title: MUC1-CD-transfected 3Y1 cells grown in vitro, biological replicate 2


title: Patient 5, post-treatment

status: Public on Apr 09 2009

type: RNA

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

description: Responder

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

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

data_processing: The data were processed using the RMA methodology without background correction using the affy package in R/Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Biopsy, Patient 5, post-treatment_Paclitaxel

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Samples with less than 1 ug quantities were amplified using 10 ng of total RNA.

extract_protocol: RNA was extracted using RNA-Easy kit from Qiagen according to manufacturer's instructions.

tag: treatment

value: Paclitaxel

tag: response

value: sensitive

tag: clinical group

tag: ca-125 coefficient


title: Patient 9, post-treatment

description: Responder

source_name: Biopsy, Patient 9, post-treatment_Paclitaxel


title: Patient 38, post-treatment

description: Non-responder. Debulking surgery was delayed past 3 cycles of Paclitaxel

source_name: Biopsy, Patient 38, post-treatment_Both_Carboplatin_Paclitaxel

value: Both

value: resistant


title: Patient 37, post-treatment

description: Non-responder. Debulking surgery was delayed past 3 cycles of Carboplatin

source_name: Biopsy, Patient 37, post-treatment_Both_Carboplatin_Paclitaxel


title: Patient 3, post-treatment

description: Responder

source_name: Biopsy, Patient 3, post-treatment_Carboplatin

value: Carboplatin


title: Patient 37, pre-treatment

description: Non-responder

source_name: Biopsy, Patient 37, pre-treatment


title: Patient 35, post-treatment

description: Responder

source_name: Biopsy, Patient 35, post-treatment_Carboplatin


title: Patient 45, pre-treatment

description: Non-responder

source_name: Biopsy, Patient 45, pre-treatment


title: Patient 36, post-treatment

description: Non-responder

source_name: Biopsy, Patient 36, post-treatment_Carboplatin


title: Patient 39, post-treatment

description: Responder

source_name: Biopsy, Patient 39, post-treatment_Paclitaxel


title: Patient 32, pre-treatment

description: Responder

source_name: Biopsy, Patient 32, pre-treatment


title: Patient 32, post-treatment

description: Responder

source_name: Biopsy, Patient 32, post-treatment_Carboplatin


title: Patient 34, post-treatment

description: Responder

source_name: Biopsy, Patient 34, post-treatment_Paclitaxel


title: Patient 35, pre-treatment

description: Responder

source_name: Biopsy, Patient 35, pre-treatment


title: Patient 3, pre-treatment

description: Responder

source_name: Biopsy, Patient 3, pre-treatment


title: Patient 30, pre-treatment

description: Responder

source_name: Biopsy, Patient 30, pre-treatment


title: Patient 29, post-treatment

description: Responder

source_name: Biopsy, Patient 29, post-treatment_Carboplatin


title: WGAAD-426

status: Public on Apr 10 2009

city: Miami

first: Amanda

last: Myers

state: FL

address: 1600 NW 10th Ave

department: Psychiatry and Behavioral Sciences

country: USA

institute: Miller School of Medicine, University of Miami

description: Human Cortex from Alzheimer's Disease

hyb_protocol: RNA: Illumina Whole Genome Gene Expression Rev. F (Illumina Doc #11763837)

scan_protocol: RNA: Illumina Beadstation

data_processing: RNA: Beadstudio software v 1.5.0.34, rank invariant normalization to extract

source_name: Alzheimer's Disease frozen cortical tissue

label_protocol: RNA: per ambion manual for cat #IL1791, biotinylated cRNA created from in vitro translation targeting poly A tail, cy3 used to image RNA signal

extract_protocol: total RNA (Qiagen Rneasy Lipid Tissue cat #cat 74804, Qiagen Rnase free dnase set- cat # 79254)

tag: tissue

tag: gender

value: Male

tag: age

tag: pmi


title: Patient 1, post-treatment

description: Non-responder

source_name: Biopsy, Patient 1, post-treatment_Carboplatin


title: Patient 28, post-treatment

description: Non-responder

source_name: Biopsy, Patient 28, post-treatment_Paclitaxel


title: Patient 29, pre-treatment

description: Responder

source_name: Biopsy, Patient 29, pre-treatment


title: Patient 31, post-treatment

description: Non-responder

source_name: Biopsy, Patient 31, post-treatment_Carboplatin


title: Patient 27, post-treatment

description: Non-responder

source_name: Biopsy, Patient 27, post-treatment_Paclitaxel


title: Patient 1, pre-treatment

description: Non-responder

source_name: Biopsy, Patient 1, pre-treatment


title: Patient 20, pre-treatment

description: Responder

source_name: Biopsy, Patient 20, pre-treatment


title: Patient 21, post-treatment

description: Responder

source_name: Biopsy, Patient 21, post-treatment_Carboplatin


title: Patient 2, post-treatment

description: Responder

source_name: Biopsy, Patient 2, post-treatment_Paclitaxel


title: Patient 24, post-treatment

description: Responder

source_name: Biopsy, Patient 24, post-treatment_Paclitaxel


title: Patient 30, post-treatment

description: Responder

source_name: Biopsy, Patient 30, post-treatment_Carboplatin


title: Patient 4, pre-treatment

description: Non-responder

source_name: Biopsy, Patient 4, pre-treatment


title: Patient 12, post-treatment

description: Non-responder

source_name: Biopsy, Patient 12, post-treatment_Paclitaxel


title: Patient 19, post-treatment

source_name: Biopsy, Patient 19, post-treatment_Both_Carboplatin_Paclitaxel


title: Patient 16, post-treatment

description: Responder

source_name: Biopsy, Patient 16, post-treatment_Paclitaxel


title: Patient 17, post-treatment

description: Responder

source_name: Biopsy, Patient 17, post-treatment_Carboplatin


title: Patient 13, pre-treatment

description: Non-responder

source_name: Biopsy, Patient 13, pre-treatment


title: Patient 13, post-treatment

description: Non-responder

source_name: Biopsy, Patient 13, post-treatment_Carboplatin


title: Patient 11, post-treatment

description: Responder

source_name: Biopsy, Patient 11, post-treatment_Carboplatin


title: Patient 10, pre-treatment

description: Responder

source_name: Biopsy, Patient 10, pre-treatment


title: Patient 11, pre-treatment

description: Responder

source_name: Biopsy, Patient 11, pre-treatment


title: Patient 10, post-treatment

description: Responder

source_name: Biopsy, Patient 10, post-treatment_Carboplatin


title: Patient 9, pre-treatment

description: Responder

source_name: Biopsy, Patient 9, pre-treatment


title: Patient 17, pre-treatment

description: Responder

source_name: Biopsy, Patient 17, pre-treatment


title: Patient 46, pre-treatment

description: Non-responder

source_name: Biopsy, Patient 46, pre-treatment


title: Patient 5, pre-treatment

description: Responder

source_name: Biopsy, Patient 5, pre-treatment


title: Patient 7, pre-treatment

description: Responder

source_name: Biopsy, Patient 7, pre-treatment


title: Patient 44, pre-treatment

description: Responder

source_name: Biopsy, Patient 44, pre-treatment


title: Patient 41, pre-treatment

description: Responder

source_name: Biopsy, Patient 41, pre-treatment


title: Patient 39, pre-treatment

description: Responder

source_name: Biopsy, Patient 39, pre-treatment


title: Patient 43, pre-treatment

description: Responder

source_name: Biopsy, Patient 43, pre-treatment


title: Patient 8, pre-treatment

description: Responder

source_name: Biopsy, Patient 8, pre-treatment


title: Patient 14, post-treatment

source_name: Biopsy, Patient 14, post-treatment_Both_Carboplatin_Paclitaxel


title: Patient 2, pre-treatment

description: Responder

source_name: Biopsy, Patient 2, pre-treatment


title: Patient 38, pre-treatment

description: Non-responder

source_name: Biopsy, Patient 38, pre-treatment


title: Patient 34, pre-treatment

description: Responder

source_name: Biopsy, Patient 34, pre-treatment


title: Patient 24, pre-treatment

description: Responder

source_name: Biopsy, Patient 24, pre-treatment


title: Patient 28, pre-treatment

description: Non-responder

source_name: Biopsy, Patient 28, pre-treatment


title: Patient 27, pre-treatment

description: Non-responder

source_name: Biopsy, Patient 27, pre-treatment


title: Patient 16, pre-treatment

description: Responder

source_name: Biopsy, Patient 16, pre-treatment


title: Patient 33, pre-treatment

description: Non-responder

source_name: Biopsy, Patient 33, pre-treatment


title: Patient 15, pre-treatment

description: Responder

source_name: Biopsy, Patient 15, pre-treatment


title: Patient 19, pre-treatment

description: Non-responder

source_name: Biopsy, Patient 19, pre-treatment


title: NOD-ES 4K

city: Cambridge

first: Albert

middle: W

last: Cheng

state: MA

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

description: Gene expression in NOD-ES 4K

hyb_protocol: Agilent (mouse 4x44k) expression arrays were hybridized according to our lab’s method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail consisted of 1.65ug cy3-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 60°C in an Agilent rotor oven set to maximum speed. The arrays were treated with Wash Buffer #1 (6X SSPE / 0.005% n-laurylsarcosine) on a shaking platform at room temperature for 2 minutes, and then Wash Buffer #2 (0.06X SSPE) for 2 minutes at room temperature. The arrays were then dipped briefly in acetronitrile before a final 30 second wash in Agilent Wash 3 Stabilization and Drying Solution, in the hood using a stir plate and stir bar at room temperature.

scan_protocol: Arrays were scanned using an Agilent scanner and the data was extracted using Agilent’s Feature Extraction software.

data_processing: Microarray data were processed and normalized between arrays using Limma package.

organism: Mus musculus

source_name: NOD-ES 4K

label_protocol: Cy3-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 0.5 µg total RNA.

