title: Synchrony 9 hr

city: Rockville

first: Ravi

last: Sanka

state: Maryland

address: 9704 Medical Center Drive

institute: JCVI

description: Tp-9hr_A_08-10-2009_(Tp_Affy1_tiling).Tp_synchronization.rma-gene-core-Signal

hyb_protocol: Hybridization of labeled targets on the arrays was carried out using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: The arrays were then scanned with the GeneChip® Scanner, to generate the probe cell intensity data files.

data_processing:
Initial analysis of gene level expression was performed using Affymetrix Expression Console Software, version 1.1. The Robust Multichip Analysis (RMA) algorithm was applied to the probe cell intensity data files for all experimental conditions, using default parameters in the RMA-sketch workflow for core gene level analysis.
probe group file: Tp_Affy1_exon.pgf
meta-probeset file: Tp_Affy1_exon.mps
Tp_Affy_GeneLevel_ProbeID_map.txt

organism: Thalassiosira pseudonana CCMP1335

source_name: synchronized cells harvested at 9 hr

label_protocol: For each hybridization, double stranded cDNA was synthesized from 7 ug of total RNA with no amplification using the GeneChip® WT Amplified Double-Stranded cDNA Synthesis Kit (Affymetrix).  Cleanup of double-stranded cDNA was done with the GeneChip® Sample Cleanup Module (Affymetrix).  Fragmentation and end-labeling was performed using the GeneChip® WT Double-stranded DNA Terminal Labeling Kit (Affymetrix).

growth_protocol: Thalassiosira pseudonana (CCMP1335) cultures were synchronized by silica starvation/repletion. Samples were taken each hr of cell cycle (0-9 hr), treated with cycloheximide, pelleted and stored at -80oC prior to RNA isolation.

extract_protocol: Total RNA extracted with Trizol reagent (Sigma) from cells harvested at each time point.

tag: cell culture

value: synchronized cell culture


title: KS06d

status: Public on Oct 01 2012

type: RNA

city: Houston

first: Govindarajan

last: Kunde Ramamoorthy

state: Texas

address: 1100 Bates Street

country: USA

institute: Baylor College of Medicine

description: Male Small litter P180 biol-rep2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation and log2 transformation with LUMI package in R

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Male Small litter P180

label_protocol: Standard Illumina labeling protocol

extract_protocol: RNA was extracted using the Rneasy Mini Kit (Qiagen). Quality control was performed by spectrophotometry (NanoDrop-1000 Spectrophotometer, Thermo Fisher Scientific).

tag: strain

value: FVB/NJ-Jax

tag: Sex

value: Male

tag: age

tag: group

value: Small litter


title: Synchrony 9 hr-replicate

description: Tp-9hr_B_08-10-2009_(Tp_Affy1_tiling).Tp_synchronization.rma-gene-core-Signal


title: 10DS

type: genomic

city: Bethesda

first: Jennifer

last: Barb

state: MD

address: 12 South Drive Bldg 12A Room 2001

department: DCB

institute: NIH

description: 16S rRNA genes are PCR amplified from DNA extracts using 16S rRNA universal forward and reverse primers and labeled via incorporation of Cy3-dCTP in a second nested PCR.

hyb_protocol: Prior to hybridization, slides were blocked with sodium borohydride (NaBH4, 1X PBS, 99% ethanol) in order to reduce unreactive aldehyde groups, thus minimizing the fluorescent background. Fourteen microliter of each labeled and purified PCR sample were mixed with 6 µl of hybridization buffer containing 2X SSC, 0.2 µg/µl yeast tRNA, 0.1% SDS, and heated for 5 minutes at 100C. After that, 10 µl of each solution were loaded slowly at one corner and under the cover slip, allowing capillary action to pull the solution over the array. Slides were then placed on incubation racks in a humidified chamber, and hybridization was then performed at 55C for 16 h in a microarray incubator. Slides were removed from the hybridization chamber and sunk into a water bath containing a washing solution (2X SSC, 10%SDS, at 55C) to remove the cover slips. The slides were washed using an automated microarray robotic instrument. A washing program was set up as follow: one washing in buffer (2X SSC, 10%SDS) at 55C for 2 minutes, a second washing in 2X SSC buffer at room temperature for 2 minutes, and a final washing in 0.1X SSC buffer at room temperature for 2 minutes. Once the slides are finished spinning in the centrifuge, they were removed and placed in a light-proof container until scanning.

scan_protocol: The microarray slides are scanned using an Axon 4000B scanner and crude data is extracted using GenePix Pro software. Data are normalized by comparing individual signal intensities to the average of signals from universal probes.

data_processing: Individual probe spot net intensity was calculated by subtracting the foreground intensity (F532) with background intensity (B532); intensity was set to 1 if net intensity is <1 or signal to noise ratio (F532/B532) < 2; between-the-array signal normalization was done based on mean universal 16S sequence probe intensities; signals were also scaled to be within the same minimal and maximal intensities range across arrays; normalized and scaled intensities of the same probe sequence were then averaged. The averaged unique probe intensities were then raised to the power of 0.3 and then converted to ordinal numbers on a 0-5 scale, with 0=not detected and 1 to 5 reflect increasing signal strength. For detail analysis procedure see: http://bioinformatics.forsyth.org/homim

molecule: genomic DNA

organism: Homo sapiens

source_name: oral sample

label_protocol: Two separate PCR reactions were set up with, respectively, forward primer 5'-CCA GAG TTT GAT YMT GGC-3' with reverse primer 5'-GAA GGA GGT GWT CCA RCC GCA -3', and forward primer 5'-GAC TAG AGT TTG ATY MTG GC-3' with reverse primer 5'-GYT ACC TTG TTA CGA CTT-3'. Two µl of genomic DNA template were added to the reaction mixture (final volume 25 µl) containing 20 pmol of each primer, 40 nmol of deoxytriphosphates, 1.5 mM Mg2+ and 1 U of Platinum High Fidelity Taq polymerase (Invitrogen, San Diego, CA). The samples were preheated at 94°C for 2 min, followed by 32 cycles of amplification under the following conditions: 94°C for 30 s, 55°C for 30 s, and 68°C for 1.5 min, with an additional 1 s for each cycle. A final 10 min elongation step at 68°C was added. The results of the PCR amplification were examined by electrophoresis in a 1% agarose gel. The two parallel PCR reactions were combined and the products purified with QIAquick PCR Purification Kit (Qiagen).Purified PCR products were labeled via the incorporation of Cy3-dCTP during a second reaction. Briefly, 7 μL of each product were added into a 25 μL reaction mixture containing 15 pmol of the forward primer 9F (5'-GAGTTTGATYMTGGCTCAG-3') , 5 pmol of the 1492R primer , 2.5 μL 10•X high fidelity PCR buffer, 2 mM MgSO4, 2.5 μL of deoxynucleotide triphosphate mixture without deoxycytidine triphosphate (10 mM, 0.2 mM final concentration of each deoxynucleotide), 2.5 μL of deoxycytidine triphosphate mixture (1 μL of 1 mM Cy3-dCTP + 4 μL of 2 mM dCTP, 0.2 mM final concentration), 0.25 μL 10% Triton X, and 1.25 U Taq polymerase. The PCR program included an initial denaturation step at 94C for 2 minutes, followed by 40 cycles of denaturation at 94oC for 30s, annealing at 55C for 30s, elongation at 68C for 1.5 minute with an additional 1 s for each cycle, and a final elongation step at 68C for 10 minutes.

growth_protocol: None; DNA was extracted directly from clinical samples

extract_protocol: Bacterial DNA was eluted from saliva that had been collected using a sterile oral suction device, supragingival plaque using sterile applicator, tongue and buccal brushing using a sterile cytotbrush respectively, per patient at each specimen collection time. Plaque, and tongue and buccal brushings were placed in 150 microliter of TE buffer. Genomic DNA was extracted using the Epicenter Masterpure Kit for DNA Extraction (Epicentre Biotechnologies, Madison, Wisconsin).

tag: time of specimen collection

value: after transplant

tag: sample type

value: saliva

tag: developed respiratory signs/symptoms (rss) or no rss

value: RSS


title: Synchrony 8 hr

description: Tp-8hr_supplement_10-10-2009_(Tp_Affy1_tiling).Tp_synchronization.rma-gene-core-Signal

source_name: synchronized cells harvested at 8 hr


title: 10DP

treatment_protocol: None; DNA was extracted directly from clinical samples

value: plaque


title: KC03i

description: Male Control P180 biol-rep1

source_name: Male Control P180

value: Control


title: KS22b

description: Female Small litter P180 biol-rep3

source_name: Female Small litter P180

value: Female


title: Synchrony 8 hr-replicate

description: Tp-8hr_supplement_10-10-2009_(Tp_Affy1_tiling)_Rep3.Tp_synchronization.rma-gene-core-Signal


title: SOIV_Animal_1012_D3_RL

city: Minato

first: Yoshihiro

last: Kawaoka

state: Tokyo

address: Shirokanedai 4-6-1

department: ERATO Influenza-induced Host Responses Project

country: Japan

institute: Japanese Science and Technology Agency

hyb_protocol: Using Agilents Gene Expression Hybridizatoin kit #4 and Gene Expression wash pack #5, Cy3-labeled cRNA preparations were hybridized with rhesus macaque arrays (Agilent Microarray Design Identification Number 015421) for 17 h at 65°C.

scan_protocol: Immediately after washing, Feature Extraction Software, version 7 (Agilent Technologies) was used for image analysis and data extraction.

data_processing: Per chip and per gene normalization was performed using GeneSpring GX version 11.0.2. Expression values were baselined to the mean of the uninfected samples

organism: Macaca mulatta

source_name: Lung

label_protocol: Using the Quick Amp Labeling Kit, T7 RNA polymerase was used to simultaneously amplify target material and incorporate cyanine 3-labeled CTP to prepare Cy3-labeled cRNA.

extract_protocol: Total RNA was extracted from homogenized lung tissues with the RNeasy Mini Kit (Qiagen, Hilden, Germany)  following the manufacturer's recommendation.

treatment_protocol: Excised lung tissues were placed in the RNA stabilization reagent RNAlater (Ambion, CA) and stored at -80°C. All tissues were thawed together and homogenized (2 minutes at 30Hz) by using a TissueLyser (Qiagen, Hilden, Germany), following the manufacturer’s instructions.

