title: WT|NEX2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: control tissue

hyb_protocol: The gene array chips were hybridized in a shaker-incubator at 37°C at 300 rpm for 18 hours and washed and stained with Cy5-Streptavidin according to the recommendations of the manufacturer (Amersham Biosciences).

scan_protocol: The DNA Microarray scanner of Agilent was used for scanning and image analysis was performed with the Codelink Expression Analysis 4.1 software.

data_processing: Statistical data analysis was performed on the mean foreground and median background intensities, as provided by the Codelink Expression Analysis 4.1 software.  All probes that were flagged as manufacturing spot removed (M), irregular (I), and saturated (S) by the Codelink Expression Analysis software, were removed, prior to the normalization. Data were background corrected; in case, this results in a negative value, the background corrected intensity for that spot was set equal to 0.5. All data were normalized with quantile normalization and base 2 log-transformed.

label: Biotin Streptavidin Cy5

source_name: neocortex and hippocampal tissue E14.5

label_protocol: Total RNA was controlled for integrity and purity using an Agilent Bioanalyzer and a NanoDrop spectrophotometer, respectively. All samples were of similar RNA quality. Starting with 1ug of total RNA, the RNA amplification was performed by in vitro transcription (IVT) with a biotin labeling reaction during the IVT, according to the recommendations of the manufacturer (Amersham Biosciences).  The probes were purified and analyzed again for yield (> 20 ug) and purity (260:280 nm and 260:230 nm >1.8). Ten micrograms of the resulting antisense RNA was fragmented according to the recommendations of the manufacturer (Amersham Biosciences) and resuspended in 260ul of hybridization buffer.

growth_protocol: Fresh frozen dissected tissue was kept at -80° till use.

extract_protocol: RNA from mouse neocortex and hippocampus tissues was isolated using RNeasy kit according to the manufacturer’s protocol (QIAGEN).Total RNA was controlled for integrity and purity using an Agilent Bioanalyzer and a NanoDrop spectrophotometer, respectively

treatment_protocol: Neocortex and hippocampal tissue was dissected in ice-cold PBS and frozen immediately at -80°C till use

value: neocortex and hippocampal tissue

tag: develomental stage

value: Embryonic day E14.5

tag: genotype/variation

value: wildtype Sip1


title: WT|Nestin2.2

status: Public on Oct 30 2009

type: RNA

description: control tissue

molecule: total RNA

organism: Mus musculus

source_name: neocortex and hippocampal tissue E18.5

tag: tissue

value: Embryonic day E18.5


title: Sip1|Nestin2.1

description: knockout tissue

value: Sip1 knockout mutant


title: Frontonasal mass prominence, biological rep3

city: Vancouver

first: Joy

last: Richman

state: BC

address: 2350 Health Sciences Mall

department: Oral Health Sciences

country: Canada

institute: University of British Columbia

description: Gene expression data from stage 18 frontonasal mass prominences, between the nasal pits

hyb_protocol: Hybridization was performed as described in the GeneChip Expression Analysis Technical Manual by the London Regional Genomics Centre, London, Ontario, Canada

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000

data_processing: The data were analyzed with GCOS1.4  using Affymetrix default analysis settings and Scaling within 3 fold of each other as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

label: biotin

organism: Gallus gallus

source_name: Stage 18 chicken embryos

label_protocol: Biotinylated cRNA were prepared according to two-cycle Affymetrix protocol from 500 ng total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Embryos were incubated at 38 degrees C until they reached Hamburger Hamilton Stage 18

extract_protocol: Qiagen RNAeasy kit was used.

treatment_protocol: No treatment was done to the embryos. These are normal tissues.

value: Mesenchyme plus epithelium

tag: genotype

value: Unknown

tag: age

value: Hamburger Hamilton stage 18


title: Mandibular prominence, biological rep1

description: Gene expression data from stage 18 mandibular prominences


title: Sip1|NEX1

description: knockout tissue


title: Sip1|NEX2

description: knockout tissue


title: P10 7d SNI; Biological replicate 6

city: London

first: Caroline

middle: Emma

last: Johnston

address: 125 Coldharbour Lane

country: United Kingdom

institute: Kings College London

description: Global gene expression

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

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

data_processing: The Bioconductor affy library was used to import CEL file data and the gcrma library was used to normalize the raw data.

label: Biotin

organism: Rattus norvegicus

source_name: Rat spinal dorsal horn

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

growth_protocol: Standard laboratory rodent housing, with free access to water and food and were exposed to a 12:12 hour on/off light cycle. Pups left with mothers following surgery.

extract_protocol: Trizol extraction of total RNA.

treatment_protocol: SNI surgery was performed where the tibial and common peroneal branches of the sciatic nerve were tightly ligated with a silk suture and transected distally, while the sural nerve was left intact (Decosterd and Woolf, 2000). In sham-operated controls, the sciatic nerve was exposed but not ligated. Operation performed under isofluorane.

tag: strain

value: Sprague-Dawley

value: spinal cord (ipsilateral dorsal horn)

tag: developmental stage

value: Neonate (P10)

tag: treatment group

value: 7 day post sciatic nerve SNI injury


title: P10 7d SNI; Biological replicate 5

description: Global gene expression


title: WT|Nestin2.1

description: control tissue


title: Sip1|Nestin1.2

description: knockout tissue


title: P10 7d SNI; Biological replicate 4

description: Global gene expression


title: Mandibular prominence, biological rep2


title: Sip1|Nestin2.2

description: knockout tissue


title: WT|Nestin1.2

description: control tissue


title: Sip1|Nestin1.1

description: knockout tissue


title: WT|NEX1

description: control tissue


title: WT|Nestin1.1

description: control tissue


title: P10 Sham; Biological replicate 3

description: Global gene expression

value: sham


title: P10 Sham; Biological replicate 4

description: Global gene expression


title: P10 Sham; Biological replicate 5

description: Global gene expression


title: P10 7d SNI; Biological replicate 3

description: Global gene expression


title: P10 Sham; Biological replicate 6

description: Global gene expression


title: P10 7d SNI; Biological replicate 2

description: Global gene expression


title: Adult 7d SNI; Biological replicate 4

description: Global gene expression

value: Adult (8-12wks)


title: P10 Sham; Biological replicate 2

description: Global gene expression


title: Adult 7d SNI; Biological replicate 3

description: Global gene expression


title: Adult 7d SNI; Biological replicate 1

description: Global gene expression


title: Adult 7d SNI; Biological replicate 5

description: Global gene expression


title: P10 7d SNI; Biological replicate 1

description: Global gene expression


title: Adult 7d SNI; Biological replicate 2

description: Global gene expression


title: P10 Sham; Biological replicate 1

description: Global gene expression


title: Adult Sham; Biological replicate 6

description: Global gene expression


title: Embryo_WT_48hpf_biological rep 4

city: Dunedin

first: Julia

last: Horsfield

address: Cnr Hanover and Great King Streets

department: Pathology Department

country: New Zealand

institute: University of Otago

description: Gene Expressiondata from WTat 48hpf

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)  using  Affymetrix GeneChip® Hybrisiation Oven 640

scan_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)  using Affymetrix GeneChip® Scanner 7G

data_processing: After QC using GCOS and dCHhip, probe level data were background corrected, normalised and summarised using the default RMA method (PM only) in the Affy package of the R statistical environment.

organism: Danio rerio

label_protocol: Total RNA was labelled using Affymetrix GeneChip® One-Cycle Target Labeling and Control Reagents Kit Cat #  900493 using standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

growth_protocol: Embryos were kept  in embryo medium at 28 degrees celcius until collected for RNA extraction.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and purfied using Qiagen Rneasy columns.

treatment_protocol: Rad21nz171 homozgous mutant embryos were compared to wild type embryos at the same developmental time.

value: Dechorionated embryo

value: wild type

tag: time point

value: 48 hours post-fertilization


title: Embryo_WT_24hpf_biological rep 4

description: Gene Expressiondata from WT at 24hpf

value: 24 hours post-fertilization


title: Embryo_Rad21 mutant_48hpf_biological rep 2

description: Gene Expressiondata from Rad21 mutants at 48hpf

source_name: Embryo_Rad21 mutant_48hpf

value: Rad21 mutant


title: Embryo_WT_48hpf_biological rep 2

description: Gene Expressiondata from WTat 48hpf


title: Embryo_WT_48hpf_biological rep 1

description: Gene Expressiondata from WTat 48hpf


title: Embryo_Rad21 mutant_48hpf_biological rep 1


title: Embryo_Rad21 mutant_48hpf_biological rep 3


title: Embryo_WT_24hpf_biological rep 3

description: Gene Expressiondata from WT at 24hpf


title: Adult Sham; Biological replicate 3

description: Global gene expression


title: Embryo_Rad21 mutant_48hpf_biological rep 4


title: Embryo_WT_24hpf_biological rep 2

description: Gene Expressiondata from WT at 24hpf


title: Adult 7d SNI; Biological replicate 6

description: Global gene expression


title: Embryo_WT_24hpf_biological rep 1

description: Gene Expressiondata from WT at 24hpf


title: Embryo_Rad21 mutant_24hpf_biological rep 3

description: Gene Expressiondata from Rad21 mutants at 24hpf

source_name: Embryo_Rad21 mutant_24hpf


title: Adult Sham; Biological replicate 4

description: Global gene expression


title: Adult Sham; Biological replicate 5

description: Global gene expression


title: Adult Sham; Biological replicate 2

description: Global gene expression


title: Adult Sham; Biological replicate 1

description: Global gene expression


title: Embryo_Rad21 mutant_24hpf_biological rep 4


title: Embryo_Rad21 mutant_24hpf_biological rep 2


title: Embryo_Rad21 mutant_24hpf_biological rep 1


title: Embryo_WT_48hpf_biological rep 3

description: Gene Expressiondata from WTat 48hpf


title: Sham 4

city: Houston

first: Scott

middle: E

last: Evans

state: TX

address: 1400 Holcombe Blvd

department: Pulmonary Medicine - Unit 1462

country: USA

institute: University of Texas-M.D. Anderson Cancer Center

description: Sham treated

hyb_protocol: cRNA was hybridized to BeadChips per Illumina instructions.

scan_protocol: Chips were scanned using level 3 signal using a BeadStation 500 scanner.

data_processing: Data was processed using Illumina BeadStudio v3.  Matrix tables were generated both without normalization and with rank invariant normalization, using sham group as the reference group.

source_name: 2h treatment of MLE-15 cells

label_protocol: cRNA was hybridized to BeadChips prior to labeling with Cy3-Streptavidin per Illumina instructions.

growth_protocol: MLE-15s grown in monolayer to approximately 80% confluence in 6 well plates

extract_protocol: total RNA extracted using Qiagen Rneasy per manufacturers instructions.  cRNA amplification using Ambion total prep kit per manufacturers instructions.

treatment_protocol: MLE-15 cells were treated with PBS, ODN2395 (0.4 ug), Pam2CSK4 (0.2 ug) or ODN2395+Pam2CSK4 for 2 hours. For each, a 20 ul volume of the treatment was added to a 500 ul volume of RPMI for each well of 6-well tissue culture plates.

tag: cell type


title: ODN2395 5

description: ODN2395 treated


title: ODN2395 4

description: ODN2395 treated


title: ODN/Pam2 5

description: Combination treated


title: SC3

city: West Vancouver

first: Wendy

last: Tymchuk

address: 4160 Marine Drive

department: Science

institute: Fisheries & Oceans Canada

hyb_protocol: Hybridization followed the procedures at http://web.uvic.ca/grasp/microarray (Genisphere Array 50 Protocol).

scan_protocol: Fluorescence images were collected at 10μm resolution using a ScanArray microarray scanner (Perkin Elmer). The same laser power (95%) and photomultiplier tube (PMT) settings were used for all slides (Cy3 PMT 75, Cy5 PMT 65).  Fluorescence intensity data were extracted from TIF images using Spotfinder (TIGR).

data_processing: TM4 Microarray Software Suite, a set of open-source freeware programs developed at the Institute for Genomics Research (TIGR), was used for quantification, normalization and analysis of microarray data. The otsu quantification method within TIGR Spotfinder was used to quantify the scanned microarray files.  Integrated intensities were corrected for background and any spots with expression levels < 2 standard deviations above background for at least 50% of the samples were removed.  TIGR Microarray Data Analysis System (MIDAS) was used to apply a locally weighted linear regression (LOWESS) normalization module. The resulting normalized and filtered expression files were analyzed using TIGR Multiexperiment Viewer (MeV).

organism: Fundulus heteroclitus

source_name: muscle, southern, control

label_protocol: Reverse transcriptase of 15ug of total RNA was performed following the SuperScript II Reverse Transcriptase protocol (Invitrogen).  Indirect labeling was performed on individual cDNA following the Array 50 kit protocol (Genisphere).