extract_protocol: RNA was isolated from MEF depleted mouse ES line by preplating on gelatin or from mechanically separated EpiSC and EpiSC-like cells lines using the RNeasy Mini Kit (Qiagen).

tag: strain

value: NOD

tag: cell line

value: ES


title: Patient 12, pre-treatment

description: Non-responder

source_name: Biopsy, Patient 12, pre-treatment


title: 129 ES (mESM P8)_1

description: Gene expression in 129 ES (mESM P8)

source_name: 129 ES (mESM P8)

value: non-NOD


title: NOD ES 43 KP/CH

description: Gene expression in NOD ES 43 KP/CH

source_name: NOD ES 43 KP/CH


title: iPS_EpiSC 3M

description: Gene expression in iPS_EpiSC 3M

source_name: iPS_EpiSC 3M

value: EpiSC iPS


title: NOD EpiSC-like ES #1 P9

description: Gene expression in NOD EpiSC-like ES #1 P9

source_name: NOD EpiSC-like ES #1 P9

value: EpiSC-like ES


title: 129 ES (epiESM P8)

description: Gene expression in 129 ES (epiESM P8)

source_name: 129 ES (epiESM P8)


title: 129 ES (mESM P8)_2

description: Gene expression in 129 ES (mESM P8)


title: iPS_EpiSC 1K

description: Gene expression in iPS_EpiSC 1K

source_name: iPS_EpiSC 1K


title: NOD ES 85 KP

description: Gene expression in NOD ES 85 KP

source_name: NOD ES 85 KP


title: NOD EpiSC-like ES #1 P10

description: Gene expression in NOD EpiSC-like ES #1 P10

source_name: NOD EpiSC-like ES #1 P10


title: NOD EpiSC-like ES #1 P5

description: Gene expression in NOD EpiSC-like ES #1 P5

source_name: NOD EpiSC-like ES #1 P5


title: EpiSC P20

description: Gene expression in EpiSC P20

source_name: EpiSC P20

value: EpiSC


title: NOD EpiSC-like iPS #6 P12

description: Gene expression in NOD EpiSC-like iPS #6 P12

source_name: NOD EpiSC-like iPS #6 P12

value: EpiSC-like iPS


title: Astrocytes_GSE_0 ug/ml

city: Kawasaki

first: Shihori

last: Tanabe

state: Kanagawa

address: 3-25-26, Tonomachi, Kawasaki-ku

department: Division of Risk Assessment

country: Japan

institute: National Institute of Health Sciences

description: Gene expression data from primary cultures of hippocampal astrocytes (control)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for aprx. 16 hr at 45C on GeneChip Rat Genome U34A Array. GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip array was scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip operating software (GCOS) version 1.4 using Affymetrix default analysis setting  and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Rattus norvegicus

source_name: Primary cultures of hippocampal astrocytes treated with 0 ug/ml of grape seed extract (GSE)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle protocol from 100 ng total RNA (GeneChip Expression Analysis Technical Manual, 702232 Rev.2, Affymetrix).

growth_protocol: Primary cultures of hippocampal neurons and astrocytes were maintained in DMEM supplementated with 1 mM glutamine, N1 supplement, 10 U/ml penicillin, and 10 ug/ml streptomycin.

extract_protocol: Total RNA extraction was performed using silica-gel-based membrane according to manufacturer's protocol (QIAGEN, RNeasy Mini Kit).

treatment_protocol: The cultures were treated with grape seed extract (GSE) at indicated concentration.

value: Wistar rats


title: NOD EpiSC-like ES #1 P7

description: Gene expression in NOD EpiSC-like ES #1 P7

source_name: NOD EpiSC-like ES #1 P7


title: NOD EpiSC-like iPS #6 P7

description: Gene expression in NOD EpiSC-like iPS #6 P7

source_name: NOD EpiSC-like iPS #6 P7


title: Astrocytes_GSE_10 ug/ml

description: Gene expression data from primary cultures of hippocampal astrocytes treated with 10 ug/ml of GSE

source_name: Primary cultures of hippocampal astrocytes treated with 10 ug/ml of grape seed extract (GSE)


title: Astrocytes_GSE_1 ug/ml

description: Gene expression data from primary cultures of hippocampal astrocytes treated with 1 ug/ml of GSE

source_name: Primary cultures of hippocampal astrocytes treated with 1 ug/ml of grape seed extract (GSE)


title: Astrocytes_GSE_100 ug/ml

description: Gene expression data from primary cultures of hippocampal astrocytes treated with 100 ug/ml of GSE

source_name: Primary cultures of hippocampal astrocytes treated with 100 ug/ml of grape seed extract (GSE)


title: Neurons_GSE_0 ug/ml

description: Gene expression data from primary cultures of hippocampal neurons (control)

source_name: Primary cultures of hippocampal neurons treated with 0 ug/ml of grape seed extract (GSE)


title: Neurons_GSE_1 ug/ml

description: Gene expression data from primary cultures of hippocampal neurons treated with 1 ug/ml of GSE

source_name: Primary cultures of hippocampal neurons treated with 1 ug/ml of grape seed extract (GSE)


title: Patient 14, pre-treatment

description: Non-responder

source_name: Biopsy, Patient 14, pre-treatment


title: EpiSC P12

description: Gene expression in EpiSC P12

source_name: EpiSC P12


title: bortezomib+PBS_4

city: Jacksonville

first: Yan

middle: W.

last: Asmann

address: 4500 San Pablo Road South

institute: Mayo Clinic

hyb_protocol: For each sample, 15 μg of fragmented, biotinylated cRNA was hybridized to a Mouse Genome 430A 2.0 array (Affymetrix Inc.), then washed with buffers of varying stringencies, stained with streptavidin-PE.

scan_protocol: Scanned with a Hewlett-Packard GeneArray Scanner (Hewlett-Packard, Santa Clara, CA). The GeneChip Microarray Suite v4.01 software program (Affymetrix Inc.) was then used to generate data for subsequent analysis.

data_processing: GC-RMA Preprocessing

label: Biotin

source_name: Spleen

label_protocol:
Synthesis and cleaning of double-stranded cDNA followed by synthesis of biotin-labeled cRNA and fragmentation of biotinylated cRNA into 100- to 150-nt fragments were carried out in the Mayo Clinic Advanced Genomics Technology Center core facility, according to protocols
described in the Affymetrix GeneChip Expression Analysis manual (Affymetrix Inc., Santa Clara, CA).

extract_protocol: Trizol, followed by Invitrogen's Rneasy Kit

treatment_protocol: Treated with bortezomib on day -1, and treated with PBS on day 0.

value: HLA-DR3 transgenic mice

value: spleen


title: cut-ligated phenanthroline exponential 4C library biological

status: Public on Apr 08 2009

type: genomic

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description: Fragments interacting with ribosomal enhancer in, Saccharomyces cerevisiae BY4741

hyb_protocol: Hybridisation was performed according to standard Affymetrix protocols. (Gene Chip Whole transcript (WT) double-stranded target assay manual. Part 702179 rev. 3)

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

data_processing: The data were analyzed in two sample comparisons using Tiling Analysis Software 1.1.02, quantile normalized, scaled together. Threshold cut-offs of 99.23%, a maximum gap of 50 and minimum run of 200.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Cut-ligated exponential yeast cells treated with phenanthroline

label_protocol: ds PCR product (7.5 ug) was prepared. DNA was fragmented and end labelled according to the GeneChip WT Double stranded target assay manual for Model Organisms, Single tiling arrays (No amplification) Affymetrix WT Procedures C and D.

growth_protocol: Yeast cells were grown in SC to an OD600 = 0.6. Cells that were treated with phenanthroline were incubated with 150ug ml-1 phenanthroline for 1 hour.

extract_protocol: Amplified samples were purified with a High Pure PCR product purification kit (Roche) and then concentrated through a DNA Clean and Concentrator™ column (Zymo Research). 7.5 ug of each sample was provided for microarray analysis.

treatment_protocol: Chromatin was cross-linked in whole cells through the addition of formaldehyde (2% v/v final) for 10 min at room temperature. Chromatin was extracted from cells using glass beads. Chromatin was digested with MspI (200U, total volume of 100 l, 2 hrs, 37 ºC) before Ligation. Ligation was performed at 16oC for 2 hours. Ligation reactions were stopped and cross links reversed by the addition of 0.2M NaCl, 4mM Tris HCl (pH 7.5), 0.025U Recombinant PCR grade Proteinase K (Roche) and incubation of samples at 65oC (overnight).     Targets interacting with the rDNA enhancer[38] (i.e. the junction between NTS1-2 and ETS2-2, Chromosome XII: 460611…460815) were amplified, by nested inverse PCR using nested primer pairs. PCR reactions (20 ul), contained 2 ul of template, primer (3mM) and 0.65 U of NEB Taq Polymerase. First round PCR conditions were 35 cycles of 98 ºC for 15 s, 59 ºC for 30 s and 72 ºC for 1 min. First round PCR product was diluted 200-fold for use in the second round. Second round PCR conditions were 30 cycles of 95 ºC for 30 s, 59 ºC for 30 s and 72 ºC for 90 s.

tag: phenanthroline treated exponential yeast cells

tag: PCR product amplified from cut-ligated 4C library

source_name: cut (background control) phenanthroline treated exponential 4C library

tag: PCR product amplified from cut 4C library


title: cut-ligated exponential 4C library

source_name: Cut-ligated 4C library prepared from exponential yeast cells untreated

tag: untreated exponential yeast cells

source_name: cut (background control) exponential 4C library


title: bortezomib+SEB_4

treatment_protocol: Treated with bortezomib on day -1, and treated with SEB on day 0.


title: bortezomib+SEB_3


title: PBS+SEB_1

treatment_protocol: Treated with PBS on day -1, and treated with SEB on day 0.


