iPS 4

description:
5991413017_J
Down's Syndrome;induced pluripotent stem cell;CCL54 C18;rep4

value: induced pluripotent stem cell

value: Down's Syndrome

value: male


title: Spleen BALB/c F1_irradiated male 2_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 2 Spleen

tag: strain


title: Spleen BALB/c F1_irradiated male 4_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 4 Spleen


title: 20024_AraC_410324

value: acute myeloid leukemia (AML)

tag: cultured

value: yes

tag: treatment dosage

tag: treatment duration

value: 3 days


title: DS2-iPS 4

description:
5991413017_G
Down's Syndrome;induced pluripotent stem cell;CCL54 C11;rep4

tag: disease state

tag: gender

tag: passage

tag: clone


title: Spleen BALB/c F1_irradiated male 1_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 1 Spleen

tag: treatment


title: UPN 410324, 3 day DAC treatment, array plate number 7

source_name: Bone marrow biopsy, DAC

value: decitabine (DAC)


title: UPN 410324, 3 day DAC treatment, array plate number 3

value: MLL translocation, poor risk


title: 20023_Mock_410324

value: DMSO vehicle (mock)


title: 20025_DAC 100_410324

source_name: Bone marrow culture, DAC


title: 20022_Unc_410324

source_name: Bone marrow, uncultured (day 0)

value: no


title: 20026_Unc_632729


title: UPN 410324, 3 day AraC treatment, array plate number 7

value: 60 years


title: UPN 410324, 3 day AraC treatment, array plate number 3


title: Spleen CBA/Ca F1_irradiated male 4_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 4 Spleen

value: CBA/Ca

value: Offspring of irradiated male, 1Gy acute X-rays


title: UPN 410324, 3 day Mock treatment, array plate number 7

source_name: Bone marrow biopsy, mock

value: mock


title: DS-Fibr 5

description:
5991413039_K
Down's Syndrome;fibroblast;CCL54;rep5

source_name: DS fibroblast

tag: cell type

value: fibroblast

tag: cell line


title: WT1-iPS 4

description:
5991413017_A
normal;induced pluripotent stem cell;CRL-2429 C11;rep4

source_name: fibroblast-derived iPSC

value: normal


title: DS-Fibr 4

description:
5991413039_J
Down's Syndrome;fibroblast;CCL54;rep4


title: JOFF [reps 1 and 2]

description:
Leaf
Samples 5,6

tag: variety

value: Ayvalık

value: Leaf

tag: tissue status

value: juvenile

tag: year

value: off-year


title: WT1-iPS 6

description:
5991413017_C
normal;induced pluripotent stem cell;CRL-2429 C11;rep6

value: induced pluripotent stem cell

value: male


title: Spleen CBA/Ca F1_irradiated male 6_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 6 Spleen

tag: tissue

value: Spleen


title: Spleen BALB/c Control male 2_tech_rep1_rep2

source_name: BALB/c Control male 2 Spleen

value: BALB/c

value: Control


title: Spleen CBA/Ca F1_irradiated male 2_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 2 Spleen


title: Spleen CBA/Ca F1_irradiated male 1_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 1 Spleen


title: Spleen BALB/c Control male 5_tech_rep1_rep2

source_name: BALB/c Control male 5 Spleen


title: Spleen CBA/Ca F1_irradiated male 3_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 3 Spleen


title: Spleen BALB/c Control male 4_tech_rep1_rep2

source_name: BALB/c Control male 4 Spleen


title: WT2-iPS 1

description:
5991413017_D
normal;induced pluripotent stem cell;CRL1502 C32;rep1

value: female


title: WT-Fibr2 1

description:
5991413039_G
normal;fibroblast;CRL-1502;rep1

source_name: fibroblast


title: DS-Fibr 6

description:
5991413039_L
Down's Syndrome;fibroblast;CCL54;rep6

value: Down's Syndrome


title: WT-Fibr2 3

description:
5991413039_I
normal;fibroblast;CRL-1502;rep3


title: WT2-iPS 3

description:
5991413017_F
normal;induced pluripotent stem cell;CRL1502 C32;rep3


title: WT1-iPS 5

description:
5991413017_B
normal;induced pluripotent stem cell;CRL-2429 C11;rep5


title: WT-Fibr1 9

description:
5991413039_F
normal;fibroblast;CRL-2429;rep8


title: Spleen BALB/c Control male 3_tech_rep1_rep2

description:
two technical replicas used to generate the data for this sample
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: BALB/c Control male 3 Spleen