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

treatment_protocol: prior to heat shock 20ºC

tag: subspecies

value: heteroclitus

source_name: muscle, pool

treatment_protocol: at 20ºC or 60 min at 34ºC

tag: type

value: Pooled RNA

value: macrolepidotus and heteroclitus


title: SC2


title: SC4


title: Pam2 4

description: Pam2CSK4 treated


title: SC1


title: S606

treatment_protocol: heat shock 60 min at 34ºC


title: Sham 5

description: Sham treated


title: Pam2 3

description: Pam2CSK4 treated


title: ODN/Pam 3

description: Combination treated


title: ODN2395 2

description: ODN2395 treated


title: ODN/Pam 2

description: Combination treated


title: Pam2 2

description: Pam2CSK4 treated


title: ODN/Pam 1

description: Combination treated


title: S604

source_name: muscle, southern, heat shock, 60 min.


title: Sham 2

description: Sham treated


title: NC3

source_name: muscle, northern, control

value: macrolepidotus


title: S601


title: NC5


title: S605


title: NC2


title: N605

source_name: muscle, northern, heat shock, 60 min.


title: ODN2395 1

description: ODN2395 treated


title: NC1


title: N604


title: N602


title: Sham 1

description: Sham treated


title: Lmono_inactivated_48h_rep2

city: Hobart

first: John

middle: Phillip

last: Bowman

state: Tasmania

address: College Road, Sandy Bay

department: School of Agricultural Science

country: Australia

institute: University of Tasmania

description: Biological replicate 2 of 2

hyb_protocol: Slides were pre-hybridized in a hybridization solution [25 %, v/v, formamide, 5x SSC buffer (0.75 M NaCl, 0.075 M trisodium citrate, pH 7.0), 0.1 % SDS] containing 10 mg BSA ml–1 for 45 min at 42 °C. Slides were then rinsed twice in distilled water and air-dried. Hybridization was performed in a humid hybridization chamber at 42 °C for 16–20 h using a hybridization solution containing 0.42 µg human Cot1 DNA µl–1, 0.62 µg polyA µl–1 and 0.83 µg salmon sperm DNA µl–1. Slides were washed at room temperature in 1x SSC buffer containing 0.2 % SDS for 5 min and again in 0.1x SSC buffer containing 0.2 % SDS for 5 min. The slides were then further washed twice in 0.1x SSC buffer at room temperature for 2 min and then air-dried.

scan_protocol: Scanned using a GenePix 4000A scanner (Axon Instruments)

data_processing: Digitized signal data was normalized using house keeping gene tufA as an internal standard to correct for experimental and chip variations. This was required due to large changes in mRNA between treatments and controls. To do this the background of both the cy3 and cy5 channels were subtracted and a raw ratio (R) was obtained for all individual chips, including technical replicates. The chip-based tufA ratio (T) was corrected to the ratio of tufA copy numbers  (TC) occurring within corresponding controls and treatments, i.e. correction factor C=TC/T, determined separately by real-time PCR analysis. The correction factor was multiplied to all other raw ratios to obtain normalized values. Variation occurring within the RT-PCR analyses ranged from 7-22%. The treatment: control RT-PCR-based ratios determined ranged from 0.47-1.09 (see file tufA_correction.txt). Variation between technical replicates was <10%.  Real-time PCR protocol for tufA is as follows - tufA forward primer (5’-AGG TGA AGC TGA CTG GGA AG-3’); tufA reverse primer (5’-CTG GAC TCA TGA ATG GTT TG-3’). RT-PCR analysis was set-up using 2 ul of RNA sample or DNA standard, 1 pmol of each tufA primer, and employing the one-step QuantiTect SYBR Green RT-PCR kit. PCR experiments were set up automatically using a liquid handling pipettor robot station (Corbett Research). PCR was performed in a Rotorgene model 3000 thermocycler (Corbett Research) with the following thermal cycling conditions: 30 min at 50ºC, 15 min at 95ºC followed by 40 repeats of 15 s at 94ºC, 30 s at 50ºC and 30 s at 72ºC. Data collection and amplification efficiency correction was performed using Rotorgene 6000 software. In each run two negative controls (RNA free water) were included. Melt curve analysis (45ºC to 95C) and agarose electrophoresis was performed following each run to ensure the formation of homogenous amplicons. For each RNA sample analyzed, measurements of mRNA copy numbers were determined in triplicate and the mean of these values was plotted against a standard curve constructed based on known amounts of RNA.

organism: Listeria monocytogenes

source_name: non-inactivated bacterial culture

label_protocol: RNA was converted to cDNA and post-labelled with Cy5 (red) and Cy3 (green) fluorescent dyes using the SuperScript Indirect cDNA Labelling System (Invitrogen).

growth_protocol: Controls grown to early stationary growth phase (approx. 10^8 cells/ml, ~12 h incubation) at 25 C in brain-heart infusion broth (Oxoid)

extract_protocol: All cultures were pelleted at 4000 rpm for 10 min and then suspended in 3 ml Bacterial RNA Protect reagent (Qiagen) for 15 min with constant agitation followed by centrifugation and storage at -80 C. Cells were defrosted and underwent a 2–3 h (25 °C) enzymic treatment in TE buffer (10 mM Tris/HCl, 1 mM disodium EDTA, pH 7.5) containing 20 mg lysozyme ml–1 and 10 mg proteinase K ml–1. Cells were fully lysed by bead beating using 0.1 mm zirconium-silica sand in RNAeasy MIDI RNA extraction kit (Qiagen) lysis buffer containing 0.1 % β-mercaptoethanol. RNA was then extracted and purified using the RNAeasy kit and subsequently stored at –80 °C. RNA quality and quantity was assessed with the Agilent Technologies bioanalyser 2100 and RNA LabChip.

treatment_protocol: Control cultures pelletd by centrifuge (4000 rpm, 10 min). Cells suspended in brain heart infusion broth adjusted to pH 3.5 and containing 2.5 M NaCl and incubated at 25 C for either 5-10 min, 24 h, 48 h or 72 h

value: non-inactivated bacterial culture

value: ScottA

source_name: low pH/aw-exposed bacterial culture (48 h)

value: low pH/aw-exposed bacterial culture


title: Lmono_inactivated_72h_rep2

description: Biological replicate 2 of 2

source_name: low pH/aw-exposed bacterial culture (72 h)


title: Pam2 1

description: Pam2CSK4 treated


title: N603


title: Lmono_inactivated_72h_rep1

description: Biological replicate 1 of 2


title: Lmono_inactivated_48h_rep1

description: Biological replicate 1 of 2


title: Lmono_inactivated_24h_rep2

description: Biological replicate 2 of 2

source_name: low pH/aw-exposed bacterial culture (24 h)


title: Lmono_inactivated_24h_rep1

description: Biological replicate 1 of 2


title: Lmono_inactivated_20min_rep2

description: Biological replicate 2 of 2

source_name: low pH/aw-exposed bacterial culture (20 min)

value: 20 min


title: Lmono_inactivated_20min_rep1

description: Biological replicate 1 of 2


title: mouse erythroleukemia_G9a knockdown_replicate 3, GCRMA

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description: G9a knockdown

hyb_protocol: Affymetrix standard.

scan_protocol: Affymetrix standard.

data_processing: GCRMA normalization using R.

source_name: MEL, G9a knockdown

label_protocol: Affymetrix standard.

growth_protocol: RPMI medium containing 10% fetal bovine serum; 1% glutamine; penicillin and streptomycin 2% DMSO were added for 4 days to induce erythroid differentiation.

extract_protocol: The RNA was extracted and purified using the RNeasy Mini Kit (Qiagen) including the on-column DNAse I digestion step.

treatment_protocol: Knock down was induced by adding 5 micrograms/ml final of Dox in the culture medium.

value: mouse erythroleukemia


title: mouse erythroleukemia_wild type_replicate 1, GCRMA

description: wild type

source_name: MEL, wild type


title: mouse erythroleukemia_G9a knockdown_replicate 1, GCRMA

description: G9a knockdown


title: mouse erythroleukemia_G9a knockdown_replicate 2, MAS5

description: G9a knockdown


title: mouse erythroleukemia_wild type_replicate 3, GCRMA

description: wild type


title: Non-small cell lung cancer cell line_HCC827 GR8_s

type: genomic

city: Boston

first: Pasi

last: Janne

state: MA

address: 44 Binney Street Dana 820

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Hybridized to 250K_Sty

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

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

data_processing:
CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the invariant set probe selection method and the running median smoothing method. The data matrix contains the normalized expression values produced by that algorithm.
primary data description: Genotype Call (SNP call): A, AB, B, and NoCall; 'Signal' = Summarized signal

molecule: genomic DNA

organism: Homo sapiens

source_name: Non-small cell lung cancer cell line

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown to approximately 70% confluency in RPMI media supplemented with 5% FBS, 100 units/ml Penicillin, and 100 ug/ml Streptomycin.

extract_protocol: Genomic DNA was extracted from cell lines using the Qiagen DNeasy Blood and Tissue Kit according to manufacturer's instructions. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: cell line

value: HCC827 GR8

tag: notable drug resistance

value: gefitinib


title: cultured epiblast cEpi#1

status: Public on Oct 29 2009

city: Cambridge

first: Fuchou

last: Tang

state: Cambridgeshire

address: Tennis Court Road

department: Wellcome Trust/Cancer Research UK Gurdon Institute

institute: University of Cambridge

description:
Epiblast from E5.5-E7.5 postimplantation embryos obtained as described above, was dissected with glass needles based on morphology, and treated with EGTA in PBS for 10min, followed by trypsin for 5min at room temperature.
Gene expression data from mouse embyronic cells using Applied Biosystems AB1700 Whole Genome Microarray

hyb_protocol: Hybridization was performed according to Applied Biosystems Chemiluminescence Detection Kit Protocol (PN 4339627) using 10 ug fragmented cRNA

scan_protocol: Image was captured using CCD camera came with AB1700 Microarray Analyzer

data_processing: Quantile normalization was performed. The normalization was performed using ABarray bioconductor package

label: digoxigenin

source_name: cultured epiblast

label_protocol: Digoxigenin labeled cRNA was prepared according to Applied Biosystems nanoamp RT-IVT protocol