title: PBS+SEB_3


title: PBS+SEB_2


title: PBS+SEB_4


title: bortezomib+SEB_1


title: PBS+PBS_3

treatment_protocol: Mouse treated with PBS on day -1, and treated with PBS on day 0


title: bortezomib+SEB_2


title: bortezomib+PBS_3


title: PBS+PBS_4


title: PBS+PBS_2


title: bortezomib+PBS_2


title: bortezomib+PBS_1


title: PSSM-Horse-44-Pool-Controls-replicate-2

city: EVRY

first: ERIC

last: BARREY

address: 3bis Christophe Colomb

country: France

institute: INSERM-INRA

description: Biological replicate PSSM muscle horse 44 against  the pool of control muscles of sound horses

hyb_protocol: The 5µg of aaRNA were completely vacuum-dried and resuspended in 9µL of coupling buffer and 11µL of dye, the tubes were mixed by vortexing and incubated for 30 minutes in the dark. The reaction was quenched by addition of 0.73 M Hydroxylamine and incubation for 15 minutes in the dark. Excess dye was removed from the labeled aaRNA by purification on a column. Purified labeled aaRNA were subsequently mixed with 10 µg poly (A) RNA, 10 µg yeast tRNA, 10 µg Cot 1 mouse RNA, then precipitated with 0.5 volumes of 7.5 M ammonium acetate and 2.5 volumes of absolute ethanol. After centrifugation at 16,000 x g for 45 minutes to 1 hour at 4°C, the supernatant was removed and the pellet was washed once with 700 µL of 70% ethanol. The samples were centrifuged at 16000 g for 15 minutes at 4°C. The aaRNA pellet was vacuum-dried for 1 minute and then dissolved in 50 µL of the hybridization mix preheated at 50°C: 2 x SSC, 0.1% SDS and 0.1% Salmon sperm DNA. It was mixed by vortexing and incubated in a water bath at 50°C to dissolve the mRNA pellet. Each slide was rehydrated in a humidified chamber for 1 hour at room temperature then dried in a dessicator for 1 hour. The slides were prehybridized in 0.3% Ethanolamine and 0.05 M Na Borate pH9. The slides were plunged 1 minute in water and dried by centrifugation for 7 minutes at 100 x g. The probe was heated for 2 minutes at 100°C and placed between the slide and a cover slip. The arrays were incubated overnight in a water bath at 50°C in a humidified slide chamber and washed in a first solution of 0.1x SSC with 0.1% SDS for 5 minutes followed by two washing steps in 0.1x SSC for 5 minutes each at room temperature, under agitation and safe from the light. The arrays were dried by centrifugation at 100 x g for 7 minutes. The image of fluorescence intensities of Cy3 (532 nm) and Cy5 (635 nm) were scanned separately with the laser scanner (GenePix® 4000B).

scan_protocol: The tiff images (10 µm/pixel) were analyzed using a specific software for microarray image analysis (GenePix® Pro 6.0 software) which allowed locating the spots automatically with manual control and quantifying the fluorescence intensity of each spot. For each microarray, the data output were the fluorescence intensities of all the spots corresponding to each gene. These data were imported in a genomic data analysis software (Gene Spring® software) to normalize the data before filtering and statistical analysis. For each sample (horse), a duplicate analysis (dye-swap) was made and the average fluorescence results were used.

data_processing: Then, all the results were normalized per spot and per microarray by the Lowess regression method in order to remove systematic variations. Finally, for each sample and each gene an expression ratio was obtained:   Ratio = Expression of each PSSM muscle / expression in the reference control muscle   For statistical analysis, a log transformation ratio was used to normalize the distribution.

organism: Equus caballus

source_name: Gluteus-medius-muscle-PSSM-horse

label_protocol: After purification of the amino-modified RNA, monofunctional forms of the Cyanine 3 (Cy3) or Cyanine 5 (Cy5) fluorochrome were coupled to 5 µg of the studied sample and control sample by an indirect method: the ester groups linked to the fluorochromes were bound on the amino-allyl groups incorporated on the RNA during the in vitro transcription. The marked targets were then mixed and hybridized on the same chip for immediate comparison of the two nucleic acid populations. For each sample, a dye-swap (duplicate measurement) was performed to avoid asymmetry of marker affinity (Cy3 and Cy5). The two results were averaged before statistical results.

extract_protocol: Total RNA was extracted from tissues by a phenol-chloroform method (TRIZOL reagent).

value: gluteus medius muscle


title: PSSM-Horse-44-Pool-Controls-replicate-1


title: PSSM-Horse-42-Pool-Controls-replicate-2

description: Biological replicate PSSM muscle horse 42 against  the pool of control muscles of sound horses


title: PSSM-Horse-54-Pool-Controls-replicate-1

description: Biological replicate PSSM muscle horse 54 against  the pool of control muscles of sound horses


title: PSSM-Horse-54-Pool-Controls-replicate-2


title: PSSM-Horse-42-Pool-Controls-replicate-1


title: RNA pool from VOT-E36 cells at 4 days in differentiating conditions

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

description: Gene expression data from 4 cochleas disected from E10.5 Ig-1 +/+ mouse embryos.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse MG_U74Av2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned at 3-mm density with a GeneChip® Scanner 3000 7G 4C (Affymetrix).

data_processing: The data were analyzed with puma package, propagating uncertainty in Microarray data (www.bioconduct.org).

source_name: RNA from VOT-E36 cell line

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

growth_protocol: the cell line was cultured in a chemically defined medium (Ultraculture) with 2 mm l-glutamine, 50 U ⁄ mL c-interferon and human plasma fibronectin at a final concentration of 5–10 lg ⁄ mL.

extract_protocol: Total RNA was prepared with Qiagen RNeasy mini-kits according to the manufacturer’s instructions. cRNA was prepared as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

treatment_protocol: cultured cells form same passage

value: VOT-E36 cells

tag: time point

value: 4 days in differentiating conditions

tag: protocol

value: conditionally immortalized cell lines by a temperaturesensitive variant of the T antigen (tsA58)


title: RNA pool from VOT-E36 cells at 7 days in differentiating conditions

value: 7 days in differentiating conditions


title: 13366466 - A13.3.2 (complemented by TSN1)-NaCl repeat2 vs double mutant A13.3.11-NaCl repeat2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Root transcriptome of the tsn1 tsn2 double mutant

hyb_protocol: 13-NaCl repeat2 Cy5 / 13+NaCl repeat2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: 13-NaCl repeat2

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: root - Media: 0,5xMS 0,5%sucrose 100mM NaCl	 hygrometry: 70%	 Temperature: 22°C	 Light: continuous

extract_protocol: 13-NaCl repeat2:25ug.

treatment_protocol: Name:TSN_FJ_NaClstress - compound based treatment - compound addition,sodium chloride:quantity 100mM time 48hour . Seeds were sown on nylon mesh on 0,5x MS medium (SIGMA) containing 0,5 % w/v sucrose and 1,2 % agar. After stratification for 48h at 4degre Celsius in the dark, plates were placed in the growth chamber for 5 days before transferring seedlings to the same medium containg 100mM NaCl. Seedlings were harvested at day 7.

tag: line

value: arabidopsis thaliana (col x ws)  mutant (tsn1-/- tsn2-/-)

tag: development stage

value: (boyes et al. plant cell 2001):boyes = 1.0

value: root

source_name: 13+NaCl repeat2

extract_protocol: 13+NaCl repeat2:25ug.

value: arabidopsis thaliana (col x ws)  mutant (tsn1-/- tsn2-/- ; ectopic tsn1+/+)


title: RNA pool from VOT-E36 cells at 1 day in differentiating conditions

value: 1 day in differentiating conditions


title: 13366332 - A13.3.2 (complemented by TSN1)-NaCl repeat1 vs double mutant A13.3.11-NaCl repeat1

hyb_protocol: 13-NaCl repeat1 Cy5 / 13+NaCl repeat1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 13-NaCl repeat1

extract_protocol: 13-NaCl repeat1:25ug.

source_name: 13+NaCl repeat1

extract_protocol: 13+NaCl repeat1:25ug.


title: Neurons_GSE_10 ug/ml

description: Gene expression data from primary cultures of hippocampal neurons treated with 10 ug/ml of GSE

source_name: Primary cultures of hippocampal neurons treated with 10 ug/ml of grape seed extract (GSE)


title: 13366335 - A10.9.5 (complemented by TSN2) repeat2 vs double mutant A10.9.3- repeat2

hyb_protocol: 10- repeat2 Cy5 / 10+ repeat2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 10- repeat2

growth_protocol: root - Media: 0,5xMS 0,5%sucrose	 hygrometry: 70%	 Temperature: 22°C	 Light: continuous

extract_protocol: 10- repeat2:25ug.

treatment_protocol: no treatment

source_name: 10+ repeat2

extract_protocol: 10+ repeat2:25ug.

value: arabidopsis thaliana (col x ws)  mutant (tsn1-/- tsn2-/- ; ectopic tsn2+/+)


title: PSSM-Horse-38-Pool-Controls-replicate-2

description: Biological replicate PSSM muscle horse 38 against  the pool of control muscles of sound horses


title: 13366465 - double mutant A13.3.11-NaCl repeat2 vs A13.3.2 (complemented by TSN1)-NaCl repeat2

hyb_protocol: 13+NaCl repeat2 Cy5 / 13-NaCl repeat2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PSSM-Horse-32-Pool-Controls-replicate-2

description: Biological replicate PSSM muscle horse 32 against  the pool of control muscles of sound horses


title: 13366339 - double mutant A13.3.11-NaCl repeat1 vs A13.3.2 (complemented by TSN1)-NaCl repeat1

hyb_protocol: 13+NaCl repeat1 Cy5 / 13-NaCl repeat1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PSSM-Horse-12-Pool-Controls-replicate-1

description: Biological replicate PSSM muscle horse 12 against  the pool of control muscles of sound horses


title: TtT/GF - 10µM NECA (5/-N-ethylcarboxamidoadenosine) 120mins - 2

city: Cardiff

first: jack

last: ham

address: Heath Park

department: Centre for Endocrine and Diabetes Sciences

institute: Cardiff University

description: Mouse TtT/GF cells treated with 10µM NECA (5/-N-ethylcarboxamidoadenosine) for 120mins - Replicate 2

hyb_protocol: 10 μg fragmented cDNA was then hybridised overnight to the murine MG_U74A v2 GeneChip

scan_protocol: GeneChips were scanned using the Agilent Gene Array Scanner controlled by Microarray Suite 5.0