title: Spleen BALB/c Control male 1_tech_rep1_rep2

source_name: BALB/c Control male 1 Spleen


title: WT-Fibr1 7

description:
5991413039_D
normal;fibroblast;CRL-2429;rep6


title: Spleen CBA/Ca Control male 6_tech_rep1_rep2

source_name: CBA/Ca Control male 6 Spleen


title: WT-Fibr1 8

description:
5991413039_E
normal;fibroblast;CRL-2429;rep7


title: Spleen CBA/Ca Control male 5_tech_rep1_rep2

source_name: CBA/Ca Control male 5 Spleen


title: euDS-iPS 2

description:
5991413039_B
Euploid Down's Syndrome;induced pluripotent stem cell;CCL54 C87;rep2

source_name: euploid DS fibroblast-derived iPSC

value: euploid induced pluripotent stem cell


title: Spleen CBA/Ca Control male 3_tech_rep1_rep2

source_name: CBA/Ca Control male 3 Spleen

value: CBA/Ca


title: euDS-iPS 3

description:
5991413039_C
Euploid Down's Syndrome;induced pluripotent stem cell;CCL54 C87;rep3


title: WT-Fibr2 2

description:
5991413039_H
normal;fibroblast;CRL-1502;rep2


title: Spleen CBA/Ca Control male 2_tech_rep1_rep2

source_name: CBA/Ca Control male 2 Spleen


title: Spleen CBA/Ca Control male 4_tech_rep1_rep2

source_name: CBA/Ca Control male 4 Spleen


title: DS1-iPS 3

description:
5445316039_L
Down's Syndrome;induced pluripotent stem cell;CCL54 C18;rep3

source_name: DS fibroblast-derived iPSC


title: euDS-iPS 1

description:
5991413039_A
Euploid Down's Syndrome;induced pluripotent stem cell;CCL54 C87;rep1


title: DS1-iPS 2

description:
5445316039_K
Down's Syndrome;induced pluripotent stem cell;CCL54 C18;rep2


title: Spleen CBA/Ca Control male 1_tech_rep1_rep2

source_name: CBA/Ca Control male 1 Spleen


title: DS1-iPS 1

description:
5445316039_J
Down's Syndrome;induced pluripotent stem cell;CCL54 C18;rep1


title: Liver BALB/c F1_irradiated male 4_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 4 Liver

value: Offspring of irradiated male, 1Gy acute X-rays

value: Liver


title: Liver BALB/c F1_irradiated male 5_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 5 Liver


title: Liver BALB/c F1_irradiated male 3_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 3 Liver


title: Liver BALB/c F1_irradiated male 6_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 6 Liver


title: WT1-iPS 2

description:
5445316039_E
normal;induced pluripotent stem cell;CRL-2429 C11;rep2

source_name: fibroblast-derived iPSC


title: WT1-iPS 1

description:
5445316039_D
normal;induced pluripotent stem cell;CRL-2429 C11;rep1


title: WT1-iPS 3

description:
5445316039_F
normal;induced pluripotent stem cell;CRL-2429 C11;rep3


title: Liver CBA/Ca F1_irradiated male 6_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 6 Liver


title: Liver BALB/c F1_irradiated male 2_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 2 Liver


title: Liver BALB/c F1_irradiated male 1_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 1 Liver


title: WT2-iPS 2

description:
5991413017_E
normal;induced pluripotent stem cell;CRL1502 C32;rep2


title: Spleen CBA/Ca F1_irradiated male 5_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 5 Spleen


title: DS2-iPS 2

description:
5491021070_K
Down's Syndrome;induced pluripotent stem cell;CCL54 C11;rep2


title: DS2-iPS 3

description:
5491021070_L
Down's Syndrome;induced pluripotent stem cell;CCL54 C11;rep3


title: DS2-iPS 1

description:
5491021070_J
Down's Syndrome;induced pluripotent stem cell;CCL54 C11;rep1


title: WT-Fibr1 5

description:
5491021070_H
normal;fibroblast;CRL-2429;rep5

source_name: fibroblast

value: fibroblast


title: Liver CBA/Ca F1_irradiated male 2_tech_rep1_rep2

description:
two technical replicas used to generate the data for this sample
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: CBA/Ca F1_irradiated male 2 Liver


title: Liver CBA/Ca F1_irradiated male 4_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 4 Liver


title: Liver CBA/Ca F1_irradiated male 1_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 1 Liver


title: WT-Fibr1 6

description:
5491021070_I
normal;fibroblast;CRL-2429;rep6

value: normal


title: Liver CBA/Ca F1_irradiated male 3_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 3 Liver


