title: SLK5dpi_MeDIP

description: Analysis of DNA methylation patterns in de novo infected SLK cells at 5 days post-infection

source_name: MeDIP of DNA from de novo infected SLK cells at 5 days post-infection

source_name: Input, DNA from de novo infected SLK cells at 5 days post-infection


title: H13: Diff [mRNA]

status: Public on Jun 07 2010

type: RNA

city: West Point

first: Michele

last: Cleary

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

country: USA

institute: Merck and Co., Inc.

description: Recent advances in the study of human embryonic stem cells (hESCs) and induced-pluripotent stem cells (iPS) highlight their importance as both model systems for basic research and avenues for therapeutic applications.  To gain better insight into the molecular properties and developmental capabilities of these cells, a clearer understanding of their molecular properties is crucial.  In this study, we analyze changes in the expression profile of microRNAs (miRNAs) and mRNAs in nine different, National Institutes of Health (NIH)-approved hESC lines.  By examining both undifferentiated hESCs and cells exposed to an undirected differentiation scheme at early stages found those miRNAs and mRNAs enriched in the hESC lines, and those miRNAs and mRNAs initially regulated upon commitment.  In comparing these profiles with those of an embryonal carcinoma (EC) cell line, NTera-2, we observed distinct patterns of miRNA expression in hESCs.  Furthermore, this analysis demonstrates that some previously identified hESC-enriched miRNAs, such as the miR-302 family and miR-17-92 miRNA cluster, are regulated at very early stages of commitment.  Additionally, we identify other early response miRNAs, not previously identified as hESC-enriched, and describe a large cluster of hESC-enriched miRNAs located on chromosome 19, whose expression changes rapidly in response to differentiation cues.  Examination of changes in mRNA expression during early commitment further reveals that many differentiation-regulated genes are possible candidates for regulation by these hESC-enriched miRNAs.

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

molecule: total RNA

organism: Homo sapiens

source_name: human embryonic stem cell line

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: cell line/type

value: H13 Diff


title: LM2 with hypoxia for 24h, repeat A

city: Princeton

first: Yibin

last: Kang

state: NJ

address: LTL 254, Washington Road

department: Molecular Biology

institute: Princeton University

description: 1% O2 level, 24h

hyb_protocol: Labeled cRNA (mixed Cy5-labeled and Cy3-labeled) was incubated with Blocking agent and Fragmentation buffer (Agilent Gene Expression Hybridization Kit) for 30min at 60°C. GEx Hybridization Buffer HI-RPM was then added to the mixture. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized for 16h. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner.Images were quantified using Agilent Feature Extraction Software (version 9.1.3).

data_processing: The data were analyzed with Genespring GX 7.3 Expression Analysis using Per Spot (divide by control channel), Per Chip (normalize to 50th percentile) and Per Gene (normalize to median) normalization methods.

source_name: LM2 with hypoxia for 24h, repeat A

label_protocol: 325ng of total RNA were primed with T7 promoter primer at 65°C for 10 min, then reversed transcribed to cDNA at 40°C for 2h with MMLV RT, and transcribed to cRNA with T7 RNA polymerase with dATP, dTTP, dGTP and Cy5-CTP(test) or Cy3-CTP (reference) at 40°C for 2. Labeled cRNA was purified with Qiagen RNeasy mini kit.

growth_protocol: These sublines were maintained in DMEM with 10% FBS and antibiotics.

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

treatment_protocol: Low oxygen (1%) was applied by placed the cells in an oxygen chamber in tissue culture incubator (37-degree) for designated period (6h or 24h). The control was cultured in the tissue culture incubator (21% oxygen, 37-degree).

tag: cell line

value: breast cancer cell MDA-MB-231

tag: subline

tag: treatment

value: 1% O2 in oxygen chamber

tag: stress

value: hypoxia

tag: time

source_name: Universal Human Reference RNA (Stratagene)

value: 10 human cell lines


title: AP3_MeDIP

type: genomic

city: Hamburg

first: Thomas

last: Guenther

department: Mechanisms of Antiviral Defense

country: Germany

institute: Heinrich-Pette-Institut

description: Analysis of DNA methylation patterns in the PEL-derived cell line AP3

hyb_protocol: Labelled input and MeDIP samples were blocked using Agilent blocking solution and human cot-1 DNA (Invitrogen), and hybridized using the Agilent Oligo aCGH/ChIP-on-chip Hybridization Kit at 65°C for 24 hrs in a rotating oven. Arrays were washed once with Oligo aCGH/ChIP-on-chip Wash Buffer 1 (Agilent 5188-5221) at RT for 5 min and in Oligo aCGH/ChIP-on-chip Wash Buffer 2 (Agilent 5188-5222) at 37°C for 1 min.

scan_protocol: Microarrays were scanned with a GenePix Personal 4100A scanner (Axon Instruments)

data_processing: Primary array analysis and data normalization was carried out using GenePix®Pro 6.0 software (Axon Instruments). All MeDIP datasets were normalized using the methylated pCR2.1 plasmid which had been added to the samples prior to the immunoprecipitation, thus controlling for differences in MeDIP efficiency as well as labelling and array hybridization. Both channels were adjusted such that the average ratio of input vs. MeDIP signals across all pCR2.1-specific spots was 1. To eliminate false positive spots, we hybridized DNA from KSHV-negative SLK cells and identified all probes which exhibited high levels of background hybridization (i.e., fluorescence levels that exceeded the mean value plus 1x the standard deviation of all KSHV-specific spots on the negative control array). These probes (which mapped almost exclusively to repeat regions) were permanently flagged in all datasets and not used for further analysis. While our arrays carry probes specific for the M and P types of the KSHV genome, the KSHV genomes from the BCBL1 and AP3 lines have not been fully sequenced and thus may deviate from the reference genomes at a few locations. To control for such sequence differences, we flagged all spots which exhibited fluorescence levels which did not exceed a background fluorescence treshold in the input channel, which was set to the mean fluorescence plus twice the standard deviation of all negative control features (i.e. empty array features as well as spots containing irrelevant sequences, corresponding to all Agilent probes in the datasets which are labeled with NC2_ and (-)3xSLv1). Note that, if sequence diversification leads to only a reduction of hybridization efficiency (e.g. due to single nucleotide polymorphism, which will not abolish hybridization), this will not falsify our results as the hybridization efficiency will be reduced in input as well as the immunoprecipitated sample; the ratio will thus be unaffected. In addition to above quality controls, in each dataset we flagged all probes which exhibited more than 30 % variance between duplicate spots. The 30% treshold corresponds to the mean variance plus twice the standard deviation exhibited by all KSHV-specific probes in all MeDIP experiments, thus removing all probes which show a significantly increased variance between individual spot repeats. MeDIP data were furthermore corrected by subtracting from each probe-specific signal the value observed in the negative control, i.e. the MeDIP sample representing the unmethylated KSHV bacmid in the background of cellular DNA. After normalization, an enrichment score was calculated for each of the probes, represented by the ratio of fluorescence signal intensities in the immunoprecipitated samples relative to the input control.

molecule: genomic DNA

source_name: MeDIP of DNA from PEL-derived AP3 cells

label_protocol: 500 ng of MeDIP-input and all of the MeDIP material were labeled with Cy3 and Cy5 using Agilent Genomic DNA Labeling Kit PLUS according to Agilents recommendations. After labeling, samples were purified using Microcon YM-30 filter columns (Milipore).

growth_protocol: established cell line; grown under standard conditions

extract_protocol: Highly pure genomic DNA serving as input for MeDIP was prepared by proteinase K digestion, followed by phenol chloroform extraction and ethanol precipitation. Negative and positive controls were prepared by mixing genomic DNA from SLK cells with unmethylated or in vitro methylated KSHV bacmid DNA (Zhou et al., J Virol. 2002 Jun;76(12):6185-96), respectively. The ratio of viral vs. cellular DNA was selected such that it mimics the episome content typically seen in KSHV-infected PEL cell lines and the SLKp line (approx. 30-40 copies per cell). The control DNA or DNA from KSHV-infected cells was resuspended in TE containing RNAseA and incubated for at least 2 hrs at 37°C to degrade RNA. DNA was sonicated to an average fragment size of 100-500 bp using a BioruptorTM (Diagenode). In order to allow quantification and normalization across multiple samples, 0.2 ng of in vitro methylated pCR2.1 plasmid (described at the end of this section) were added to 5 µg of sheared DNA and diluted in TE to a final volume of 250 µl. 50 µl (1 µg) of the dilution were saved as an input control, and another 250 µl TE were added to the remaining 200 µl. Denaturing of DNA was performed by incubation at 98°C for 10 min, followed by incubation on ice for 10 min. Subsequently, 51 µl 10x IP-buffer (100 mM Na-phosphate buffer, pH 7.0, 1.4 mM NaCl, 0.5 % Triton X-100) were added. Immunoprecipitation was performed by addition of 2.5 µg of a 5´-methylcytidine specific antibody (MAb-5MECYT-100, Diagenode) and incubation for 2 hrs on a rotating wheel at 4°C. 50 µl Dynabeads® M-280 Sheep anti-Mouse IgG (Invitrogen) were washed once with 0.1 % BSA in PBS, resuspended in 50 µl 1x IP-buffer, added to the DNA-antibody complexes and incubated for 2 hrs. Samples were washed three times with 1x IP-buffer for 10 min. Beads were resuspended in 150 µl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.5 % SDS) and 3.5 µl proteinase K were added. Samples were incubated shaking at 55°C for 15 min followed by 2 min at 65°C. Eluate was collected, elution was repeated once and the eluates were combined. DNA was purified twice by phenol-chloroform extraction, followed by a single chloroform extraction. DNA (300 µl in total) was precipitated with 810 µl ethanol (100 %), 24 µl NaCl (5 M) and 3 µl glycogen (10 mg/ml) at -80°C for at least 30 min. After centrifugation (20.000 x g, 4°C, 15 min), pellets were washed once with ethanol (70 %) centrifuged again, dried in a speedvac and resuspended in 15.5 µl H2O. Input controls were prepared by adding 250 µl water to 50 µl of the sheared DNA input samples and treated identical to the IP samples, starting with the ethanol precipitation step. The samples were subsequently analyzed by qPCR or microarray hybridization. For control and normalization purposes, we prepared in vitro methylated DNA from a bacmid containing the complete KSHV genome and the pCR2.1 vector (Invitrogen). DNA was methylated by incubating 15 µg of DNA with 40 units of the CpG methyltransferase M.SssI (NEB) for 2 hrs in 1x NEBuffer 2 containing 160 µM S-adenosylmethionine (SAM). Fresh SAM was added and reactions were incubated for another 2 hrs. DNA was purified and the reaction was repeated once to ensure complete methylation. Quantitative methylation was confirmed by restriction analysis using methylation sensitive enzymes (HpaII and MspI, Fermentas), and/or bisulfite sequencing of specific loci.