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling (TGT 100) as normalization method.

source_name: Folicullostellate cell line TtT/GF

label_protocol: 10 μg RNA was used to generate double-stranded cDNA by using a T7-linked oligo(dT) primer. Biotinylated cRNA was synthesised using the T7 RNA transcript labelling kit (Enzo Diagnostics, Farmingdale NY, USA)

growth_protocol: TtT/GF cells were cultured in 2% (v/v) heat-inactivated (HI) FBS (fetal bovine serum).

extract_protocol: RNA was extracted using TriZol reagent performed according to the manufacturer's instructions.

tag: cell type

value: TtT/GF cells

tag: agent

tag: time

tag: replicate


title: RNA pool from VOT-E36 cells at proliferating conditions

value: proliferating conditions


title: PSSM-Horse-38-Pool-Controls-replicate-1

tag: tissue


title: TtT/GF - 10µM NECA (5/-N-ethylcarboxamidoadenosine) 120mins - 1

description: Mouse TtT/GF cells treated with 10µM NECA (5/-N-ethylcarboxamidoadenosine) for 120mins - Replicate 1


title: 13366463 - double mutant A10.9.3- repeat2 vs A10.9.5 (complemented by TSN2) repeat2

hyb_protocol: 10+ repeat2 Cy5 / 10- repeat2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: PBS+PBS_1


title: PSSM-Horse-32-Pool-Controls-replicate-1


title: PSSM-Horse-5-Pool-Controls-replicate-1

description: Biological replicate PSSM muscle horse 5 against  the pool of control muscles of sound horses


title: 13366166 - A10.9.5 (complemented by TSN2) repeat1 vs double mutant A10.9.3- repeat1

hyb_protocol: 10- repeat1 Cy5 / 10+ repeat1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 10- repeat1

extract_protocol: 10- repeat1:25ug.

source_name: 10+ repeat1

extract_protocol: 10+ repeat1:25ug.


title: RNA pool from VOT-E36 cells at 2 days in differentiating conditions

value: 2 days in differentiating conditions


title: 13366165 - double mutant A10.9.3- repeat1 vs A10.9.5 (complemented by TSN2) repeat1

hyb_protocol: 10+ repeat1 Cy5 / 10- repeat1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366164 - A13.3.2 (complemented by TSN1) repeat2 vs double mutant A13.3.11- repeat2

hyb_protocol: 13- repeat2 Cy5 / 13+ repeat2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 13- repeat2

extract_protocol: 13- repeat2:25ug.

source_name: 13+ repeat2

extract_protocol: 13+ repeat2:25ug.


title: RNA pool from VOT-E36 cells at 14 days in differentiating conditions

value: 14 days in differentiating conditions


title: PSSM-Horse-12-Pool-Controls-replicate-2


title: TtT/GF - 10µM NECA (5/-N-ethylcarboxamidoadenosine) 30mins - 1

description: Mouse TtT/GF cells treated with 10µM NECA (5/-N-ethylcarboxamidoadenosine) for 30mins - Replicate 1


title: PSSM-Horse-5-Pool-Controls-replicate-2


title: HEK293 in low glucose #2

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description: Gene expression data from cells cultivated in low glucose

hyb_protocol: For hybridization, 15 µg of fragmented cRNA were incubated with the chip (Human Genome U133 Plus 2.0 Array) in 200 µl of the hybrization solution in a Hybridization Oven 640 (Affymetrix) for 16 h at 45 °C. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual (Rev. 5).

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

data_processing: The signals were processed using Affymetrix GeneChip Operating Software (GCOS; v.1.4; Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 200.

source_name: Human embryonic kidney cells (HEK293) cultivated for 7 days in DMEM containing low (100 mg/dl) glucose.

label_protocol: Biotinylated cRNA were prepared according to the protocol of the manufacturer (Affymetrix; GeneChip Expression Analysis Technical Manual; Rev. 5).

growth_protocol: Human embryonic kidney (HEK293) cells were grown for 7 days in DMEM (supplemented with 10 % FCS) containing 450 mg/dl glucose (high glucose) or 100 mg/dl glucose (low glucose).

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

value: HEK 293

tag: glucose concentration

value: low glucose (100 mg/dl)


title: TtT/GF - 10µM NECA (5/-N-ethylcarboxamidoadenosine) 120mins - 3

description: Mouse TtT/GF cells treated with 10µM NECA (5/-N-ethylcarboxamidoadenosine) for 120mins - Replicate 3


title: 13365869 - A13.3.2 (complemented by TSN1) repeat1 vs double mutant A13.3.11- repeat1

hyb_protocol: 13- repeat1 Cy5 / 13+ repeat1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 13- repeat1

extract_protocol: 13- repeat1:25ug.

source_name: 13+ repeat1

extract_protocol: 13+ repeat1:25ug.


title: 13365883 - double mutant A13.3.11- repeat1 vs A13.3.2 (complemented by TSN1) repeat1

hyb_protocol: 13+ repeat1 Cy5 / 13- repeat1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HEK293 in low glucose #1


title: TtT/GF - no treatment - 3

description: Mouse TtT/GF cells no treatment - Replicate 3

value: no treatment


title: HEK293 in high glucose #1

description: Gene expression data from cells cultivated in high glucose

source_name: Human embryonic kidney cells (HEK293) cultivated for 7 days in DMEM containing high (450 mg/dl) glucose.

value: high glucose (450 mg/dl)


title: TtT/GF - no treatment - 1

description: Mouse TtT/GF cells no treatment - Replicate 1


title: HEK293 in high glucose #2


title: SAGE_IPF_11

status: Public on Apr 07 2009

type: SAGE

anchor: NlaIII

city: Research Triangle Park

first: Kathy

last: Boon

state: NC

address: 111 TW Alexander Dr

department: Division of Intramural Research

institute: NHLBI/NIEHS

description: SAGE library generated from lung biopsy sample

data_processing: The SAGE 2000 software version 4.12 (available at http://www.sagenet.org) was used to extract SAGE tags from the original sequence files and remove duplicate ditags.

source_name: Lung biopsy

extract_protocol: Total RNA was extracted from frozen lung tissue using the RNAgents total RNA isolation system (Promega, Madison, WI, USA)

tag: Gender

value: male

tag: Age

tag: Tissue

value: lung


title: 13366162 - double mutant A13.3.11- repeat2 vs A13.3.2 (complemented by TSN1) repeat2

hyb_protocol: 13+ repeat2 Cy5 / 13- repeat2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: SAGE_IPF_12


title: SAGE_NT29

source_name: Normal lung

value: normal lung parenchyma, 17 year old male, non-smoker


title: SAGE_NT12

value: normal lung parenchyma, 69 year old male, non-smoker


title: TtT/GF - no treatment - 2

description: Mouse TtT/GF cells no treatment - Replicate 2


title: SAGE_IPF_8


title: SAGE_IPF_9


title: SAGE_IPF_6


title: SAGE_IPF_1


title: TtT/GF - 10µM NECA (5/-N-ethylcarboxamidoadenosine) 30mins - 2

description: Mouse TtT/GF cells treated with 10µM NECA (5/-N-ethylcarboxamidoadenosine) for 30mins - Replicate 2


title: SAGE_IPF_7


title: Control Caco2A

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

description: Adenocarcinoma control

hyb_protocol: 0.85 microgram of biotin-labeled cRNA was hybridized to Illumina Mouse Ref-8 BeadChips at 55 °C overnight. BeadChips were incubated with Cy3 streptavidin and washed according to the manufacturer’s protocol.

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan confocal scanner and Illumina BeadStudio version 1.5.13

data_processing: Scan outputs were analyzed with Illumina BeadStudio version 1.5.13  without normalization

source_name: Caco-2 cell line, control

label_protocol: Five hundred ng of total RNA was reverse transcribed and amplified overnight with T7 RNA polymerase and labeled with biotin following the manufacturer’s protocol.

growth_protocol: Growth to 70% confluency in D-MEM supplemented with  10% FBS and amino acids.

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).

treatment_protocol: None.

tag: Colon cancer adenocarcinoma cell line control.


title: Ki-Ras transformed CacoK15B

description: Rapidly growing colon cancer cell line.

data_processing: Scan outputs were analyzed with Illumina BeadStudio version 1.5.13, without normalization

source_name: Caco-2 cell line Ki-Ras-transformed

tag: Colon cancer adenocarcinoma cell line transformed to express Ki-RASV12


title: TtT/GF - 10µM NECA (5/-N-ethylcarboxamidoadenosine) 30mins - 3

description: Mouse TtT/GF cells treated with 10µM NECA (5/-N-ethylcarboxamidoadenosine) for 30mins - Replicate 3


title: Control Caco2B

description: Adenocarcinoma control

data_processing: Scan outputs were analyzed with Illumina BeadStudio version 1.5.13 without normalization


title: SAGE_IPF_10

value: female


title: SAGE_IPF_2


title: SAGE_IPF_4


title: Ki-Ras transformed CacoK15A

description: Rapidly growing colon cancer cell line.