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

value: cultured epiblast


title: cultured epiblast cEpi#3

description:
Epiblast from E5.5-E7.5 postimplantation embryos obtained as described above, was dissected with glass needles based on morphology, and treated with EGTA in PBS for 10min, followed by trypsin for 5min at room temperature
Gene expression data from mouse embyronic cells using Applied Biosystems AB1700 Whole Genome Microarray


title: reprogrammed epiblast ES-like cells passage 24 rEpiES#2

description:
epiblast from e5.5-e7.5 postimplantation embryos obtained as described above, was dissected with glass needles based on morphology, and treated with egta in pbs for 10min, followed by trypsin for 5min at room temperature. epiblast cells were then dissociated into single cells by pipeting with glass capillary. these of epiblast cells were cultured in ‘es’ medium (dmem/f12 medium plus 20% fetal bovine serum and 1000u/ml lif) on mitomycin treated mouse embryonic fibroblast (mefs) feeder cells. these epiblast cells grew efficiently as epithelial colonies after 4-5 days culture. the resulting colonies were treated with 1mg/ml collagenase for 10min at room temperature and picked, dissociated into smaller clumps by mechanically cutting them into smaller pieces using glass needles, and similarly passaged at every 5-6 days intervals. these referred to as primary repi cell lines, could be passaged extensively in es medium, following treatment with collagenase and mechanical dissociation. the morphology of repi colonies was overall similar to that of episcs and not es cells; they were flatter and bigger than es colonies and positive for alkaline phosphatase, but were negative for oct4-gfp expression. following culture of repi cell lines for 14-35 days, a few gfp-positive cells appeared in repi colonies. the clones bearing gfp-positive cells were isolated using glass needles, and passaged following treatment with collagenase and dissociated mechanically. when these colonies were large enough with gfp positive cells, they were treated with trypsin which on subsequent culture produced gfp positive colonies. we refer to these cells as repies cells. these repies have so far been propagated for more than 40 passages (1: 10 to 1:20 dilution each passage). The number of cell lines we derived from postimplantation embryos is summarized
Gene expression data from mouse embyronic cells using Applied Biosystems AB1700 Whole Genome Microarray

value: reprogrammed epiblast ES-like cells

value: passage 24


title: reprogrammed epiblast ES-like cells passage 24 rEpiES#3


title: mouse erythroleukemia_wild type_replicate 2, MAS5

description: wild type


title: cultured epiblast cEpi#2


title: Non-small cell lung cancer cell line_HCC827 PFR-1_s

description: Hybridized to 250K_Sty

value: HCC827 PFR-1


title: Non-small cell lung cancer cell line_HCC827 PFR-3_s

description: Hybridized to 250K_Sty

value: HCC827 PFR-3


title: Non-small cell lung cancer cell line_HCC827 GR7_s

description: Hybridized to 250K_Sty

value: HCC827 GR7


title: reprogrammed epiblast ES-like cells passage 24 rEpiES#1


title: mouse embryonic stem cell ES#3

description:
Mouse embryos were isolated from E5.5-E7.5 129/sv or ROSA 129/Sv females mated with Oct4-△PE-EGFP transgenic males
Gene expression data from mouse embyronic cells using Applied Biosystems AB1700 Whole Genome Microarray

source_name: mouse embryonic stem cell

value: ES cell


title: Non-small cell lung cancer cell line_HCC827 GR5_s

description: Hybridized to 250K_Sty

value: HCC827 GR5


title: reprogrammed epiblast ES-like cells passage 4 rEpiES#3

description:
epiblast from e5.5-e7.5 postimplantation embryos obtained as described above, was dissected with glass needles based on morphology, and treated with egta in pbs for 10min, followed by trypsin for 5min at room temperature. epiblast cells were then dissociated into single cells by pipeting with glass capillary. these of epiblast cells were cultured in ‘es’ medium (dmem/f12 medium plus 20% fetal bovine serum and 1000u/ml lif) on mitomycin treated mouse embryonic fibroblast (mefs) feeder cells. these epiblast cells grew efficiently as epithelial colonies after 4-5 days culture. the resulting colonies were treated with 1mg/ml collagenase for 10min at room temperature and picked, dissociated into smaller clumps by mechanically cutting them into smaller pieces using glass needles, and similarly passaged at every 5-6 days intervals. these referred to as primary repi cell lines, could be passaged extensively in es medium, following treatment with collagenase and mechanical dissociation. the morphology of repi colonies was overall similar to that of episcs and not es cells; they were flatter and bigger than es colonies and positive for alkaline phosphatase, but were negative for oct4-gfp expression. following culture of repi cell lines for 14-35 days, a few gfp-positive cells appeared in repi colonies. the clones bearing gfp-positive cells were isolated using glass needles, and passaged following treatment with collagenase and dissociated mechanically. when these colonies were large enough with gfp positive cells, they were treated with trypsin which on subsequent culture produced gfp positive colonies. we refer to these cells as repies cells. these repies have so far been propagated for more than 40 passages (1: 10 to 1:20 dilution each passage). The number of cell lines we derived from postimplantation embryos is summarized.
Gene expression data from mouse embyronic cells using Applied Biosystems AB1700 Whole Genome Microarray

value: passage 4


title: Non-small cell lung cancer cell line_HCC827 PFR-5_s

description: Hybridized to 250K_Sty

value: HCC827 PFR-5


title: Non-small cell lung cancer cell line_HCC827 GR6_s

description: Hybridized to 250K_Sty

value: HCC827 GR6


title: reprogrammed epiblast ES-like cells passage 4 rEpiES#1


title: Non-small cell lung cancer cell line_HCC827 PFR-4_s

description: Hybridized to 250K_Sty

value: HCC827 PFR-4


title: Non-small cell lung cancer cell line_HCC827 PFR-6_s

description: Hybridized to 250K_Sty

value: HCC827 PFR-6


title: Non-small cell lung cancer cell line_HCC827 GR2_s

description: Hybridized to 250K_Sty

value: HCC827 GR2


title: mouse embryonic stem cell ES#2

description:
Mouse embryos were isolated from E5.5-E7.5 129/sv or ROSA 129/Sv females mated with Oct4-△PE-EGFP transgenic males.
Gene expression data from mouse embyronic cells using Applied Biosystems AB1700 Whole Genome Microarray


title: reprogrammed epiblast ES-like cells passage 4 rEpiES#2


title: Non-small cell lung cancer cell line_HCC827 GR1_s

description: Hybridized to 250K_Sty

value: HCC827 GR1


title: mouse embryonic stem cell ES#1

source_name: embyronic mouse ES cell


title: Gold induction of C. metallidurans CH34 with 50µM - 30min.

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

institute: SCK-CEN

description: Gold induction of C. metallidurans CH34 with 50µM Au(III) - 30min.

hyb_protocol: Labeled cDNA was re-suspended in the universal hybridization buffer (Pronto kit), mixed and added to the spotted slide for overnight hybridization at 42°C in a Tecan HS4800 Pro hybridization station (Tecan Group Ltd, Switzerland). Afterwards, the slide was washed according to Pronto kit's protocol.

scan_protocol: Slides were scanned (at 532 and 635 nm) using the GenePix Personal 4100A microarray scanner (Molecular Devices©, USA). Micro-array spot-signals were analyzed using the GenePix Pro v.6.0.1 software and flagged according to build-in quality criteria.

data_processing: Raw median intensity data were imported into R version 2.7.0 for statistical analysis using the LIMMA package version 2.15.15 as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50. Data were normalized within each array using the printing-tip loess normalization algorithm. The in-slide replicate correlations were calculated using the duplicate correlation function in the LIMMA package. The log expression values were fitted to a linear model and moderated t-statistics were calculated using empirical Bayes method. P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate.

organism: Cupriavidus metallidurans CH34

source_name: Cupriavidus metallidurans CH34 uninduced mid-exponential phase culture

label_protocol: Ten micrograms of RNA were reverse transcribed using Pronto kit (Promega, United States) following manufacturer’s instructions. Two color labeling, green for control samples and red for condition (metal challenge) samples, was performed using respectively Cy3-dCTP and Cy5-dCTP nucleotides (Amersham BioSciences, United Kingdom).

growth_protocol: Bacteria culture was grown on TrisMM medium until OD reached 0.58 at 30°C.

extract_protocol: Total RNA extraction was conducted using the SV Total RNA Isolation system (Promega Corporation, cat# Z3100, USA). The quality and quantity control of total RNA was monitored using the BioAnalyser 2100 (Agilent Technologies, USA) and NanoDrop 1000 spectrophotometer (Thermo Scientific, USA) respectively.

treatment_protocol: no treatment

tag: strain CH34, culture in mid-exponential phase, OD 0.58

source_name: Cupriavidus metallidurans CH34 induction 50µM Au(III) - 30min.

growth_protocol: acteria culture was grown on minimal medium until OD reached 0.58 at 30°C. Au(III) was added to the culture and incubated for 30 minutes.

treatment_protocol: 10 ml of bacterial culture was grown on TrisMM until OD reached 0.58. Then, 50µM of Au(III) was added to the culture and incubated for 30 min.


title: Gold induction of C. metallidurans CH34 with 100µM - 10min.

description: Gold induction of C. metallidurans CH34 with 100µM Au(III) - 10min.

source_name: Cupriavidus metallidurans CH34 induction 100µM Au(III) - 10min.

growth_protocol: Bacteria culture was grown on minimal medium until OD reached 0.58 at 30°C. Au(III) was added to the culture and incubated for 10 minutes.

treatment_protocol: 10 ml of bacterial culture was grown on TrisMM until OD reached 0.58. Then, 100µM of Au(III) was added to the culture and incubated for 10 min.


title: Gold induction of C. metallidurans CH34 with 50µM - 10min.

description: Gold induction of C. metallidurans CH34 with 50µM Au(III) - 10min.

source_name: Cupriavidus metallidurans CH34 induction 50µM Au(III) - 10min.

growth_protocol: acteria culture was grown on minimal medium until OD reached 0.58 at 30°C. Au(III) was added to the culture and incubated for 10 minutes.

treatment_protocol: 10 ml of bacterial culture was grown on TrisMM until OD reached 0.58. Then, 50µM of Au(III) was added to the culture and incubated for 10 min.


title: Gold induction of C. metallidurans CH34 with 10µM - 10min.

description: Gold induction of C. metallidurans CH34 with 10µM Au(III) - 10min.

source_name: Cupriavidus metallidurans CH34 induction 10µM Au(III) - 10min.

treatment_protocol: 10 ml of bacterial culture was grown on TrisMM until OD reached 0.58. Then, 10µM of Au(III) was added to the culture and incubated for 10 min.