tag: sample type

value: biological sample

tag: cell type

value: B cells

source_name: Input, DNA from PEL-derived AP3 cells


title: LM2 with hypoxia for 6h, repeat B

description: 1% O2 level, 6h

source_name: LM2 with hypoxia for 6h, repeat B


title: RA wt rep5

city: Münster

first: Peter

middle: Christian

last: Kahr

address: Grevener Straße 1

institute: University Hospital Münster

description:
replicate 5
SAMPLE 20

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genespring

label: biotin

organism: Mus musculus

source_name: isolated RA of wild-type mouse

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit from Ambion

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

tag: genotype

value: wild-type

tag: age

value: 12 weeks

tag: tissue

value: Right atrial appendage


title: BCBL1_H3K9/14Ac

description: Analysis of H3K9/14Ac patterns in the PEL-derived cell line BCBL1

hyb_protocol: Labelled input and ChIP samples were blocked using Agilent blocking solution and human cot-1 DNA (Invitrogen), and hybridized using the Agilent Oligo aCGH/ChIP-on-chip Hybridization Kit at 65°C for 24 hrs in a rotating oven. Arrays were washed once with Oligo aCGH/ChIP-on-chip Wash Buffer 1 (Agilent 5188-5221) at RT for 5 min and in Oligo aCGH/ChIP-on-chip Wash Buffer 2 (Agilent 5188-5222) at 37°C for 1 min.

scan_protocol: Microarrays were scanned using a GenePix Personal 4100A scanner (Axon Instruments)

data_processing: Primary array analysis and data normalization was carried out using GenePix®Pro 6.0 software (Axon Instruments). All ChIP datasets were normalized using the adenovirus type 5 DNA that was added as a spike-in prior to labeling, hence correcting for errors during labelling, hybridization or scanning of the samples (probes Ad5f/r_K_475 to _590 were excluded due to a sequence deletion). To eliminate false positive spots, we hybridized DNA from KSHV-negative SLK cells and identified all probes which exhibited high levels of background hybridization (i.e., fluorescence levels that exceeded the mean value plus 1x the standard deviation of all KSHV-specific spots on the negative control array). These probes (which mapped almost exclusively to repeat regions) were permanently flagged in all datasets and not used for further analysis. While our arrays carry probes specific for the M and P types of the KSHV genome, the KSHV genomes from the BCBL1 and AP3 lines have not been fully sequenced and thus may deviate from the reference genomes at a few locations. To control for such sequence differences, we flagged all spots which exhibited fluorescence levels which did not exceed a background fluorescence treshold in the input channel, which was set to the mean fluorescence plus twice the standard deviation of all negative control features (i.e. empty array features as well as spots containing irrelevant sequences, corresponding to all Agilent probes in the datasets which are labeled with NC2_ and (-)3xSLv1). Note that, if sequence diversification leads to only a reduction of hybridization efficiency (e.g. due to single nucleotide polymorphism, which will not abolish hybridization), this will not falsify our results as the hybridization efficiency will be reduced in input as well as the immunoprecipitated sample; the ratio will thus be unaffected. In addition to above quality controls, in each dataset we flagged all probes which exhibited more than 30 % variance between duplicate spots. The 30% treshold corresponds to the mean variance plus twice the standard deviation exhibited by all KSHV-specific probes in all ChIP experiments, thus removing all probes which show a significantly increased variance between individual spot repeats. After normalization, an enrichment score was calculated for each of the probes, represented by the ratio of fluorescence signal intensities in the immunoprecipitated samples relative to the input control.

source_name: H3K9/14Ac ChIP DNA from BCBL1 cells

label_protocol: 500 ng of amplified ChIP-input controls and 500 ng of amplified immunoprecipitated ChIP material were labeled with Cy3 and Cy5 using Agilent Genomic DNA Labeling Kit PLUS according to Agilents recommendations. For normalization purposes, 0.1 ng of Adenovirus Type 5 DNA were added to each samples prior to the labeling procedure. After labeling, samples were purified using Microcon YM-30 filter columns (Milipore).

extract_protocol: ChIP analysis was performed as described by Si et al. (J Virol. 2006 Sep;80(18):9017-30) and recommended by the array manufacturer (Agilent Mammalian ChIP-on-chip protocol V10.0, May 2008), with some modifications. For chromatin immunoprecipitation, protein from 5x10^6 to 2x10^7 cells was cross-linked to DNA with 1 % formaldehyde in PBS for 10 min (adherent cells) or 20 min (suspension cells) at room temperature. The reaction was quenched by adding 1/20th volume 2.5 M glycine, cells were washed with PBS, scraped off the dish and collected. Cells were washed twice with ice cold PBS. All following steps were performed at 4°C. Lysis and wash buffers contained 1x protease inhibitor cocktail (Roche) and 1 mM Pefabloc® SC-Protease Inhibitor (Roth). Nuclei were isolated by incubation of cross-linked cells with 1 ml buffer I (50 mM Hepes-KOH, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10 min on ice and pelleted by centrifugation (1,350 x g 5 min). The nuclei were subsequently washed with 1 ml buffer II (10 mM Tris-HCl, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), pelleted again and resuspended in 1 ml buffer III (1% SDS, 10 mM EDTA, 50 mM Tris-HCL). Chromatin was fragmented by sonication using a BioruptorTM (Diagenode) to an average length if 100-500 bp. After addition of 100 µl 10% Triton X-100, cell debris was pelleted by centrifugation (20,000 x g, 4°C) and supernatants were collected. For each individual IP, chromatin from 1x106 cells in a maximum volume of 200µl was diluted with dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16,7 mM Tris-HCl, 167 mM NaCl) to a final volume of 2 ml. To reduce non-specific background, chromatin was pre-incubated with 60 µl salmon-sperm DNA protein-A agarose beads (Upstate). Antibodies (2 to 10 µg, depending on the antibody) specific for the histone modifications H3K9/K14-Ac (Upstate: #06-599), H3K4-me3 (Upstate: #04-745), H3K9-me3 (Upstate: #17-625) or H3K27-me3 (Upstate: #07-449) were added and incubated for 16 hrs at 4°C on a rotating wheel. 60 µl agarose beads were added to precipitate the chromatin-immunocomplexes for 1 hr at 4°C. Beads were washed once with low-salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, 150 mM NaCl), once with high-salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, 500 mM NaCl), once with LiCl-wash buffer (0.25 M LiCl, 1 % Nonidet P-40, 1 % Na-deoxycholate, 1 mM EDTA, 10 mM Tris-HCl) and twice with TE buffer. Chromatin was eluted from the beads in 210 µl elution-buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS) for 30 min at 65°C. 8 µl of a 5 M NaCl solution were added to 200 µl of the supernatant, and chromatin was de-crosslinked overnight at 65°C. Samples were diluted by adding 200 µl TE and RNA was degraded with 8 µl RNAseA (10 mg/ml) for 2 hrs at 37°C. For degradation of protein, 7 µl of CaCl2 solution (300 mM CaCl2 in 10 mM Tris-HCl) and 4 µl ProteinaseK (20 mg/ml Peqlab) were added and samples were incubated for 1h at 55°C. DNA was purified two times by phenol-chloroform extraction followed by a single chloroform extraction. DNA (400 µl in total) was precipitated with 1055 µl ethanol (100 %), 24 µl NaCl (5 M) and 3 µl glycogen (10 mg/ml) at -80°C for at least 30 min. After centrifugation (20.000 x g, 4°C, 15 min), pellets were washed once with ethanol (70 %) centrifuged again and dried in a vacuum centrifuge. DNA was resuspended in 70 µl of 10 mM Tris-HCl. For preparation of input controls, 1/4th of the amount of chromatin that was used in the immunopreciptations was employed. Input samples were diluted in dilution buffer to a final volume of 200 µl and were treated identical to IP samples, starting with the decrosslinking step. Both samples were subsequenctly subjected to whole genome amplification and labeling using a linker mediated PCR protocol (Agilent Mammalian ChIP-on-chip protocol V10.0, May 2008), followed by microarray hybridization.

tag: antibody

source_name: Input DNA from BCBL1 cells


title: LM2 with hypoxia for 24h, repeat B

description: 1% O2 level, 24h

source_name: LM2 with hypoxia for 24h, repeat B


title: RA wt rep4

description:
replicate 4
SAMPLE 19


title: RA wt rep3

description:
replicate 3
SAMPLE 18


title: Diffuse Intrinsic Pontine Glioma 9 - Tumour-6.0

status: Public on Jun 08 2010

city: Toronto

first: Pawel

last: Buczkowicz

state: Ontario

address: 686 Bay Street

department: Paediatric Laboratory Medicine

country: Canada

institute: Hospital for Sick Children

description: Hybridized to 6.0

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  were processed using Partek Genome Suite V6.4 and Genotyping Console V2.1 using Segmentation and Hidden-Markov Model Analysis. Tumour samples were normalized to their matched normal. Tumour samples with no corresponding matched normal were normalized using HapMap.
CHP files for samples analyzed on the 250K platform were normalized using BRLMM algorithm. CHP files for samples analyzed on the 6.0 platform were normalized using Birdseed algorithm.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from snap frozen biopsy and autopsy samples from DIPG patients using the acidic phenol-chloroform method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: DIPG

tag: gender

value: M

tag: age at dx (years)

tag: os (months)

tag: symptoms

value: LTS, ataxia, CN

tag: symptom duration (days)

tag: tmz during rt

value: Yes

tag: tmz post rt

tag: other chemo


title: SLKP_MeDIP

description: Analysis of DNA methylation patterns in long-term infected SLKP cells

source_name: MeDIP of DNA from SLKP cells (long-term KSHV infected SLK cells)

tag: cell line

value: SLKP

value: endothelial cells

source_name: Input, DNA from SLKP cells (long-term KSHV infected SLK cells)


title: LM2 with hypoxia for 0h, repeat B

description: 21% O2 level

source_name: LM2 with hypoxia for 0h, repeat B

tag: subline

tag: treatment

tag: time

value: 0h (without treatment)


title: RA wt rep2

description:
replicate 2
SAMPLE 17

tag: strain


title: RA wt rep1

description:
replicate 1
SAMPLE 16

tag: genotype


title: LA wt rep4

description:
replicate 4
SAMPLE 14

source_name: isolated LA of Pitx2c wild-type mouse

tag: age

value: Left atrial appendage


title: LA wt rep5

description:
replicate 5
SAMPLE 15

tag: tissue


title: BCBL1_MeDIP

description: Analysis of DNA methylation patterns in the PEL-derived cell line BCBL1

source_name: MeDIP of DNA from PEL-derived BCBL1 cells

tag: sample type

tag: cell type

source_name: Input, DNA from PEL-derived BCBL1 cells


title: SLK_BacM_pos_control_MeDIP

description: MeDIP positive control sample: prior to MeDIP, in vitro methylated KSHV bacmid Bac36 DNA was spiked into genomic SLK DNA and adjusted via real time PCR to mimic KSHV copy numbers as seen in BCBL1 and SLKP cells.