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan confocal scanner and Illumina's BeadStudio version 1.5.13


title: SE_induction_C15_4days_with_Yariv-treatment

status: Public on Apr 06 2009

city: Villeneuve d'Ascq

first: Anca

last: Lucau

address: Cité Scientifique

department: Biology

institute: University Lille 1

description: Artefactual, saturated, or low-signal spots were eliminated from the analysis and the background subtracted median intensities used for calculations.

hyb_protocol: 14-18 h hybridization (DigEasy hybridization buffer; Roche) at 42°C in a Corning chamber. Slides were washed successively in 4x, 2x (with SDS 0.1x), 0.2x, and 0.1x SSC.

scan_protocol: Images were acquired with a GenePix4000B scanner and analyzed with GenePix Pro 6.0 (Axon Downingtown, PA, USA) software.

data_processing:
For each slide a global lowess followed by a print-tip median normalization was performed using R (http://cran.r-project.org/) packages as implemented in Goulphar (Lemoine et al. 2006). Expression values for replicated spots on the array were averaged. In order to exclude possible dye effects, all probes exhibiting an opposite behaviour in the swapped-dye experiment were eliminated from the final analysis. For missing value handling, gene expression patterns with more than two missing values (33%) were excluded from subsequent analysis. The remaining missing values were replaced by using the KNN-imputation method (Troyanskaya et al. 2001). The SAM (Tusher et al. 2001) was used to identify differentially expressed genes over different conditions. We fixed the false discovery rate at 5% using the 90th percentile of falsely called genes. Only genes with smooth expression profiles over repetitions were retained.
The VALUE column reports the averaged results of the replicas [log2(CH1/CH2) ratios].

organism: Cichorium intybus

source_name: leaf explants of C15D4_with_Yariv

label_protocol: Ten μg of total RNA were used for each experiment. Reverse transcription and fluorochrome incorporation were performed in a MJ PTC-200 Peltier Thermal Cycler, using oligo-dT (Roche), the Superscript II Kit (Invitrogen) and CY3- and CY5-labelled d-CTP (Amersham). The QIAquick PCR Purification Kit (Qiagen) was used for target purification.

growth_protocol: 4 days of culture at 35°C in obscurity with orbital shaking

extract_protocol: Total RNA was extracted using a Tri reagent kit (Euromedex) and purified with the RNeasy MinElute kit (Qiagen). RNA integrity was checked by capillary electrophoresis (Agilent 2100 Bioanalyser, Agilent technologies).

treatment_protocol: Leaf explants were excised from 2-months-old in vitro plantlets and placed in 20 mL SE induction medium (Belettre et al. 2001) containing 250 µM B-Glc Yariv reagent. Twelve plants of each genotype were used per replica.

value: leaf explants

tag: genotype

value: cultured 4 days

value: somatic embryogenesis induction in presence of Yariv reagent (Y+)

source_name: leaf explants of C15D4 without Yariv

treatment_protocol: Leaf explants were excised from 2-months-old in vitro plantlets. Twelve plants of each genotype were used per replica.

value: somatic embryogenesis induction in absence of Yariv reagent (Y-)


title: Ha-Ras transformed CacoH2A

source_name: Caco-2 cell line Ha-Ras-transformed

tag: Colon cancer adenocarcinoma cell line transformed to express Ha-RASV12


title: Ha-Ras transformed CacoH2B

description: Rapidly growing colon cancer cell line with EMT phenotype


title: SAGE_IPF_3


title: K59_D0_vs_C15_D0

source_name: leaf explants of K59DO

growth_protocol: no culture in SE induction medium and no treatment

value: no induction

source_name: leaf explants of C15D0


title: SE_induction_K59_4days

data_processing:
For each slide a global lowess followed by a print-tip median normalization was performed using R (http://cran.r-project.org/) packages as implemented in Goulphar (Lemoine et al. 2006). Expression values for replicated spots on the array were averaged. In order to exclude possible dye effects, all probes exhibiting an opposite behaviour in the swapped-dye experiment were eliminated from the final analysis. For missing value handling, gene expression patterns with more than two missing values (33%) were excluded from subsequent analysis. The remaining missing values were replaced by using the KNN-imputation method (Troyanskaya et al. 2001). The SAM (Tusher et al. 2001) was used to identify differentially expressed genes. We fixed the false discovery rate at 5% using the 90th percentile of falsely called genes. Only genes with smooth expression profiles over repetitions were retained.
The VALUE column reports the averaged results of the replicas [log2(CH1/CH2) ratios].

source_name: leaf explants of K59D4

label_protocol: Ten μg of total RNA were used. Reverse transcription and fluorochrome incorporation were performed in a MJ PTC-200 Peltier Thermal Cycler, using oligo-dT (Roche), the Superscript II Kit (Invitrogen) and CY5-labelled d-CTP (Amersham). The QIAquick PCR Purification Kit (Qiagen) was used for target purification.

treatment_protocol: Leaf explants were excised from 2-months-old in vitro K59 plantlets and placed in 20 mL SE induction medium (Belettre et al. 2001). Twelve plants were used per replica.

value: somatic embryogenesis induction

source_name: leaf explants of K59D0

growth_protocol: no culture in SE induction medium.

treatment_protocol: Leaf explants were excised from 2-months-old in vitro K59 plantlets. Twelve plants were used per replica.


title: SE_induction_K59_4days_with_Yariv-treatment

source_name: leaf explants of K59D4_with_Yariv

source_name: leaf explants of K59D4 without Yariv


title: Crypt part of rats jejunum villi

status: Public on Apr 05 2009

city: Shizuoka

first: Toshinao

last: Goda

address: 52-1 Yada, suruga-ku

department: Department of Nutrition

institute: University of Shizuoka

description: The entire small intestine was removed, and the region extending from the pylorus to the ligament of Treitz was discarded. The jejunoileum was divided into three segments of equal length. The proximal one-third (jejunum) of the jejunoileum was flushed with ice cold diethylpyrocarbonate (DEPC) in 0.154 mol/L NaCl solution. A segment was excised from the middle region of the jejunal segment for total RNA extraction. This segment was opened longitudinally and flattened on a glass slide, serosal-side down, and immediately frozen in liquid nitrogen. For RNA extraction, frozen tissue blocks of approximately 7×7 mm2 were covered with a supporting medium (OCT Compound, Miles laboratories, IN, USA) and then transferred serosal-side down to a pre-flattened supporting surface of 1 g/L of agar inside a cryostat at -18°C. Transverse sections of 10 µm thickness were taken through the submucosa into the muscular layer, as described previously. At various depths on the villus-crypt unit, one section was attached to a microscope slide for inspection of the presence of the villus and the crypt architecture after staining with 3 g/L of methylene blue. Frozen tissue sections (10 µm section ×10) were collected (100  m as one fractionation). Typically, the villus-crypt column was divided into seven fractions, three of which were used for further analysis; the first fraction from the top of the villi was labeled "top of the villi", the fourth fraction from the top of the villi was labeled "middle of the villi", and the sixth fraction from the top of the villi was labeled "crypt".

hyb_protocol: Aliquots of Cy3 or Cy5-labeled cRNA of several fractions were separately hybridized to Agilent Rat Oligo Microarrays (22.5 K) according to the manufacturer's hybridization protocol.

scan_protocol: Scanned on Scan Array Lite (PerkinElmer). Images were quantified using Scan Array Express (PerkinElmer).

data_processing: Data analysis was performed using ScanArray Express (PerkinElmer) and Excel (Microsoft). Cy3 or Cy5 values were corrected by Cy3 median value of Top of villi and represented as Ch1_log2 and Ch2_log2, respectively. Variability spots were removed by algorism in ScanArray express, and less-than-or-equal-to 2 signal/noise ratio in the spots in base 2 logarithms was removed. After removing variability spots, signals between Cy3- and Cy5-labeling did not differ, indicating high reproducibility of the microarray analyses. Normalization of Cy3 or Cy5 signals was carried out by global median normalization. Data was averaged for each signal of Cy3 and Cy5 and represented by base 2 logarithms.  Specifically, Sample VALUEs (signals) = Average (Ch1_log2, Ch2_log2)-2*SD (Ch1_log2, Ch2_log2).

label: Cy3, Cy5

source_name: Crypt part of jejunum villi

label_protocol: Total RNA was labeled using the Agilent Linear Amplification/Labeling Kit according to the instructions of manufacturer.

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

value: Crypt part of villi of jejunum

tag: age

value: six-weeks-old

tag: gender

tag: strain

value: Sprague-Dawley


title: Middle part of rats jejunum villi

source_name: Middle part of jejunum villi

value: Middle part of villi of jejunum


title: Top part of rats jejunum villi

source_name: Top part of jejunum villi

value: Top part of villi of jejunum


title: Artery_atherosclerotic_rep3

status: Public on Apr 04 2009

city: COPENHAGEN

first: Silvio

last: Zaina

address: Blegdamsvej 9

department: Clinical Biochemistry

country: Denmark

institute: Rigshospitalet

hyb_protocol: The hybridization was performed on the Advalytix SlideBooster™ (Advalytix, Germany) using AdvaHybC hybridization solution, incubated at 42°C for 16 hours.

scan_protocol: The slides were scanned on the Agilent G2565BA scanner and quantified using GenePix v.3.0.

data_processing: Intensity-based normalization was performed. Background-subtracted Alexa647 intensity was normalized to overall median Alexa555 intensity calculated on all arrays, and log2 ratio (Alexa647/Alexa555) was calculated.

label: Alexa 647 (red)

source_name: Methylated (filtered) genomic DNA from Atherosclerotic artery

label_protocol: Samples were labeled with amino-allyl-dUTP, coupled to alexa dyes, following the Bioprime Plus Array CGH Indirect Genomic labeling system protocol, the labeled probes were then purified and hybridized to human 15K CpG microarrays at the UHN microarray center, Toronto, Canada.

extract_protocol: Genomic DNA was prepared with DNeasy (Qiagen). DNA was pooled to equally represent every sample within either group (i.e. normal and atherosclerotic arteries) and filtered to eliminate the unmethylated fraction according to Shann et al. Genome Res. 2008;18:791-801. Mock digestions were performed to prepare unfiltered, reference DNA. Samples were amplified by WGA (Sigma) and primers were eliminated using ExcelaPure 96-well UF plates (EdgeBio).