title: Liver BALB/c Control male 4_tech_rep1_rep2

source_name: BALB/c Control male 4 Liver


title: Liver BALB/c Control male 5_tech_rep1_rep2

source_name: BALB/c Control male 5 Liver


title: WT-Fibr1 4

description:
5491021070_G
normal;fibroblast;CRL-2429;rep4


title: DS-Fibr 2

description:
5491021070_E
Down's Syndrome;fibroblast;CCL54;rep2

source_name: DS fibroblast


title: WT-Fibr1 3

description:
5491021070_C
normal;fibroblast;CRL-2429;rep3


title: WT-Fibr1 2

description:
5491021070_B
normal;fibroblast;CRL-2429;rep2


title: Liver BALB/c Control male 3_tech_rep1_rep2

source_name: BALB/c Control male 3 Liver


title: WT-Fibr1 1

description:
5491021070_A
normal;fibroblast;CRL-2429;rep1


title: Liver BALB/c Control male 1_tech_rep1_rep2

source_name: BALB/c Control male 1 Liver


title: Liver BALB/c Control male 2_tech_rep1_rep2

source_name: BALB/c Control male 2 Liver


title: Liver CBA/Ca Control male 5_tech_rep1_rep2

source_name: CBA/Ca Control male 5 Liver


title: Liver BALB/c Control male 6_tech_rep1_rep2

source_name: BALB/c Control male 6 Liver


title: DS-Fibr 3

description:
5491021070_F
Down's Syndrome;fibroblast;CCL54;rep3


title: Liver CBA/Ca Control male 4_tech_rep1_rep2

source_name: CBA/Ca Control male 4 Liver


title: DS-Fibr 1

description:
5491021070_D
Down's Syndrome;fibroblast;CCL54;rep1


title: Liver CBA/Ca Control male 6_tech_rep1_rep2

source_name: CBA/Ca Control male 6 Liver


title: WT-Fibr2 5

description:
5445316044_K
normal;fibroblast;CRL-1502;rep5


title: WT-Fibr2 4

description:
5445316044_J
normal;fibroblast;CRL-1502;rep4


title: MEL1 ES 2

description:
5445316044_H
normal;human embryonic stem cell;MEL-1;rep2

source_name: embryonic stem cell

value: human embryonic stem cell


title: Spleen BALB/c Control male 6_tech_rep1_rep2

source_name: BALB/c Control male 6 Spleen


title: WT-Fibr2 6

description:
5445316044_L
normal;fibroblast;CRL-1502;rep6

source_name: fibroblast


title: Liver CBA/Ca Control male 2_tech_rep1_rep2

source_name: CBA/Ca Control male 2 Liver


title: Brain BALB/c F1_irradiated male 5_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 5 Brain

value: Brain


title: Brain BALB/c F1_irradiated male 4_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 4 Brain


title: Liver CBA/Ca Control male 3_tech_rep1_rep2

source_name: CBA/Ca Control male 3 Liver


title: Liver CBA/Ca Control male 1_tech_rep1_rep2

source_name: CBA/Ca Control male 1 Liver


title: WT4-iPS 2

description:
5445316044_E
normal;induced pluripotent stem cell;CRL-1502 C29;rep2

source_name: fibroblast-derived iPSC


title: Brain CBA/Ca F1_irradiated male 4_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 4 Brain


title: WT3-iPS 2

description:
5445316044_B
normal;induced pluripotent stem cell;CRL-2429 C16;rep2


title: Brain CBA/Ca F1_irradiated male 6_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 6 Brain


title: WT4-iPS 1

description:
5445316044_D
normal;induced pluripotent stem cell;CRL-1502 C29;rep1


title: Brain BALB/c F1_irradiated male 3_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 3 Brain


title: MEL1 ES 3

description:
5445316044_I
normal;human embryonic stem cell;MEL-1;rep3


title: MEL1 ES 1

description:
5445316044_G
normal;human embryonic stem cell;MEL-1;rep1


title: WT4-iPS 3

description:
5445316044_F
normal;induced pluripotent stem cell;CRL-1502 C29;rep3


title: Brain BALB/c F1_irradiated male 2_tech_rep1_rep2

description:
two technical replicas used to generate the data for this sample
NimbleGen Mus musculus MM8 Expression Array (12x135k) [090901_mm8_60mer_expr_HX12]

source_name: BALB/c F1_irradiated male 2 Brain


title: WT3-iPS 3

description:
5445316044_C
normal;induced pluripotent stem cell;CRL-2429 C16;rep3


title: Brain CBA/Ca F1_irradiated male 5_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 5 Brain


title: WT3-iPS 1

description:
5445316044_A
normal;induced pluripotent stem cell;CRL-2429 C16;rep1


title: Brain BALB/c F1_irradiated male 6_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 6 Brain


title: Brain BALB/c F1_irradiated male 1_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 1 Brain


title: Ssalar_7daypostSBMfeed_rep7_tank1

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

hyb_protocol: Each experimental sample and reference pool (825 ng each) was fragmented for 30 minutes at 60°C, mixed with an equal amount of 2x GEx Hybridization buffer HI-RPM (Agilent Gene Expression Hybridization Kit, No. 5188-5242) and loaded onto a cGRASP 44k Salmonid oligonucleotide microarray (Agilent Technologies, [21]). The hybridization was incubated for 17 hrs (10 rpm at 65°C) in a hybridization oven (Agilent). Slides were washed immediately after hybridization using wash buffers, acetonitrile and Stabilization and Drying Solution, as per manufacturer’s instructions to prevent ozone-related problems. Slides were then kept in the dark at low ozone (<9 ppb) and scanned as soon as possible.