tag: tissue

value: Lung

tag: monkey

tag: influenza a virus titer

value: Yes

tag: strains

value: SOIV

tag: day

tag: lung lobe

value: Right Lower


title: KS10b

description: Female Small litter P180 biol-rep2


title: SOIV_Animal_1012_D3_LM

value: Left Middle


title: KC07i

description: Male Control P180 biol-rep2


title: Synchrony 7 hr

description: Tp-7hr_A_08-10-2009_(Tp_Affy1_tiling).Tp_synchronization.rma-gene-core-Signal

source_name: synchronized cells harvested at 7 hr


title: 10D2S


title: 10D2Ton

value: tongue brushing


title: Synchrony 7 hr-replicate

description: Tp-7hr_A_08-10-2009_(Tp_Affy1_tiling)_Rep2.Tp_synchronization.rma-gene-core-Signal


title: Synchrony 4 hr-replicate

description: Tp-4hr_B_08-10-2009_(Tp_Affy1_tiling).Tp_synchronization.rma-gene-core-Signal

source_name: synchronized cells harvested at 4 hr


title: 10D2P


title: KUTK4_Animal_1011_D7_RL


title: KS08b

description: Female Small litter P180 biol-rep1


title: 10D2Buc

value: buccal brushings


title: KC17c

description: Female Control P180 biol-rep3

source_name: Female Control P180


title: 10D1Ton


title: KUTK4_Animal_1011_D7_LM


title: 10D1S


title: Synchrony 2 hr

description: Tp-2hr_A_08-10-2009_(Tp_Affy1_tiling).Tp_synchronization.rma-gene-core-Signal

source_name: synchronized cells harvested at 2 hr

value: synchronized cell culture


title: Synchrony 4 hr

description: Tp-4hr_A_08-10-2009_(Tp_Affy1_tiling).Tp_synchronization.rma-gene-core-Signal


title: KC05c

description: Female Control P180 biol-rep2

value: FVB/NJ-Jax


title: KUTK4_Animal_1002_D3_RL


title: KUTK4_Animal_1002_D3_LM


title: KUTK4_Animal_1010_D3_LM


title: KUTK4_Animal_1010_D3_RL


title: 10D1P


title: PFR32_1_rep1

city: Boston

first: Pasi

last: Janne

state: MA

address: 44 Binney Street Dana 820

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: PF299804 Resistant, persistent exposure to PF299804

hyb_protocol: The fragmented cRNA ws added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution was then removed. The chips were transferred to a fluidics instrument that performs washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured. These measures provide the basis of subsequent biostatistical analysis. The data was transferred to a file-system from which it can be downloaded via a password-protected URL.

data_processing: Normalized and analyzed using GenePattern (http://www.broadinstitute.org/cancer/software/genepattern/), selecting RMA method

source_name: NSCLC cells

label_protocol: At DFCI Microarray core, RNA was converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis was then carried out. The double-stranded cDNA was used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) was purified from the IVT reaction mixture using magnetic particles. The cRNA was quantified spectrophotometrically and purity of the cRNA was also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range was not routinely carried forward in the analysis. The purified cRNA was fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: Cells were grown in RPMI supplemented with 10% FBS and antibiotics (PC9 and PFR3) or RPMI supplemented with 10% FBS, antibiotics and PF299804 (PFR3+). Cells were growing exponentially before the harvest

extract_protocol: RNA was isolated using trizol and clened up with RNAeasy kit (Qiagen)

tag: cell type

value: Non-Small Cell Lung Cancer (NSCLC)

value: Resistant


title: Control_Animal_0_D0_RL


title: Synchrony 0 hr

description: Tp-0hr_A_08-10-2009_(Tp_Affy1_tiling).Tp_synchronization.rma-gene-core-Signal

source_name: synchronized cells harvested at 0 hr


title: Synchrony 2 hr-replicate

description: Tp-2hr_B_08-10-2009_(Tp_Affy1_tiling).Tp_synchronization.rma-gene-core-Signal


title: PFR32_1_rep3


title: 10D1Buc

value: after transplant


title: PFR32_1_rep2


title: KC01c

description: Female Control P180 biol-rep1


title: Synchrony 0 hr- replicate

description: Tp-0hr_B_08-10-2009_(Tp_Affy1_tiling).Tp_synchronization.rma-gene-core-Signal


title: 10CS

value: saliva


title: 10CTon

value: RSS


title: M1_3

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

description: Gene expression of primary motor cortex

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner with the Scan Control software (Agilent Technologies).

data_processing: The resulting images were processed, and raw data were collected using Agilent’s Feature Extraction software. The gene expression data were analyzed using GeneSpring GX 12 (Agilent). The signal intensity for each probe was normalized by a percentile shift, in which each measurement was divided by the 75th percentile of all measurements in its array.

source_name: cerebral cortex, M1, reprecate3

label_protocol: Five hundred ng of the RNA sample was transcribed using oligo(dT)-based T7 promoter primer and MMLV-RT in the first- and second-strand cDNA synthesis reactions. The double-stranded cDNAs were used as templates in the preparation of fluorescent complementary RNAs (cRNAs) in the presence of T7 RNA polymerase and cyanine 3-CTP dye in an in vitro transcription reaction.

extract_protocol: The tissues were homogenized using a conventional rotor-stator homogenizer. Then total RNA was extracted from tissues using RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA). RNA was treated with DNase 1 (Qiagen) and was cleaned up using Qiagen RNeasy mini kit or Qiagen RNeasy MinElute kit (Qiagen). The purity and integrity of the isolated total RNA was analyzed with ultraviolet spectrophotometry and an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). All RNA samples showed a 260/280 ratio between 1.7 and 1.9 and 28S:18S ratio of 1.5 and higher and the RNA Integrity Number showed between 8.0 and 9.5.

value: cerebral cortex

tag: tissue region

value: primary motor cortex (M1)


title: Control_Animal_0_D0_LM

value: Control


title: M1_4

description: Gene expression of primary motor cortex

source_name: cerebral cortex, M1, reprecate4


title: 10CP

value: plaque


title: 10CBuc


title: PFR31_1_rep3

description: PF299804 Resistant, maintained in normal media after the resistant cells are established


title: 10ATon

value: before transplant


title: 10AS


title: PFR31_1_rep1


title: 10AP


title: M1_2

description: Gene expression of primary motor cortex

source_name: cerebral cortex, M1, reprecate2


title: PC9_1_rep1

description: Parental Cells

value: Sensitive


title: A46_4

description: Gene expression of area 46

source_name: cerebral cortex, A46, reprecate4


title: PC9_1_rep2

description: Parental Cells


title: A46_3

description: Gene expression of area 46

source_name: cerebral cortex, A46, reprecate3


title: PFR31_1_rep2


title: A46_2

description: Gene expression of area 46

source_name: cerebral cortex, A46, reprecate2


title: M1_1

description: Gene expression of primary motor cortex

source_name: cerebral cortex, M1, reprecate1


title: NCI-H1975_WZR6_rep3

description:
WZR6-3
WZ4002-resistant Clone6.

hyb_protocol: The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution was then removed. The chips were transferred to a fluidics instrument that performs washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing: Normalized and analyzed using GenePattern (http://www.broadinstitute.org/cancer/software/genepattern/), selecting the RMA method.

source_name: NCI-H1975 NSCLC cells, WZ4002 resistant

label_protocol: At the Dana-Farber Cancer Institute (DFCI) Microarray core, RNA was converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis was then carried out. The double-stranded cDNA was used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) was purified from the IVT reaction mixture using magnetic particles. The cRNA was quantified spectrophotometrically, and the purity of the cRNA was also assessed by spectrophometric measurements. Those cRNAs that fall outside of an acceptable range were not routinely carried forward in the analysis. The purified cRNA was fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: Cells were grown in RPMI supplemented with 5% FBS. Cells were growing exponentially before the harvest.

extract_protocol: RNA was isolated using Trizol and cleaned up with the RNeasy kit (Qiagen).

tag: cell line

tag: wz4002 resistant

value: yes


title: 10ABuc

source_name: oral sample


title: NCI-H1975_WZR6_rep2

description:
WZR6-2
WZ4002-resistant Clone6.


title: NCI-H1975_parental_rep3

description:
H1975-3
Parental cells.

source_name: NCI-H1975 NSCLC cells, WZ4002 sensitive

value: no


title: F30-2

city: Braunschweig

first: Anna

last: Buschart

address: Inhoffenstr. 7

department: BiSA

country: Germany

institute: Helmholtz-Centre for Infection Research

description:
mode of action studies – fludioxonil
Agilent Custom Array 028105

data_processing: Data from gProcessedSignal column are loaded into R/Bioconductor, quantile-normalization, average of replicate spots, limma for biological replicates and FC + statistics

organism: Candida albicans SC5314

label_protocol: QuickAmp Kit, Agilent, 500 ng total RNA input

growth_protocol: o/n in YPD, p/c in YNB+2g/L glucose, m/c in RPMI-1640 + 20 µg/ml Fludioxonil, for 30 min from OD 0,1

extract_protocol: Vortex with beads + RNeasy (+ in most cases Dnase)

treatment_protocol: 20 µg/ml fludioxonil

tag: treatment

value: fludioxonil

tag: date of cultivation

tag: date of isolation

tag: dnase treatment

tag: date of quality check

tag: date of scan


title: U30-3

description:
mode of action studies
Agilent Custom Array 028105

growth_protocol: o/n in YPD, p/c in YNB+2g/L glucose, m/c in RPMI-1640, for 30 min from OD 0,1

value: untreated


title: U30-1


title: F30-1


title: HaCaT cells treated with S.aureus planktonic-conditioned media from cultures spiked with DMSO control, replicate 3

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

hyb_protocol: Labeled and fragmented cRNA was hybridized for 16 hr at 45C to the Affymetrix Human Genome U133A 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix 7G scanner and GCOS version 1.4.

data_processing:
Microarray data were analyzed using FlexArray version 1.6. The Affymetrix CEL files were imported and normalized using GC-RMA.
Matrix files include scaled MAS5 (linked to the Series record) and GC-RMA (contained in the data table below) normalized (log2) values.

source_name: Primary human keratinocytes were cultured from newborn foreskin.

label_protocol: Total RNA (500ng) was reverse transcribed, and amplified and biotin-labeled via in vitro transcription using the MessageAmp Premier kit

growth_protocol: HaCaT keratinocytes were cultured in 6 well plates using EpiLife growth medium supplemented with human keratinocyte growth supplement. Cells were maintained at 37C in a humidified, 5% CO2 atmosphere.

extract_protocol: After treatment, the medium was removed and RNA was isolated using an RNeasy minikit following the manufacturer’s instructions for adherent cells. Extracted RNA was then ethanol precipitated.

treatment_protocol: After growing HaCaT cells to confluence, cells were treated for 4 hours at 37C, 5% CO2.

value: Conditioned medium from planktonic S. aureus cultures spiked with DMSO during exponential phase growth.

value: Human Foreskin Keratinocytes were isolated at the University of Washington.


title: NCI-H1975_parental_rep2

description:
H1975-2
Parental cells.


title: F30-3


title: NCI-H1975_parental_rep1

description:
H1975-1
Parental cells.


title: HaCaT cells treated with S.aureus planktonic-conditioned media from cultures spiked with DMSO control, replicate 2


title: HaCaT cells treated with S.aureus planktonic-conditioned media from cultures spiked with DMSO control, replicate 1


title: A46_1

description: Gene expression of area 46

source_name: cerebral cortex, A46, reprecate1

tag: age


title: U30-2


title: NCI-H1975_WZR6_rep1

description:
WZR6-1
WZ4002-resistant Clone6.


title: HaCaT cells treated with S.aureus planktonic-conditioned media from cultures exposed to phevalin, replicate 3

value: Conditioned medium from planktonic S. aureus cultures spiked with phevalin during exponential phase growth.