treatment_protocol: Atherosclerotic arteries: obtained from revascularization surgery of coronary arteries with obstructive atherosclerotic lesions; normal arteries: aortic tissue adjacent to valve, obtained from aortic valve replacement surgery in subject with no evidence of coronary atherosclerosis by cardiac catheterism and examination during surgery.

value: 22-79 years, p>0.05 between the two groups

tag: sex

value: mixed, 50% each in both groups

tag: atherosclerotic lesion stage

value: advanced, ischemic cardiopathy requiring bypass

label: alexa 555 (green)

source_name: undigested (reference) DNA from Atherosclerotic artery

value: 22-79 años, p>0.05 between the two groups


title: SAGE_IPF_5

source_name: Lung biopsy

value: lung


title: Artery_atherosclerotic_rep2


title: Artery_normal_rep3

source_name: Methylated (filtered) genomic DNA from Normal artery

source_name: undigested (reference) DNA from Normal artery


title: Artery_normal_rep2


title: SE_induction_C15_4days

source_name: leaf explants of C15D4

treatment_protocol: Leaf explants were excised from 2-months-old in vitro plantlets and placed in 20 mL SE induction medium (Belettre et al. 2001). Twelve plants of each genotype were used per replica.

tag: protocol

growth_protocol: no culture in SE induction medium


title: Artery_atherosclerotic_rep1


title: Transcriptional profiling of the drug-resistant mycobacterium tuberculosis clinical isolates

city: Beijing

first: Zhaogang

last: Sun

state: Beijing

address: No. 97, Machang Road, Tongzhou District

department: Microbiology and Immunology

country: China

institute: Beijing Tuberculosis & Thotacic Tumor research Institute

description: the bacilli were inoculated on the L-J slant and then cultured in Middlebrook 7H9 plus OADC into log phage,and harvested for total RNA .

hyb_protocol: 1. Add the following to the 5µl labeled sample.    i. 0.5µl 10 mg/ml tRNA  ii. 1.0µl 20X SSC  iii. 2.5ul Formamide  iv. 1.0µl 1% SDS     2. Heat to 98 oC for 2 minutes. Spin in centrifuge for 1 min at 12,000 Xg.  Let cool for 5 min.  3. Pipette cooled 10µl hybridization solution on microarray.  Apply 22 x 22 coverslip to cover array (if bubbles appear under the cover slip, they will slowly migrate to the edges provided that the volume is accurate).   4. OPTIONAL:  Apply thin wall of rubber cement around the 4 corners of the coverslip to avoid movement.  This step is recommended if your waterbath is not perfectly level.    5. Hybridize in standard hyb. chambers with ~40µl water under each slide (20ul under both ends of each slide) overnight in 50oC water bath    6. Remove cover slip while array is submerged in first wash solution (2XSSC + 0.1% SDS), transfer to submerged microscope slide staining racks and rinse for 1 min in 1X SSC+0.05% SDS with agitation/shaking.     7. Rinse in 0.06X SSC with shaking. Transfer to another submerged staining rack and wash 2 min in fresh 0.06X SSC with shaking.    8. Centrifuge 3 min at 1000 rpm in a 50ml conical (array edge up) to dry.  Scan immediately.

scan_protocol: the Mycobacterium whole Genome Array fluorescence intensities of Cy3 and Cy5 dyes at each spot were scanned and quantified by double tunnel laser scanning LuxScan 10KA (CapitalBio)

data_processing: The gene expression scanning data were analyzed by the program LuxScan 3.0 (CapitalBio).The gene-expression data from the microarray test were further analyzed using Michiel de Hoon’s Cluster and TreeView programs.

organism: Mycobacterium tuberculosis

source_name: mycobacterium tuberculosis clinical isolates in China

label_protocol: 1. Bring 1.5µg of RNA to a volume of 11µl (in a PCR tube) with nucleotide-free water and add 2.2µl (2mg/ml) random primers (pulse spin to collect contents).  2. Heat 2 min at 98oC, snap cool on ice.  3. (Keep on ice) and add 11.1µl of the following reaction mix:   5.0µl 5X First-Strand buffer    2.5µl 100 mM DTT       2.3µl low dTdNTP mix (5mM A,G,C and 0.2mM T stock)   1.5ul Cy3 or Cy5     Then add 1.2ul Superscript, vortex to mix and spin to collect contents    4. Incubate 10 min at 25oC followed by 90 min at 42oC in PCR machine.    **Can freeze or leave at 4oC overnight if necessary    5. Prime a microcon10 column (YM10 from Millipore) with 400µl TE and spin for 10 min at 10,000 Xg.  Empty flow-through in collection tube and return primed column.  Add both reactions (cy3 and cy5) to column and centrifuge at 10,000 Xg until ~25µl remaining (~20-30 min).  Wash with 200µl TE and spin until almost dry (<5µl).  6. Recover cDNA by inverting microcon into new collection 1.5 ml tube and centrifuge at half max speed 1 min.  7. Bring sample to 5µl with TE.

growth_protocol: the bacilli were first inoculated on the L-J slant and then further cultured in Middlebrook 7H9 plus OADC mid-exponential phase (OD600 0.4–0.5) at 37 uC with shaking,and harvested for total RNA .

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

treatment_protocol: Total RNA was isolated using TRIzol LS Reagent (Invitrogen) according to the manufacturer’s  instruction,except for the ultrasonating to disrupt the mycobacteria.

value: extensively drug-resistant strains from clinic

value: drug-sensitive strains from clinic


title: Endometrium, mild negative energy balance_UCIC1106

city: Hatfield

first: Zhangrui

state: Hertfordshire

address: Hawkshead Lane

department: Production and Population Health

institute: Royal Veterinary College

description:
Gene expression data of endometrial tissue from mild negative energy balance cow
Multiparous Holstein-Friesian cows with a mean parity of 4.7 and an average previous lactation yield of 6,477 ± 354 kg were used. Cows were blocked two weeks prior to expected calving according to parity, body condition score and previous yield and randomly allocated to 2 treatments designed to produce mild (n=5) or severe NEB (n=6).

hyb_protocol: Based on the established ARK-Genomics protocols (http://www.ark-genomics.org/protocols).

scan_protocol: GeneChips were scanned using Affymetrix 3000 7G, Fluidics station.

data_processing: CHP files were not used for data analysis. The CEL files were processed using S+ArrayAnalyzer 2.1 (Insightful Corporation, Seattle, Washington). The raw data were summarized using Robust Multichip Analysis (RMA) with a primary Quantile normalization. The summarized data were further normalized with a Median Inter-quartile Range (IQR).

organism: Bos taurus

source_name: Endometrium from cow 1106 with mild negative energy balance

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

treatment_protocol: From day 2 after calving mild (MNEB) cows were fed ad lib grass silage with 8 kg/day of a 21% crude protein dairy concentrate and milked x1 daily; severe (SNEB) cows were fed 25 kg/day silage with 4 kg/day concentrate and milked x3 daily. The chemical composition of silage and concentrate offered (as previously described (53)) was the same across treatment groups. Daily measurements of milk yield, milk composition, dry matter intake (DMI), body weight, and dietary energy intake were used to calculate EB, based on the French net energy for lactation (NEL) system. Net EB was calculated as UFL/day in which 1 unité fourragère lait (UFL) is the NEL equivalent of 1 kg of standard air-dry barley as described previously (29). Samples of uterine endometrium were collected from all cows following slaughter at 14 ± 0.4 days postpartum.

value: uterine endometrial tissue

value: Holstein-Friesian cow, black and white

value: 4.7 lactations


title: Endometrium, severe negative energy balance_UCIC231

description:
Gene expression data of endometrial tissue from severe negative energy balance cow
Multiparous Holstein-Friesian cows with a mean parity of 4.7 and an average previous lactation yield of 6,477 ± 354 kg were used. Cows were blocked two weeks prior to expected calving according to parity, body condition score and previous yield and randomly allocated to 2 treatments designed to produce mild (n=5) or severe NEB (n=6).

source_name: Endometrium from cow 231 with severe negative energy balance

label_protocol: Based on the established ARK-Genomics protocols (http://www.ark-genomics.org/protocols).


title: Day10 50mg

city: Daejon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

description: Day10 normal level

hyb_protocol: Labeled cRNA (750 ng) were hybridized to a Mouse-8 Expression BeadChip for 16-18 h at 58 °C, according to the manufacturer's instructions (Illumina).

scan_protocol: Following attachment of Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences), arrays were scanned with an Illumina bead array reader.

data_processing: Signal intensities of genes were normalized by the quantile method.

source_name: brain

label_protocol: Total RNA was amplified and purified to yield biotinylated cRNA using an Ambion Illumina RNA amplification kit (Ambion).

growth_protocol: Mice were maintained for two weeks prior to the experiment in a controlled environment of 22 ± 2 °C with a 12 h dark/light cycle.

extract_protocol: Total RNA from the brain tissue was isolated using TriPure Isolation Reagent according to the manufacturer's instructions (Roche Applied Science).

treatment_protocol: Aqueous extracts of Ephedra herba were administered orally at dosage of 50 or 1,250 mg/kg once daily for 1, 3 and 10 consecutive days.

tag: treatment time

tag: dose

value: Five-week-old

value: female

tag: agent

value: aqueous extracts of Ephedra herba


title: Artery_normal_rep1


title: THP-1-DS-TB-18h-rep2

description: Biological replicate 2 of 3. THP-1 cells infected with DS-TB were tested, with the THP-1 cells treated with PBS as control.

hyb_protocol: 1. Add the following to the 5µl labeled sample.  0.5µl 10 mg/ml tRNA  1.0µl 20X SSC  2.5ul Formamide  1.0µl 1% SDS     2. Heat to 98 oC for 2 minutes. Spin in centrifuge for 1 min at 12,000 Xg.  Let cool for 5 min.  3. Pipette cooled 10µl hybridization solution on microarray.  Apply 22 x 22 coverslip to cover array (if bubbles appear under the cover slip, they will slowly migrate to the edges provided that the volume is accurate).  4. Hybridize in standard hyb. chambers with ~40µl water under each slide (20ul under both ends of each slide) overnight in 50oC water bath

scan_protocol: the 22K Human Genome Array fluorescence intensities of Cy3 and Cy5 dyes at each spot were scanned and quantified by double tunnel laser scanning LuxScan 10KA (CapitalBio)

source_name: THP-1 cells,infected with DS-TB of A36, 4h

growth_protocol: THP-1 cells were subcultured every third day for an initial density of 2 X 105 cells/ml. Prior to plating of the cell lines, viability was assessed by trypan blue exclusion staining. THP-1 cells were differentiated into adherent, well spread macrophages by the addition of 100 nM phorbol myristate acetate (PMA) and maintained for 3 days at 37°C, 5% CO2.