scan_protocol: All slides were scanned using a ScanArray® Express scanner (PerkinElmer®; 5μm resolution; PMTs: Cy5: 60, Cy3: 65) in a low-ozone environment (<9 ppb).

data_processing: Scanned images were processed in the ImaGene® software (V 8.0; Biodiscovery, El Segundo, CA, USA) using the 44K salmonid GAL file (11/09) (http://web.uvic.ca/grasp/microarray/array.html). The raw data was imported into GeneSpring GX11.5 (Agilent). Annotation files and specifications of the microarray can be found at the cGRASP microarray page (http://web.uvic.ca/grasp/microarray/array.html). All spots were thresholded to 1.0, samples were normalized using an intensity-dependent LOWESS normalization and a per gene baseline to median normalization. Control spots were removed and all entities were filtered to retain only those entities in which 80% of the biological replicates had raw values ≥500 in any one of the six conditions (i.e. time points). Entities were then filtered to retain the entities in which at least 80% were flagged as ‘present’ in six of six conditions. The remaining entities were tested for significant differential expression by comparing each of the time points (day one, two, three, five, seven) to day zero using the Mann-Whitney test (p<0.05) without multiple test correction. Only genes that changed more than 1.5 fold were considered for further analysis.

organism: Salmo salar

source_name: Distal intestine

label_protocol: Reverse transcription and labeling of the RNA was done according to Agilent’s two color Low Input Quick Amp labeling protocol (Version 6.5, May 2010).cRNA was quantified using spectrophotometry (NanoDrop1000™, Thermo Fisher Scientific). All samples had specific activity >6 pmol dye per µg cRNA. Labeled cRNA was stored at -80°C in the dark until hybridization.

growth_protocol: Atlantic salmon (Salmo salar L.) of the Sunndalsøra breed held in 1 m3 fiberglass tanks with running seawater (25-30 fish per tank) at the research facilities of Nofima Marin, Sunndalsøra, Norway. Initial body weight of 500-600 g. Two diets, the reference (FM) diet contained 563 g kg-1 fishmeal meal as the sole protein source while the test diet contained 200 g kg-1 hexane-extracted (defatted) soybean meal, partially replacing the fishmeal in the FM diet. Both diets were approximately iso-nitrogenous and iso-energetic on a crude protein and gross energy basis, containing 28% lipid and 43% crude protein. All fish were adapted to the FM diet for seven days.

extract_protocol: For RNA extraction, sections of distal intestinal tissue (distal-most region of the post-gastric intestinal tract defined by appearance of annular mucosal folds and widening of intestinal diameter) were taken and placed in RNAlater at 4°C for 24h and then stored at -80°C. To ensure exposure to SBM, only fish that had content throughout the intestinal tract were sampled. From ten fish per time point (five from each tank duplicate) approximately 20 mg of sample tissue was immersed in 1 ml TRIzol® (Invitrogen), homogenized with a mixermill (Retsch MM301) and total RNA was extracted as per manufacturers protocol. Total RNA was purified using RNeasy columns as per manufacturer’s instructions (Qiagen), including an optional on-column DNase I digestion step. Samples were quantified by spectrophotometry (NanoDrop1000™, Thermo Fisher Scientific) and quality checked by agarose gel electrophoresis. Samples confirmed free of genomic DNA by PCR with and without reverse transcriptase. Samples were stored at -80°C until further use.

treatment_protocol: Day zero in this experiment marks the sampling of FM fed fish. Duplicate tanks of the remaining fish received the SBM test diet from day zero and were sampled after one, two, three, five and seven days of exposure.

source_name: Pooled 3 indiv intestine samples from each condition (n=18)

tag: reference

value: Reference pool


title: Ssalar_7daypostSBMfeed_rep8_tank1


title: Brain CBA/Ca F1_irradiated male 1_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 1 Brain


title: Brain CBA/Ca F1_irradiated male 3_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 3 Brain


title: Brain BALB/c Control male 5_tech_rep1_rep2

source_name: BALB/c Control male 5 Brain


title: Ssalar_7daypostSBMfeed_rep9_tank1


title: Ssalar_7daypostSBMfeed_rep4_tank2


title: Brain BALB/c Control male 4_tech_rep1_rep2

source_name: BALB/c Control male 4 Brain


title: Ssalar_7daypostSBMfeed_rep5_tank2


title: Brain BALB/c Control male 3_tech_rep1_rep2

source_name: BALB/c Control male 3 Brain


title: Ssalar_7daypostSBMfeed_rep3_tank2


title: Brain CBA/Ca Control male 6_tech_rep1_rep2

source_name: CBA/Ca Control male 6 Brain


title: Ssalar_7daypostSBMfeed_rep1_tank2


title: Ssalar_5daypostSBMfeed_rep7_tank1


title: Brain CBA/Ca Control male 5_tech_rep1_rep2

source_name: CBA/Ca Control male 5 Brain


title: Brain CBA/Ca F1_irradiated male 2_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 2 Brain