title: HaCaT cells treated with S.aureus biofilm-conditioned media from cultures spiked with DMSO control, replicate 2

value: Conditioned medium from biofilm S. aureus cultures.


title: HaCaT cells treated with S.aureus biofilm-conditioned media from cultures spiked with DMSO control, replicate 1


title: HaCaT cells treated with S.aureus planktonic-conditioned media from cultures exposed to phevalin, replicate 1


title: HaCaT cells treated with S.aureus biofilm-conditioned media from cultures spiked with DMSO control, replicate 3


title: HaCaT cells treated with S.aureus planktonic-conditioned media from cultures exposed to phevalin, replicate 2


title: 10 uM phevalin (0.1%DMSO) in EpiLife growth medium supplemented with human keratinocyte growth supplement, replicate 2

value: 10uM phevalin in growth media


title: 10 uM phevalin (0.1%DMSO) in EpiLife growth medium supplemented with human keratinocyte growth supplement, replicate 3


title: Theileria annulata infected Bos taurus TBL20 LPS 18h rep3

city: Glasgow

first: William

last: Weir

address: Room 220, Henry Wellcome Building, Garscube Campus, Bearsden Road

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 18 hours post LPS stimulation, this is the 3rd of 3 replicates

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

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

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

organism:
Theileria annulata
Bos taurus

source_name: T. annulata infected bovine cells, 18 hours post LPS stimulation

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

growth_protocol: BL20, an uninfected bovine lymphosarcoma cell line (Olobo and Black, 1989. Vet. Immunol. Immunopathol. 20, 165-172) and TBL20, a T. annulata (Ankara strain) infected BL20 cell line (Shiels et al., 1986. Vet. Parasitol. 21, 1-10.) were cultured in standard complete medium (Swan et al., 1999. Mol. Biochem. Parasitol. 101, 117-129) except that heat-inactivated foetal bovine serum (FBS; Sigma) was used. Cultures were seeded with 200,000 cells/ml and maintained by feeding with fresh medium every two to three days (Schmuckli-Maurer et al., 2010. Cell Microbiol. 12, 158-173).

extract_protocol: Total RNA was extracted using Triazol (ref) and this was cleaned up using an RNeasy Mini kit (Qiagen Inc., CA, USA) . RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer (ref)

treatment_protocol: Stimulation of cells was carried out for up to 48 hours in six well plates with 5,000,000 cells/well in a total of 5 ml medium, set up immediately prior to addition of 1 μg/ml LPS (Sigma: L2630).

tag: infection

value: T. annulata infected

value: LPS

tag: time

value: 18 hours


title: Theileria annulata infected Bos taurus TBL20 LPS 18h rep1

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 18 hours post LPS stimulation, this is the 1st of 3 replicates


title: Theileria annulata infected Bos taurus TBL20 LPS 18h rep2

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 18 hours post LPS stimulation, this is the 2nd of 3 replicates


title: Bos taurus BL20 LPS 18h rep3

description: This sample is of the bovine lymphosarcoma cell line BL20, 18 hours post LPS stimulation, this is the 3rd of 3 replicates

organism: Bos taurus

source_name: Bovine cells, 18 hours post LPS stimulation

value: uninfected


title: Bos taurus BL20 LPS 18h rep2

description: This sample is of the bovine lymphosarcoma cell line BL20, 18 hours post LPS stimulation, this is the 2nd of 3 replicates


title: 1 uM phevalin (0.1%DMSO) in EpiLife growth medium supplemented with human keratinocyte growth supplement, replicate 3

value: 1uM phevalin in growth media


title: Bos taurus BL20 LPS 18h rep1

description: This sample is of the bovine lymphosarcoma cell line BL20, 18 hours post LPS stimulation, this is the 1st of 3 replicates


title: 10 uM phevalin (0.1%DMSO) in EpiLife growth medium supplemented with human keratinocyte growth supplement, replicate 1


title: Theileria annulata infected Bos taurus TBL20 LPS 4h rep3

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 4 hours post LPS stimulation, this is the 3rd of 3 replicates

source_name: T. annulata infected bovine cells, 4 hours post LPS stimulation

value: 4 hours


title: 1 uM phevalin (0.1%DMSO) in EpiLife growth medium supplemented with human keratinocyte growth supplement, replicate 2


title: 1 uM phevalin (0.1%DMSO) in EpiLife growth medium supplemented with human keratinocyte growth supplement, replicate 1


title: Theileria annulata infected Bos taurus TBL20 LPS 4h rep1

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 4 hours post LPS stimulation, this is the 1st of 3 replicates


title: Theileria annulata infected Bos taurus TBL20 LPS 4h rep2

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 4 hours post LPS stimulation, this is the 2nd of 3 replicates


title: Bos taurus BL20 LPS 4h rep1

description: This sample is of the bovine lymphosarcoma cell line BL20, 4 hours post LPS stimulation, this is the 1st of 3 replicates

source_name: Bovine cells, 4 hours post LPS stimulation


title: 0.1%DMSO in EpiLife growth medium supplemented with human keratinocyte growth supplement, replicate 1

value: Vehicle control


title: 0.1%DMSO in EpiLife growth medium supplemented with human keratinocyte growth supplement, replicate 3


title: Bos taurus BL20 LPS 4h rep3

description: This sample is of the bovine lymphosarcoma cell line BL20, 4 hours post LPS stimulation, this is the 3rd of 3 replicates


title: 0.1%DMSO in EpiLife growth medium supplemented with human keratinocyte growth supplement, replicate 2


title: Bos taurus BL20 LPS 4h rep2

description: This sample is of the bovine lymphosarcoma cell line BL20, 4 hours post LPS stimulation, this is the 2nd of 3 replicates


title: Theileria annulata infected Bos taurus TBL20 control rep2

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 without any treatment, this is the 2nd of 3 replicates

source_name: T. annulata infected bovine cells, no treatment


title: Theileria annulata infected Bos taurus TBL20 control rep3


title: Theileria annulata infected Bos taurus TBL20 control rep1

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 without any treatment, this is the 1st of 3 replicates


title: WZR11

description:
PC9 WZR11
GR4 cells made resistant to WZ4002, Clone11.

hyb_protocol: Hybridization was done at the Dana-Farber Cancer Institute (DFCI) molecular biology core. Briefly, the biotinylated fragments are added to a hybridization solution containing a biotinylated control oligonucletide (for quality control), and hybridized to a microarray chip overnight at 49°C. The chips are then transferred to a fluidics instrument that performs washes to remove DNA that has not hybridized to its complementary oligonucleotide probe. The bound DNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE), followed by biotinylated anti-streptavidin, followed by SAPE.

scan_protocol: Scanning of the microarray chips was done at the Dana-Farber Cancer Institute (DFCI) molecular biology core. Briefly, each DNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.

data_processing: The scanned data was analyzed using D-Chip. The CHP files are the original files from the DFCI core.

source_name: PC9 NSCLC cells, WZ4002 resistant

label_protocol: Labelling was done at the Dana-Farber Cancer Institute (DFCI) molecular biology core. Briefly, the Mapping 250K analysis begins with one aliquot of 250 ng of DNA and is cleaved with StyI. Linkers are ligated to the restriction fragments using T4 DNA ligase. The linkers provide a primer site for the subsequent PCR reaction. The fragments are amplified using Taq polymerase. The PCR products are purified from the primers and free nucleotides by ultrafiltration. They are then quantified spectrophotometrically, and are also assayed using size fractionation on a microfluidics device to determine whether the size distribution of products is as expected. The purified PCR products are fragmented by DNase I in order to provide 3' hydroxyl groups for subsequent labeling, and to facilitate the subsequent hybridization step. The fragmented PCR products are labeled with a single biotin at each free 3'OH using terminal deoxynucleotidyl transferase and a dideoxy biotinylated nucleoside triphosphate.

extract_protocol: DNA was isolated using the DNeasy Blood-Tissue kit (Qiagen).


title: WZR12

description:
PC9 WZR12
GR4 cells made resistant to WZ4002, Clone12.


title: 3744_MMTV2

city: Ithaca

first: John

last: Schimenti

state: NY

department: Biomedical Sciences

institute: Cornell University

scan_protocol: Scanning was performed in accordance with the NimbleGen protocol (performed by Cornell CLC).

data_processing: Analyzed with  NimbleScan (v2.5)-segmentation algorithm. Copy number changes were identified and segmented with Nimblegen CGH-segMNT algorithm using unaveraged and 10x averaging windows. The significance threshold was set at +/- 0.15 Log2 ratio and required a minimum of two consecutive probes to exhibit change in order to call a segment.

source_name: MMTV-Neu Mammary Tumor

label_protocol: Performed according to NimbleGen protocols (performed by Cornell CLC). Five micrograms of genomic DNA from tumor and reference samples were labeled and hybridized to 3x720K mouse Nimblegen CGH whole genome tiling arrays.

tag: strain background

value: C3H (C3H/HeNCrl)

tag: genotype/variation

value: MMTV-Neu

tag: gender

value: female

tag: tissue

value: Mammary Tumor

source_name: C3H congenic Chaos3+/+ mouse control

value: congenic Chaos3+/+ mouse control

tag: sample type

value: reference


title: NiV_ΔC_2

city: LYON

first: HORVAT

last: Branka

address: 21 avenue Tony Garnier

department: human virology

country: France

institute: INSERM

hyb_protocol: 10 µg of biotin-labeled RNA were fragmented using 5 µl fragmentation buffer in a final volume of 20 µl, then mixed with 240 µl Amersham hybridization solution and injected onto Codelink Uniset Human Whole Genome bioarrays. Arrays were hybridized overnight at 37°C, then washed in stringent TNT buffer at 46°C for 1 h before performing a streptavidin-cy5 detection step. Each array was incubated for 30 min in 3,4 ml streptavidin-cy5 solution, washed four times in 240 ml TNT buffer, rinsed twice in 240 ml water containing 0.2M Triton X-100, and then, dried by centrifugation at 650g.

scan_protocol: Arrays were then scanned at 635nm using an Axon Genepix 4000B Scanner (Axon).

data_processing: Data extraction and raw data normalization were performed using the CodeLink Gene Expression Analysis v4.0 software. Normalization was performed by the global method. The threshold was calculated using the normalized signal intensity of the negative controls supplemented by 3 times the standard deviation. Spots with signal intensity below this threshold were referred to as “absent”.

source_name: ΔC NiV-infected HUVEC

label_protocol: Amplified and biotin-labeled RNAs were obtained from 2µg of total RNA, by a round of in vitro transcription (dIVT) using the Message Amp a RNA kit version II (Ambion), following the manufacturer’s protocol.