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

treatment_protocol: The adherent cells were washed twice prior to the addition of XDR-TB or DS-TB at an MOI of 10. The bacteria and the cells were then gently rocked for 4h at 37°C, 5% CO2, and then the bacteria not associated with the cells were removed by repeated washing of the monolayers with binding medium. The infected THP-1 cells were collected for toatal RNA after further culture for 18h.

tag: cell line

value: human macrophage-like cell line THP-1

tag: infection

value: DS-TB of A36, 4h

source_name: THP-1 cells without any infection by mycobacterium tuberculosis


title: Day3 50mg

description: Day3 normal level


title: Endometrium, severe negative energy balance_UCIC3156

source_name: Endometrium from cow 3156 with severe negative energy balance

tag: tissue


title: Day10 1250mg

description: Day10 high level


title: Day1 50mg

description: Day1 normal level


title: Endometrium, severe negative energy balance_UCIC214

source_name: Endometrium from cow 214 with severe negative energy balance


title: Endometrium, severe negative energy balance_UCIC2463

source_name: Endometrium from cow 2463 with severe negative energy balance


title: Endometrium, severe negative energy balance_UCIC51

source_name: Endometrium from cow 51 with severe negative energy balance


title: Endometrium, severe negative energy balance_UCIC11

source_name: Endometrium from cow 11 severe negative energy balance


title: Day1 1250mg

description: Day1 high level


title: Day3 1250mg

description: Day3 high level


title: Endometrium, mild negative energy balance_UCIC330B

source_name: Endometrium from cow 330B with mild negative energy balance


title: THP-1-DS-TB-18h-rep1

description: Biological replicate 1 of 3. THP-1 cells infected with DS-TB were tested, with the THP-1 cells treated with PBS as control.


title: Endometrium, mild negative energy balance_UCIC3110

source_name: Endometrium from cow 3310 with mild negative energy balance


title: Untreated control

description: control

value: Untreated

value: none, control


title: Endometrium, mild negative energy balance_UCIC245

source_name: Endometrium from cow 245 with mild negative energy balance


title: Endometrium, mild negative energy balance_UCIC109B

source_name: Endometrium from cow 109B with mild negative energy balance


title: THP-1-XDR-TB-18h-rep2

description: Biological replicate 2 of 3. THP-1 cells infected with XDR-TB were tested, with the THP-1 cells treated with PBS as control.

source_name: THP-1 cells,infected with XDR-TB of B42, 4h

value: XDR-TB of B42, 4h


title: THP-1-XDR-TB-18h-rep1

description: Biological replicate 1 of 3. THP-1 cells infected with XDR-TB were tested, with the THP-1 cells treated with PBS as control.


title: siCypB.PRL2

status: Public on Apr 03 2009

city: Chicago

first: Feng

last: Fang

state: IL

address: 303 E Superior St Lurie 4-225

department: Department of Pathology

institute: Northwestern University

description: The pHIV-7/Puro vectors (si-Luc to target luciferase gene and si-CypB to target CypB gene) were used to generate stable cell lines. Cells were treated with or without prolactin (PRL, 100ng/ml) for 2 hours.

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 1.5.11). It was vst transformed and rsn normalized.

source_name: T47D breast cancer cells - si-CypB - treated with prolactin

label_protocol: standard as recommended by illumina

extract_protocol: RNA was isolated using Qiagen RNeasy Micro Kit (Qiagen).

tag: cell type

value: T47D breast cancer cells stably overexpressing CypB small interfering siRNA


title: siCypB.PRL3


title: siCypB.PRL1


title: siLuc.PRL2

source_name: T47D breast cancer cells - si-Luc - treated with prolactin

value: T47D breast cancer cells stably overexpressing luciferase small interfering siRNA


title: siLuc.PRL3


title: siCypB2

description: The pHIV-7/Puro vectors (si-Luc to target luciferase gene and si-CypB to target CypB gene) were used to generate stable cell lines

source_name: T47D breast cancer cells - si-CypB - untreated


title: siLuc.PRL1


title: siCypB3


title: siCypB1


title: siLuc3

source_name: T47D breast cancer cells - si-Luc - untreated


title: Littermate control menstruating uterus 4

city: Cambridge

first: Ching-wen

last: Cheng

address: Robinson Way

department: Obstetrics and Gynaecology

institute: University of Cambridge

description: Control biological replicate 4

hyb_protocol: Standard hybridization protocol by Centre for Microarray Resources, Department of Pathology, University of Cambrdge, UK.

scan_protocol: Standard Illumina scanning protocol by Centre for Microarray Resources, Department of Pathology, University of Cambrdge, UK.

data_processing: Data were normalized in R environment using the Lumi Bioconductor package.

source_name: Uterus / decidualized and mentruating - control

label_protocol: Standard label protocol by Centre for Microarray Resources, Department of Pathology, University of Cambrdge, UK.

extract_protocol: Total RNA from individual uteri was isolated by homogenising one of uterine horn in TRIZOL (Invitrogen, Paisley, United Kingdom) and further purified using Qiagen RNeasy Mini kit (Qiagen, West Sussex, United Kingdom) following the manufacturer’s instructions. The Quality of purified RNA was examined using Agilent 2100 Bioanalyzer (Agilent Technologies UK, Stockport, United Kingdom).

treatment_protocol: Ovariectomized mice were treated sequentially with steroid hormones and then, to induce decidualization and K-ras activation, oil containing beta-NF was injected into the uterine lumen.The menstruation was induced by progesterone withdrawal after the induction of decidualization.

value: Female

value: around 12 weeks

value: Uterus


title: K-ras activated menstruating uterus 5

description: K-ras biological replicate 5

source_name: Uterus / decidualized and mentruating - K-ras activated


title: Littermate control menstruating uterus 5

description: Control biological replicate 5


title: K-ras activated menstruating uterus 2

description: K-ras biological replicate 2


title: siLuc2


title: Littermate control menstruating uterus 1

description: Control biological replicate 1


title: Littermate control menstruating uterus 3

description: Control biological replicate 3


title: K-ras activated menstruating uterus 6

description: K-ras biological replicate 6


title: Littermate control menstruating uterus 2

description: Control biological replicate 2


title: K-ras activated menstruating uterus 3

description: K-ras biological replicate 3


title: Littermate control menstruating uterus 6

description: Control biological replicate 6


title: K-ras activated menstruating uterus 4

description: K-ras biological replicate 4


title: 25whole_flies_Df(3L)ED4543_12

city: Johnson City

first: Lev

last: Yampolsky

state: TN

address: ETSU

department: Biological Sciences

institute: East Tennessee State University

hyb_protocol: See Neal, S.J., Gibson, M.L., So, A.K. & Westwood, J.T. Genome 46, 879-892. (2003)

data_processing: Background subtracted, repeated intensities for multiple probes averaged by gene, data normalized by ANOVA normalization with arrays and channels as factors. AutoBlank subtracted from each observation.

organism: Drosophila melanogaster

source_name: 25 whole flies

label_protocol: Lines Df(3L)ED4475 and Df(3L)ED4543 alternated for Cy3 and Cy5. For details see Neal, S.J., Gibson, M.L., So, A.K. & Westwood, J.T. Genome 46, 879-892. (2003)

growth_protocol: Standard SCY Drosophila medium, 26oC

extract_protocol: Twenty five adult flies 2-5 days after eclosion frozen in liquid nitrogen immediately prior to extraction by Trizol method (Invitrogen ®, Carlsbad, CA)

treatment_protocol: the two lines compared are heterozygous for different long deletions in chromosome 3L

tag: isogenic line


title: small_intestinal_crypt_vs_cultured_crypt-organoid_2

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

country: Germany

institute: University Clinic Dresden

description: crypt vs. crypt-organoid 2

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using Feature Extraction (V.9.5.3, Agilent Technologies). All data analyses were performed using ArrayAssist (5.5.1, Stratagene Inc.) and Microsoft Excel (Microsoft Corporation). Raw signal intensities were corrected by subtracting local background. Negative values were changed into a positive value close to zero (standard deviation of the local background) in order to allow calculation of ratios between intensities for features only present in one channel (small intestinal crypts or organoids). Normalization was performed by applying a Lowess algorithm and individual features were filtered if both (small intestinal crypts or organoids) intensities were changed or if both intensities were less than two times the background signal. Furthermore, non-uniform features were filtered.

label_protocol: 500 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

growth_protocol: Isolated crypts were counted and pelleted. 500 crypts were mixed with 50 ul Matrigel (BD Bioscience) and plated in 24 well plates. After polymerization of Matrigel, 500 ul of crypt culture medium (Advanced DMEM/F12 with growth factors (10-50 ng/ml EGF (Peprotech), 500 ng/ml R-spondin 111 and 100 ng/ml Noggin (Peprotech)) was added.   For passage, organoids were removed from Matrigel and mechanically dissociated into single-crypt domains, and transferred to new Matrigel. Passage was performed every 1-2 weeks with 1:5 split ratio.