source_name: MeDIP of DNA from KSHV-negative SLK cells spiked with in vitro methylated KSHV Bacmid (Bac36) DNA

value: SLK

value: positive control

source_name: Input, DNA from KSHV-negative SLK cells spiked with in vitro methylated KSHV Bacmid (Bac36) DNA


title: LA wt rep1

description:
replicate 1
SAMPLE 11


title: broth vs swarm array #5

city: Ann Arbor

first: Melanie

middle: M

last: Pearson

state: MI

address: 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

description: Five independent arrays were each analyzed for broth-cultured versus swarming P. mirabilis.

hyb_protocol: Labeled cDNA was mixed and hybridized to an array slide using TIGR SOP#M008 (ftp://ftp.jcvi.org/pub/data/PFGRC/pdf_files/protocols/M008.pdf).

scan_protocol: The microarray was scanned using a ScanArray Express microarray scanner (Perkin Elmer) at 10 μm resolution and quantified using the ScanArray Express software.

data_processing: The total normalization algorithm (ScanArray Express, Perkin Elmer) was used to normalize microarray data.  Median spot values for each triplicate probe were extracted using MIDAS (TIGR).  A gene was considered differentially regulated if it was greater than 2-fold changed in 4 or more of the arrays and with the median greater than a 2-fold change.

organism: Proteus mirabilis HI4320

source_name: broth

label_protocol: RNA (4 μg), obtained from broth-cultured P. mirabilis, was used as a template for cDNA synthesis and was labeled with Cyanine 3 dye (GE Healthcare) according to SOP#M007 from The Institute for Genomic Research (TIGR).

growth_protocol: P. mirabilis HI4320 cultured to mid-log phase (OD600 = 0.8) in LB broth.

extract_protocol: 1 ml of culture was added to 2 ml RNA Protect.  RNA was isolated using the RNEasy kit (Qiagen) according to the manufacturer’s instructions, except that 3 mg/ml lysozyme was added to cells for 15 min.  DNA was digested using Turbo-DNAfree DNase (Ambion).

tag: growth protocol

value: broth-cultured

source_name: swarm

label_protocol: RNA (4 μg), obtained from swarm-phase P. mirabilis, was used as a template for cDNA synthesis and was labeled with Cyanine 5 dye (GE Healthcare) according to SOP#M007 from The Institute for Genomic Research (TIGR).

growth_protocol: Swarming motility was assessed by spotting 5 μl late logarithmic-phase bacterial culture (OD600 = 1.0) onto the center of an LB swarm plate (1% tryptone, 0.5% yeast extract, 1% NaCl, 1.5% agar) followed by overnight incubation at 30°C.  P. mirabilis was assessed for swarm or consolidation behavior by morphology of the colony edge, motility (using an inverted microscope), and by Gram stain.

extract_protocol: Bacteria from the outermost edge of a swarming colony were scraped with a plastic loop into 1.5 ml RNA Protect (Qiagen); four 7.5 cm diameter plates were scraped for each RNA sample.

value: swarming-phase


title: RA het rep2

description:
replicate 2
SAMPLE 7

source_name: isolated RA of Pitx2c heterozygous mouse

value: Pitx2c heterozygous


title: broth vs swarm array #2


title: Dendritic cells day7 rep1 (MO MAC DC)

city: Regensburg

first: Maja

last: Klug

address: Franz-Josef-Strauss-Allee 11

department: Hematology

institute: University Hospital Regensburg

description: gender: male; sample was hybridized to the Agilent GPL6848 (1x244K)  expression array but adapted to the GPL6480 (4x44K) platform by GeneSpring version 7

hyb_protocol: Samples were hybridized for 16h at 65°C using a stringent protocol according to the manufacture's instructions (Agilent).  Arrays were disassembled and washed for 1 minute in Agilent gene Expression (GE)  wash buffer 1 followed by washing 1 minute in prewarmed (37°C) GE wash buffer 2.

scan_protocol: Images were scanned immediately after washing using a DNA microarray scanner (Agilent) at 5 µm resolution.

data_processing: Data was processed using Feature Extraction Software (Agilent) and further analyzed using GeneSpring GX software version 10.0.2 (worksheet1: DC_kinetic) or version 7 (worksheet 2: MO_MAC_DC). Data were normalized to the 75 th percentile and baseline transformed to the median of freshly isolated monocytes. The sorted CD14+ cells (DC kinetic and MO MAC DC) and the elutriated monocytes (MO MAC DC) were considered as one monocyte population).

source_name: Monocyte-derived dendritic cell

label_protocol: Labeling and hybridization were performed using the Agilent Gene Expression system according to the manufacturer’s instructions. In brief, 200 ng to 1000 ng of high-quality RNA were amplified and Cyanine 3-CTP labeled with the One Color Low RNA Input Linear Amplification Kit (Agilent). Labeling efficiency was controlled using the NanoDrop spectrophotometer.

growth_protocol: Monocyte-derived dendritic cells (DC) were obtained by culturing elutriated monocytes with 20U/ml IL-4, 280U/ml GM-CSF and 10% FCS; monocyte-derived macrophages (MAC) were obtained by culturing elutriated monocytes with 2% AB serum

extract_protocol: Total cellular RNA of the different cell types (monocytes, macrophages dendritic cells) was isolated after different time points (6h, 18h, 27h, 42h, 51h, 66h, day7) using the RNeasy Kit (Qiagen). RNA concentration was measured with a ND-1000 Spectrophotometer (NanoDrop, Thermo Fisher Scientific) and quality was controlled on agarose gels or using the Agilent Bioanalyzer.

treatment_protocol: Peripheral blood mononuclear cells were obtained from healthy donors by leukapheresis; elutriated monocytes were obtained form peripheral blood mononuclear cells by counter current elutriation; CD14+ sorted monocytes were isolated from peripheral blood mononuclear cells with the FACS_ARIA system

tag: gender

value: male

value: primary cells

tag: disease state

value: healthy donor

value: Monocyte-derived dendritic cell


title: broth vs swarm array #1


title: RA het rep3

description:
replicate 3
SAMPLE 8

value: 12 weeks

value: Right atrial appendage


title: Macrophages day7 rep3 (MO MAC DC)

source_name: Monocyte-derived macrophages

value: Monocyte-derived macrophages


title: Macrophages day7 rep5 (MO MAC DC)


title: broth vs consolidate array #5

description: This array compared the P. mirabilis transcriptome during logarithmic-phase broth culture with P. mirabilis in the consolidation phase (short rods, little motility) on swarm agar.  This is array #5 of 5.

label_protocol: RNA (4 μg), obtained from broth-cultured P. mirabilis was used as a template for cDNA synthesis and was labeled with Cyanine 3 (GE Healthcare) according to SOP#M007 from The Institute for Genomic Research (TIGR).

source_name: consolidate

label_protocol: RNA (4 μg), obtained consolidation-phase P. mirabilis was used as a template for cDNA synthesis and was labeled with Cyanine 5 dye (GE Healthcare) according to SOP#M007 from The Institute for Genomic Research (TIGR).  Samples were processed at the same time as the broth (channel 1) samples.

extract_protocol: Bacteria from the outermost edge of a swarming or consolidating colony were scraped with a plastic loop into 1.5 ml RNA Protect (Qiagen); four 7.5 cm diameter plates were scraped for each RNA sample.  RNA was isolated using the RNEasy kit (Qiagen) according to the manufacturer’s instructions, except that 3 mg/ml lysozyme was added to cells for 15 min.  DNA was digested using Turbo-DNAfree DNase (Ambion).

value: consolidation-phase


title: broth vs swarm array #3


title: Dendritic cells day7 rep5 (MO MAC DC)


title: LA wt rep2

description:
replicate 2
SAMPLE 12

value: wild-type


title: Dendritic cells day7 rep4 (MO MAC DC)


title: LA het rep5

description:
replicate 5
SAMPLE 5

source_name: isolated LA of Pitx2c heterozygous mouse


title: broth vs consolidate array #1

description: This array compared the P. mirabilis transcriptome during logarithmic-phase broth culture with P. mirabilis in the consolidation phase (short rods, little motility) on swarm agar.  This is array #1 of 5.


title: broth vs consolidate array #4

description: This array compared the P. mirabilis transcriptome during logarithmic-phase broth culture with P. mirabilis in the consolidation phase (short rods, little motility) on swarm agar.  This is array #4 of 5.


title: broth vs consolidate array #2

description: This array compared the P. mirabilis transcriptome during logarithmic-phase broth culture with P. mirabilis in the consolidation phase (short rods, little motility) on swarm agar.  This is array #2 of 5.


title: DC and MAC - hypermethylated pools Replicate 1

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

description: single experiment

hyb_protocol: Comparative MCIp hybridizations on CpG island oligonucleotide microarrays (Agilent) were performed using the standard CGH protocol (Agilent).

scan_protocol: Scanned on an Agilent scanner at 5 µm resolution. Images were analysed and data extracted using Agilent Feature Extraction Software (version 9.5.1).

data_processing: Linear normalized (CGH-v4_95_Feb07), background subtracted VALUE data were obtained from log10 transformed, processed Red signal/processed Green signal values derived from image analysis with Agilent Feature Extraction Software (version 9.5.1).  Processed signal intensities were imported into Microsoft Office Excel 2007 for further analysis.

label: Alexa Fluor 5–dCTP

source_name: monocyte-derived DC

label_protocol: MCIp-enriched genomic DNA pools were fluorescently labeled for microarray hybridization with Alexa Fluor 5–dCTP (DC) and Alexa Fluor 3–dCTP (MAC) using the BioPrime Total Genomic Labeling System (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

growth_protocol: Peripheral blood monocytes were separated by leukapheresis of healthy donors followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge (Beckman Instruments) as previously described. Supernatants of monocyte cultures were routinely collected and analysed for the presence of interleukin 6, which was usually low, indicating that monocytes were not activated before or during elutriation. To generate immature dendritic cells, 1×10^6 monocytes/ml were cultured in RPMI 1640 medium (HyClone) supplemented with 10% fetal calf serum (FCS; Biowhittaker, Verviers, Belgium), 20 U/ml IL-4 (Promokine, Heidelberg, Germany) and 280 U/ml GM-CSF (Berlex, Seattle, USA). For generating macrophages, 1×10^6 monocytes/ml were seeded in RPMI 1640 medium (HyClone) supplemented with 2% human pooled AB-group serum (Cambrex) and cultured on teflon foils.