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen) according to the manufacturer’s protocol

value: HUVEC

value: NiV ΔC


title: Bos taurus BL20 control rep2

description: This sample is of the bovine lymphosarcoma cell line BL20 without any treatment, this is the 2nd of 3 replicates

source_name: Bovine cells, no treatment


title: Bos taurus BL20 control rep1

description: This sample is of the bovine lymphosarcoma cell line BL20 without any treatment, this is the 1st of 3 replicates


title: Cerebellum_Transgenic_REP3

status: Public on Sep 30 2012

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description:
L33-3_Mousegenome430_2.0.CEL
Gene expression data from, transgenic (daDREAM) cerebellum cells replicate 3

hyb_protocol: Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix chips (GeneChip Mouse Genome 430 2.0 Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

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

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

source_name: cerebellum transgenic

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cerebellar tissue from wild type or transgenic mice was dissected and immediatelly frozen.

extract_protocol: RNA was prepared using TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen). RNA was quantified and the RNA quality was assessed with a 2100 Bioanalyzer from Agilent Technologies

tag: hybrid C57BL/6 x CBA

value: daDREAM

value: cerebellum


title: WZR9

description:
PC9 WZR9
GR4 cells made resistant to WZ4002, Clone9.

tag: cell line

value: yes


title: NiV_ΔC_1


title: Cerebellum_WildType_REP1

description:
Wt1_Mousegenome430_2.0.CEL
Gene expression data from, wild type cerebellum cells replicate 1

source_name: cerebellum wild type

value: Wild Type


title: Cerebellum_Transgenic_REP1

description:
L33-1_Mousegenome430_2.0.CEL
Gene expression data from, transgenic (daDREAM) cerebellum cells replicate 1


title: Cerebellum_Transgenic_REP2

description:
L33-2_Mousegenome430_2.0.CEL
Gene expression data from, transgenic (daDREAM) cerebellum cells replicate 2


title: WZR10

description:
PC9 WZR10
GR4 cells made resistant to WZ4002, Clone10.

tag: wz4002 resistant


title: 10658

hyb_protocol: Performed according to NimbleGen protocols (performed by Cornell CLC)

source_name: Chaos3 Bone Tumor

value: Mcm4Chaos3/Chaos3 ('Chaos3') mouse

value: Bone Tumor


title: 16862

source_name: Chaos3 Histiocytic Sarcoma in Uterus

extract_protocol: Performed according to NimbleGen protocols (performed by Cornell CLC)

value: Histiocytic Sarcoma in Uterus


title: 3750_MMTV1


title: 17883

source_name: Chaos3 Mediastinal Tumor

value: Mediastinal Tumor


title: 16898_F1

source_name: F1 Mammary Tumor

value: F1 Mammary Tumor


title: pig 1366 at 28 day vs. at 0 day  1366_28_0

status: Public on Sep 26 2012

city: East Lansing

first: juan

middle: p

last: steibel

state: MI

address: 1205 I Anthony Hall

institute: Michigan State University

description: BLOOD EXPRESSION PRRSV infection title indicates pig ID and days post infection

hyb_protocol: Labeled aRNAs were purified and combined with 70 µl of Slide Hyb #1 solution (Ambion, Inc.) and denatured at 70C for 3 min. Hybridizations were performed in sealed hybridization cassettes (ArrayIt, TeleChem International, Inc., Sunnyvale, CA, USA) for 18 h at a humid 54C. Following hybridization, slides were washed in 2X SSC/0.5% SDS and 0.1X SSC/0.1% SDS solutions for 10 min each. The slides were rinsed in a 0.1X SSC solution and nuclease-free water and dried by centrifugation.

scan_protocol: Fluorescent images were detected by a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) and fluorescence intensity data were collected using GenePix software (Molecular Devices) after spot alignment. Median intensity values for each dye channel were stored as comma-separated values data files.

data_processing: Median intensities were extracted and normalized using a within print-tip loess location normalization implemented in NormalizeWithinArrays() in LIMMA. Background was corrected following  Ritchie  et al. (2007) method using normexp() function of LIMMA with offset=50. The resulting normalized ratios were expressed in the log2 scale.

organism: Sus scrofa

label_protocol: One µg of total RNA was reverse transcribed with a T7 oligo(dT) primer using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Inc., Austin, TX, USA) according to the manufacturer’s instructions. Following first-strand and second-strand synthesis and purification, the cDNAs were in vitro transcribed to synthesize multiple copies of amino allyl-modified aRNAs. After purification, 10 ug of aRNA was labeled with N-hydroxysuccinate (NHS) ester Cy3 or Cy5 (GE Healthcare, UK).

growth_protocol: Crossbred commercial pigs (~200) from PPRS Host Genetics Consortium (PHGC) trial one were transported to a Kansas State University bio-secure testing facility at weaning (11 to 21 d. old) and allocated to pens (10 to 15 pigs/pen). Pigs came from PRRSV-, Influenza virus- and Mycoplasma hyopneumoniae-free farms.

extract_protocol: Tempus tube collected blood samples of PHGC pigs were stored at -20 until RNA was extracted

treatment_protocol: After a 7-day acclimation period and antibiotic treatments, pigs were intramuscularly and intranasally infected with a known isolate of the Porcine Reproductive and Respiratory Syndrome virus (PRRSV) (105 tissue culture infectious dose50 of NVSL 97-7985).Blood samples were collected in Tempus™ Blood RNA Tubes (Life Technologies, Carlsbad, CA) at several time-points post-infection, including 0, 4, 7, 11, 14, 21, 28 and 42 days post-infection (DPI). Individual animal weight was measured at weekly intervals. Serum viral level was quantified using a semi-quantitative TaqMan PCR assay.

tag: animal id

tag: response

value: low viral load + low weight gain

value: Porcine Reproductive and Respiratory Syndrome Virus

tag: time (d)

value: blood

tag: breed

value: commercial crossbred pigs


title: pig 1456 at 0 day vs. at 42 day 1456_0_42

value: low viral load + high weight gain


title: pig 1456 at 0 day vs. at 28 day 1456_0_28


title: Cerebellum_WildType_REP2

description:
Wt2_Mousegenome430_2.0.CEL
Gene expression data from, wild type cerebellum cells replicate 2


title: Bos taurus BL20 control rep3

description: This sample is of the bovine lymphosarcoma cell line BL20 without any treatment, this is the 3rd of 3 replicates

value: uninfected

tag: treatment


title: pig 1366 at 4 day vs. at 0 day 1366_4_0


title: Cerebellum_WildType_REP3

description:
Wt3_Mousegenome430_2.0.CEL
Gene expression data from, wild type cerebellum cells replicate 3


title: 2044B

source_name: Chaos3 Mammary Tumor Cell Line

value: C3H (C3H/HeNCrl)

value: female

value: Mammary Tumor

source_name: C3H WT Control

value: WT Control

value: reference


title: 12353A

source_name: Chaos3 Mammary Tumor


title: pig 1405 at 0 day vs. at 11 day 1405_0_11


title: 12115B

value: congenic Chaos3+/+ mouse control


title: pig 1405 at 0 day vs. at 14 day 1405_0_14


title: 12352

value: Mcm4Chaos3/Chaos3 ('Chaos3') mouse


title: pig 1366 at 42 day vs. at 0 day  1366_42_0


title: pig 1405 at 0 day vs. at 7 day 1405_0_7


title: pig 1456 at 0 day vs. at 11 day 1456_0_11


title: pig 1456 at 0 day vs. at 14 day 1456_0_14


title: pig 1366 at 7 day vs. at 0 day 1366_7_0


title: pig 1405 at 0 day vs. at 4 day 1405_0_4


title: 16168


title: pig 1405 at 0 day vs. at 42 day 1405_0_42


title: pig 1456 at 0 day vs. at 7 day 1456_0_7


title: pig 1491 at 28 day vs. at 0 day 1491_28_0

value: high viral load + low weight gain


title: pig 1405 at 0 day vs. at 28 day 1405_0_28


title: pig 1491 at 42 day vs. at 0 day 1491_42_0


title: pig 1366 at 11 day vs. at 0 day  1366_11_0


title: pig 1502 at 0 day vs. at 42 day 1502_0_42


title: pig 1456 at 0 day vs. at 4 day 1456_0_4


title: pig 1491 at 11 day vs. at 0 day 1491_11_0


title: pig 1366 at 14 day vs. at 0 day  1366_14_0


title: 15259


title: GR4

description:
PC9 GR4
Gefitinib-resistant PC9 cells with EGFR Del E746_A750/T790M.

source_name: PC9 NSCLC cells, WZ4002 sensitive

value: no


title: 11929A


title: pig 1491 at 14 day vs. at 0 day 1491_14_0


title: pig 1502 at 0 day vs. at 28 day 1502_0_28


title: pig 1491 at 7 day vs. at 0 day 1491_7_0


title: pig 1502 at 0 day vs. at 7 day 1502_0_7


title: pig 1502 at 0 day vs. at 4 day 1502_0_4


title: pig 1502 at 0 day vs. at 14 day 1502_0_14


title: pig 1502 at 0 day vs. at 11 day 1502_0_11


title: pig 1491 at 4 day vs. at 0 day 1491_4_0


title: pig 1540 at 0 day vs. at 4 day 1540_0_4

value: high viral load + high weight gain


title: pig 1540 at 0 day vs. at 7 day 1540_0_7


title: pig 1540 at 0 day vs. at 14 day 1540_0_14


title: pig 1530 at 0 day vs. at 42 day 1530_0_42


title: pig 1540 at 0 day vs. at 28 day 1540_0_28


title: pig 1402 at 0 day vs. at 42 day 1402_0_42


title: pig 1402 at 0 day vs. at 11 day 1402_0_11


title: pig 1402 at 0 day vs. at 7 day 1402_0_7


title: 12351L


title: pig 1530 at 0 day vs. at 14 day 1530_0_14


title: pig 1402 at 0 day vs. at 28 day 1402_0_28


title: pig 1540 at 0 day vs. at 11 day 1540_0_11


title: pig 1540 at 0 day vs. at 42 day 1540_0_42


title: pig 1530 at 0 day vs. at 28 day 1530_0_28


title: pig 1518 at 42 day vs. at 0 day 1518_42_0


title: pig 1402 at 0 day vs. at 14 day 1402_0_14


title: pig 1522 at 28 day vs. at 0 day 1522_28_0


title: pig 1402 at 0 day vs. at 4 day 1402_0_4


title: pig 1530 at 0 day vs. at 7 day 1530_0_7


title: pig 1530 at 0 day vs. at 4 day 1530_0_4


title: pig 1518 at 11 day vs. at 0 day 1518_11_0


title: pig 1522 at 42 day vs. at 0 day 1522_42_0


title: pig 1522 at 14 day vs. at 0 day 1522_14_0


title: pig 1530 at 0 day vs. at 11 day 1530_0_11


title: pig 1518 at 7 day vs. at 0 day 1518_7_0


title: shRNA-Control- pSUPER gfp-neo transfected SMS-CTR cells

status: Public on Sep 13 2012

city: suzhou

first: shouli

last: wang

address: renai road 199, suzhou industrial park

department: pathology

country: China

institute: soochow university school of medicine

description: replicate 1

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal.

scan_protocol: Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: SMS-CTR cells,stably transfected with shRNA-Control- pSUPER gfp-neo vector