title: M. tuberculosis - cholesterol 24hrs_experiment 3

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

description:
Original gpr file: 08-30-07_Comparison 3.gpr
17(24hr+Tween,Cult3)Cy3 vs. 18(24hr+Cho,Cult3)Cy5

hyb_protocol: II. Prehybridization 1. Prepare Prehybridization Solution (Fresh Each Time) **this volume is based on a glass dish with a base measurement of 11x8cm. This dish allows for a pre-hyb of 1-4 slides. Adjust volume accordingly based on size of dish and/or number of slides. 106.0ml dH2O 3.0g BSA 1.2ml 10%SDS 2. Add Prehybridization solution to a glass slide-staining dish and place post-processed slides array side up into solution. Make sure there are no bubbles on the surfaces of the slides. 3. Place the staining jar containing the Prehybridization solution and slides into a waterbath and hybridize for 1 hour at 42oC. 4. Take the prehybridized slides out of the Prehybridization solution and place into a slide holder submerged in a slide-washing tray containing nuclease-free water. Wash slides for 2 minutes with constant shaking up and down. 5. Transfer slide rack to a slide washing tray containing isopropanol and wash for 2 minutes with constant shaking up and down. 6. Take the slides in the isopropanol bath to the centrifuge to keep the slides wet until you can dry them rapidly. Spin at 600 RPM in a 50ml conical for 3 minutes to dry. **Complete this step within one hour of hybridization III. Hybridization 1. Add the following to the 5µl labeled sample. 0.5µl 10 mg/ml tRNA 1.0µl 20X SSC 2.5ul Formamide 1.0µl 1% SDS 2. Heat to 98 oC for 2 minutes. Spin in centrifuge for 1 min at 12,000 Xg. Let cool for 5 min. 3. Pipette cooled 10µl hybridization solution on microarray. Apply 22 x 22 coverslip to cover array (if bubbles appear under the cover slip, they will slowly migrate to the edges provided that the volume is accurate). 4. OPTIONAL: Apply thin wall of rubber cement around the 4 corners of the coverslip to avoid movement. This step is recommended if your waterbath is not perfectly level. 5. Hybridize in standard hyb. chambers with ~40µl water under each slide (20ul under both ends of each slide) overnight in 50oC water bath **Bubbles (esp. large ones) can be troublesome for your arrays since they can cause areas of non-hybridization. To avoid bubbles, do not use the blowout feature of the pipette when adding the probe to the slide. Also, clean your coverslips with alcohol and lint-free wipes before placing over probe. IV. Post Hyb washes (next day) 1. Remove cover slip while array is submerged in first wash solution (2XSSC + 0.1% SDS), transfer to submerged microscope slide staining racks and rinse for 1 min in 1X SSC+0.05% SDS with agitation/shaking. 2. Rinse in 0.06X SSC with shaking. Transfer to another submerged staining rack and wash 2 min in fresh 0.06X SSC with shaking. 3. Centrifuge 3 min at 1000 rpm in a 50ml conical (array edge up) to dry. Scan immediately.

scan_protocol: After washing, the arrays were scanned with a GenePix4000B scanner (Molecular Devices, Sunnyvale, CA). The images were processed using GenePix 6.1 and the resulting text files were exported to Microsoft Excel.

data_processing: The data were filtered by removing all spots that were below the background noise or flagged as ‘bad’. Spots were considered to be below the background noise if the sum of the median intensities of the two channels was less than twice the highest average background of the chip. The chips were normalized by the print-tip Lowess method {Dudoit, 2000 #200}.

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis, grown in Tween, 24hrs

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

growth_protocol: M. tb cultures were grown to the exponential stage in 40ml cultures using the standard 7H9 supplemented with ADC, glycerol and .05% Tween. 2 ml 20% Tween were added to the control cultures.

extract_protocol: RNA from M. tb grown in liquid cultures for microarray and qRT-PCR analysis was extracted by resuspending the pellets in 1 ml of Trizol reagent (Gibco BRL (Invitrogen)). Cells were disrupted using 0.5 ml of 0.1 mm-diameter glass beads (Biospec Products) by pulsing twice for one min in a BioSpec Products bead beater. After 10 min incubation at room temperature, cellular debris was removed by centrifuging the samples at 16,000 rpm for 15 min. The RNA containing supernatant was transferred to a fresh tube containing 100 ml of 1-bromo-3-chloropropane (BCP) (Molecular Research Center, Inc), incubated at room temperature for 10 min and centrifuged at 16,000 rpm for 15 min at 4 °C. Isopropanol (0.5 ml) was added to the samples and RNA was precipitated overnight at -80 °C. After centrifugation, as described above, the RNA was washed twice with cold 75% ethanol. The pellet was allowed to dry and was resuspended in 90 ml of diethylpyrocarbonate (DEPC)-treated water. Rehydration was allowed to take place overnight at -80 °C, followed by treatment with 1ml of Dnase (TurboDnase, Ambion), after the addition of 10ml buffer, for 30 min at 37 °C. The RNA was further purified using the RNeasy kit according to manufacturers instructions (Qiagen).

treatment_protocol: The bacterial cultures were centrifuged at room temperature and the pellets frozen on dry ice before being transferred to -80deg.C.

tag: wild type M.tuberculosis H37Rv without the addition of 1mg/ml cholesterol made in 20% Tween-80 for 24 hrs

source_name: M. tuberculosis, grown in Tween with Cholesterol added, 24hrs

growth_protocol: M. tb cultures were grown to the exponential stage in 40ml cultures using the standard 7H9 supplemented with ADC, glycerol and .05% Tween. 2 ml cholesterol (20mg/ml in 20% Tween) were added when the cultures were growing exponentially (OD about 0.4-0.6).

tag: wild type M.tuberculosis H37Rv with the addition of 1mg/ml cholesterol made in 20% Tween-80 for 24 hrs


title: CDC1551 (146) vs CDC1551 kstR mutant (162)_24hrs plus cholesterol_experiment 1

description:
Original gpr file: 02-15-08_Comparison4.gpr
146#1+cho(Cy5) vs. 162#1+cho(Cy3)

source_name: M. tuberculosis, CDC1551 (146), grown in Tween + Cholesterol

growth_protocol:
M. tb cultures were grown to the exponential stage in 40ml cultures
using the standard 7H9 supplemented with ADC, glycerol and .05% Tween. 2
ml cholesterol (20mg/ml in 20% Tween) were added when the cultures were
growing exponentially (OD about 0.4-0.6).

tag: with the addition of 1mg/ml cholesterol made in 20% Tween-80 for 24 hrs

source_name: M. tuberculosis, CDC1551 kstR mutant (162), grown in Tween + Cholesterol


title: CDC1551 (146) vs CDC1551 kstR mutant (162)_24hrs plus cholesterol_experiment 3

description:
Original gpr file: 02-15-08_Comparison6.gpr
146#3+cho(Cy5) vs. 162#3+cho(Cy3)


title: CDC1551 (146) vs CDC1551 kstR mutant (162)_24hrs_experiment 1

description:
Original gpr file: 02-15-08_Comparison1.gpr
146#1(Cy3) vs. 162#1(Cy5)

source_name: M. tuberculosis, CDC1551 (146), grown in Tween

growth_protocol: M. tb cultures were grown to the exponential stage in 40ml cultures using the standard 7H9 supplemented with ADC, glycerol and .05% Tween. 2 ml 20%

tag: without the addition of 1mg/ml cholesterol made in 20% Tween-80 for 24 hrs

source_name: M. tuberculosis, CDC1551 kstR mutant (162), grown in Tween


title: CDC1551 (146) vs CDC1551 kstR mutant (162)_24hrs_experiment 2

description:
Original gpr file: 02-15-08_Comparison2.gpr
146#2(Cy5) vs. 162#2(Cy3)


title: CDC1551 (146) vs CDC1551 kstR mutant (162)_24hrs plus cholesterol_experiment 2

description:
Original gpr file: 02-15-08_Comparison5.gpr
146#2+cho(Cy3) vs. 162#2+cho(Cy5)


title: M. tuberculosis - cholesterol 24hrs_experiment 2

description:
Original gpr file: 08-30-07_Comparison 2.gpr
15(24hr+Tween,Cult2)Cy5 vs. 16(24hr+Cho,Cult2)Cy3


title: M. tuberculosis - cholesterol 24hrs_experiment 1

description:
Original gpr file: 08-30-07_Comparison 1.gpr
13(24hr+Tween,Cult1)Cy3 vs. 14(24hr+Cho,Cult1)Cy5

scan_protocol: After washing, the arrays were scanned with a GenePix4000B scanner (Molecular Devices, Sunnyvale, CA). The images were processed using GenePix 5.1 and the resulting text files were exported to Microsoft Excel.


title: Non-small cell lung cancer cell line_HCC827

description: Hybridized to 250K_Sty


title: CDC1551 (146) vs CDC1551 kstR mutant (162)_24hrs_experiment 3

description:
Original gpr file: 02-15-08_Comparison3.gpr
146#3(Cy3) vs. 162#3(Cy5)


title: M. tuberculosis - cholesterol 3hrs_experiment 2

description:
Original gpr file: 05-08-07_Comparison 2.gpr
3(3hr+Tween,Cult2)Cy3 vs. 4(3hr+Cho,Cult2)Cy5

source_name: M. tuberculosis, grown in Tween, 3hrs

tag: wild type M.tuberculosis H37Rv without the addition of 1mg/ml cholesterol made in 20% Tween-80 for 3 hrs

source_name: M. tuberculosis, grown in Tween with Cholesterol added, 3hrs

tag: wild type M.tuberculosis H37Rv with the addition of 1mg/ml cholesterol made in 20% Tween-80 for 3 hrs


title: M. tuberculosis - cholesterol  3hrs_experiment 1

description:
Original gpr file: 05-08-07_Comparison 1.gpr
1(3hr+Tween, culture1)cy3 vs 2(3hr+Cholesterol, culture1)cy5

growth_protocol: M. tb cultures were grown to the exponential stage in 40ml cultures using the standard 7H9 supplemented with ADC, glycerol and .05% Tween.  2 ml 20% Tween were added to the control cultures.

extract_protocol: RNA from M. tb grown in liquid cultures for microarray and qRT-PCR analysis was extracted by resuspending the pellets in 1 ml of Trizol reagent (Gibco BRL (Invitrogen)).  Cells were disrupted using 0.5 ml of 0.1 mm-diameter glass beads (Biospec Products) by pulsing twice for one min in a BioSpec Products bead beater.  After 10 min incubation at room temperature, cellular debris was removed by centrifuging the samples at 16,000 rpm for 15 min.  The RNA containing supernatant was transferred to a fresh tube containing 100 ml of 1-bromo-3-chloropropane (BCP) (Molecular Research Center, Inc), incubated at room temperature for 10 min and centrifuged at 16,000 rpm for 15 min at 4 °C.  Isopropanol (0.5 ml) was added to the samples and RNA was precipitated overnight at -80 °C.    After centrifugation, as described above, the RNA was washed twice with cold 75% ethanol.  The pellet was allowed to dry and was resuspended in 90 ml of diethylpyrocarbonate (DEPC)-treated water.  Rehydration was allowed to take place overnight at -80 °C, followed by treatment with 1ml of Dnase (TurboDnase, Ambion), after the addition of 10ml buffer, for 30 min at 37 °C.  The RNA was further purified using the RNeasy kit according to manufacturers instructions (Qiagen).


title: C2C12 GTP-treated cells 24 h differentiation

city: Chieti

first: Rosa

last: Mancinelli

state: Chieti

address: via Dei Vestini 29

department: Dept. Basic and Applied Medical Sciences

country: Italy

institute: University "G. d'Annunzio" Chieti-Pescara, Chieti

hyb_protocol: MWG Hybridization Service

scan_protocol: For each microarray slide The MWG Hybridization Service performs multiple scans with a dual  laser scanner using different photomultiplier amplification settings.