title: Ssalar_5daypostSBMfeed_rep5_tank2


title: Ssalar_5daypostSBMfeed_rep9_tank1


title: Ssalar_5daypostSBMfeed_rep8_tank1


title: Brain BALB/c Control male 6_tech_rep1_rep2

source_name: BALB/c Control male 6 Brain


title: Ssalar_7daypostSBMfeed_rep2_tank2


title: Ssalar_5daypostSBMfeed_rep6_tank1


title: Ssalar_5daypostSBMfeed_rep10_tank1


title: Brain BALB/c Control male 1_tech_rep1_rep2

source_name: BALB/c Control male 1 Brain


title: Ssalar_7daypostSBMfeed_rep10_tank1


title: Brain BALB/c Control male 2_tech_rep1_rep2

source_name: BALB/c Control male 2 Brain


title: Ssalar_7daypostSBMfeed_rep6_tank1


title: Brain CBA/Ca Control male 4_tech_rep1_rep2

source_name: CBA/Ca Control male 4 Brain


title: Liver CBA/Ca F1_irradiated male 5_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 5 Liver


title: Brain CBA/Ca Control male 2_tech_rep1_rep2

source_name: CBA/Ca Control male 2 Brain


title: Brain CBA/Ca Control male 1_tech_rep1_rep2

source_name: CBA/Ca Control male 1 Brain


title: Ssalar_5daypostSBMfeed_rep3_tank2

source_name: Distal intestine


title: Kidney BALB/c F1_irradiated male 6_tech_rep1_rep2

description:
two technical replicas used to generate the data for this sample
NimbleGen Mus musculus MM8 Expression Array (12x135k) [080925_mm8_60mer_expr_HX12]

source_name: BALB/c F1_irradiated male 6 Kidney

value: Kidney


title: Kidney BALB/c F1_irradiated male 5_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 5 Kidney


title: Ssalar_5daypostSBMfeed_rep4_tank2

source_name: Pooled 3 indiv intestine samples from each condition (n=18)


title: Kidney BALB/c F1_irradiated male 2_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 2 Kidney


title: Brain CBA/Ca Control male 3_tech_rep1_rep2

source_name: CBA/Ca Control male 3 Brain


title: Ssalar_3daypostSBMfeed_rep6_tank1


title: Ssalar_5daypostSBMfeed_rep1_tank2


title: Ssalar_3daypostSBMfeed_rep8_tank1


title: Ssalar_3daypostSBMfeed_rep4_tank2


title: Kidney CBA/Ca F1_irradiated male 4_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 4 Kidney


title: Kidney BALB/c F1_irradiated male 1_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 1 Kidney


title: Kidney CBA/Ca F1_irradiated male 5_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 5 Kidney


title: Ssalar_3daypostSBMfeed_rep9_tank1


title: Kidney BALB/c F1_irradiated male 4_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 4 Kidney


title: Ssalar_3daypostSBMfeed_rep2_tank2


title: Ssalar_3daypostSBMfeed_rep7_tank1


title: Ssalar_3daypostSBMfeed_rep3_tank2


title: Ssalar_3daypostSBMfeed_rep10_tank1


title: Ssalar_3daypostSBMfeed_rep5_tank2


title: Ssalar_3daypostSBMfeed_rep1_tank2


title: Kidney CBA/Ca F1_irradiated male 2_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 2 Kidney


title: Ssalar_2daypostSBMfeed_rep10_tank1


title: Kidney CBA/Ca F1_irradiated male 3_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 3 Kidney


title: Ssalar_2daypostSBMfeed_rep8_tank1


title: Kidney BALB/c F1_irradiated male 3_tech_rep1_rep2

source_name: BALB/c F1_irradiated male 3 Kidney


title: Kidney BALB/c Control male 4_tech_rep1_rep2

source_name: BALB/c Control male 4 Kidney


title: Ssalar_2daypostSBMfeed_rep1_tank2


title: Ssalar_2daypostSBMfeed_rep4_tank2


title: Leaves_CaLam_control_rep1

city: Cordeirópolis

first: Valéria

last: Mafra

state: São Paulo

address: Rod. Anhanguera

country: Brazil

institute: Centro de Citricultura Sylvio Moreira

description: This sample is of uninoculated sweet orange. It is the first of two biological replicates used in this experiment as control.