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis. Please refer to “RNA_QC.pdf”

value: SMS-CTR

tag: cell type

value: rhabdmyosarcoma

tag: stable transfection

value: shRNA-Control-pSUPER gfp-neo vector


title: pig 1518 at 4 day vs. at 0 day 1518_4_0

tag: infection

value: Porcine Reproductive and Respiratory Syndrome Virus

value: blood


title: pig 1518 at 28 day vs. at 0 day 1518_28_0

value: low viral load + high weight gain

value: commercial crossbred pigs


title: pig 1522 at 4 day vs. at 0 day 1522_4_0


title: pig 1421 at 42 day vs. at 0 day 1421_42_0


title: pig 1522 at 7 day vs. at 0 day 1522_7_0


title: pig 1420 at 11 day vs. at 0 day 1420_11_0

value: low viral load + low weight gain


title: pig 1420 at 7 day vs. at 0 day 1420_7_0


title: pig 1518 at 14 day vs. at 0 day 1518_14_0


title: pig 1420 at 42 day vs. at 0 day 1420_42_0


title: pig 1421 at 4 day vs. at 0 day 1421_4_0


title: pig 1421 at 11 day vs. at 0 day 1421_11_0


title: pig 1522 at 11 day vs. at 0 day 1522_11_0


title: pig 1421 at 14 day vs. at 0 day 1421_14_0


title: pig 1421 at 7 day vs. at 0 day 1421_7_0


title: pig 1420 at 14 day vs. at 0 day 1420_14_0


title: pig 1420 at 28 day vs. at 0 day 1420_28_0


title: shRNA-Control- pSUPER gfp-neo transfected RD cells

description: replicate 1

source_name: RD cells, stably transfected with shRNA-Control- pSUPER gfp-neo vector

value: RD


title: shRNA-TGF-β1- pSUPER gfp-neo transfected SMS-CTR cells

description: replicate 1

source_name: SMS-CTR cells, stably transfected with shRNA-TGF-β1- pSUPER gfp-neo vector

value: SMC-CTR

value: shRNA-TGF-β1- pSUPER gfp-neo vector


title: shRNA-TGF-β1- pSUPER gfp-neo transfected RH28 cells

source_name: RH28 cells, stably transfected with shRNA-TGF-β1- pSUPER gfp-neo vector


title: shRNA-Control- pSUPER gfp-neo transfected RH28 cells

description: replicate 1

source_name: RH28 cells,stably transfected with shRNA-Control- pSUPER gfp-neo vector


title: SAHA ic10 72 TYPE3 GluMspI

status: Public on Aug 24 2012

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

country: Canada

institute: University of Toronto

description: Transformed human B-lymphocyte cells (GM10851, Coriell Cell Repositories) were treated with the histone deacteylase inhibitor suberoylanilide hydroxamic acid. Treated and untreated DNA was then separately processed using the standard protocol of this study (3 conditions, including genomic DNA glucosylation followed by restriction enzyme digestion).

hyb_protocol: Approximately 9 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. All array sets were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned on an Affymetrix Gene Chip Scanner 3000 7G

data_processing:
We distinguished between three types of probes on the tiling microarray: “target probes”, which contain the restriction site CCGG, “flanking probes”, which do not contain the recognition sequence but could lie up to 200 bp upstream or downstream of a target probe (sheared DNA fragments were of average 200 bp), and “non-target probes” that neither contain a target sequence nor are within 200 bp (on either side) of the target sequence. After comparing different array preprocessing algorithms, we chose to use a sequence-based algorithm after Potter et al (Supplementary Note). The model (Supplementary Note, equation 1) was applied to non-target probes matched proportionally to target probes by GC content.  Normalized intensities were obtained by subtracting the fitted value from raw probe intensities, resulting in a normal distribution of probe-level intensities.  Each chip was independently normalized.  All downstream analyses were carried out at the single-probe level (i.e. without windowing or peak-calling) and solely on target probes. Probes overlapping repeats were excluded. Probes were required to have a ‘CCGG’ in both the Affymetrix probe sequence and the chromosomal sequence downloaded from UCSC; probes that did not meet this criterion were excluded.
EXP2_Human_BrainLiver_sample_metadata.xls, HumanBrain_sample_metadata.xls
BED files of normalized intensities for target probes. Unless otherwise specified, probes overlapping repeats are excluded. Unless otherwise specified, target probes that did not contain a CCGG in the UCSC genome sequence were also excluded.

source_name: Transformed B-lymphocytes (GM10851 cell line)

label_protocol: 9 ug of PCR amplified DNA products were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

growth_protocol: Human and mouse untreated tissues were analyzed in this study

extract_protocol: Genomic DNA was extracted applying standard phenol chloroform and isopropanol precipitation method. Genomic DNA was then sheared to 200bp fragment length on Covaris S2 sonifier (Covaris, USA); blunt ended and ligated to adaptors before subjecting for glucosylation and restriction enzyme digestion. Glucosylation reaction was performed in presence of 200 µM uridine-5’-diphospho-α -D-glucose (UDP-Glc, Sigma) and 80ng BGT (Lariviere, Kurzeck et al. 2002) in 100mM Tris-HCl (pH 8.0) and 25mM MgCl2 for 3 h at 37ºC.

treatment_protocol: No treatment for human and mouse tissues. Only one human cell line underwent SAHA treatment protocol; stated in the sample description.

tag: age (y)

tag: Sex

tag: post-mortem interval

tag: enzymatic digestion

value: 200 ng of glucosylated sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: SAHA ic10 72 TYPE2 GluMspI

tag: tissue

value: Transformed B-lymphocytes (GM10851 cell line)


title: pig 1421 at 28 day vs. at 0 day 1421_28_0


title: CFU-M at day4, biological rep A

first: Wenlian

last: Qiao

state: Ontario

address: Room 1110, 160 College Street

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 machine

data_processing: Gene expression values were normalized using the justRMA function of the affy package from BioConductor

source_name: Lin- cell culture derived samples, day4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Lineage negative cells derived from fresh human umbilical cord blood were cultured in serum free condition supplemented with SCF, THPO and FLT3LG.

extract_protocol: Total RNA was extracted using the RNeasy® Mini kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: CD34-CD33+CD13+ colony forming unit-monocytes (CFU-M) and CD34-CD41+CD61+CD45- megakaryocytes were sorted from pooled fresh cord blood samples on BD FACS Aria (CD34: PE; CD33: APC; CD13: PERCP; CD41: PE; CD61: FITC; CD45: APC. All antibodies were purchased from BD BioScience)

tag: time

value: 4 days in culture


title: pb rep1

status: Public on Sep 12 2012

city: Edinburgh

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

description: gene expression data of phenobarbital treated liver

hyb_protocol: The arrays were washed and stained with the GeneChip® Hybridization Wash and Stain kit (Affymetrix). The washing and staining steps were performed with GeneChip® Fluidics Workstation 450 (Affymetrix).

scan_protocol: Arrays were scanned using a solid-state laser scanner (GeneArray® Scanner 3000 combined with the GeneChip® autoloader, Affymetrix).

data_processing: The Affymetrix GeneChip® Operating Software (GCOS) was used to generate the primary and secondary raw data files.

source_name: whole liver extract

label_protocol: Processing of GeneChip® experiments was conducted as recommended by the manufacturer of the GeneChip® system (Affymetrix). For tissue samples, double stranded cDNA was synthesized with a starting amount of 0.1 µg total RNA. For RNA reverse transcription, the GeneChip® 3′ IVT Express Labelling Assay (lot ID 0904012, Affymetrix) was used in the presence of a T7-(dT)24 DNA oligonucleotide primer (Affymetrix). The cDNA was then transcribed in vitro in the presence of biotinylated ribonucleotides to form biotin-labelled amplified RNA (aRNA). The labelled aRNA was then purified and quantified by UV spectrophotometry at 260 nm and fragmented

growth_protocol: 29–32 days old male B6C3F1/Crl (C57BL/6 ♂ x C3H/He ♀) mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divided into two treatment groups of five animals each. Phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days. Mice were checked daily for activity and behaviour and sacrificed on the last day of dosing (day 28)

extract_protocol: Frozen liver and kidney samples were homogenized in TRIzol reagent (Invitrogen) and subsequently purified on a silica-gel-based-membrane (RNeasy, Qiagen) according to the manufacturer's instructions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer. RNA was stored at −80°C until GeneChip® experiment analysis.

value: Liver

tag: gender

value: male

value: phenobarbital

tag: age

tag: strain

value: B6C3F1/Crl (C57BL/6 male x C3H/He female)


title: CFU-M at day4, biological rep B

value: CD34-CD33+CD13+ colony forming unit-monocytes


title: ndf + progerin

status: Public on Aug 31 2012

city: Los Angeles

first: Lucio

last: Comai

address: 2250 Alcazar Street

institute: University of Southern California

description: Gene Expression data

hyb_protocol: Three micrograms of total RNA was then submitted to the University of Southern California Affymetrix MicroArray Core Facility at Children's Hospital Los Angeles for processing, chip hybridization, and scanning. Gene expression was analyzed on an Affimetrix gene chip Human Genome U133 Plus 2.0 Array,

scan_protocol: A Fluidics Station 400 (Affymetrix) was used to wash and stain the chips and fluorescence was detected using a G2500 GeneArray Scanner (Hewlett-Packard).

data_processing: Raw data were analyzed initially using Microarray Suite version 5.0 (MAS 5.0, Affymetrix)

source_name: human fibroblasts overexpressing progerin

label_protocol: standard Affymetrix protocol

growth_protocol: Primary dermal fibroblast cell line (GM00038) from healthy individual was obtained from the Coriell Cell Repository. Cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% fetal bovine serum, 2 mm l-glutamine, 100 U mL−1 penicillin and 100 µg mL−1 streptomycin at 37 °C in 5% CO2, and 3% O2. Cells seeded at 1.4 × 10exp5 per 100-mm-diameter dish were passaged when cultures reached 85% confluency.

extract_protocol: Total RNA was isolated from each fibroblast line at passage 10 using RNeasy kit from QIAGEN according to the manufacture’s protocol and quantitated by assessing absorbance at 260 and 280 nm using a NanoDropTM 1000 spectrophotometer.

treatment_protocol: When indicated, cells were grown in DMEM supplemented with either 10 nm farnesyltransferase inhibitor L-744832 (Biomol, Plymouth Meeting, PA, USA) or DMSO and 15% fetal bovine serum, 2 mm l-glutamine, 100 U mL−1 penicillin and 100 µg mL−1 streptomycin at 37 °C in 5% CO2, and 3% O2. Media was changed every 4 days.