data_processing: The ImaGeneTM software (BioDiscovery) is used to calculate the intensity of each spot and the corresponding background from the individual scanner tiff images. The ImaGene result files are further processed using an MWG proprietary software, MAVI Pro. MAVI Pro also calculates the background subtraction and normalization of the intensity data. The normalized and background corrected intensities are used to calculate a ratio value. The ratio values directly show up- and down regulation of genes in the experiment.

source_name: C2C12 cells 24 h differentiation in absence of GTP

label_protocol: The RNA amplification and labelling reaction was carried out using the 2-step amino-allyl labelling.

growth_protocol: C2C12 cells (American Type Culture Collection) were cultured as exponentially growing myoblasts in growth medium (GM), specifically, Dulbecco’s modified Eagle’s medium (DMEM, Euroclone, Pero, MI, Italy) containing 20% foetal bovine serum (FBS, Euroclone), 4 mM L-glutamine (Euroclone) and 100 IU ml−1–100 μg ml−1 penicillin–streptomycin (Euroclone). Cells were seeded in Petri dishes at a density of 1500–2000 cells cm−2 in GM, and subcultured by standard trypsinization every three days. After two days in GM, differentiation was induced using normal differentiation medium (DM) containing DMEM with 2% horse serum (Euroclone), L-glutamine and antibiotics, as previously described, or synthetic differentiation medium (SM) consisting of DMEM plus 1% (w/v) bovine serum albumin (BSA, SIGMA Chemical Co.; St. Louis, MO, USA), L-glutamine and antibiotics, where specified.

extract_protocol: Total RNA from C2C12 cells, cultured for 4 h and 24 h in absence or in presence of 500 μM GTP in presence of synthetic medium, was purified using NucleoSpin® RNA II kit (# 740955.10, Macherey-Nagel, Duren, Germany), according to the manufacturer’s instructions.

treatment_protocol: C2C12 cells were plated in Petri dishes (100 mm diameter) at a density of 2500 cells cm-2 and grown for 48 h in GM. The differentiation was induced using SM. Experiments were performed at two stages: at 4 h and 24 h of differentiation in absence or in presence of 500 μM GTP (# G5884, Sigma-Aldrich).

tag: passage

value: Mouse C2C12 myoblasts

source_name: C2C12 cells 24 h differentiation in presence of GTP


title: C2C12 GTP-treated cells 4 h differentiation

source_name: C2C12 cells 4 h differentiation in absence of GTP

value: C2C12 cells (American Type Culture Collection)

source_name: C2C12 cells 4 h differentiation in presence of GTP


title: liver_14days_1000ppm_replicate3

status: Public on Oct 28 2009

city: Bracknell

first: Richard

last: Currie

address: Jealott's Hill

institute: Syngenta

description: 051011_RAC 80

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat Genome 230 v2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: left laterial lobe of liver, 14 days of dietary dosing, 1000 ppm sodium phenobarbital

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

growth_protocol: Rats were maintained on CT1 diet and water, ad lib

extract_protocol: total RNA was extracted using Qiagen midi RNA extraction kits as per the manufacturer's instructions

treatment_protocol: Left lateral lobe of liver was cut into approxiamtely 5mm wide strips; each strip quarted and snap frozen in liquid nitrogen

tag: dose

tag: tissue

value: liver

tag: lobe


title: M. tuberculosis - cholesterol 3hrs_experiment 3

description:
Original gpr file: 05-08-07_Comparison 3.gpr
5(3hr+Tween,Cult3)Cy3 vs. 6(3hr+Cho,Cult3)Cy5


title: liver_7days_1000ppm_replicate1

source_name: left laterial lobe of liver, 7 days of dietary dosing, 1000 ppm sodium phenobarbital

tag: time point


title: liver_14days_1000ppm_replicate1

description: 051011_RAC 76


title: liver_14days_1000ppm_replicate2

description: 051011_RAC 78


title: C2C12 GTP-treated cells 4 h differentiation in DM tech rep 1

hyb_protocol: Optimal amount of aRNA-Cy3 and aRNA-Cy5 were co-precipitated adding 4/5 volume of ammonium acetate 5 M and 2.5 volumes of absolute ethanol. The sample was dissolved using 120 μl of hybridization buffer (SSC 20 x 500 μL, SDS 10% 20 μL, formamide 1000 μL, distilled water 480 μL) and 3 μL of RNase-free water, denatured at 90 °C for 2 min and applied directly to the microarray slides then covered with a coverslip. The microarray slide was seeded and sealed in the hybridization chamber and incubate for two days in a bath at 48 °C. After hybridization, slides were washed sequentially with a 1 x SSC/0.2% (w/v) SDS solution, a 0.1 x SSC/0.2% (w/v) SDS solution, a 0.2 x SSC solution and a 0.1 x SSC solution (4 min for each wash) in the dark at room temperature.

scan_protocol: Array was scanned using a GSI Lumonics LITE dual confocal laser scanner with a ScanArray Microarray Analysis System (PerkinElmer).

data_processing: Raw images were analyzed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). The expression levels of all spot replicates were normalized by applying the Lowess (Locfit) normalization procedure using MIDAS (the TIGR Microarray Data Analysis System) before performing any statistical analyses. The normalized and background corrected intensities are used to calculate a ratio value. Differentially expressed genes were identified using the SAM (Significant Analysis of Microarrays) permutation test procedure (STANFORD software, http://www-stat.stanford.edu/_tibs/SAM), which defines genes with a computed score larger than the threshold value as significant. Log base-2 of the ratio values > 1 (two fold up-regulated) represent up-regulated gene expression (experimental data vs. control data); while log base-2 of the ratio values < -1 (two fold down-regulated) represent down-regulated gene expression. Log base-2 of the ratio values between 1 and -1 correspond to genes that are not regulated in the experiment.

label_protocol: Aliquots (1 μg) of each RNA sample were reverse transcribed using the Amino Allyl MessageAmp II aRNA Amplification kit (#1753, Ambion). An aliquot of aaRNA modified was coupled with fluorofores Cy3 and Cy5 (CyDye Post-Labeling Reactive Dye Packs, # RPN5661, GE Healthcare).

treatment_protocol: C2C12 cells were plated in Petri dishes (100 mm diameter) at a density of 2500 cells cm-2 and grown for 48 h in GM. The differentiation was induced using DM. Experiments were performed at  4 h of differentiation in absence or in presence of 500 μM GTP (# G5884, Sigma-Aldrich).

tag: cell type

label_protocol: Aliquots (1 ug) of each RNA sample were reverse transcribed using the Amino Allyl MessageAmp II aRNA Amplification kit (#1753, Ambion). An aliquot of aaRNA modified was coupled with fluorofores Cy3 and Cy5 (CyDye Post-Labeling Reactive Dye Packs, # RPN5661, GE Healthcare).

extract_protocol: Total RNA from C2C12 cells, cultured for 4 h and 24 h in absence or in presence of 500 ?M GTP in presence of synthetic medium, was purified using NucleoSpin® RNA II kit (# 740955.10, Macherey-Nagel, Duren, Germany), according to the manufacturer's instructions.


title: liver_3days_1000ppm_replicate3

source_name: left laterial lobe of liver, 3 days of dietary dosing, 1000 ppm sodium phenobarbital


title: liver_7days_1000ppm_replicate2


title: liver_7days_1000ppm_replicate3


title: liver_1day_1000ppm_replicate1

source_name: left laterial lobe of liver, 1 day of dietary dosing, 1000 ppm sodium phenobarbital


title: liver_3days_1000ppm_replicate2


title: liver_3days_1000ppm_replicate1


title: liver_7days_500ppm_replicate2

description: 051011_RAC 51

source_name: left laterial lobe of liver, 7 days of dietary dosing, 500 ppm sodium phenobarbital


title: liver_14days_500ppm_replicate2

source_name: left laterial lobe of liver, 14 days of dietary dosing, 500 ppm sodium phenobarbital


title: liver_14days_500ppm_replicate1


title: liver_1day_1000ppm_replicate2


title: liver_7days_500ppm_replicate1


title: liver_14days_500ppm_replicate3


title: liver_3days_500ppm_replicate3

source_name: left laterial lobe of liver, 3 days of dietary dosing, 500 ppm sodium phenobarbital


title: liver_3days_500ppm_replicate2


title: WT_Stat_BR2

type: mixed

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

institute: Institute of Food Research

description: Total array is 16 blocks arranged in 4X4 configuration.

hyb_protocol: Slides blocked with DCE according to protocol at PMID 11266573. For hybridisation and washing protocols see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: Axon GenePix4000A, 10um resolution scan & see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Intensity ratios of channel 1 (cDNA) divided by channel 2 (reference gDNA) signals are calculated using BlueFuse 3.01 (BlueGnome, Cambridge, UK). Data centring was subsequently performed using the block median.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

label_protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

growth_protocol: Strain was grown in LB inoculated 1:1000 from an overnight culture for 22hrs to reach the late-stationary phase of growth.

extract_protocol: Total RNA isolation protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

tag: strain

value: Salmonella enterica serovar Typhimurium SL1344

tag: growth stage

value: late-stationary

tag: genotype/variation

value: wild type

source_name: Reference genomic DNA

growth_protocol: S. Typhimurium grown to stationary phase

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns)


title: WT_Stat_BR3


title: liver_7days_500ppm_replicate3

description: 051011_RAC 53


title: liver_1day_500ppm_replicate3

source_name: left laterial lobe of liver, 1 day of dietary dosing, 500 ppm sodium phenobarbital


title: liver_1day_1000ppm_replicate3


title: liver_3days_500ppm_replicate1


title: WT_EEP_BR2

growth_protocol: Strain was grown in LB inoculated 1:1000 from an overnight culture for 60min to reach the early-exponential phase of growth.

value: early-exponential


title: WT_EEP_BR3


title: WT_Stat_BR1


title: WT_EEP_BR1


title: liver_14days_50ppm_replicate1

source_name: left laterial lobe of liver, 14 days of dietary dosing, 50 ppm sodium phenobarbital


title: liver_14days_50ppm_replicate3


title: liver_7days_50ppm_replicate2

description: 051011_RAC 30

source_name: left laterial lobe of liver, 7 days of dietary dosing, 50 ppm sodium phenobarbital


title: liver_1day_500ppm_replicate2


title: StpA_Stat_BR2

value: ΔstpA


title: StpA_Stat_BR1


title: StpA_EEP_BR2


title: StpA_Stat_BR3


title: StpA_EEP_BR3


title: liver_14days_50ppm_replicate2


title: StpARpoS_MEP_BR3

description: Intensity ratios of channel 1 (cDNA) divided by channel 2 (gDNA) signals minus respective background signals. Total array is 16 blocks arranged in 4X4 configuration.

data_processing: Data centring was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios. Flagged features are omitted from the data centring process. Because we used a microarray based on S. Typhimurium strain LT2 to analyse the transcriptional response of a different strain (S. Typhimurium strain SL1344), we removed all the data corresponding to genes present in LT2, but absent from SL1344.

growth_protocol: Strain was grown in LB inoculated 1:1000 from an overnight culture for 160min to reach the mid-exponential phase of growth.

value: ΔrstpA ΔrpoS


title: StpARpoS_MEP_BR2


title: liver_7days_50ppm_replicate1


title: liver_7days_50ppm_replicate3


title: StpARpoS_MEP_BR1


title: StpA_EEP_BR1


title: liver_3days_50ppm_replicate2

source_name: left laterial lobe of liver, 3 days of dietary dosing, 50 ppm sodium phenobarbital


title: WT_noAntibody

description: Total array is 25 blocks arranged in 5X5 configuration.