extract_protocol: Genomic DNA was prepared using the Blood and Cell Culture Midi Kit from Qiagen (Hilden, Germany). DNA concentration was determined with the NanoDrop spectrophotometer and quality was assessed by agarose gel electrophoresis. Purified genomic DNA of dendritic cells and macrophages was sonicated to a mean fragment size of 350 - 400 bp using a Branson Sonifier 250 (Danbury, CT). 4 µg of each sample were rotated with 200 µl protein A Sepharose 4 Fast Flow beads (GE Healthcare) coated with 70 µg purified MBD-Fc protein in 2 ml Ultrafree MC centrifugal devices (Amicon/Millipore) for 3 h at 4°C in a buffer containing 250 mM NaCl (Buffer A). Beads were centrifuged to recover unbound DNA fragments (250 mM fraction) and subsequently washed with buffers containing increasing NaCl concentrations (300, 350, 400, 450, 500 mM; Buffers B   F). Densely CpG methylated DNA was eluted with 1000 mM NaCl (Buffer G) and all fractions were desalted using the QIAquick PCR purification Kit (Qiagen). The separation of CpG methylation densities of individual MCIp fractions was controlled by qPCR using primers covering the imprinted SNRPN and a region lacking CpGs (Empty), respectively. Fractions containing unmethylated DNA (250 – 350 mM NaCl) or methylated DNA (400 – 1000 mM NaCl) fractions were pooled before subsequent labelling.

value: monocyte-derived dendritic cells

tag: enrichment

value: MCIp

label: Alexa Fluor 3–dCTP

source_name: monocyte-derived MAC

value: monocyte-derived macrophages


title: Elutriated monocytes rep1 (MO MAC DC)

source_name: Monocytes obtained after counter current centrifugal elutriation

value: primary cells, CD14+


title: DC and MAC - hypermethylated pools Replicate 2

description: single experiment


title: DC and MAC - hypomethylated pools Replicate 2

description: single experiment


title: LA het rep2

description:
replicate 2
SAMPLE 2

value: Left atrial appendage


title: LA het rep4

description:
replicate 4
SAMPLE 4


title: Elutriated monocytes rep3 (MO MAC DC)

value: Monocytes obtained after counter current centrifugal elutriation


title: Mouse heart, KD-fed, rep 4

city: St. Louis

last: Crawford

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

description: Gene expression data from mouse heart

hyb_protocol: Following fragmentation, 20 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.

scan_protocol: GeneChips were scanned using the Affymetrix GS300

data_processing: The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The datasets submitted here were co-normalized and compared to datasets within the following groups: control, polysaccharide-rich chow (CONV-D CARB-1, CONV-D CARB-2, CONV-D CARB-3, CONV-D CARB-4, CONV-D CARB-5); and 24h fast from polysaccharide-rich chow (CONV-D 24h Fast-1, CONV-D 24h Fast-2, CONV-D 24h Fast-3, CONV-D 24h Fast-4, and CONV-D 24h Fast-5). These 10 comparision datasets, which originated from strain, gender, and housing condition-matched groups, were previously submitted within submission GSE14929.

source_name: Mouse heart, KD-fed

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

growth_protocol: C57Bl/6 wild-type male mice were used for this study.  Mice were maintained under specific pathogen free conditons, lights on 0600-1800, provided autoclaved water ad libitum, and maintained on sawdust bedding.

extract_protocol: Qiagen RNeasy fibrous tissue mini-prep kit.

treatment_protocol: 12 week-old mice were maintained on a standard polysacchardide-rich chow until the age of 8 weeks, at which time they were switched to a ketogenic diet (ad libitum, see above) and maintained for 4 additional weeks prior to collection of tissues (hearts used for this study were snap frozen in liquid N2 within 30 seconds of initiation of CO2 asphyxiation, which was the method of euthanasia)

value: heart


title: DC and MAC - hypomethylated pools Replicate 1

description: single experiment


title: broth vs swarm array #4

value: broth-cultured

value: swarming-phase


title: LA het rep3

description:
replicate 3
SAMPLE 3

value: Pitx2c heterozygous


title: Mouse heart, KD-fed, rep 1

description: Gene expression data from mouse heart


title: LA het rep1

description:
replicate 1
SAMPLE 1


title: Elutriated monocytes rep6 (MO MAC DC)

value: male

value: healthy donor


title: RA het rep5

description:
replicate 5
SAMPLE 10

value: 12 weeks


title: Mouse heart, KD-fed, rep 2

description: Gene expression data from mouse heart


title: Macrophages day7 rep1 (MO MAC DC)

value: primary cells


title: Macrophages day7 rep4 (MO MAC DC)

value: Monocyte-derived macrophages


title: LA wt rep3

description:
replicate 3
SAMPLE 13


title: Dendritic cells day7 rep3 (MO MAC DC)

value: Monocyte-derived dendritic cell


title: Mouse heart, KD-fed, rep 3

description: Gene expression data from mouse heart


title: RA het rep1

description:
replicate 1
SAMPLE 6

value: Right atrial appendage


title: SPF BXN#3

status: Public on Jun 05 2010

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Biotin-labeled cRNA was fragmented and hybridized to the array in a cocktail containing control oligos at 45°C for 16 hours, rotated at 60rpm, in the Affymetrix GeneChip Hybridization Oven 640. After hybridization, the arrays were automatically cycled through buffer washes and stained with streptavidin R-phycoerythrin conjugate (Invitrogen) in the Affymetrix GeneChip Fluidics Station 400 (EukGE-WS2v4 protocol).

scan_protocol: After staining and washing, the arrays were scanned in the Affymetrix GeneChip Scanner 3000 using the Affymetrix GCOS (GeneChip Operating Software) to automatically generate .CEL files.

data_processing: RMA

label_protocol: standard Affymetrix protocol

extract_protocol: RNA isolated with Trizol reagent and amplified twice with the MessageAmp aRNA Kit (Ambion)

value: CD4+CD3+B220- T cell

value: 5 wk

tag: genetic background

value: WT

tag: status

value: specific pathogen free

tag: absent pathogen

value: Sendai virus, Pneumonia virus of mice (PVM), Mouse hepatitis virus (MHV), Minute virus of mice (MVM), GD-7 virus, Reo-3 virus, Epizootic diarrhea of infant mice (EDIM), Mouse Parvovirus (MPV), Mycoplasma pulmonis, ectromelia virus and lymphocytic choriomeningitis virus


title: cardiac arrest + rosc 180 min + methylene blue: biol rep1

city: Uppsala

first: Cecile

last: Martijn

address: FOA2, Ing70, 3tr

department: Surgical Sciences

country: Sweden

institute: Uppsala University

description: cerebral gene expression data after 180 min of restoration of spontaneous circulation with therapeutical injection of methylene blue

hyb_protocol: Hybridization cocktail for single standard probe array (Porcine Genome Array, Affymetrix) was made by mixing 15 µg of fragmented cRNA with control oligonucleotide B2, 20x eukaryotic hybridization controls, herring sperm DNA (10 mg/ml), acetylated BSA (50 mg/ml) 2x hybridization buffer, and RNase-free water. The arras were washed and stained with streptavidin-phycoerythrin solution using the Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: GeneChip Operating Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 300.

organism: Sus scrofa

source_name: porcine cerebral cortex after 180 min rosc treated by methylene blue

label_protocol: Total RNA was first converted to double-stranded cDNA (One-cycle cDNA synthesis kit, Affymetrix UK Ltd) and then to biotinylated cRNA (IVT labeling kit, Affymetrix UK Ltd) as described in the One-cycle Target Labeling protocol (Affymetrix UK Ltd). The cRNA was then fragmented according to the Affymetrix protocol. Quality and fragmentation of cRNA was confirmed using Agilent 2100 Bioanalyzer.

growth_protocol: Briefly, Swedish triple breed of both sexes aged 12-14 weeks and with a mean weight of 25.8 kg ± 1.3 kg were anesthetized with pentobarbital (8 mg/kg/h iv), intubated and mechanically ventilated (Servo-i V3.1,  Siemens Medical, Solna, Sweden) with 30% oxygen in air. Thereafter, ventricular fibrillation was induced by a 50-Hz, 40-60-V alternating transthoracic current applied via two subcutaneous needle electrodes. Cardiopulmonary arrest was defined as a decrease in aortic blood pressure to below 25 mm Hg and the presence of ventricular fibrillation on the ECG. After completion of study, all animals received an injection of 10 mL potassium chloride 20 mmol/mL and were sacrificed before removing the brain.

extract_protocol: Total RNA was extracted using RNeasy Lipid Tissue kit (Qiagen)according to the manufacturer’s instructions. Contaminating genomic DNA was removed during RNA purification by addition of an on-column DNase digestion step with RNase-Free Dnase I (Qiagen). RNA quality was verified on an Agilent 2100 Bioanalyzer (Agilent)

treatment_protocol: In the animals from the Ca groups, the brain was removed immediately  after cardiac arrest (Ca0),  at 5 min (Ca5), at 20 min (Ca20) or 30 min (Ca30) after cardiac arrest. The other groups underwent cardiac arrest for 12 min before closed-chest cardiopulmonary resuscitation (CPR) was performed with a pneumatically driven automatic piston device for CPR (Lucas, Jolife AB, Lund, Sweden).  After 8 min of external chest compressions, a  monophasic countershock was delivered through defibrillation electrode pads. Restoration of spontaneous circulation (ROSC) was defined as return of co-ordinated electrical activity resulting in a systolic blood pressure greater than 60 mm Hg for at least 10 consecutive minutes. After the start of CPR the animals in the last two groups were randomly assigned to receive an infusion of 55 mL/kg/h normal saline (Rosc groups) or the same dose of saline infusion with 7.5 mg/kg/h methylene blue (MB groups). Brains were removed for expression analysis at each of the following time points: 30, 60, 180 min after ROSC.

value: cerebral cortex

tag: animal

value: farm pig

tag: development

value: prepubertal


title: cardiac arrest + rosc 60 min + methylene blue: biol rep1

description: cerebral gene expression data after 60 min of restoration of spontaneous circulation with therapeutical injection of methylene blue

source_name: porcine cerebral cortex after 60 min rosc treated by methylene blue


title: cardiac arrest + rosc 60 min + methylene blue: biol rep3


title: SPF K/BXN#2

value: KRN


title: cardiac arrest + rosc 180 min + methylene blue: biol rep2


title: SPF K/BXN#1


title: WT-whole fruit at breaker stageC

city: Potsdam

first: Björn

last: Usadel

address: Am Mühlenberg 1

institute: Max Planck Institute of Molecular Plant Physiology

description:
Gene expression data of wt tomato fruits
AH90

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedure

data_processing: The data were analyzed with Bioconductor using the RMA normalization procedure (affy package).