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

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

organism: Citrus sinensis

source_name: Three uninoculated leaves, harvested 80 weeks after the inoculation of the other leaves

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

growth_protocol: Once CaLam are uncultured, inoculations were performed using bark or bud pieces harvested from infected plants used as inoculum source.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA)  and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). Total RNA concentration and purity were determined from the ratio of absorbance readings at 260 and 280 nm using a NanoDrop 8000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, USA), and RNA integrity was tested in a denaturing agarose gel. RNA quality and concentrations were again evaluated by Nimblegen  with an Agilent 2100 bioanalyzer () and Nanodrop spectrophotometer (Thermo Scientific).

treatment_protocol:
Pera sweet orange grafted onto Rangpur lime, with four-month-old non-infected with CaLam (control)
After inoculation, plants were monitored by end-point PCR bimonhtly until the detection of the bacterium. PCR positive plants were challenged again by new grafting with infected budwoods, and pruned. CaLam is heat sensitive; therefore, all plants were kept in growth chambers at 22 to 24 °C for six months. Fully expanded leaves of two plants displaying initial symptoms of HLB and that were PCR positive for the bacterium, and leaves of two healthy plants grown under the same conditions were collected, ground in liquid nitrogen, and stored at -80° C.

value: leaves

value: uninoculated


title: Kidney CBA/Ca F1_irradiated male 6_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 6 Kidney


title: Ssalar_2daypostSBMfeed_rep5_tank2


title: Ssalar_2daypostSBMfeed_rep2_tank2


title: Ssalar_2daypostSBMfeed_rep3_tank2


title: Ssalar_2daypostSBMfeed_rep9_tank1


title: Kidney BALB/c Control male 3_tech_rep1_rep2

source_name: BALB/c Control male 3 Kidney


title: Ssalar_2daypostSBMfeed_rep7_tank1

source_name: Distal intestine


title: Ssalar_1daypostSBMfeed_rep9_tank1


title: Ssalar_1daypostSBMfeed_rep10_tank1


title: Leaves_CaLam_symptomatic_rep1

description: This sample is of sweet orange inoculated with CaLam. It is the first of two biological replicates used in this experiment.

source_name: Three symptomatic leaves, harvested 80 weeks after inoculation

treatment_protocol:
Pera sweet orange grafted onto Rangpur lime, with four-month-old challenged with CaLam by grafting infected (PCR positive) budwoods
After inoculation, plants were monitored by end-point PCR bimonhtly until the detection of the bacterium. PCR positive plants were challenged again by new grafting with infected budwoods, and pruned. CaLam is heat sensitive; therefore, all plants were kept in growth chambers at 22 to 24 °C for six months. Fully expanded leaves of two plants displaying initial symptoms of HLB and that were PCR positive for the bacterium, and leaves of two healthy plants grown under the same conditions were collected, ground in liquid nitrogen, and stored at -80° C.

value: inoculated with CaLam


title: Kidney BALB/c Control male 1_tech_rep1_rep2

source_name: BALB/c Control male 1 Kidney

value: BALB/c


title: Kidney BALB/c Control male 5_tech_rep1_rep2

source_name: BALB/c Control male 5 Kidney

value: Control


title: Ssalar_1daypostSBMfeed_rep8_tank1

source_name: Pooled 3 indiv intestine samples from each condition (n=18)


title: Kidney CBA/Ca Control male 6_tech_rep1_rep2

source_name: CBA/Ca Control male 6 Kidney


title: Leaves_CaLam_symptomatic_rep2

description: This sample is of sweet orange inoculated with CaLam. It is the second of two biological replicates used in this experiment.


title: Ssalar_1daypostSBMfeed_rep6_tank2


title: Kidney BALB/c Control male 2_tech_rep1_rep2

source_name: BALB/c Control male 2 Kidney


title: Leaves_CaLam_control_rep2

description: This sample is of uninoculated sweet orange. It is the second of two biological replicates used in this experiment as control.


title: Kidney BALB/c Control male 6_tech_rep1_rep2

source_name: BALB/c Control male 6 Kidney


title: Ssalar_1daypostSBMfeed_rep7_tank1


title: Ssalar_1daypostSBMfeed_rep3_tank2


title: Ssalar_0daypostSBMfeed_rep9_tank1


title: Kidney CBA/Ca Control male 4_tech_rep1_rep2

source_name: CBA/Ca Control male 4 Kidney


title: delN-high_Cy3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

hyb_protocol: Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction, LOWESS normalization, and dye-normalization .