hyb_protocol: Labelled samples were resuspended in hybridization buffer (1 M NaCl; 50 mM Mes, pH 7.0; 20% formamide; 1% Triton X-100). The hybridization was performed in microarray chambers (Agilent Technologies) and rotated at 55° over 48 h. The arrays were then washed with Wash 1 [6× standard saline phosphate/EDTA (0.18 M NaCl/10 mM phosphate, pH 7.4/1 mM EDTA] (SSPE)/0.005% N-lauryl sarcosine] and Wash 2 (0.06% SSPE/0.18% polyethylene glycol 200), both for 5 min at room temperature.

scan_protocol: Axon GenePix Autoloader 4200AL 10um resolution scan & see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Intensity ratios of channel 1 (coIP-DNA) divided by channel 2 (reference gDNA) signals are calculated using BlueFuse 3.1 (BlueGnome, Cambridge, UK). Data centring was subsequently performed using the block median.

molecule: other

label_protocol: 1/5 of the immunoprecipitated DNA was labelled using the 'Direct labelling of DNA' protocol that can be found at http://www.ifr.bbsrc.ac.uk/safety/microarrays/protocols.html.

growth_protocol: Over-night cultures were diluted 1000-fold into 250ml flasks containing 25ml of LB and grown at 37oC under aeration for 160min to reach the mid-exponential phase of growth.

extract_protocol: After reaching early exponential growth (OD600 0.12), formaldehyde was added to reach a 1% final concentration and the cultures incubated for 15 min at 37oC. The cross-linking was then stopped by adding 1/4 vol. 1M glycine. Cells were washed three times in ice-cold PBS (pH7.4), resuspended in 500ul lysis buffer (10mM Tris pH8.0; 50mM NaCl; 10mM EDTA; 20% sucrose; 20 mg/ml lysozyme) and incubated 45 min at 37oC at which point 500ul 2x RIPA (100mM Tris pH8.0; 300mM NaCl; 2% Nonidet P40; 1% sodium deoxycholate; 0.2% SDS) was added. Chromatin was solubilised by sonication until DNA fragments were between 300 and 750 bp, and the lysate centrifuged at 12000g for 10 min to remove debris.  Cell extracts were then incubated with the appropriate antibody (or no antibody for -CTRL) for 4h at 4oC. After the incubation of the cell extracts with the antibody, 50ul protein G beads were added and left for 16h at 4oC. The protein G beads were then washed twice in 1xRIPA, twice in wash solution (10mM Tris pH8.0; 250mM LiCl; 1mM EDTA; 0.5% Nonidet P40; 0.5% sodium deoxycholate) and twice in TE (10mM Tris pH8.0; 1mM EDTA). The immunoprecipitate was eluted in 150ul of elution buffer (50mM Tris pH8.0; 10mM EDTA; 1% SDS) prewarmed at 65oC. Cross-linking was reversed by incubating the eluate in 0.5x elution buffer containing 0.8mg/ml pronase (Sigma) and DNA purified using the Qiagen PCR purification kit.

tag: antibody

value: no Antibody

growth_protocol: S. Typhimurium grown to stationary phase in LB-broth


title: RpoS_MEP_BR3

value: ΔrpoS


title: RpoS_MEP_BR2


title: WT_antiFLAG_BR2

extract_protocol: After reaching early exponential growth (OD600 0.12), formaldehyde was added to reach a 1% final concentration and the cultures incubated for 15 min at 37oC. The cross-linking was then stopped by adding 1/4 vol. 1M glycine. Cells were washed three times in ice-cold PBS (pH7.4), resuspended in 500ul lysis buffer (10mM Tris pH8.0; 50mM NaCl; 10mM EDTA; 20% sucrose; 20 mg/ml lysozyme) and incubated 45 min at 37oC at which point 500ul 2x RIPA (100mM Tris pH8.0; 300mM NaCl; 2% Nonidet P40; 1% sodium deoxycholate; 0.2% SDS) was added. Chromatin was solubilised by sonication until DNA fragments were between 300 and 750 bp, and the lysate centrifuged at 12000g for 10 min to remove debris.  Cell extracts were then incubated with the appropriate antibody for 4h at 4oC. After the incubation of the cell extracts with the antibody, 50ul protein G beads were added and left for 16h at 4oC. The protein G beads were then washed twice in 1xRIPA, twice in wash solution (10mM Tris pH8.0; 250mM LiCl; 1mM EDTA; 0.5% Nonidet P40; 0.5% sodium deoxycholate) and twice in TE (10mM Tris pH8.0; 1mM EDTA). The immunoprecipitate was eluted in 150ul of elution buffer (50mM Tris pH8.0; 10mM EDTA; 1% SDS) prewarmed at 65oC. Cross-linking was reversed by incubating the eluate in 0.5x elution buffer containing 0.8mg/ml pronase (Sigma) and DNA purified using the Qiagen PCR purification kit.

value: anti-FLAG


title: liver_3days_50ppm_replicate3


title: RpoS_MEP_BR1


title: Roots_Control vs Drought Stressed_Replicate 3_Swap

city: Seibersdorf

first: Silvia

last: Fluch

address: Campus Seibersdorf

department: Biogenetics/Natural Resources

country: Austria

institute: Austrian Research Centers GmbH

hyb_protocol: The mixture of Cy3- and Cy5-labelled cDNA was denatured for 3 min at 95°C and mixed with 4x hybridisation mix (GE Life Science) and formamide at a ratio 1:2. Hybridizations were carried at 42°C for 15 h. The arrays were washed with 0.1% SDS in 1x SSC at 50°C for 15 min followed by 0.1% SDS in 0.1x SSC for 10 min at room temperature. After two washes with 0.2x SSC for 5 min at room temperature slides were dried with pressure air.

scan_protocol: The slides were scanned with an LS Reloaded scanner (Tecan)

data_processing: Images were processed with GenPixPro 6.0 software (Axon Instruments Inc.). A spatial and intensity-dependent (LOWESS) normalisation method was employed to normalise the ratio values of the raw data, which were afterwards statistically analysed using LIMMA software package in R (Smyth 2004) from the Bioconductor project (http://www.bioconductor.org). The cut off value was set to p <0.01

organism: Capsicum annuum

source_name: roots of control plants

label_protocol: Labelled cDNA was prepared using the template-switch-PCR method according to Petalidis et al. (2003) with 500 ng total RNA. Double stranded cDNA was purified using a QIAquick purification Kit (Quiagen). Labelling with Cy3- and Cy5-dyes (GE Life Science) was performed using BioPrime Array CGH Genomic Labeling System (Invitrogen).

growth_protocol: Plants of Capsicum annuum L. cv. Ziegenhorn Bello were placed into 0.5-l-container with commercial soil and perlit (1:1 v/v). Four plants per pot were kept in a greenhouse with natural light conditions and 10 h dark period. Temperature was kept at 18-22°C and relative air humidity varied between 60% and 80% during day and night respectively.

extract_protocol: A modified method of Chang et al. (1993) was used to extract RNA from leaves and washed roots.

treatment_protocol: Upon full development of 6 to 7 leaves of the main shoot watering of the pots was suspended for one week, whereas control plants were further watered to maintain the water content of the substrate between 40-60%. The youngest fully expanded leaves were harvested.

tag: cultivar

value: Variety Ziegenhorn Bello

value: full development of 6-7 roots

source_name: roots of drought-stressed plants

tag: stress

value: drought-stressed


title: WT_mH-NS

value: mH-NS


title: WT_antiFLAG_BR1


title: Roots_Control vs Drought Stressed_Replicate 2


title: liver_3days_50ppm_replicate1

description: 051011_RAC 26


title: Roots_Control vs Drought Stressed_Replicate 4_Swap


title: liver_1day_50ppm_replicate2

source_name: left laterial lobe of liver, 1 day of dietary dosing, 50 ppm sodium phenobarbital


title: StpA_MEP_BR3


title: liver_1day_50ppm_replicate3


title: Roots_Control vs Drought Stressed_Replicate 1


title: WT_antiFLAG_BR3


title: Leaf_Control vs Drought Stressed_Replicate 4_Swap

source_name: leaves of control plants

value: full development of 6-7 leaves

source_name: leaves of drought-stressed plants


title: StpA_MEP_BR2


title: Leaf_Control vs Drought Stressed_Replicate 3_Swap


title: liver_1day_50ppm_replicate1


title: StpA3xFLAG_antiFLAG_BR2


title: StpA3xFLAG_antiFLAG_BR3


title: liver_14days_control_replicate3

source_name: left laterial lobe of liver, 14 days of dietary dosing, control


title: Leaf_Control vs Drought Stressed_Replicate 2


title: StpA3xFLAG_antiFLAG_BR1


title: Leaf_Control vs Drought Stressed_Replicate 1


title: StpA_MEP_BR1


title: WT_MEP_BR3


title: WT_MEP_BR1

growth_protocol: Strain was grown in LB inoculated 1:1000 from an overnight culture for 160min to reach the early-exponential phase of growth.


title: WT_MEP_BR2


title: liver_7days_control_replicate3

source_name: left laterial lobe of liver, 7 days of dietary dosing, control


title: liver_7days_control_replicate2


title: liver_7days_control_replicate1


title: liver_14days_control_replicate1


title: liver_14days_control_replicate2


title: WT_LEP_B1T2

growth_protocol: Strain was grown in LB inoculated 1:1000 from an overnight culture for 250min to reach the late-exponential phase of growth.

value: late-exponential


title: WT_LEP_B2T1


title: E0xZSP Glucose 3000209725_L

city: São Paulo

first: André

last: Vieira

state: São Paulo

address: Av. Prof. Lineu Prestes 748

department: Bioquímica

country: Brazil

institute: Instituto de Química - USP

description: Fluorescence mean intensity and surrounding median background from each spot were obtained with ArrayVision v6.0 (Imaging Research, Inc). Unreliable spots, having intensities too similar to local background or saturated were filtered out. Spots presenting mean intensity below 2 times the standard deviation of its background in Cy3 and Cy5 simultaneously were eliminated from the subsequent analysis since their expression ratio is meaningless,. Saturated signals [intensity greater than >990 fluorescence units] were also discarded. Normalization was carried out by LOWESS fitting on a M versus S plot, where M is the fluorescence log-ratio of the heat shock time-point relative to the control condition [M=log2(ratio)] and S is the log-mean fluorescence intensity [S = log2((cy3+cy5)/2)].

hyb_protocol: Cy3 and Cy5 fluorescent labeled cDNAs were ressuspended in 13ul of water and mixed in a solution containing 25% of Hybridization Buffer (Amersham Biosciences) and 50% formamide, in a final volume of 56ul. Samples were denatured by heating at 95oC for 2 min and immediately chilled on ice. The targets were applied on the microarray slides, covered with a 24 x 60 mm coverslip (Corning) and hybridized at 42oC for 16h. Washing was performed once in 1xSSC, 0.1% SDS for 10 min, twice in 0.1xSSC, 0.01% SDS for 10 min and in 0.1xSSC for 1 min. The slides were shrinked in water for 10s and dried with nitrogen gas.

scan_protocol: Microarray slides were scanned with a Generation III DNA Scanner (Amersham Biosciences).