organism: Solanum lycopersicum

source_name: tomato fruit WT-whole fruit at breaker stage

label_protocol: standard Affymetrix procedures

growth_protocol: Plants were greenhouse grown

extract_protocol: hot phenol method (Verwoerd et al., 1989)

treatment_protocol: Fruits were harvested at the breaker stage

tag: genotype/variation

value: wildtype

tag: variety

value: MicroTom

value: breaker stage

value: fruit


title: Splenic CD11c+ DCs

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

description: Gene expression from freshly isolated mouse splenic CD11c+ DCs

hyb_protocol: As per Vanderbilt Microarray Shared Resource Standard Protocol

data_processing: RMA-normalized expression values were obtained for all probe sets using Expression Console software (Affymetrix Inc)

source_name: Spleen

extract_protocol: CD11c+ DCs were FACS-sorted and the RNA extracted using the Qiagen RNeasy Mini Kit protocol according to the manufacturer’s instructions. Samples were treated with DNase.

tag: strain

value: Splenic CD11c+ DCs (freshly-isolated)


title: cardiac arrest + rosc 30 min + methylene blue: biol rep2

description: cerebral gene expression data after 30 min of restoration of spontaneous circulation with therapeutical injection of methylene blue

source_name: porcine cerebral cortex after 30 min rosc treated by methylene blue


title: GF K/BXN#4

tag: genotype

value: male

value: germ free


title: cardiac arrest + rosc 60 min + methylene blue: biol rep2


title: ex-35S-451- whole fruit at breaker stageC

description:
Gene expression data of orr excision line tomato fruits
AH91

source_name: tomato fruit ex-35S-451- whole fruit at breaker stage

value: ex-35S-451 Orr excision line

tag: age


title: cardiac arrest + rosc 180 min + methylene blue: biol rep3

tag: tissue


title: GF K/BXN#1

value: CD4+CD3+B220- T cell


title: GF K/BXN#3

value: 5 wk


title: cardiac arrest + rosc 30 min + methylene blue: biol rep1


title: GF BXN#1

value: WT


title: cardiac arrest + rosc 30 min + methylene blue: biol rep3


title: SPF BXN#2

value: specific pathogen free


title: GF BXN#2


title: cardiac arrest + rosc 180 min + saline: biol rep3

description: cerebral gene expression data after 180 min of restoration of spontaneous circulation with injection of control saline

source_name: porcine cerebral cortex after 180 min rosc treated by saline


title: SPF BXN#1

value: Sendai virus, Pneumonia virus of mice (PVM), Mouse hepatitis virus (MHV), Minute virus of mice (MVM), GD-7 virus, Reo-3 virus, Epizootic diarrhea of infant mice (EDIM), Mouse Parvovirus (MPV), Mycoplasma pulmonis, ectromelia virus and lymphocytic choriomeningitis virus


title: RA het rep4

description:
replicate 4
SAMPLE 9

value: Pitx2c heterozygous

value: 12 weeks

value: Right atrial appendage


title: GF K/BXN#2

value: KRN


title: ex-35S-451- whole fruit at breaker stageB

description:
Gene expression data of orr excision line tomato fruits
AH92


title: Hetero-whole fruit at breaker stageB

description:
Gene expression data of orr heterozygous tomato fruits
AH87

source_name: tomato fruit Hetero-whole fruit at breaker stage

value: heterozygous ORR mutant


title: WT-whole fruit at breaker stageB

description:
Gene expression data of wt tomato fruits
AH89

value: wildtype

value: MicroTom


title: cardiac arrest + rosc 180 min + saline: biol rep2

value: cerebral cortex

value: farm pig

value: prepubertal


title: cardiac arrest + rosc 60 min + saline: biol rep2

description: cerebral gene expression data after 60 min of restoration of spontaneous circulation with injection of control saline

source_name: porcine cerebral cortex after 60 min rosc treated by saline


title: Hetero-whole fruit at breaker stage

description:
Gene expression data of orr heterozygous tomato fruits
AH107

value: breaker stage

value: fruit


title: homo-whole fruit at breaker stage

description:
Gene expression data of orr homozygous tomato fruits
AH106

source_name: tomato fruit homo-whole fruit at breaker stage

value: homozygous ORR mutant


title: cardiac arrest + rosc 30 min + saline: biol rep2

description: cerebral gene expression data after 30 min of restoration of spontaneous circulation with injection of control saline

source_name: porcine cerebral cortex after 30 min rosc treated by saline


title: cardiac arrest + rosc 60 min + saline: biol rep3


title: WT-whole fruit at breaker stage

description:
Gene expression data of wt tomato fruits
AH105


title: cardiac arrest + rosc 180 min + saline: biol rep1


title: homo-whole fruit at breaker stageC

description:
Gene expression data of orr homozygous tomato fruits
AH86


title: homo-whole fruit at breaker stageB

description:
Gene expression data of orr homozygous tomato fruits
AH85


title: GF BXN#3

value: CD4+CD3+B220- T cell

value: 5 wk

value: male

value: germ free


title: 30 min untreated cardiac arrest: biol rep1

description: cerebral gene expression data after 30 min untreated cardiac arrest

source_name: porcine cerebral cortex after 30 min untreated cardiac arrest


title: cardiac arrest + rosc 60 min + saline: biol rep1


title: ex-35S-451- whole fruit at breaker stage

description:
Gene expression data of orr excision line tomato fruits
AH108

value: ex-35S-451 Orr excision line


title: Hetero-whole fruit at breaker stageC

description:
Gene expression data of orr heterozygous tomato fruits
AH88


title: 20 min untreated cardiac arrest: biol rep3

description: cerebral gene expression data after 20 min untreated cardiac arrest

source_name: porcine cerebral cortex after 20 min untreated cardiac arrest


title: 20 min untreated cardiac arrest: biol rep2


title: 30 min untreated cardiac arrest: biol rep2


title: SLE

city: Lund

first: Christian

last: Lood

address: Sölvegatan 23

department: Laboratory Medicine

institute: Lund University

description: gene expression data

hyb_protocol: samples were hybridized onto Affymetrix HG-U133 Plus 2.0 GeneChip® (HG-U133) arrays containing more than 47,000 gene transcripts. All microarray hybridizations were carried out at the Swegene Microarray Resource Centre according to the manufacturer's instructions.

scan_protocol: Scanned on an Affymetrix scanner at the Swegene Microarray Resource Centre according to the manufacturer's instructions.

data_processing: All microarray data was analyzed using the MAS5 algorithm with Affymetrix GeneChip operating system 1.2 (GCOS 1.2) and SpotFire Decisionsite for functional Genomics 8.0 (Spotfire Inc., Mass, USA). Spotfire results are available on the Series record as a supplementary file.

source_name: platelets

label_protocol: Standard Affymetrix labeling protocol

growth_protocol: Primary cells, no culture. Isolated according to Amisten et al 2008 (PMID: 17920662).

extract_protocol: Platlet RNA was isolated using the TRIzol method according to the manufacturer's instructions. For each microarray hybridization, platelet  RNA was pooled from 10 unique individuals, and purified on RNEasy MinElute Cleanup column (Qiagen, Venlo, The Netherlands) according to the manufacturer's instructions.

treatment_protocol: No treatment

value: platelets

value: female

value: 36 years, range:22-70

tag: disease status

value: SLE


title: cardiac arrest + rosc 30 min + saline: biol rep3


title: Mutant thoracic spinal cord 4 hours after sham operation

city: London

first: ANDREA

last: MALASPINA

state: England

address: 4 Newark Street

department: Neuroscience

country: United Kingdom

institute: Institute of Cell and Molecular Science

description: thoracic cord

hyb_protocol: 500 ng from each of the 12 RNA pools were hybridised simultaneously to 12 arrays, using a standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol, Illumina Bead-Chip Reader

data_processing: Output files were processed using the Gene Expression BeadStudio 3.2.6, with background subtraction

organism: Rattus norvegicus

source_name: Rat spinal cord

label_protocol: cRNA labeling was performed with 750 ng of pooled RNA, using the Ambion Total Prep kit. cRNA purity and labelling was checked using the Nanodrop and Agilent bioanalyser.

extract_protocol: RNA was extracted from the thoracic spinal cord samples obtained from injured and uninjured rats, and from animals subjected to laminectomy, using the SV total RNA isolation system (Promega, UK). RNA quantification was performed using a Nanodrop ND-1000 spectrophotometer and quality was checked using the Agilent bioanalyser system (Agilent).

value: thoracic spinal cord

value: G93A SOD1

tag: protocol

value: 4 hours after sham operation

value: Sprague-Dawley

value: 10 weeks

tag: geneder


title: Control

description: gene expression data

tag: cell type

tag: gender

value: Control


title: broth vs consolidate array #3

description: This array compared the P. mirabilis transcriptome during logarithmic-phase broth culture with P. mirabilis in the consolidation phase (short rods, little motility) on swarm agar.  This is array #3 of 5.

source_name: broth

tag: growth protocol

value: broth-cultured

source_name: consolidate

value: consolidation-phase


title: 5 min untreated cardiac arrest: biol rep3

description: cerebral gene expression data after 5 min untreated cardiac arrest

source_name: porcine cerebral cortex after 5 min untreated cardiac arrest

value: cerebral cortex

value: farm pig

value: prepubertal


title: 20 min untreated cardiac arrest: biol rep1


title: 30 min untreated cardiac arrest: biol rep3


title: cardiac arrest + rosc 30 min + saline: biol rep1


title: hTERT LATE PASSAGE REP1

city: Chapel Hill

first: Laura

last: Bonifacio

state: NC

address: 308 Beard Hall

department: Medicinal Chemistry and Natural Products

institute: UNC Eshelman School of Pharmacy

description: miRNA expression in late passage immortalized fibroblasts

hyb_protocol: Samples were labeled and hybridized as described in Agilent Protocol 1.5.

scan_protocol: Slides were scanned on an Agilent Scanner.

data_processing: Mean signal for each probe was quantile normalized and the log2 was taken.  Probes were collapsed to individual miRNAs by averaging.  Each cell line high passage miRNA array was normalized to its corresponding low passage miRNA array.

source_name: hTERT+ foreskin fibroblasts passage 17

growth_protocol: Fibroblasts were cultured at 37 degrees and 5% CO2 in MEMα supplemented with 1mM sodium pyruvate, 1.5 g/L sodium bicarbonate, and 10% fetal bovine serum.

extract_protocol: Total RNA was isolated with mirVana Total RNA Isolation Kit (Ambion).

treatment_protocol: BJ-hTERT cells were immortalized by stable transfection with pBabe-hTERT.  Replicative senescence was confirmed by morphology change, beta-gal stainng, and growth curve plateau.

value: foreskin

value: late passage immortalized fibroblasts

tag: passage number


title: hTERT EARLY PASSAGE REP1

description: miRNA expression in early passage immortalized fibroblasts

source_name: hTERT+ foreskin fibroblasts passage 3

label_protocol: Samples were labeled and hybridized as described in Agilent Protocol 1.5.