tag: passage

value: fibroblast

value: overexpressing progerin

tag: cell line


title: ndf + FTI

description: Gene Expression data

source_name: human fibroblasts overexpressing prelamin A treated with FTI


title: pb rep5

treatment_protocol: Phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days

tag: animal id


title: SAHA ic10 30 TYPE3 GluMspI


title: CFU-M at day0, biological rep B

source_name: umbilical cord blood

value: 0 day in culture


title: pb rep4


title: control rep5

description: gene expression data of control liver

value: control


title: control rep2

description: gene expression data of control liver


title: pb rep3


title: SAHA ic10 30 TYPE1 GluMspI


title: SAHA ic10 30 TYPE2 GluMspI


title: ndf + preLA

description: Gene Expression data

source_name: human fibroblasts overexpressing prelamin A

value: overexpressing prelamin A


title: control rep3

description: gene expression data of control liver


title: control rep4

description: gene expression data of control liver


title: pb rep2


title: ndf + progerin + FTI

description: Gene Expression data

source_name: human fibroblasts overexpressing progerin treated with FTI


title: CFU-M at day0, biological rep A


title: ndf control1

description: Gene Expression data

source_name: human fibroblasts


title: ndf + preLA + ZMPSTE24

description: Gene Expression data

source_name: human fibroblasts overexpressing prelamin A and ZMPSTE24

value: overexpressing prelamin A and ZMPSTE24


title: SAHA ctrl 72 TYPE12 GluMspI


title: SAHA ctrl 72 TYPE10 GluMspI


title: SAHA ctrl 72 TYPE11 GluMspI


title: SAHA ctrl 30 TYPE11 GluMspI


title: ndf control 2

description: Gene Expression data


title: SAHA 15 72 TYPE4 GluMspI


title: pig 1420 at 4 day vs. at 0 day 1420_4_0

tag: response

value: low viral load + low weight gain

value: Porcine Reproductive and Respiratory Syndrome Virus

tag: time (d)

value: blood

tag: breed

value: commercial crossbred pigs


title: SAHA 15 72 TYPE5 GluMspI

value: Transformed B-lymphocytes (GM10851 cell line)

value: 200 ng of glucosylated sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: SAHA 15 30 TYPE6 GluMspI


title: SAHA 15 30 TYPE4 GluMspI


title: SAHA 110 72 TYPE9 GluMspI


title: SAHA 15 30 TYPE5 GluMspI


title: SAHA 110 72 TYPE7 GluMspI


title: SAHA 110 72 TYPE8 GluMspI


title: SAHA 110 30 TYPE9 GluMspI


title: SAHA 110 30 TYPE8 GluMspI


title: SAHA 110 30 TYPE7 GluMspI


title: SAHA ctrl 30 TYPE12 GluMspI


title: SAHA ic10 72 TYPE3 HpaII

value: 200 ng of native sheared DNA were subjected to 10 U of HpaII digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: SAHA ic10 72 TYPE1 HpaII


title: SAHA ic10 72 TYPE2 HpaII


title: SAHA 15 72 TYPE6 GluMspI


title: SAHA ctrl 30 TYPE10 GluMspI


title: SAHA ic10 30 TYPE3 HpaII


title: SAHA ctrl 72 TYPE10 HpaII


title: SAHA ic10 30 TYPE1 HpaII


title: SAHA ic10 30 TYPE2 HpaII


title: SAHA ctrl 30 TYPE12 HpaII


title: SAHA ctrl 72 TYPE12 HpaII


title: SAHA ctrl 72 TYPE11 HpaII


title: SAHA ctrl 30 TYPE10 HpaII


title: SAHA 15 72 TYPE4 HpaII


title: SAHA 15 72 TYPE5 HpaII


title: SAHA 15 72 TYPE6 HpaII


title: SAHA 15 30 TYPE5 HpaII


title: SAHA 110 72 TYPE8 HpaII


title: SAHA 15 30 TYPE6 HpaII


title: SAHA 110 72 TYPE9 HpaII


title: SAHA 15 30 TYPE4 HpaII


title: SAHA 110 72 TYPE7 HpaII


title: SAHA 110 30 TYPE9 HpaII


title: SAHA 110 30 TYPE7 HpaII


title: SAHA ic10 72 TYPE3 MspI

value: 200 ng of native sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: SAHA 110 30 TYPE8 HpaII


title: SAHA ic10 72 TYPE2 MspI


title: SAHA ic10 72 TYPE1 MspI


title: SAHA ic10 30 TYPE2 MspI


title: SAHA ic10 30 TYPE3 MspI


title: SAHA ic10 30 TYPE1 MspI


title: SAHA ctrl 72 TYPE11 MspI


title: SAHA ctrl 72 TYPE10 MspI


title: SAHA ctrl 30 TYPE11 MspI


title: SAHA ctrl 30 TYPE11 HpaII


title: SAHA ctrl 72 TYPE12 MspI


title: SAHA ctrl 30 TYPE12 MspI


title: SAHA 15 72 TYPE4 MspI


title: SAHA 15 30 TYPE6 MspI


title: SAHA 15 72 TYPE5 MspI


title: SAHA 15 30 TYPE5 MspI


title: SAHA 15 30 TYPE4 MspI


title: SAHA 110 72 TYPE8 MspI


title: SAHA 110 30 TYPE8 MspI


title: SAHA 110 30 TYPE7 MspI


title: shRNA-TGF-β1- pSUPER gfp-neo transfected RD cells

description: replicate 1

source_name: RD cells, stably transfected with shRNA-TGF-β1- pSUPER gfp-neo vector

value: RD

tag: cell type

value: rhabdmyosarcoma

tag: stable transfection

value: shRNA-TGF-β1- pSUPER gfp-neo vector


title: SAHA ctrl 30 TYPE10 MspI

tag: age (y)


title: SAHA 110 72 TYPE9 MspI

tag: Sex


title: SAHA 15 72 TYPE6 MspI

tag: post-mortem interval


title: SAHA 110 30 TYPE9 MspI

tag: enzymatic digestion


title: hepatocytes_control_biological rep1

status: Public on Aug 22 2012

city: Gliwice

first: Joanna

last: Polanska

address: Akademicka 16

department: Automatic Control

country: Poland

institute: Silesian University of Technology

description: Gene expression data from untreated cells that are able to induce cytoprotective mechanisms following heat shock (somatic cells, in this case - hepatocytes)

hyb_protocol: Biotin-labeled cRNA probe samples were purified, fragmented and hybridized (without DMSO) at 45°C overnight to the Affymetrix GeneChip® Mouse Genome 430 2.0 Array. The arrays were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: The arrays were scanned using a microarray scanner, which is component of the Affymetrix GeneChip Instrument System

data_processing: The data was analyzed with R/Bioconductor and Matlab softwares, RMA algorithm with Dai annotation (Brainarray, version 15.1 dated Jan 2012) were used for data normalization.

source_name: untreated, isolated mouse hepatocytes

label_protocol: cDNA was synthesized from 8 ug of total RNA using the One-Cycle cDNA Synthesis Kit with SuperScriptII polymerase then reverse-transcribed with a T7 RNA polymerase incorporating biotin-labeled nucleotides using the GeneChip IVT Labeling Kit.

extract_protocol:
Hepatocytes were isolated by collagenase type IA perfusion of the liver
Total RNA was isolated using RNeasy® Mini Kit spin columns (Qiagen) according to the manufacturer's instructions.

treatment_protocol: untreated (control)

value: FVB/N

value: male

tag: tissue type

value: liver

value: hepatocytes


title: hepatocytes_heat shock_43_biological rep1

description: Gene expression data from isolated somatic cells (hepatocytes) subjected to heat shock at temperature six centigrade's above physiological

source_name: isolated mouse hepatocytes, heat shock: 43°C

extract_protocol:
Hepatocytes were isolated (after heat shock and recovery) by collagenase type IA perfusion of the liver
Total RNA was isolated using RNeasy® Mini Kit spin columns (Qiagen) according to the manufacturer's instructions.

treatment_protocol: heat shock performed in vivo at 43°C for 30 minutes and 2 hours of recovery


title: SAHA 110 72 TYPE7 MspI

tag: tissue


title: hepatocytes_heat shock_43_biological rep2

tag: gender


title: hepatocytes_control_biological rep3

tag: age


title: spermatocytes_heat shock_43_biological rep2

description: Gene expression data from cells sensitive to damage in elevated temperatures (spermatocytes) after a severe heat shock treatment

source_name: isolated mouse spermatogenic cells enriched with spermatocytes (~80%), heat shock: 43°C

extract_protocol:
Spermatocytes were isolated by unit gravity sedimentation of spermatogenic cells (obtained after collagenase type IA/trypsin/DNase I digestion of decapsulated testes) in 1-3% w/v linear BSA gradient. Finally cells were suspended in RPMI medium supplemented with 10% fetal bovine serum, ,  0.004% gentamycin and 6mM sodium lactate
Total RNA was isolated using RNeasy® Mini Kit spin columns (Qiagen) according to the manufacturer's instructions.

treatment_protocol: heat shock performed on isolated cells at 43°C for 1 hour and 2 hours of recovery at physiological temperature (32°C)

tag: strain

value: testes

value: spermatocytes


title: hepatocytes_control_biological rep2


title: control rep1

description: gene expression data of control liver

value: Liver

tag: treatment

value: control

value: B6C3F1/Crl (C57BL/6 male x C3H/He female)


title: spermatocytes_heat shock_38_biological rep1

description: Gene expression data from cells sensitive to damage in elevated temperatures (spermatocytes) after a mild heat shock treatment

source_name: isolated mouse spermatogenic cells enriched with spermatocytes (~80%), heat shock: 38°C

treatment_protocol: heat shock performed on isolated cells at 38°C for 1 hour and 2 hours of recovery at physiological temperature (32°C)


title: spermatocytes_control_biological rep3

description: Gene expression data from untreated cells sensitive to damage in elevated temperatures (spermatocytes)

source_name: untreated, isolated mouse spermatogenic cells enriched with spermatocytes (~80%)


title: hepatocytes_heat shock_43_biological rep3


title: spermatocytes_heat shock_38_biological rep3


title: spermatocytes_heat shock_43_biological rep3


title: spermatocytes_control_biological rep1

label_protocol: cDNA was synthesized from 8 ug of total RNA using the One-Cycle cDNA Synthesis Kit with SuperScriptII polymerase then reverse-transcribed with a T7 RNA polymerase incorporating biotin-labeled nucleotides using the GeneChip IVT Labeling Kit


title: spermatocytes_heat shock_38_biological rep2


title: spermatocytes_heat shock_43_biological rep1


title: Fibroblast Day zero, Experiment 3

status: Public on Aug 09 2012

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

address: 733 N. Broadway

department: Oncology

institute: Johns Hopkins School of Medicine

description: Individual sample

hyb_protocol: For array assay, 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed. Illumina HumanHT-12 V4.0 expression beadchips were used for each assay.

scan_protocol: Fluorescent signals were obtained by scanning with the iScan System.

data_processing: Data were extracted with Gene Expression Module 1.0.6 in GenomeStudio 1.0.2 and signal intensities from multiple chips comprising this single series were normalized without background subtraction to obtain non-normalized data. Signals for each gene were then log 2 transformed and mean subtracted across all conditions to obtain processed data.

source_name: adult fibroblasts, Coriell Institute, Cat # AG07714, treated as described

label_protocol: 500 ng total RNA from each sample was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) as described in the instruction manual.

extract_protocol: Total RNA was prepared as described in the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion. RNA quality was assessed by Nanodrp-1000 spectrometer for OD260/280 and OD260/230 ratio and Bioanalyzer (Agilent Technologies).