data_processing: filtering low intensity spots, LOWESS normalization.

organism: Blastocladiella emersonii

label_protocol: 10ug of total RNA was reverse transcribed and labeled using “Superscript® Plus Indirect cDNA Labeling System” (Invitrogen®). Unincorporated dye was removed by purification in Millipore filters MAFB000 in guanidine buffer pH 4.8 followed by 4 washes with ethanol 80%. Labeled cDNA was eluted with 90 ul of Tris 10mM, pH8.0 and dried in speed vac.

extract_protocol: total RNA was extracted using Trizol regent (Invitrogen)

tag: growth protocol

value: Zero min sporulation cells in the presence of 1% glucose.

source_name: ZSP

value: ZSP min sporulation cells in the presence of 1% glucose.


title: E0xZSP Glucose 3000209725_R

value: ZSP cells in the presence of 1% glucose.


title: E0xE150 Glucose 3000209699_L

value: 150 min sporulation cells in the presence of 1% glucose.


title: liver_3days_control_replicate2

source_name: left laterial lobe of liver, 3 days of dietary dosing, control

value: liver


title: E0xZSP Glucose 3000209199_L


title: E0xE150 Glucose 3000209731_R


title: E0xE150 Glucose 3000209731_L


title: E0xZSP Glucose 3000209199_R


title: E0xE150 Glucose 3000209198_R


title: E0xZSP Glucose 3000209700_L


title: liver_3days_control_replicate3


title: E0xE150 Glucose 3000209699_R


title: E0xE150 Glucose 3000148624_R


title: WT_LEP_B1T1

value: Salmonella enterica serovar Typhimurium SL1344

value: wild type


title: liver_1day_control_replicate3

description: 051011_RAC 05

source_name: left laterial lobe of liver, 1 day of dietary dosing, control


title: StpA_LEP_B2T2

value: ΔstpA


title: liver_3days_control_replicate1


title: StpA_LEP_B2T1


title: WT_LEP_B2T2


title: StpA_LEP_B1T1


title: E0xE150 Glucose 3000148624_L


title: liver_1day_500ppm_replicate1


title: E0xE120 Glucose 3000209746_R

value: 120 min sporulation cells in the presence of 1% glucose.


title: liver_1day_control_replicate2

description: 051011_RAC 03


title: E0xE120 Glucose 3000209730_L


title: E0xE120 Glucose 3000209746_L


title: StpA_MEP_B2T2

value: mid-exponential


title: E0xE120 Glucose 3000209197_L


title: StpA_LEP_B1T2


title: E0xE120 Glucose 3000209730_R


title: E0xE120 Glucose 3000209197_R


title: liver_1day_control_replicate1


title: Nucleus accumbens acute cocaine 3

city: New York

first: Ian

middle: Sutherland

last: Maze

state: NY

address: 1425 Madison Ave.

department: Neuroscience

institute: Mount Sinai School of Medicine

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Beadstudio software from illumina

source_name: Mouse nucleus accumbens 1 hr

label_protocol: Standard Illumina labelling protocol

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

treatment_protocol: Animals were treated daily with either 'saline' (15 treatments saline, i.p.), 'acute' cocaine (14 treatments saline + 1 treatment 20 mg/kg cocaine-HCl, i.p.), 'repeated + acute' cocaine (7 treatments saline + 8 treatments 20 mg/kg cocaine-HCl, i.p.) or 'repeated withdrawal + acute' cocaine (7 treatments 20 mg/kg cocaine-HCl + 7 treatments saline + 1 challenge treatment 20 mg/kg cocaine-HCl, i.p.) and were sacrificed 1 hour after the final treatment.

tag: agent

tag: age

value: 8-10 week old

value: Bilateral, 1mm-thick, 15-gauge punches, pooled together from 4 animals


title: StpA_MEP_B2T1


title: Nucleus accumbens repeated + acute cocaine 3

description: Replicate 3

value: 7 treatments saline + 8 treatments 20 mg/kg cocaine-HCl, i.p.


title: Nucleus accumbens salline 3

description: Replicate 3

value: 15 treatments saline, i.p.


title: E0xE60 Glucose 3000209741_R

value: 60 min sporulation cells in the presence of 1% glucose.


title: E0xE60 Glucose 3000209745_R


title: E0xE120 Glucose 3000148622_L


title: E0xE120 Glucose 3000148622_R


title: E0xE60 Glucose 3000209729_R


title: E0xE60 Glucose 3000209741_L


title: Nucleus accumbens repeated + acute cocaine 2

description: Replicate 2


title: E0xZSP Glucose 3000209700_R


title: StpA_MEP_B1T2


title: Nucleus accumbens repeated wd + acute cocaine 3

description: Replicate 3

value: 7 treatments 20 mg/kg cocaine-HCl + 7 treatments saline + 1 challenge treatment 20 mg/kg cocaine-HCl, i.p.


title: E0xE60 Glucose 3000209729_L

value: Zero min sporulation cells in the presence o 1% glucose.


title: WT_MEP_B2T1


title: Nucleus accumbens repeated wd + acute cocaine 2

description: Replicate 2


title: Nucleus accumbens acute cocaine 2

description: Replicate 2

value: 14 treatments saline + 1 treatment 20 mg/kg cocaine-HCl, i.p.


title: WT_MEP_B2T2


title: E0xZSP 3000148632_R

value: Zero min sporulation cells.

value: Zoospore cells.


title: E0xZSP 3000148630_L


title: E0xE60 Glucose 3000148620_R

value: Zero min sporulation cells in the presence of 1% glucose.


title: StpA_MEP_B1T1


title: E0xE60 Glucose 3000148620_L


title: Nucleus accumbens salline 2

description: Replicate 2


title: WT_MEP_B1T2


title: Nucleus accumbens acute cocaine 1

description: Replicate 1


title: E0xZSP 3000148640_R


title: E0xZSP 3000148630_R


title: Nucleus accumbens repeated + acute cocaine 1

description: Replicate 1


title: E0xZSP 3000148640_L


title: E0xZSP 3000148632_L


title: E0xZSP 3000148608_R


title: E0xZSP 3000148608_L


title: Nucleus accumbens salline 1

description: Replicate 1


title: E0xE150 3000148631_L

value: 150 min sporulation cells.


title: E0xE150 3000148631_R


title: E0xE150 3000148638_L


title: E0xE150 3000148638_R


title: E0xE150 3000148642_R


title: E0xE150 3000148642_L


title: E0xE60 3000148605_L

value: 60 min sporulation cells.


title: E0xE60 3000148605_R


title: E0xE60 3000148643_R

value: Zero min sporulation cells

value: 60 min sporulation cells


title: E0xE60 3000148348_L


title: E0xE60 3000148348_R


title: PTIP deficient DT40 cell

city: Kyoto

first: XIN

last: WANG

address: Yoshida Konoe, Sakyo-ku

department: Graduate School of Medicine

country: Japan

institute: Kyoto University

description: no additional information

hyb_protocol: Following fragmentation,  cRNA  were hybridized  on Genechip® Chicken Genome Array (Affymetrix Cat#900590). GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix P/N00-0079).

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G System w/Workstation and AutoLoader (Affymetrix P/N00-0218)

data_processing: The data were analyzed with GeneChip® Operating Software (GCOS) (Affymetrix P/N690-036)

source_name: Gallus gallus DT40 B cell PTIP deficient clone

label_protocol: Biotinylated cRNA were prepared using GeneChip® Expression 3’ Amplification One-Cycle Target Labeling and Control Reagents  (Affymetrix Cat#900493)

growth_protocol: Both wild-type and PTIP deficient DT40 cells were cultured at 39°C

extract_protocol: The total RNAs were isolated from wild-type and PTIP-/-/- cells using Sepasol®-RNA I (Nacalai tesque, Japan).

value: bursa of Fabricius

tag: cell line

value: DT40 B cell line

value: PTIP deficient


title: E0xE60 3000148606_L


title: E0xE120 3000148607_700_R

value: 120 min sporulation cells


title: E0xE120 3000148641_L


title: E0xE120 3000148641_R


title: E0xE60 3000148606_R


title: E0xE120 3000148347_R


title: H.pylori strain HPAG (HopZ) 1hr in rich media, pH 5, replicate 3

status: Public on Oct 27 2009

city: Saint Louis

first: Jeremiah

middle: J

last: Faith

state: MO

address: Campus Box 8510

institute: Washington University in St. Louis

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 16 hr at 45C on GeneChips Hp-AG78a520172F. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GS300

data_processing: The data were normalized using the justRMA() function [with default parameters] from the Bioconductor R package.

organism: Helicobacter pylori

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

growth_protocol: Bacterial cells were grown to log phase in BB medium and then added to mGEPs cells in RPMI 1640 medium supplemented with 10% FBS at 37C or just RPMI 1640 medium supplemented with 10% FBS at 37C (no mGEP cells)

extract_protocol: Qiagen RNeasy mini-prep kit

treatment_protocol: After 24h of infection, medium and non-attached bacteria were washed off and the bacterial and mammalian cells harvested by trypsinization (5mins at 37C). Following neutralization with ice-cold medium, and a PBS wash, cells were flash frozen in liquid nitrogen

value: H.pylori HPAG


title: wild-type DT40 cell

description: no additional information

source_name: Gallus gallus DT40 B cell wild-type clone

value: wildtype


title: E0xE120 3000148347_L


title: E0xE120 3000148607_700_L

extract_protocol: 120 min sporulation cells


title: H.pylori strain HPAG (HopZ) 1hr in rich media, pH 5, replicate 2


title: Tetrahymena_hht2-K4Q

city: Rochester

first: Martin

last: Gorovsky

address: Hutchison Hall 432

department: Department of Biology

institute: University of Rochester

description: references: Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.

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

scan_protocol: Sample scan protocol provided and performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Array normalization was performed using the quantile normalization method of Bolstad et al. (2003). Normalized expression values for the individual probes were used to obtain the expression values for a given open reading frame (ORF) by using the robust multiarray average (RMA) procedure as previously described by Irizarry et al. (2003).

organism: Tetrahymena thermophila

source_name: Tetrahymena thermophila hht2-K4Q

label_protocol: Sample labeling protocol provided and performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Super proteose peptone (SPP) medium (1% proteose peptone, 0.1% yeast extract, 0.2% glucose, 90 µM EDTA ferric sodium salt), 30°C, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks), 200,000 cells/ml.

extract_protocol: Homogenization was done using a Qiashredder spin column and total RNA was extracted using the RNeasy Protect Cell Mini Kit (Qiagen, Valenica, CA) according to manufacturer’s instructions. The concentration of total RNA was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE) and RNA integrity was verified using a Bioanalyzer 1000 (Agilent, Palo Alto, CA).


title: Tetrahymena_htb1-K115R

source_name: Tetrahymena thermophila htb1-K115R


title: Tetrahymena_deltaBRE1

source_name: Tetrahymena thermophila delta-BRE1


title: Tetrahymena_HTB1

source_name: Tetrahymena thermophila HTB1


title: H.pylori strain HPAG (HopZ) 1hr in rich media, pH 5 replicate 1


title: Tetrahymena_deltaUBC2

source_name: Tetrahymena thermophila delta-UBC2


title: WT_MEP_B1T1

value: Salmonella enterica serovar Typhimurium SL1344

value: mid-exponential

value: wild type

source_name: Reference genomic DNA


title: naive B cells from PP

city: Yokohama

first: Keiichiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN

description: from C57BL6/J wild type mice, without any treatment

hyb_protocol: The labeled cRNA was hybridized with Mouse Genome 430 2.0 Arrays (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The image was quantified by using GCOS software.

source_name: mouse naive B cells from Peyer's patches

label_protocol: RNA was subjected to biotinilated cRNA synthesis by using Target Labeling lit (Affymetrix).

growth_protocol: C57BL6/J wild type mice were maintained in specific pathogen-free conditions (SPF) at the animal facility of the Research Center for Allergy and Immunology.