value: early passage immortalized fibroblasts


title: hTERT EARLY PASSAGE REP2


title: untreated cardiac arrest control (0 min): biol rep3

description: cerebral gene expression data from controls after 0 min untreated cardiac arrest

source_name: Control porcine cerebral cortex after 0 min untreated cardiac arrest


title: SPF K/BXN#3

value: CD4+CD3+B220- T cell

value: 5 wk

tag: genetic background

value: KRN

value: male

tag: status

value: specific pathogen free

value: Sendai virus, Pneumonia virus of mice (PVM), Mouse hepatitis virus (MHV), Minute virus of mice (MVM), GD-7 virus, Reo-3 virus, Epizootic diarrhea of infant mice (EDIM), Mouse Parvovirus (MPV), Mycoplasma pulmonis, ectromelia virus and lymphocytic choriomeningitis virus


title: Mutant thoracic spinal cord 30 minutes after sham operation

description: thoracic cord

value: thoracic spinal cord

value: G93A SOD1

value: 30 minutes after sham operation

value: Sprague-Dawley

value: female


title: Wild type thoracic spinal cord 30 minutes after sham operation

description: thoracic cord

value: WT

value: 10 weeks


title: Wild type thoracic spinal cord 30 minutes after SCI

description: thoracic cord

value: 30  minutes after SCI


title: Mutant thoracic spinal cord 4 hours after SCI

description: thoracic cord

value: 4 hours after SCI


title: 5 min untreated cardiac arrest: biol rep1

value: cerebral cortex

tag: animal

value: farm pig

value: prepubertal


title: BJ SENESCENT REP2

description: miRNA expression in senescent fibroblasts

source_name: foreskin fibroblasts passage 8

value: foreskin

value: senescent fibroblasts


title: Mutant thoracic spinal cord 30 minutes after SCI

description: thoracic cord

value: 30  monutes after SCI


title: Wild type thoracic spinal cord 4 hours after sham operation

description: thoracic cord

value: 4 hours after sham operation


title: untreated cardiac arrest control (0 min): biol rep2

tag: development


title: Wild type thoracic spinal cord 7 days after SCI

description: thoracic cord

value: 7 days after SCI


title: 5 min untreated cardiac arrest: biol rep2


title: Tgfbr2-fspKO/Tgfbr2-flox prostate epithelial cell replicate 3

city: Nashville

first: Neil

last: Bhowmick

state: TN

address: A1302 Medical Center North

department: Urologic Surgery

institute: Vanderbilt University

description: Biological replicate 3 of 3. KE vs pooled wt E.

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Epithelial cells from tissue with Tgfbr2 knocked out (KO) in the stromal compartment

label_protocol: mRNA was amplified and primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase  and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label or Cy5-lable.

growth_protocol: Tgfbr2-fspKO and Tgfbr2-flox mice were aged to 6 weeks. The prostates were dissected out and flash frozen in OCT. Laser capture microdissection of the stromal compartment was performed on 10 µm tissue sections.

extract_protocol: mRNA was isolated by oligo dT magnetic separation.

tag: genotype/variation

value: 6 wk

value: prostate epithelial cells

source_name: pooled wt epithelial cells


title: Mutant thoracic spinal cord 7 days after SCI

description: thoracic cord

value: thoracic spinal cord

value: G93A SOD1


title: Tgfbr2-fspKO/Tgfbr2-flox prostate epithelial cell replicate 2

description: Biological replicate 2 of 3. KE vs pooled wt E.


title: untreated cardiac arrest control (0 min): biol rep1


title: Wild type thoracic spinal cord 24 hours minutes after SCI

description: thoracic cord

value: 24 hours  minutes after SCI

value: Sprague-Dawley

value: female


title: Intestinal lamina propria CD11c+ CD11b+ DCs

description: Gene expression from freshly isolated mouse small intestine CD11c+ CD11b+ DCs

scan_protocol: As per Vanderbilt Microarray Shared Resource Standard Protocol

source_name: Small Intestine

extract_protocol: CD11c+ CD11b+ DCs were FACS-sorted and the RNA extracted using the Qiagen RNeasy Mini Kit protocol according to the manufacturer’s instructions. Samples were treated with DNase.

value: Intestinal CD11c+ CD11b+ DCs (freshly-isolated)


title: pollinated pop2-1 flowers, biological rep3

city: Tucson

first: RAVISHANKAR

last: PALANIVELU

state: AZ

address: 1140 E. South Campus Drive P.O. Box 210036

department: Plant Sciences

institute: University of Arizona

description: Gene expression data from pop2-1 pollinated stage 15 flowers.

hyb_protocol: Labeled cRNA was fragmented and 15 µg of fragmented cRNA (25-200nt as per Agilent 2100 Bioanalyzer RNA 6000 Nano Chip Series II Assay, Agilent Technologies, Waldbronn, Germany) was hybridized to the GeneChip® Arabidopsis ATH1 genome arrays (http://www.affymetrix.com) for 20 hours at 45oC. Standard washing and staining procedures were performed using the GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA).

scan_protocol: The arrays were then scanned using the GeneChip Scanner 3000 with 7G upgrade (Affymetrix, Santa Clara, CA).

data_processing: Signal intensities from each of the 15 arrays were converted to raw expression data (with Present, "P", Absent, "A" and Marginal, "M" scores) using Microarray Suite 5.0 (MAS 5.0; Affymetrix, Santa Clara, CA).

organism: Arabidopsis thaliana

source_name: pollinated flowers from Arabidopsis mutant pop2-1

label_protocol: After first and second strand cDNA synthesis with total RNA, the cDNAs were used to generate cRNA labeled with biotin in an in vitro transcription reaction.

growth_protocol: pop2-1 homozygous mutant plants (Ler accession) were grown in chambers at 21°C under illumination (100 µmol m-2 s-1 with a 16-hour photoperiod).

extract_protocol: Total RNA was extracted from collected flowers using the Qiagen RNeasy kit (http://www.qiagen.com). Total RNA (10 µg) was prepared for microarray experiment as per the Affymetrix GeneChip Expression Analysis protocol (Part#701071, Rev 5, Affymetrix, Santa Clara, CA).

treatment_protocol: Stage 14-15 pollinated flowers from pop2-1/pop2-1 homozygous mutant plants were collected and frozen in liquid nitrogen until RNA isolation.

value: pop2-1 mutant

value: Ler

value: flowers

tag: developmental stage

value: stage 14-15 flowers


title: Tgfbr2-fspKO/Tgfbr2-flox prostate epithelial cell replicate 1

description: Biological replicate 1 of 3. KE vs pooled wt E.

tag: strain


title: BJ SENESCENT REP1

value: foreskin


title: pollinated wild-type flowers, biological rep1

source_name: pollinated wild-type flowers from Arabidopsis

value: wild-type


title: BJ EARLY PASSAGE REP1

description: miRNA expression in early passage fibroblasts

source_name: foreskin fibroblasts passage 2

value: early passage fibroblasts


title: Wild type thoracic spinal cord 4 hours after SCI

description: thoracic cord

tag: genotype

value: WT

value: 4 hours after SCI

value: 10 weeks


title: Mutant thoracic spinal cord 24 hours after SCI

description: thoracic cord

value: 24 hours after SCI

tag: age


title: pollinated wild-type flowers, biological rep3

tag: tissue


title: pollinated wild-type flowers, biological rep2


title: pollinated pop2-1 flowers, biological rep2


title: LEC pre-control, rep2

status: Public on Jun 04 2010

city: Zurich

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

hyb_protocol: Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer’s protocol.

scan_protocol: Scan protocol Chemiluminescent Detection Kit (P/N 4339627) and Chemiluminescent Microarray Analyzer User Guide (P/N 4338852B).

data_processing: The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation. The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values. The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise. In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV.

label: digoxigenin

source_name: Dermal Lymphatic Endothelial cells, transfected with pre-negative control

label_protocol: Digoxigenin-UTP labeled cRNA was generated from 0.5 µg of total RNA for each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit (P/N 4363105) according to the manufacturer’s protocol.

growth_protocol: LEC were seeded onto fibronectin-coated culture dishes (10 µg/ml; BD Biosciences, Bedford, MA) and were cultured in endothelial cell basal medium (EBM; Cambrex Bio Science, Walkersville, MD) supplemented with 20% fetal bovine serum (FBS; Invitrogen, Grand Island, NY), 2 mM L glutamine, antibiotic-antimycotic solution, 10 µg/ml hydrocortisone and N6,2'-O-dibutyryl-adenosine 3',5'-cyclic monophosphate (25 µg/ml; all from Fluka, Buchs, Switzerland).

extract_protocol: Isolate total cellular RNA with 1 ml of the Trizol reagent (Invitrogen) after washing one 80-90 % confluent 10 cm culture dish with PBS. Homogenize the sample using a cell scraper and add 0.2 ml of chloroform in a 1.5 ml tube. Shake the sample vigorously for 15 seconds and allow standing for 5 minutes. Centrifuge the resulting mixture at 12,000 x g for 15 minutes at 4 degree Celsius. Transfer the aqueous phase to a fresh tube and add 0.5 ml of iso-propanol and mix. Allow the sample to stand for 5 minutes at room temperature and centrifuge at 12,000 x g for 10 minutes at 4 degrees Celsius. Remove the supernatant and wash the RNA pellet by adding 1 ml of 75% ethanol. Vortex the sample and then centrifuge at 12,000 x g for 5 minutes at 4 degrees Celsius. Remove the ethanol and briefly dry the RNA pellet for 5 minutes and add 50 micro-liter of RNAase/DNAase free water and mix by repeated pipetting until RNA pellet is fully dissolved.

treatment_protocol: To assess the effects of miR-31 overexpression on LECs, primary LECs were transfected with Pre-miR-31 precursor or Pre-miR-Neg control molecules using Amaxa and the transcriptome profiles defined after 48 hours.

value: male

value: foreskin dermis

value: CD45-/CD34-/CD31+ lymphatic endothelial cell (LEC)

tag: passage

tag: transfection

value: control


title: LEC pre-miR31, rep2

source_name: Dermal Lymphatic Endothelial cells, transfected with pre-miR31


title: Intestinal lamina propria CD11c+ CD11b- DCs

description: Gene expression from freshly isolated mouse small intestine CD11c+ CD11b- DCs

label_protocol: As per Vanderbilt Microarray Shared Resource Standard Protocol

extract_protocol: CD11c+ CD11b- DCs were FACS-sorted and the RNA extracted using the Qiagen RNeasy Mini Kit protocol according to the manufacturer’s instructions. Samples were treated with DNase.

value: Intestinal CD11c+ CD11b- DCs (freshly-isolated)


title: Golden Retriever_Bitsy_marginal zone lymphoma

city: Denver

first: Beth

last: Tamburini

state: CO

address: 1400 Jackson Street, K503

department: Immunology

institute: University of Colorado Denver

description: Gene expression data from dogs with hemangiosarcoma of different breeds