treatment_protocol: Fibroblasts passaged 2-3 days prior to day 0 and then harvested on day zero

value: no 4F no BMSC

tag: time

value: Day +3

value: fibroblast

tag: sample type


title: spermatocytes_control_biological rep2


title: Fibroblast Day+3 +4F Experiment 3

description: Individual sample

treatment_protocol: Fibroblasts passaged 2-3 days prior to day zero, nucleofected with 4F (SOKM) on day zero, and then harvested on day +3

value: Day zero


title: Fibroblast Day+3 +4F Experiment 1

description: Individual sample

value: Fibroblasts passaged 2-3 days prior to day zero, nucleofected with 4F (SOKM) on day zero, and then harvested on day +3


title: Fibroblast Day zero, Experiment 2

description: Individual sample

value: Fibroblasts passaged 2-3 days prior to day 0 and then harvested on day zero


title: Fibroblast Day+3 +4F Experiment 2

description: Individual sample


title: Disc Cells in 3D Control (154)

status: Public on Jun 27 2012

city: Charlotte

first: Helen

last: Gruber

state: NC

address: 1542 Graden Terrace

department: Orthopaedic Surgery

institute: Carolinas HealthCare System

hyb_protocol: Fragmented cRNA was hybridized to the  X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned once via the Affymetrix 3000G scanner.

data_processing: The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).

source_name: Disc Cells in 3D Control

label_protocol: Biotin-labeled cRNA were prepard according to the Affymetrix protocol for IVT labeling.

growth_protocol: Human annulus disc cells (100,000) were seeded into each piece (~0.5 cm3) of a collagen construct (Gelfoam; Pharmacia & Upjohn Co., Kalamazoo, MI). They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 102 pM IL-1beta. Cells were allowed to grow an additional 5 days without changing the media.

extract_protocol: Each piece of Gelfoam was homongenized and RNA isolated using TRIzol reagent

value: annulus disc cells

tag: tissue grade

value: IV

tag: feed media


title: LU998

status: Public on May 17 2012

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Illumina hybridization protocol (Manuell 11322187 Revision A)

scan_protocol: Standard Illumina iScan scanning protocol Scan setting file: Direct Hyb

data_processing: The data were normalised using quantile normalisation implemented in BASE, http://base.thep.lu.se/

source_name: Lung tumor, small cell lung cancer, smoker

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevB

extract_protocol: Total RNA from fresh frozen lung tumor tissue was extracted as described PMID:17334996. RNA concentrations were measured using a Nanodrop (NanoDrop Technologies). RNA integrity was determined by an Agilent Bioanalyzer.

value: lung carcinoma

tag: assay

tag: osbin

tag: os

value: F

tag: smoking

value: smoker

tag: tnm

tag: Stage

value: IA

tag: histology

value: LCNEC


title: SAHA ic10 72 TYPE1 GluMspI

source_name: Transformed B-lymphocytes (GM10851 cell line)

tag: age (y)

tag: Sex

tag: post-mortem interval

tag: cell line

tag: enzymatic digestion

value: 200 ng of glucosylated sheared DNA were subjected to 10 U of MspI digestion in a final volume of 20 µl for 12 h at 37ºC (50 fold surplus of the enzyme over the DNA substrate), followed by enzyme inactivation at 80ºC for 10 min.


title: LU804

source_name: Lung tumor, adenocarcinoma, never smoker

tag: tissue

tag: age

value: IB

value: AC


title: LU89

value: M

value: neo

value: SCLC


title: LU80

value: IIB


title: LU821


title: LU87


title: LU79


title: LU887


title: Fibroblast Day zero, Experiment 1

description: Individual sample

tag: time

value: Day -3

tag: cell type

value: fibroblast

tag: sample type


title: Disc Cells in 3D Control (95)

treatment_protocol: They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 102 pM IL-1beta. Cells were allowed to grow an additional 5 days without changing the media.

tag: tissue grade

tag: feed media


title: LU583

tag: assay

tag: osbin

tag: os

value: IIA


title: LU635

tag: smoking

tag: tnm

tag: Stage


title: LU740

source_name: Lung tumor, small cell lung cancer

tag: Sex

value: IIIA

tag: histology


title: LU702


title: LU628


title: Disc Cells in 3D Control (126)

value: annulus disc cells

value: III


title: LU70

source_name: Lung tumor, adenocarcinoma, smoker

value: lung carcinoma


title: LU510

value: F

value: smoker


title: LU485


title: LU468

source_name: Lung tumor, squamous cell carcinoma, smoker


title: LU473


title: LU464


title: LU500

value: SqCC


title: LU48


title: LU66


title: LU460

value: IA


title: LU427


title: LU486

source_name: Lung tumor, squamous cell carcinoma, never smoker


title: LU449


title: LU444

value: IB


title: LU418

value: AC


title: LU434


title: LU436

value: LCNEC


title: LU409

source_name: Lung tumor, squamous cell carcinoma

value: M


title: LU382


title: LU375


title: LU352


title: LU376


title: LU324


title: LU398


title: LU318


title: LU38

source_name: Lung tumor, adenocarcinoma


title: LU330


title: LU348


title: LU454


title: LU350

value: SCLC


title: LU372


title: LU355

value: neo


title: LU324492


title: LU295


title: LU402


title: LU370


title: LU320

value: IIB


title: LU302


title: LU276


title: LU257


title: LU272


title: LU2


title: LU262


title: LU271


title: LU277

value: IA-IIIA


title: LU219


title: LU164


title: LU190


title: LU145


title: Anaplastic thyroid carcinoma biological replicate 2

status: Public on Mar 14 2012

city: Bronx

first: Antonio

last: Di Cristofano

address: 1301 Morris Park Ave Price 302

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Analized with Expression Console (RMA).

source_name: thyroid gland

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

extract_protocol: Trizol extraction followed by Quiagen Rneasy column purification.

tag: tumor type

value: anaplastic tumor

value: 8-10 months


title: LU111

value: IIIA


title: LU1054


title: Anaplastic thyroid carcinoma biological replicate 3


title: LU136


title: LU123


title: LU971


title: Anaplastic thyroid carcinoma biological replicate 4


title: LU137


title: LU143


title: Anaplastic thyroid carcinoma biological replicate 5


title: Follicular thyroid carcinoma biological replicate 5

value: follicular tumor

value: 16-20 months


title: LU14

value: lung carcinoma

value: F


title: LU16

value: smoker


title: Follicular thyroid carcinoma biological replicate 4


title: Anaplastic thyroid carcinoma biological replicate 1


title: Pten-/- male biological replicate 1

description: Pten-/- male 1

tag: strain background

tag: genotype/variation

value: Pten-/-

value: male

value: 2-4 months


title: Follicular thyroid carcinoma biological replicate 1

tag: age


title: p53-/- female biological replicate 2

description: p53-/- female 2

value: female

value: 2 months


title: Pten,p53-/- female biological replicate 3

description: Pten,p53-/- female 3


title: Pten-/- female biological replicate 1

description: Pten-/- female 1


title: Pten-/- male biological replicate 2

description: Pten-/- male 2


title: Pten,p53-/- female biological replicate 1

description: Pten,p53-/- female 1


title: Pten-/- male biological replicate 3

description: Pten-/- male 3


title: Follicular thyroid carcinoma biological replicate 3


title: Pten,p53-/- female biological replicate 2

description: Pten,p53-/- female 2


title: p53-/- female biological replicate 1

description: p53-/- female 1


title: Follicular thyroid carcinoma biological replicate 2


title: p53-/- female biological replicate 3

description: p53-/- female 3


title: Pten-/- female biological replicate 3

description: Pten-/- female 3


title: Pten-/- female biological replicate 2

description: Pten-/- female 2


title: wild type female biological replicate 3

description: wild type female 3

value: wild type


title: 2.7_1

status: Public on Jan 11 2012

city: Santiago

first: Felipe

middle: F

last: Aceituno

address: Vicuña Mackena 4860

department: Chemical Engineering and Bioprocesses

country: Chile

institute: PUC

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Yeast Genome 2,0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000 7G.

data_processing: The data were analyzed in R with the affy, affyQCReport and simpleaffy packages from Bioconductor. Data was normalized using the RMA algorithm.

organism: Saccharomyces cerevisiae EC1118

source_name: nitrogen-limited cultures sparged with 5% oxygen, with 4 micromolar dissolved oxygen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: cells were grown in chemostats with a  syntethic must medium (MS300), custom modified to achieve nitrogen limitation  with d=0.1 h-1, pH=3.5

extract_protocol: RNA was extracted from frozen cell pellets using the AxyPrep Multisource RNA kit (Axygen Biosciences, USA), modified for the use with glass beads for cell lysis. Briefly, we resuspended the cell pellet in the R-I kit buffer, added it to a screw-cap tube containing 250 µl of 500 µm acid-washed glass beads (Sigma, USA). We stirred the tubes in three cycles of 45 s in a Mini Bead BeaterTM (Biospec), standing an equivalent time in ice between cycles. Later, the lysate was centrifuged at 10.000 x g and supernatant was transferred to a tube with 250 µl of isopropanol. After this point, we followed the kit manufacturer instructions.

treatment_protocol: cultures were sparged with different oxygen/nitrogen mixtures to achieve different dissolved oxygen concentration. When reached the culture steady state for each level, samples were taken and inmediately placed on crushed ice. Afterwards, they were centrifuged at max. speed, eliminated the supernatant and the cell pellet frozen in liquid nitrogen and stored at -80ºC until analysis

tag: condition


title: 2.7_2

value: nitrogen-limited cultures sparged with 5% oxygen, with 4 micromolar dissolved oxygen


title: 2.7_3


title: 5_1

source_name: nitrogen-limited cultures sparged with 20% oxygen, with 11 micromolar dissolved oxygen


title: 5_3

value: nitrogen-limited cultures sparged with 20% oxygen, with 11 micromolar dissolved oxygen


title: 5_2


title: wild type male biological replicate 2

description: wild type male 2


title: wild type female biological replicate 1

description: wild type female 1


title: wild type female biological replicate 2

description: wild type female 2


title: wild type male biological replicate 1

description: wild type male 1


title: 1.2_3

source_name: nitrogen-limited cultures sparged with 1% oxygen, with 0.8 micromolar dissolved oxygen


title: LU415

tag: tissue

value: IB

value: AC


title: wild type male biological replicate 3

description: wild type male 3


title: 1.2_2

value: nitrogen-limited cultures sparged with 1% oxygen, with 0.8 micromolar dissolved oxygen


title: 0_3

source_name: nitrogen-limited cultures in fully anaerobic conditions


title: 1.2_1


title: 0_1

value: nitrogen-limited cultures in fully anaerobic conditions


title: 0_2


title: WT_40 vs dh_40 hyb23

status: Public on Jan 01 2012

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

hyb_protocol: Hybridization buffer (Agilent In Situ Hybridization Kit Plus) was added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers at 65 degrees Celcius for 17 h. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: scanned slides were Lowess normalised using Prep (van Hijum, Applied Bioinformatics 2003 2(4):241-244). Interslide scaling was performed using Postprep (van Hijum, Applied Bioinformatics 2003 2(4):241-244).