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen).

treatment_protocol: Single cell suspensions were prepared from mouse pLN or Peyer's patches, stained with anti-B220,PNA,anti-Fas antibodies, and then purified by using FACS ARIA.

tag: tissues

value: Adult mouse Peyer's patches

value: C57BL6/J wild type

value: B cells


title: H.pylori strain HPAG (HopZ) 1hr in rich media, pH 7, replicate 3


title: H.pylori strain HPAG (HopZ) 1hr in rich media, pH 7, replicate 1


title: naive B cells from pLN

department: Research Center for Allergy and Immunology

description: from C57BL6/J wild type mice, immunized with TNP-KLH with incomplete Freund's adjuvant

source_name: mouse naive B cells from immunized peripheral lymph nodes

value: Adult mouse peripheral lymph nodes


title: H.pylori strain HPAG (HopZ) 0hr in rich media, pH 7, replicate 3


title: H.pylori strain HPAG (HopZ) 0hr in rich media, pH 7, replicate 2


title: Tetrahymena_wild-type_CU428

source_name: Tetrahymena thermophila wild-type CU428

value: wild-type CU428


title: H.pylori strain HPAG (ChAG associated) 1hr in rich media, pH 5 replicate 2


title: H.pylori strain HPAG (HopZ) 1hr in rich media, pH 7, replicate 2


title: H.pylori strain HPAG (ChAG associated) 1hr in rich media, pH 5 replicate 3


title: H.pylori strain HPAG (HopZ) 0hr in rich media, pH 7, replicate 1


title: H.pylori strain HPAG (ChAG associated) 1hr in rich media, pH 5 replicate 1


title: GC B cells from pLN

source_name: mouse germinal center B cells from immunized peripheral lymph nodes


title: H.pylori strain 488_Kx2 (gastric cancer associated) in mammalian cell media, replicate 1

value: H.pylori 488_Kx2


title: H.pylori strain 488_Kx2 (gastric cancer associated) in mammalian cell media, replicate 3


title: H.pylori strain HPAG (ChAG associated) 1hr in rich media, pH 7, replicate 3


title: H.pylori strain HPAG (ChAG associated) 1hr in rich media, pH 7, replicate 2


title: H.pylori strain HPAG (ChAG associated) 1hr in rich media, pH 7, replicate 1


title: GC B cells from PP

source_name: mouse germinal center B cells from Peyer's patches


title: H.pylori strain 488_Kx1 (ChAG associated) in mammalian cell media, replicate 2

value: H.pylori 488_Kx1


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx2 (gastric cancer associated) replicate 2

description: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx1 (ChAG associated)


title: H.pylori strain 488_Kx1 (ChAG associated) in mammalian cell media, replicate 1


title: H.pylori strain 488_Kx2 (gastric cancer associated) in mammalian cell media, replicate 2


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx2 (gastric cancer associated) replicate 1

source_name: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx1 (ChAG associated)


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx2 (gastric cancer associated) replicate 3


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx1 (ChAG associated) replicate 2


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx1 (ChAG associated) replicate 3


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx1 (ChAG associated) replicate 1


title: H.pylori strain HPAG (with HopZ knockout) in mammalian cell media, replicate 1


title: H.pylori strain HPAG (with HopZ knockout) in mammalian cell media, replicate 2


title: H.pylori strain HPAG (ChAG associated) in mammalian cell media, replicate 6


title: H.pylori strain HPAG (ChAG associated) in mammalian cell media, replicate 5


title: H.pylori strain HPAG (ChAG associated) in mammalian cell media, replicate 3


title: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain HPAG (ChAG associated) replicate 3


title: H.pylori strain HPAG (ChAG associated) in mammalian cell media, replicate 1


title: H.pylori strain HPAG (with HopZ knockout) in mammalian cell media, replicate 3


title: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain HPAG (ChAG associated) replicate 2


title: H.pylori strain HPAG (ChAG associated) in mammalian cell media, replicate 4


title: H.pylori strain HPAG (ChAG associated) in mammalian cell media, replicate 2


title: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain HPAG (ChAG associated) replicate 1


title: Mouse non-progenitor gastric epithelial cells (no H.pylori), replicate 1


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (with HopZ knockout) replicate 2


title: Nucleus accumbens repeated wd + acute cocaine 1

description: Replicate 1

value: 7 treatments 20 mg/kg cocaine-HCl + 7 treatments saline + 1 challenge treatment 20 mg/kg cocaine-HCl, i.p.

value: 8-10 week old

value: Bilateral, 1mm-thick, 15-gauge punches, pooled together from 4 animals


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (with HopZ knockout) replicate 1


title: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain 488_Kx2 replicate 1

description: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain 488_Kx2 (gastric cancer associated)

hyb_protocol: Following fragmentation, 25 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

molecule: polyA RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA.

growth_protocol: Cells were grown to 70% confluence in RPMI 1640 medium supplemented with 10% FBS at 37C

extract_protocol: Qiagen RNeasy mini-prep kit.

treatment_protocol: After 24h of infection, medium and non-attached bacteria were washed off and the mouse cells harvested by trypsinization (5mins at 37C). Following neutralization with ice-cold medium, and a PBS wash, cells were flash frozen in liquid nitrogen

tag: treatment

value: Cells grown in T75 cell culture flasks

value: 24 hrs


title: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain 488_Kx2 replicate 3

source_name: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain 488_Kx2 (gastric cancer associated)


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (ChAG associated) replicate 5


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (ChAG associated) replicate 6


title: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain 488_Kx1 (ChAG associated) replicate 1


title: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain 488_Kx1 (ChAG associated) replicate 3


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx2 (gastric cancer associated) replicate 3


title: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain 488_Kx1 (ChAG associated) replicate 2


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx2 (gastric cancer associated) replicate 2


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx2 (gastric cancer associated) replicate 1


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (ChAG associated) replicate 4


title: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain 488_Kx2 replicate 2


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (ChAG associated) replicate 1


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (ChAG associated) replicate 2


title: Mouse gastric epithelial progenitor cells (no H.pylori), replicate 2


title: Mouse gastric epithelial progenitor cells (no H.pylori), replicate 1


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx1 (ChAG associated) replicate 2


title: E0xE60 3000148643_L

value: Zero min sporulation cells

value: 60 min sporulation cells


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx1 (ChAG associated) replicate 3


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 488_Kx1 (ChAG associated) replicate 1


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (ChAG associated) replicate 3


title: Mouse non-progenitor gastric epithelial cells, uninfected, replicate 3


title: Mouse non-progenitor gastric epithelial cells, uninfected, replicate 1


title: RZ-6

city: Houston

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

hyb_protocol: Following fragmentation, hybridization was performed according to standard Affymetrix (Santa Clara, CA) protocols (http://www.affymetrix.com/support/technical/manuals/affx).

scan_protocol: GeneChips were scanned at high resolution using an Affymetrix GeneChip Scanner 3000.

data_processing: Results were analyzed using GeneSpring GX version 7.2 software (Agilent Technologies, Redwood City, CA). Data, chip and genes were normalized in three stages (log transformed raw data < .01 set to .01, global normalization to the 50th percentile, followed by gene level normalization) using the recommended GeneSpring default settings for data transformation.

organism: Bos taurus

source_name: growth plate chondrocytes, reserve zone

label_protocol: Biotinylated cRNA were prepared using the MessageAmp II-Biotin Enhanced Kit from Ambion

extract_protocol: RNA was extracted from cells using RNA STAT-60 (Tel-Test, Inc.) per the manufacturer’s instructions.  Samples were analyzed with an Agilent 2100 Bioanalyzer to confirm RNA integrity.

value: growth plate chondrocytes, reserve zone

value: < 10 months

tag: gender

value: male


title: Mouse gastric epithelial progenitor cells, uninfected, replicate 2


title: HZ-6

source_name: growth plate chondrocytes, hypertrophic zone


title: Mouse non-progenitor gastric epithelial cells, uninfected, replicate 2


title: Mouse gastric epithelial progenitor cells, uninfected, replicate 1


title: RZ-5


title: HEK293 in NOD.Scid, rep2

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description: Gene expression data from in vivo expanded HEK293 cells.

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

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

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

source_name: Human embryonic kidney cells (HEK293) expanded for three weeks in immunodeficient NOD.Scid mice

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

growth_protocol: Human embryonic kidney (HEK293) cells were grown in DMEM (glucose concentration 450 mg/dl), either injected in NOD.Scid mice and expanded for three weeks in vivo, or cultivated in vitro.

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

value: embryonic kidney cells

tag: growth

value: in vivo cell expansion


title: HZ-5

value: growth plate chondrocytes, hypertrophic zone


title: HEK293 cells in vitro, rep1

description: Gene expression data from in vitro cultivated HEK293 cells.

source_name: Human embryonic kidney cells (HEK293) in vitro cultivated in DMEM (450 mg/dl glucose)

value: in vitro cell cultivation


title: HZ-4


title: RZ-4


title: Mouse gastric epithelial progenitor cells, uninfected, replicate 3


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (with HopZ knockout) replicate 3


title: Anti-mir-210 replicate 2

city: rotterdam

first: Mario

last: Pescatori

address: Westplein 11

country: Netherlands

institute: Health e-genomics

description: Gene expression data from HUVEC in which miR-210 activity was blocked by a complementary anti-miR-210-LNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  HG-U133_Plus_2.1sq. GeneChip.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Summarized signal intensities were generated in BRB ArrayTools using justRMA

source_name: HUVEC transfected with anti-miR-210-LNA

growth_protocol: HUVEC were grown in EGM-2 (Lonza) containing 2% FBS

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy mini kit following standard RNA cleanup protocol

treatment_protocol: To obtain stable miR-210 over-expressing cells, HUVEC were infected by retroviral vectors bearing pre-miR-210 sequence or a control scramble sequence. To inhibit miR-210, Locked Nucleic Acid (LNA) oligonucleotides against miR-210 or a control scramble sequence (Exiqon) were transfected by siRNA Transfection Reagent (Santa Cruz), following manufacturer instructions, in 40% confluent HUVEC (4X103/cm2) at the final concentration of 40 nM.

value: HUVEC


title: HZ-3


title: Anti-mir-210 replicate 3


title: Anti-mir-210 replicate 1


title: Anti-scramble replicate 2

description: Gene expression data from HUVEC transfected with a scramble-LNA

source_name: HUVEC transfected with a scramble-LNA


title: HEK293 in NOD.Scid, rep1


title: Anti-scramble replicate 1


title: Anti-scramble replicate 3


title: RZ-2


title: RZ-3


title: HEK293 cells in vitro, rep2


title: HZ-1


title: pSUPER-mir-210 replicate 3

description: Gene expression data from HUVEC over-expressing miR-210

source_name: HUVEC infected by retroviral vectors bearing pre-miR-210 sequence


title: RZ-1


title: pSUPER-mir-210 replicate 2


title: HZ-2