extract_protocol: RNA was isolated using Trizol (Invitrogen)

treatment_protocol: Isolated small intestines were opened longitudinally, and washed with cold PBS. The tissue was chopped into around 5 mm pieces, and further washed with cold PBS. The tissue fragments were incubated in 2 mM EDTA with PBS for 30 min on ice. After removal of EDTA medium, the tissue fragments were vigorously suspended by 10 ml pipette with cold PBS. The supernatant was the villous fraction and was discarded; the sediment was resuspended with PBS. After further vigorous suspension and centrifugation, the supernatant was enriched for crypts. This fraction was passed through a 70-um cell strainer (BD bioscience) to remove residual villous material. Isolated crypts were centrifuged at 300 rpm for 3 min to separate crypts from single cells.  The final fraction consisted of essentially pure crypts and was used for culture or direct RNA isolation.

tag: epithelial cells from small intestine crypts isolated by EDTA and separated from villus by a cell strainer

source_name: cells from cultured crypt organoids

tag: cells isolated form cultured crypt-organoids grown in crypt culture medium (Advanced DMEM/F12 with growth factors (10-50 ng/ml EGF (Peprotech), 500 ng/ml R-spondin 111 and 100 ng/ml Noggin (Peprotech))


title: cultured_crypt-organoid_vs_small_intestinal_crypt_ 2

description: crypt vs. crypt-organoid 2 dyeswap

source_name: epithelial cells from small intestine crypts


title: 25whole_flies_Df(3L)ED4475_11

scan_protocol: See Neal, S.J., Gibson, M.L., So, A.K. & Westwood, J.T. Genome 46, 879-892. (2003)


title: small_intestinal_crypt_vs_cultured_crypt-organoid_1

description: crypt vs. crypt-organoid 1


title: 25whole_flies_Df(3L)ED4475_12


title: Infested Brahman 3

city: Brisbane

first: Emily

middle: Kate

last: Piper

address: Seddon Buildings (Bldg 82)

department: School of Veterinary Science

country: Australia

institute: University of Queensland

hyb_protocol: As per GeneChip expression manual, performed by the Australian Genome Research Facility

scan_protocol: Agilent Microarray Scanner (Agilent Technologies) as per Affymetrix GeneChip manual

data_processing: The data were analyzed with R/Bioconductor using RMA normalization. Additional parameters: background correction was convolution, quantile normalization and summarization with median polish.

organism: Bos indicus

source_name: Skin biopsy

growth_protocol: Whole skin tissue sample (8 mm diameter and 10 mm deep) obtained with biopsy punch, no growth protocol or treatment

extract_protocol: Skin tissue frozen in liquid nitrogen, wrapped in heavy duty aluminium and pulverised with hammer on metal block at -80°C. Returned to LN2. Pulverised tissue transferred to 1500 μl chilled Trizol reagent (Invitrogen) with four small glass beads and homogenised in tissue homogeniser for 1 min, returned to ice. Total RNA extracted using protocol for Trizol reagent as per manufacturer's instructions. RNA resuspended in 30 μl RNase-free H20 and treated with 0.75 μl Turbo DNase (Ambion) according to the manufacturer's instructions. RNA sample cleaned with RNeasy mini columns (Qiagen) and eluted from column in 50 μl RNase-free H20.

value: 6 months

value: skin

tag: disease state

value: heavy challenge with R.microplus

tag: genotype

value: Brahman


title: cultured_crypt-organoid_vs_small_intestinal_crypt_ 1

description: crypt vs. crypt-organoid 1 dyeswap


title: Infested Brahman 2

label_protocol: As per GeneChip expression manual, performed by the Australian Genome Research Facility

tag: gender

tag: age


title: 25whole_flies_Df(3L)ED4543_11


title: siLuc1


title: 25whole_flies_Df(3L)ED4543_10


title: K-ras activated menstruating uterus 1

description: K-ras biological replicate 1

tag: strain

tag: sex


title: Infested Holstein 3

value: Holstein-Friesian


title: 25whole_flies_Df(3L)ED4543_8


title: 25whole_flies_Df(3L)ED4475_8


title: 25whole_flies_Df(3L)ED4543_7


title: Infested Holstein 2

value: female


title: 25whole_flies_Df(3L)ED4543_9


title: 25whole_flies_Df(3L)ED4475_9


title: 25whole_flies_Df(3L)ED4475_7


title: wt_48h_B

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: Following fragmentation, 4 microg of cDNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

organism: Mycobacterium tuberculosis H37Rv

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA (Prokaryotic Expression Analysis, Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: minimal medium with nitrate; incubated for 48 hours

extract_protocol: RNeasy (Qiagen)

tag: genetic modification

value: none (wild type)


title: Naïve Brahman 2

value: 18 months

value: control


title: Infested Brahman 1


title: Naïve Brahman 3


title: 25whole_flies_Df(3L)ED4475_5


title: 25whole_flies_Df(3L)ED4475_6


title: Null glnR_18h_B

source_name: Null glnR_18h_B

growth_protocol: minimal medium with nitrate; incubated for 18 hours

value: deletion of glnR (Rv0818)


title: Infested Holstein 1


title: Naïve Holstein 1

value: 12 months


title: Naïve Brahman 1


title: Naïve Holstein 2


title: wt_18h_B


title: Null glnR_48h_B

source_name: Null glnR_48h_B


title: Naïve Holstein 3


title: 25whole_flies_Df(3L)ED4543_4


title: wt_48h_A


title: 25whole_flies_Df(3L)ED4543_6


title: 25whole_flies_Df(3L)ED4475_4


title: 25whole_flies_Df(3L)ED4475_3


title: 25whole_flies_Df(3L)ED4475_1


title: oxLDL-stimulated 6h-rep3 Vs oxLDL-stimulated 12h-rep3

city: shanghai

first: ting

last: chen

address: kongjiang road 1665

institute: shanghaixinhua hospital

description: Compared between biological replicate 3 of 3 human primary monocytes for oxLDL-stimulating 6h and biological replicate 3 of 3 human primary monocytes for oxLDL-stimulating 12h

hyb_protocol: Hybridization was performed overnight on a µParafloTM microfluidic chip

scan_protocol: Array images were obtained using an Axon GenePix 4000B laser scanner and digitized using the Array-Pro image software (Media Cybernetics).

data_processing: Total Data on all five chips were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

label_protocol: Total RNA was extracted using Trizol (Invitrogen). The assay started from 2 to 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.

extract_protocol: Total RNA was extracted using Trizol (Qiagen). The assay started from 2 to 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3ºC-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments

value: oxLDL-stimulated 6h

tag: replicate

value: human primary monocytes

value: oxLDL-stimulated 12h


title: Null glnR_18h_A

source_name: Null glnR_18h_A


title: wt_18h_A


title: 25whole_flies_Df(3L)ED4543_2


title: 25whole_flies_Df(3L)ED4543_3


title: control-rep1 Vs oxLDL-stimulated 12h-rep2

description: Compared between biological replicate 1 of 3 Control human primary monocytes and biological replicate 2 of 3 human primary monocytes for oxLDL-stimulating 12h

source_name: human primary monocytes


title: 25whole_flies_Df(3L)ED4543_1


title: oxLDL-stimulated 12h-rep1 Vs control-rep3

description: Compared between biological replicate 1 of 3 human primary monocytes for oxLDL-stimulating 12h and biological replicate 3 of 3 Control human primary monocytes


title: control-rep1 Vs oxLDL-stimulated 6h-rep1

description: Compared between biological replicate 1 of 3 Control human primary monocytes and biological replicate 1 of 3 human primary monocytes for oxLDL-stimulating 6h


title: oxLDL-stimulated 6h-rep2 Vs control-rep2

description: Compared between biological replicate 2 of 3 human primary monocytes for oxLDL-stimulating 6h and biological replicate 2 of 3 Control human primary monocytes


title: 25whole_flies_Df(3L)ED4475_10


title: 25whole_flies_Df(3L)ED4475_2


title: Normal RLL pairing AS4 at Day 15, biological rep1

status: Public on Apr 02 2009

city: Jacksonville

first: Catherine

last: Dumur

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

description: Gene expression data from Normal RLL at Day 15 from rat# 4

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

scan_protocol: GeneChips were scanned using the GCS 3000 scanner.

data_processing: The data were analyzed using the Robust Multiarray Analysis (RMA) method.

source_name: Normal RLL, Day 15

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tissues were snap-frozen immediately after extirpation from the animal.

extract_protocol: Trizol extraction of total RNA was performed followed by a Qiagen cleanup step, according to manufacturers' instructions.

tag: rat number

value: normal liver

value: Fischer 344

value: male

value: Young adult


title: Normal RLL pairing AS8 and AS11 at Day 25, biological rep2

description: Gene expression data from Normal RLL at Day 55 from rat# 8

source_name: Normal RLL, Day 25


title: Normal RLL pairing AS9 and AS12 at Day 25, biological rep3

description: Gene expression data from Normal RLL at Day 55 from rat# 9


title: Normal RLL pairing AS6 at Day 15, biological rep3

description: Gene expression data from Normal RLL at Day 15 from rat# 6


title: BDEneu Met at Day 25, biological rep3

description: Gene expression data from BDEneu Met at Day 25 from rat# 9

source_name: BDEneu Met, Day 25

value: peritoneal metastase


title: Normal RLL pairing AS1 at Day 10, biological rep1

description: Gene expression data from Normal RLL at Day 10 from rat# 1

source_name: Normal RLL, Day 10


title: Normal RLL pairing AS7 and AS10 at Day 25, biological rep1

description: Gene expression data from Normal RLL at Day 55 from rat# 7


title: Normal RLL pairing AS2 at Day 10, biological rep2

description: Gene expression data from Normal RLL at Day 10 from rat# 2


title: BDEneu Met at Day 25, biological rep2

description: Gene expression data from BDEneu Met at Day 25 from rat# 8


title: Normal RLL pairing AS5 at Day 15, biological rep2

description: Gene expression data from Normal RLL at Day 15 from rat# 5


title: BDEneu Met at Day 25, biological rep1

description: Gene expression data from BDEneu Met at Day 25 from rat# 7