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were background corrected with the RMA algorithm using R and the Bioconductor's affy package.  All parameters were set at its default settings

organism: Canis lupus familiaris

source_name: marginal zone lymphoma primary tumor cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cryopreserved cultured cells from the earliest available passages were used or primary tumor cells

extract_protocol: RNA was prepared using the RNEasy Mini Kit and QIAshredder columns (QIAGEN, Valencia, CA)

tag: breed

value: Golden Retriever

tag: id

value: Bitsy

tag: tumor type

value: marginal zone B cell lymphoma

tag: tumor origin

value: B cell


title: Golden Retriever_Snuggles_diffuse large B cell lymphoma

source_name: diffuse large B cell lymphoma primary tumor cells

value: Snuggles

value: diffuse large B cell lymphoma


title: LEC pre-control, rep1

tag: gender

tag: cell type


title: LEC pre-miR31, rep1


title: Golden Retriever_Shilo_T-zone lymphoma

source_name: T-zone lymphoma primary tumor cells

value: Shilo

value: T-zone lymphoma

value: T cell


title: Golden Retriever_Cooper_diffuse large B cell lymphoma

value: Cooper


title: Golden Retriever_Chieftain_diffuse large B cell lymphoma

value: Chieftain


title: Keeshond_Kylie_splenic hematoma

source_name: splenic hematoma cultured cells

value: Keeshond

value: Kylie

value: hematoma

value: spleen


title: Golden Retriever_OSCA20_osteosarcoma

source_name: osteosarcoma tumor cell line

value: osteosarcoma

value: bone


title: Golden Retriever_Benson_diffuse large B cell lymphoma

value: Golden Retriever

value: Benson


title: Golden Retriever_Thunder_T-zone lymphoma

value: Thunder


title: Golden Retriever_Sally_diffuse large B cell lymphoma

value: Sally

value: B cell


title: Golden Retriever_Forrest_chronic lymphocytic leukemia

source_name: chronic lymphocytic leukemia primary tumor cells

value: Forrest

value: chronic lymphocytic leukemia

value: lymphocyte


title: Golden Retriever_Fire_T-zone lymphoma

value: Fire

value: T-zone lymphoma

value: T cell


title: Golden Retriever_OSCA75_osteosarcoma


title: Golden Retriever_Rose_T-zone lymphoma

value: Rose


title: Golden Retriever_Niki_T-zone lymphoma

value: Niki


title: Golden Retriever_Maddle_chronic lymphocytic leukemia

value: Maddle


title: pollinated pop2-1 flowers, biological rep1

value: pop2-1 mutant

value: Ler

value: flowers

value: stage 14-15 flowers


title: Golden Retriever_OSCA23_osteosarcoma

value: Golden Retriever

value: osteosarcoma

value: bone


title: Golden Retriever_Newman_T-zone lymphoma

value: Newman


title: Golden Retriever_OSCA71_osteosarcoma


title: Golden Retriever_Kaycee_diffuse large B cell lymphoma

value: Kaycee

value: diffuse large B cell lymphoma

value: B cell


title: Golden Retriever_OSCA59_osteosarcoma


title: Golden Retriever Mix_Rascal_acute lymphoblastic leukemia

source_name: acute lymphoblastic leukemia primary tumor cells

value: Golden Retriever mix

value: Rascal

value: acute lymphoblastic leukemia

value: lymphoblast


title: Standard Poodle_Baxter_splenic hematoma

value: Standard Poodle

value: Baxter

value: hematoma

value: spleen


title: Golden Retriever_Pippin_splenic hematoma

value: Pippin


title: Dalmatian_Dal4_hemangiosarcoma

source_name: hemangiosarcoma tumor cell line

value: Dalmation

value: hemangiosarcoma


title: GR X Great Pyrenees_DD1_hemangiosarcoma

value: Golden Retriever x Great Pyrenees


title: Golden Retriever_Frog_hemangiosarcoma

value: Golden Retriever

value: Frog


title: mPFC_IsoP30_6

city: Dublin

first: Keith

middle: J

last: Murphy

address: UCD Conway Institute, Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University College Dublin

description: Sample name: cl10120572

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Data filtering criteria linked as supplementary file on Series GSE19653 record.

source_name: Brain, fresh dissection immedited following cull

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Half the rats were housed on isolation see Murphy et al., 2010. At the appropriate postnatal age animals were culled and the medial prefrontal cortex dissected rapidly nad snap frozen in liquid nitrogen.

value: Wistar

value: brain (medial prefrontal cortex)

tag: growth protocol

value: isolation-reared

value: postnatal day 30


title: Rottweiler_Joey_hemangiosarcoma

value: Rottweiler

value: Joey


title: mPFC_IsoP30_4

description: Sample name: cl10120570


title: Golden Retriever_ChadG8_hemangiosarcoma


title: Golden Retriever_Journey_hemangiosarcoma

value: Journey


title: mPFC_IsoP30_5

description: Sample name: cl10120571


title: mPFC_SocP30_6

description: Sample name: cl10120560

value: socially-reared


title: mPFC_IsoP30_3

description: Sample name: cl10120569


title: Golden Retriever_ChadG6_hemangiosarcoma


title: Golden Retriever_ChadG4_hemangiosarcoma


title: mPFC_SocP30_5

description: Sample name: cl10120559


title: mPFC_SocP30_3

description: Sample name: cl10120557


title: mPFC_IsoP30_1

description: Sample name: cl10120567


title: mPFC_IsoP40_5

description: Sample name: cl10120553

value: postnatal day 40


title: mPFC_IsoP40_1

description: Sample name: cl10120549


title: Portuguese Water Dog_ChadP9_hemangiosarcoma

value: Portuguese Water Dog


title: mPFC_SocP30_1

description: Sample name: cl10120555


title: mPFC_SocP30_2

description: Sample name: cl10120556


title: mPFC_SocP30_4

description: Sample name: cl10120558


title: mPFC_IsoP40_3

description: Sample name: cl10120551


title: mPFC_IsoP40_4

description: Sample name: cl10120552


title: mPFC_IsoP40_2

description: Sample name: cl10120550


title: mPFC_SocP40_5

description: Sample name: cl10120541


title: mPFC_SocP40_4

description: Sample name: cl10120540


title: mPFC_SocP40_6

description: Sample name: cl10120542


title: mPFC_SocP40_2

description: Sample name: cl10120538


title: mPFC_IsoP30_2

description: Sample name: cl10120568


title: mPFC_IsoP60_5

description: Sample name: cl10120535

value: postnatal day 60


title: mPFC_IsoP60_4

description: Sample name: cl10120534


title: mPFC_SocP40_1

description: Sample name: cl10120537


title: mPFC_IsoP60_2

description: Sample name: cl10120532


title: mPFC_IsoP60_6

description: Sample name: cl10120536


title: hTERT LATE PASSAGE REP2

source_name: hTERT+ foreskin fibroblasts passage 17

value: foreskin

value: late passage immortalized fibroblasts

tag: passage number


title: mPFC_SocP40_3

description: Sample name: cl10120539


title: mPFC_IsoP60_1

description: Sample name: cl10120531


title: mPFC_SocP60_5

description: Sample name: cl10120523


title: mPFC_SocP60_6

description: Sample name: cl10120524


title: mPFC_SocP60_4

description: Sample name: cl10120522


title: mPFC_IsoP80_5

description: Sample name: cl10120517

value: postnatal day 80


title: mPFC_SocP60_3

description: Sample name: cl10120521


title: mPFC_SocP60_2

description: Sample name: cl10120520


title: mPFC_IsoP60_3

description: Sample name: cl10120533


title: mPFC_SocP80_6

description: Sample name: cl10120506


title: mPFC_SocP60_1

description: Sample name: cl10120519


title: mPFC_SocP80_4

description: Sample name: cl10120504


title: mPFC_SocP80_3

description: Sample name: cl10120503


title: mPFC_SocP80_5

description: Sample name: cl10120505


title: mPFC_IsoP80_6

description: Sample name: cl10120518


title: mPFC_IsoP80_4

description: Sample name: cl10120516


title: mPFC_IsoP80_3

description: Sample name: cl10120515


title: mPFC_IsoP80_2

description: Sample name: cl10120514


title: mPFC_IsoP80_1

description: Sample name: cl10120513


title: mPFC_SocP80_1

description: Sample name: cl10120501


title: mPFC_SocP80_2

description: Sample name: cl10120502


title: proximal-colon-saline-rat-30

city: Sydney

first: Caroline

middle: Audrey

last: Kerr

state: NSW

address: 11 Julius Ave North Ryde

department: Moelcular health Technologies

country: Australia

institute: CSIRO

description: Gene expression data from saline-treated rat colonic epithelium.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: The data-set was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Rat scraped colonic epithelium (proximal)

label_protocol: Approximately 4.5ug of total RNA was processed to produce biotinylated cRNA targets according to the standard Affymetrix protocol.

growth_protocol: Rat was housed in wire-bottomed caging in a temperature controlled room (22-24C) with a 12 h light/dark cycle. Rat was given free access to water and modified AIN-93G diet. Rat was fed this diet for 28 days.

extract_protocol: RNAlater and stored at -80C.

treatment_protocol: Rat was injected with saline subcutaneously. Six hours after injection rat was anaesthetised with isoflurane and killed by exsanguination.

value: proximal colon

value: epithelium

value: male

value: Sprague Dawley

tag: weight

value: 176 +- 2.4g (mean weight)

tag: treatment

value: saline


title: distal-colon-saline-rat-29

source_name: Rat scraped colonic epithelium (distal)

value: distal colon


title: distal-colon-saline-rat-27


title: proximal-colon-saline-rat-27


title: distal-colon-saline-rat-31


title: proximal-colon-saline-rat-31


title: proximal-colon-saline-rat-23


title: proximal-colon-saline-rat-21


title: proximal-colon-saline-rat-25


title: proximal-colon-AOM-rat-12

description: Gene expression data from AOM-treated rat colonic epithelium.

treatment_protocol: Rat was injected with azoxymethane (15 mg/kg) subcutaneously. Six hours after injection rat was anaesthetised with isoflurane and killed by exsanguination.

value: azoxymethane (AOM)


title: proximal-colon-AOM-rat-11


title: proximal-colon-saline-rat-24


title: proximal-colon-AOM-rat-19


title: distal-colon-saline-rat-24


title: proximal-colon-saline-rat-28


title: proximal-colon-AOM-rat-15


title: distal-colon-AOM-rat-12


title: proximal-colon-saline-rat-29


title: proximal-colon-AOM-rat-13


title: distal-colon-saline-rat-21


title: distal-colon-AOM-rat-15


title: distal-colon-saline-rat-28


title: distal-colon-AOM-rat-19


title: distal-colon-AOM-rat-13


title: distal-colon-saline-rat-25


title: distal-colon-saline-rat-23


title: distal-colon-saline-rat-30


title: distal-colon-AOM-rat-11


title: Golden Retriever_Tucker_hemangiosarcoma

value: Golden Retriever

value: Tucker

value: hemangiosarcoma

value: spleen


title: proximal-colon-AOM-rat-9


title: distal-colon-AOM-rat-9


title: proximal-colon-AOM-rat-8


title: proximal-colon-AOM-rat-7


title: proximal-colon-AOM-rat-5


title: distal-colon-AOM-rat-8


title: distal-colon-AOM-rat-1


title: distal-colon-AOM-rat-7


title: distal-colon-AOM-rat-5


title: proximal-colon-AOM-rat-1


title: Yersinia pestis CO92 LPP mutant 37°C replicate 1

city: Galveston

first: Ashok

middle: K

last: Chopra

state: TX

address: 301 University Blvd.