source_name: Embryonic fibroblast cells derived from Lats1ΔN/ΔN C57BL/6J mice under high cell density

label_protocol: 500 ng of total RNA was labeled using Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 500ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 5-CTP (Cy5-CTP) or 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A650nm for Cy5-CTP and  at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Lats1+/+ and Lats1ΔN/ΔN MEFs were under both high and low cell density conditions

extract_protocol: Total RNAs were extracted from MEFs derived from LATS1+/+ and LATS1ΔNΔN mice using miRNeasy extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: no teatment

tag: background strain

tag: genotype/variation

value: embryonic fibroblasts

tag: cell density

value: high


title: delN-high_Cy5


title: Ssalar_1daypostSBMfeed_rep5_tank2


title: Ssalar_0daypostSBMfeed_rep8_tank1


title: Kidney CBA/Ca Control male 5_tech_rep1_rep2

source_name: CBA/Ca Control male 5 Kidney

tag: strain


title: Kidney CBA/Ca F1_irradiated male 1_tech_rep1_rep2

source_name: CBA/Ca F1_irradiated male 1 Kidney


title: delN-low_Cy5

value: low


title: Ssalar_1daypostSBMfeed_rep2_tank2


title: WT-low_Cy5

source_name: Embryonic fibroblast cells derived from Lats1+/+ C57BL/6J mice under high cell density


title: Ssalar_0daypostSBMfeed_rep7_tank1


title: Ssalar_0daypostSBMfeed_rep6_tank1


title: Ssalar_0daypostSBMfeed_rep5_tank2


title: Kidney CBA/Ca Control male 3_tech_rep1_rep2

source_name: CBA/Ca Control male 3 Kidney

value: CBA/Ca


title: delN-low_Cy3


title: Ssalar_1daypostSBMfeed_rep4_tank2


title: Ssalar_0daypostSBMfeed_rep4_tank2


title: WT-high_Cy3


title: Ssalar_1daypostSBMfeed_rep11_tank1


title: Ssalar_0daypostSBMfeed_rep2_tank2


title: Kidney CBA/Ca Control male 1_tech_rep1_rep2

source_name: CBA/Ca Control male 1 Kidney


title: Ssalar_1daypostSBMfeed_rep1_tank0


title: Control vs Sox17 LOF 3

city: Daejeon

first: Hanseul

last: Yang

address: Korea Advanced Institute of Science and Technology

description: Biological replicate 3 of 3.

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 sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

source_name: NC 2

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: HUVECs were cultured on 0.1% gelatin coated dishes and incubated with EGM-2 media(Lonza) at humidifed 37℃, 5% CO2 incubator

extract_protocol: Total RNA extracted using RNeasy plus mini kit following manufacturer's instructions

treatment_protocol:
siRNAs against Sox17 or scrambled siRNAs for controls were transfected into HUVECs using LipofectaminTM RNAiMAX (invitrogen). After 24 hours, cells were plated on cell culture plate at 10-20% confluency.
After 8 hours, cells were incubated with 0.2% FBS in EBM-2 for overnight. Then cells were stimulated by 50 ng/ml of VEGF for 2 hours and used for analysis

value: primary  HUVEC

value: scrambled siRNA treatment

source_name: LoF 2

value: Sox17 siRNA treatment


title: WT-high_Cy5


title: WT-low_Cy3


title: Ssalar_0daypostSBMfeed_rep1_tank2

source_name: Distal intestine


title: Control vs Sox17 LOF 2

institute: Korea Advanced Institute of Science and Technology

description: Biological replicate 2 of 3.

source_name: Con 3

source_name: LoF 3


title: Nupr1het2;KIC

status: Public on Dec 16 2012

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

hyb_protocol: The cRNA hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven. After 16 h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix-recommended protocol(http://media.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf.

scan_protocol: The arrays were scanned using the Affymetrix GCS 3000 7G

data_processing: The Gene-Chip Operating Software (Affymetrix, Santa Clara, CA), was used to produce the intensity files. The background subtraction and normalization of probe set intensities was performed using the method of Robust Multiarray Analysis (RMA)

source_name: C57BL/6 mice bearing a heterozygous deletion of exon 2 of the Nupr1 gene

label_protocol: Arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix-recommended protocol(http://media.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf.

growth_protocol: not applicable

extract_protocol: All samples were snap frozen in liquid N2 until RNA extraction.RNA were processed and profiled on Affymetrix Mouse Gene 1.0, according to the Affymetrix standard protocol. Briefly. total RNA (200 ng per sample) was labeled using the Affymetrix GeneChip® WT cDNA Synthesis and Amplification Kit protocol, and hybridized to the arrays as described by the manufacturer (Affymetrix, Santa Clara, CA).

treatment_protocol: not applicable

tag: genotype

value: Pancreatic tumor


title: Nupr1wt1;KIC

source_name: C57BL/6 mice wild type


title: Nupr1wt3;KIC


title: Nupr1ko1;KIC

source_name: C57BL/6 mice bearing a homozygous deletion of exon 2 of the Nupr1 gene


title: Control vs Sox17 LOF 1

description: Biological replicate 1 of 3.