organism: Lactiplantibacillus plantarum WCFS1

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Cultures were grown in a fermentor in MRS with a of pH 5.8, at 125 rpm, and at 28 or 40 degrees Celcius

extract_protocol: Cultures were lysed by beat-beating and total RNA was isolated by subsequent fenol extraction

treatment_protocol: Harvested cultures were quenced in extraction mix containing Phenol/Chloroform, SDS, Na-acetate, glass-beads and TE buffer.

tag: strain

tag: genotype

value: WT

tag: treatment

value: dh


title: dcdh_28 vs dc_28 hyb19

value: dcdh

value: dc


title: DC_28 vs dc_40 hyb17

value: DC


title: dcdh_40 vs WT_28 hyb24


title: dh_28 vs dc_40 hyb22


title: dc_28 vs WT_28 hyb18


title: dh_40 vs dh_40 hyb15


title: dc_40 vs WT_40 hyb16


title: dcdh_40 vs dcdh_40 hyb11


title: dcdh_40 vs dc_40 hyb9


title: WT_40 vs dh_40 hyb10


title: dc_28 vs dcdh_28 hyb8


title: dh_40 vs dcdh_28 hyb20


title: WT_28 vs dh_28 hyb12


title: dh_40 vs dcdh_40 hyb13


title: dh_28 vs WT_40 hyb7


title: WT_40 vs WT_28 hyb14


title: dH28 vs WT_28 hyb4


title: WT_40 vs dc_40 hyb5


title: CRD vs 332NT

status: Public on Mar 10 2012

city: Daejeon

first: Myung Soon

last: Kim

address: Yeusung-gu

department: R&D

country: South Korea

institute: Genomictree

description: methylation profiling in 332NT sample

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential Oligo aCGH/ChIP-on-chip Wash buffer1, 2, ACN, and Stabilization and Drying Solution as following manufacturer's instructions.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.3.2.1).

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

source_name: CRD

label_protocol: 4 µg of amplified enriched DNA were labeled using Bioprime kit as following manufacturer's instructions

extract_protocol:
genomic DNA extracted using Qiaquick DNA mini kit following manufacturer's instructions
enrichment protocol: 0.5ug sonicated gDNA was incubated with MBD2bt protein, and then purification using Magnetic bead.

tag: sample type

value: pooled DNA of 12 adjacent normal samples

value: enriched methylated DNA of adjacent normal tissue


title: WT_28 vs dh_28 hyb2


title: dcdh_40 vs dc_28 hyb21


title: dc_40 vs dcdh_28 hyb3


title: dcdh_28 vs dc_28 hyb1


title: dhdc_28 vs dh_28 hyb6

value: dhdc


title: P1 mouse eyeball extracted total RNA_wt3

status: Public on Jan 01 2011

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

hyb_protocol: 2.2 micrograms of cDNA was hybridized for 17 hr to the Affymetrix array as described in the Ovation™ Biotin RNA Amplification and Labeling System manual. Genechips® were processed using protocol EukGE_WS2v4 450 for Genechip® fluidics station 450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring 7.2 program. No further adjustments were made to the data in the table.

label_protocol: 50 ng total RNA was amplified using the NUGEN Ovation™ Biotin RNA Amplification and Labeling System. Amplified cDNA was fragmented and biotin labeled according to manufacturer's instructions.

growth_protocol: Newborn Brg1 lens-conditional knockout and wildtype mouse pups were used.

extract_protocol: Total RNA was extracted using RNeasy micro-elute columns (QIAGEN), according to manufacturer's instructions.

treatment_protocol: Newborn Brg1 lens-conditional knockout and wildtype mouse eyeballs were dissected.

value: eyeballs

value: mixed background (Gebuhr TC, Kovalev GI, Bultman S, Godfrey V, Su L, Magnuson T. The role of Brg1, a catalytic subunit of mammalian chromatin-remodeling complexes, in T cell development. J Exp Med. 2003 Dec 15;198(12):1937-49.)


title: P1 mouse eyeball extracted total RNA_Brg1_cKO1

value: Brg1 cKO


title: P1 mouse eyeball extracted total RNA_Brg1_cKO2


title: P1 mouse eyeball extracted total RNA_wt2

value: wild type


title: P1 mouse eyeball extracted total RNA_Brg1_cKO3


title: C2 corrected_A2_tumor

status: Public on Mar 07 2011

city: Hannover

first: Astrid

last: Rohrbeck

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Department of Toxicology

institute: Medizinische Hochschule Hannover

description:
Lung samples were derived from SP-C/c-raf mice in the C57BL/6 background for at least five generations (aged 5 – 14 months); tumor cells were isolated from 11 – 14 month old mice, unaltered lung tissue were isolated from the dysplasia-bearing transgenic mouse (aged 5 – 7 months). Endogenous normal lung tissue was studied of non-transgenic mice (aged 7 – 10 months). The non-transgenic littermates (wild-type) served as control for transgenic effects.
Mice were sacrificed and the lung tissues were immediately frozen on dry ice and stored at -80°C until further analysis.

hyb_protocol: Following fragmentation, labeled cRNA of each sample was hybridized to Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays covering over 34.000 genes and stained according to the manufacturer's instructions. The hybridization was performed for 16 hours at 60 rpm and 45°C in the GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays were done on the Gene Chip® Fluidics Station 400 (Affymetrix) according to the manufacturers recommendation. The antibody signal amplification, washing and staining protocol (Affymetrix) was used to stain the arrays with streptavidin R-phycoerythrin (SAPE). To amplify staining, SAPE solution was added twice with a biotinylated anti-streptavidin antibody (Vector Laboratories, CA) staining step in between

scan_protocol: The arrays were scanned using the Affymetrix GeneChip® Scanner 7G. Scanned image files was visually inspected for artefacts and then analyzed, each image being scaled to the same target value for comparison between chips. The GeneChip® Operating Software (GCOS) was used to control the fluidics station and the scanner, to capture probe array data and to analyze hybridization intensity data.

data_processing:
Array data was normalized using scaling or per-chip normalization to adjust the total or average intensity of each array to be approximately the same.
Microarray chips were analyzed by the GCOS (GeneChip Operating Software) from Affymetrix with the default settings except that the target signal was set to 500 and used to generate a microarray quality control and data report.
CEL files exported from GCOS were uploaded into ArrayTrack software (National Center for Toxicological Research, U.S. FDA, Jefferson, AR, USA (NCTR/FDA)) and normalized using Total Intensity Normalization after subtracting backgrounds for data management and analysis. ArrayTrack software includes some tools common to other bioinformatics software (e.g., ANOVA, T-test and SAM).To compare the normalized data from dysplasia, normal lung tissue from transgenic mouse, tumor cells and non-transgenic of different mice, we used the Significance Analysis of Microarrays (SAM) algorithm (ArrayTrack), which contains a sliding scale for false discovery rate (FDR) of significantly up- and down-regulated genes. All data were permuted 100 cycles by using the two classes, unpaired data mode of the algorithm. As cut-off for significance an estimated FDR of 0.001 was chosen. Moreover, a cut-off for fold-change of differential expression of 2 was used.
Two clustering approaches were used to determine components of variation in the data in this study as follows.
A) Principal-component analysis (PCA) that was used to obtain a simplified visualization of entire datasets. PCA is a useful linear approach to obtain a simplified visualization of entire datasets, without losing experimental information (variance). PCA allowed the dimension of complex data to be reduced and highlights the most relevant features of a given dataset to be highlighted.
B) Hierarchical gene clustering (HCA) where the data points were organized in a phylogenetic tree in which the branch lengths represent the degree of similarity between the values.

label: Biotin

source_name: C2 corrected_A2_tumor, lung tissue

label_protocol: Total RNA (175ng) was used to generate biotin-labeled cRNA (10 µg) by means of Message Amp aRNA Premium Amplification Kit (Ambion, Austin, TX). Quality control of cRNA was performed using a bioanalyzer (Agilent 2001 Biosizing, Agilent Technologies).

extract_protocol:
From each frozen lung tissue 10-µm thick sections were prepared and transferred on polyethylene napthalate foil-covered slides (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany).
The sections were fixed in methanol / acetic acid and stained in hematoxylin. The desired cells were microdissected using the PALM MicroLaser systems (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany) and collected in an adhesive cap (Zeiss, P.A.L.M. Microlaser Technologies GmbH, Bernried, Germany). Microdissected cells were resuspended in a guanidine isothiocyanate-containing buffer (RLT buffer from RNeasy MikroKit, Qiagen, Santa Clarita, CA, USA) with 10 µl/ml β-mercaptoethanol to ensure isolation of intact RNA. Approximately an area of 6 x 106 µm2 were pooled from a specific layer of interest in the same animal and used for RNA extraction.
Following microdissection, total RNA-extraction was performed with the RNeasy Micro Kit (RNeasy MicroKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction. A standard quality control of the total RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

tag: spc-c-raf transgenic mice, age

value: 7 month old, Gender:male, Tissue:unaltered


title: Macrophage culture, ID 6, TNFa

status: Public on Mar 01 2010

city: New York

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: Macrophage culture, ID 6, TNFa

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with lumi package in R.

source_name: Macrophages culture

label_protocol: Biotinylated cRNA were prepared with the Ambion Message Amp Premier RNA Amplification kit.

growth_protocol: Peripheral blood mononuclear cells from normal blood donor buffy coats were purified by gradient centrifugation with Ficoll-Paque Plus, and collected at the interface. Monocytes were isolated by plastic adherence. Macrophages were generated by culturing monocytes for 7 days in RPMI  supplemented with Human M-CSF (50ng/ml) plus 1% HSA.

extract_protocol: Cells were harvested in RLT buffer and stored in -800C for RNA extraction.RNA was extracted from cultured macrophages using the RNeasy Mini KIT (Qiagen, Valencia, CA, U.S.A.).

treatment_protocol: Macrophages were cultured for an additional 24 hours in RPMI supplemented with 20 ng/ml IFN-g (for M1 polarization), 25ng/ml IL-4 (for M2 polarization), 20ng/ml TNF-a, 1 ug/ml LPS, and 1 ug/ml LPS plus 20ng/ml IFN-g.

tag: ID

tag: treatment group

value: TNFa

tag: cell type

value: cultured macrophages

tag: batch

tag: line

value: L


title: Macrophage culture, ID 6, LPSandIFNg

description: Macrophage culture, ID 6, LPSandIFNg

value: LPS and IFNg

value: B


title: P1 mouse eyeball extracted total RNA_wt1

city: LYON


title: Psoriasis skin, ID P 002, LS

description: Psoriasis skin, ID P 002, LS

source_name: Psoriasis Lesional skin

value: skin

tag: disease status

value: lesional psoriasis

value: D


title: Psoriasis skin, ID P 004, LS

description: Psoriasis skin, ID P 004, LS

value: F


title: Psoriasis skin, ID P 001, NL

description: Psoriasis skin, ID P 001, NL

source_name: Psoriasis Non-lesional skin

value: non-lesional psoriasis

value: C


title: Psoriasis skin, ID P 005, NL

description: Psoriasis skin, ID P 005, NL

value: G


title: Psoriasis skin, ID P 003, NL

description: Psoriasis skin, ID P 003, NL

value: E