source_name: Con 2

source_name: LoF 4


title: Liver_WT_Chow_Biolrep5

city: Portland

first: Harini

last: Sampath

state: OR

address: 3181 SW Sam Jackson Park Rd

department: CROET

institute: OHSU

hyb_protocol: 1.8 ug of target was hybridized with the GeneChip Mouse Gene ST Array (Affymetrix) overnight, followed by washing, staining with streptavidin-phycoerythrin (Affymetrix), signal amplification with biotinylated anti-streptavidin antibody (Affymetrix), and a final staining step on the Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip 3000 laser scanner (Affymetrix) with the 7G upgrade.

data_processing: Data visualization and exploratory analysis were conducted using GeneSifter web-based software, release 59.0 (GeoSpiza Inc., Seattle, WA). Affymetrix .cel files were uploaded to the GeneSifter web site with GC robust multiarray average (RMA) normalization

source_name: Chow-fed wild-type liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol with 125 ng input RNA

growth_protocol: 10 week old male mice were individually housed for 10 weeks

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

treatment_protocol: Mice were given ad libitum access to chow or HFD for 10 weeks

value: male

value: liver

tag: diet

value: Chow-fed

value: wild-type


title: Liver_Ogg1-/-_HFD_Biolrep6

source_name: HFD-fed Ogg1-/- liver

tag: gender

value: HFD-fed


title: Liver_Ogg1-/-_HFD_Biolrep1


title: Ssalar_5daypostSBMfeed_rep2_tank2

source_name: Pooled 3 indiv intestine samples from each condition (n=18)

value: Reference pool


title: Liver_WT_Chow_Biolrep4


title: Nupr1ko2;KIC


title: Kidney CBA/Ca Control male 2_tech_rep1_rep2

source_name: CBA/Ca Control male 2 Kidney

value: Kidney


title: Nupr1het1;KIC


title: Liver_WT_HFD_Biolrep3

source_name: HFD-fed wild-type liver


title: Liver_Ogg1-/-_Chow_Biolrep3

source_name: Chow-fed Ogg1-/- liver


title: Liver_WT_Chow_Biolrep2


title: Liver_Ogg1-/-_HFD_Biolrep2


title: Liver_WT_Chow_Biolrep6


title: Liver_Ogg1-/-_Chow_Biolrep2


title: Liver_Ogg1-/-_HFD_Biolrep3


title: Liver_WT_HFD_Biolrep1


title: Liver_Ogg1-/-_Chow_Biolrep5


title: Liver_WT_HFD_Biolrep4


title: Liver_WT_HFD_Biolrep2


title: Ssalar_2daypostSBMfeed_rep6_tank1


title: Liver_Ogg1-/-_Chow_Biolrep6


title: Nupr1wt2;KIC


title: Mammoplastic reduction (control) N. 98

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

description: Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

hyb_protocol: Labeled RNA was hybridized to Agilent miRNA arrays for 22 hours at 55°C using the Agilent's Hybridization Oven that is suited for bubble-mixing and microarray hybridization processes. Washing was performed using the Gene Expression Wash Buffer kit (Agilent Technologies) following the manufacturer's instructions.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 5% sensitivity settings.

data_processing: Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 60% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were and inter-array normalized with cyclic Lowess (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed.

source_name: Frozen mammoplastic reduction sample was provided from the NCCR Molecular Oncology (Prof. Cathrin Brisken), Lausanne, Switzerland.

label_protocol: We performed miRNA expression profiling from 100 ng of total RNA and following the miRNA Microarray System protocol v. 1.5 (Agilent Technologies). Total RNA was dephosphorylated and ligated with pCp-Cy3. Unincorporated dyes were removed with MicroBioSpin6 columns (BioRad).

extract_protocol: After surgical removal, sample was macro-dissected by pathologists, quickly frozen and stored at –80°C. Total RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissue, according to the manufacturer's guidelines. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), while RNA integrity and content of microRNAs (%) in each sample was assessed by capillary electrophoresis using the RNA 6000 Nano LabChip and the Small RNA Nano LabChip respectively using the Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Only total RNA sample with R.I.N. (RNA Integrity Number) values of 6, or higher, and the percentage of miRNA < 30% were used for microarray analysis.

tag: - sex

value: female

tag: - date of birth

tag: - date of surgery


title: Liver_Ogg1-/-_Chow_Biolrep1


title: Liver_Ogg1-/-_HFD_Biolrep5


title: Mammoplastic reduction (control) N. 99


title: Mammoplastic reduction (control) N. 97


title: Liver_WT_HFD_Biolrep5


title: Mammoplastic reduction (control) N. 100


title: Liver_WT_Chow_Biolrep3


title: Mammoplastic reduction (control) N. 95


title: Liver_Ogg1-/-_Chow_Biolrep4