department: Microbiology & Immunology

institute: University of Texas Medical Branch

description: Performed by UTMB microarray core laboratory, per standard procedures

hyb_protocol: Kit:  Genisphere's random prime kits: Cy3 Array 900 MPX (20 assay), W599130 and Cy5 Array 900 MPX (20 assay), W599140 Protocol:  Followed Manufacture's suggested protocol (label & hyb) RNA input: 2ug

scan_protocol: Scanner:  GenePix 4000B scanner and GenePix Pro software

data_processing: GeneSpring GX 10 (Agilent Techologies) was used to perform Lowess normalization, followed by log transformation

organism: Yersinia pestis CO92

source_name: Yersinia pestis CO92 LPP mutant cultured at 37°C

label_protocol: Microarray chips to Y. pestis are available to our laboratory through the NIAID’s Pathogen Functional Genomics Resource Center at The Institute for Genomic Research (TIGR). RNA was processed and hybridized by the Molecular Genomics Core Facility at UTMB (Dr Thomas Wood, director).

growth_protocol: WT Y. pestis CO92 was obtained from the Centers for Disease Control and Prevention (CDC, Atlanta, GA) and maintained in our restricted access biosafety level (BSL)-2 laboratory. The creation and characterization of strains deficient in the expression of the lpp gene were described in detail previously [Sha J, Agar SL, Baze WB, et al. Braun lipoprotein (Lpp) contributes to virulence of yersiniae: potential role of Lpp in inducing bubonic and pneumonic plague. Infect Immun 2008;76:1390-409]. All Yersinia strains were grown in either brain, heart, infusion broth (BHI, Difco, Voigt Global Distribution Inc, Lawrence, KS) or heart infusion broth (HIB, Difco) at 26 °C prior to RNA isolation or infection of macrophages.

extract_protocol: Prior to RNA isolation, bacteria were grown in BHI broth overnight at 26 °C. The overnight culture was diluted 1:20 dilution in BHI broth and grown at 26 °C for an additional 2 h. The temperature was shifted to 37 °C for 4 h to facilitate activation of the type 3 secretion system (T3SS) and expression of the Yersinia outer membrane proteins (Yops). Bacteria were harvested and RNA was isolated using RiboPure (Ambion/Applied Biosystems, Austin, TX).

treatment_protocol: Cultured at 26 oC

tag: genome/variation

value: LPP mutant

tag: culture condition

value: cultured at 37°C

source_name: Yersinia pestis CO92 wild-type cultured at 37°C

value: wild-type


title: Yersinia pestis CO92 LPP mutant 37°C replicate 3

tag: strain

label_protocol: Prior to RNA isolation, bacteria were grown in BHI broth overnight at 26 °C. The overnight culture was diluted 1:20 dilution in BHI broth and grown at 26 °C for an additional 2 h. The temperature was shifted to 37 °C for 4 h to facilitate activation of the type 3 secretion system (T3SS) and expression of the Yersinia outer membrane proteins (Yops). Bacteria were harvested and RNA was isolated using RiboPure (Ambion/Applied Biosystems, Austin, TX).


title: Yersinia pestis CO92 LPP mutant 26°C replicate 2

source_name: Yersinia pestis CO92 LPP mutant cultured at 26°C

value: cultured at 26°C

source_name: Yersinia pestis CO92 wild-type cultured at 26°C


title: Yersinia pestis CO92 LPP mutant 26°C replicate 3


title: Yersinia pestis CO92 LPP mutant 37°C replicate 2


title: control_littermates_WT3

city: Chicago

last: Yun

state: IL

address: 303 E.  Superior St.

department: Neurology and The Center for Genetic Medicine

institute: Northwestern University

description: Sciatic Nerve, Female and Male, Post natal day 14, Tissue was collected from control littermates

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 1.8.3). It was vst transformed and quantile normalized.

label_protocol: standard as recommended by illumina

extract_protocol:
Tissue was collected from control littermates
We used the miRVana miRNA isolation kit from Ambion®.  We used the protocol to extract total RNA.  Briefly, fresh frozen sciatic nerves were homogenization in lysis buffer followed by a phenol/chloroform extraction.  The sample was then combined with 1.25 volumes of 100% ethanol, and passed through a filter. After several washes, the RNA was eluted using elution buffer.

value: Sciatic Nerve

value: female and male

tag: age

value: Post natal day 14

tag: genotype

value: control littermates


title: Roots, Cd treatment, biological rep2

city: Shanghai

first: Jian Yong

last: Li

address: 300 Feng lin road

country: China

institute: Institute of Plant Physiology and Ecology, SIBS, CAS

description: Gene expression data from roots under Cd treatment situatioin in rep1.

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

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

source_name: Cd treatment

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: Arabidopsis thaliana plants were grown in quarter-strength sterile hydroponic solution at 28 0C with 16-h-light/8-h-dark cycles as described (Arteca and Arteca, 2000; Gong et al., 2003).

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

treatment_protocol: 200um Cd for 6 hours

tag: tissue

value: Root

tag: ecotype

value: 4 weeks (adult)


title: Roots, control, biological rep3

description: Gene expression data from roots in the control situatioin in rep2.

source_name: control


title: Roots, Cd treatment, biological rep3

description: Gene expression data from roots under Cd treatment situatioin in rep2.


title: Roots, control, biological rep2

description: Gene expression data from roots in the control situatioin in rep1.


title: HepG2 low glucose rep5

city: incheon

first: DeokHoon

last: Kim

address: 7-45 songdo-dong yeonsu-ku

country: South Korea

institute: Lee Gil Ya cancer and diabets institute

description: replicate 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile in Illumina genome studio v2010.1

source_name: HepG2 cell line

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

growth_protocol: HepG2 celline was cultured in 25mM glucose DMEM with 10% FBS and 100U/ml penicillin/streptomycin.

extract_protocol: RNA was extracted with RNeasy kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Experion (Bio-rad)

treatment_protocol: 2.7mM glucose was treated in low glucose condition. 25mM glucose was treated in high glucose condition.

tag: cell line

tag: cell culture condition

value: low glucose


title: HepG2 low glucose rep4

description: replicate 4


title: Yersinia pestis CO92 LPP mutant 26°C replicate 1


title: HepG2 low glucose rep6

description: replicate 6


title: Roots, Cd treatment, biological rep1

description: Gene expression data from roots under Cd treatment situatioin in rep3.


title: control_littermates_WT2


title: Roots, control, biological rep1

description: Gene expression data from roots in the control situatioin in rep3.


title: control_littermates_WT1


title: HepG2 low glucose rep3

description: replicate 3


title: HepG2 low glucose rep1

description: replicate 1


title: P0_Cre_Dicer_MT3

description: Sciatic Nerve, Female and Male, Post natal day 14, Tissue was collected from P0 Cre Dicer F or N

extract_protocol:
Tissue was collected from P0 Cre Dicer F or N
We used the miRVana miRNA isolation kit from Ambion®.  We used the protocol to extract total RNA.  Briefly, fresh frozen sciatic nerves were homogenization in lysis buffer followed by a phenol/chloroform extraction.  The sample was then combined with 1.25 volumes of 100% ethanol, and passed through a filter. After several washes, the RNA was eluted using elution buffer.

value: P0 Cre Dicer F or N


title: HepG2 low glucose rep2

description: replicate 2


title: P0_Cre_Dicer_MT2


title: Soybean_Nanahomare_Fullygrown2

city: Bunkyo-ku yayoi

first: Tomoyo

last: Narikawa

state: Tokyo

country: Japan

institute: University of Tokyo

description: Gene expression data from beans of Nanahomare at reproductive development

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Soybean Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AFFYMETRIX GeneChip Scanner 3000.

data_processing:
MAS5.0 was used to format the microarray data into CHP files.
The data were subsequently analyzed with Normalized Message Router (NMR) using Bioconductor and R.

organism: Glycine max

source_name: soybean seed green and fully grown

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

growth_protocol: Both species were geown under the same condition.

extract_protocol: total RNAwas extracted using RNeasy Plant Mini Kit (QIAGEN).

treatment_protocol: Samples were stored at -80C until RNA extraction.

tag: cultivar

value: Nanahomare

tag: developmental stage

value: Fully grown


title: islet of 12.5 dpc pregnant mice 3

city: Bunkyo-Ku

first: Hirotaka

last: Watada

address: 2-1-1 Hongo

department: Medicine, Metabolism and Endocrinology

institute: Juntendo University

description: Gene expression data from islet of 12.5 dpc pregnant mice.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 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 set to 500.

source_name: islet of 12.5 dpc pregnant mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

extract_protocol: RNA was extracted using the QIAGEN Rneasy mini kit (QIAGE N, Valencia, CA) according to the manufacture's instructions.

treatment_protocol: Pancreatic islet were isolated from control and 12.5 dpc mice by collagenase digestion method.

value: pancreatic islet

tag: status

value: pregnant

tag: time


title: HIEG clamp Muscle 1-2 canada Control

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

description:
Simple annotation: hormone treatment, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68074.gif

hyb_protocol: The labelled cDNA with cy5 ( before HIEG clamp) and cy3 (after HIEG clamp) from the same subject were pooled and hybridized simultaneously on Stanford microarray.

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 5760; Parameter Feature Extraction date = 2006-04-18; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Karine,,Clement Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.63; Parameter Scan Time = 10:47:09; Parameter PMT Volts = 550; Parameter Scan Date = 2006-04-12; Parameter Pixel Size = 10; Parameter Laser on time = 5549; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [114647]; Parameter Laser Power = 3.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Karine,,Clement Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 26.63; Parameter Scan Time = 10:47:09; Parameter PMT Volts = 540; Parameter Scan Date = 2006-04-12; Parameter Pixel Size = 10; Parameter Laser on time = 5555; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [114647]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Karine,,Clement

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Muscle 2 Control canada after HIEG clamp

label_protocol: 10ug aRNA were labeled with cyanine (Cy) 3 or Cy5 dyes during a random-primed reverse transcription reaction using the superscript II (Invitrogen, France).

extract_protocol: Total RNA was extracted from basal and after HIEG clamp biopsies with guanidinium thiocyanate method. RNA concentrations and integrity were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France. 500ng of total RNA were amplified using the MessageAmp antisense RNA kit (Ambion, Austin, TX).

tag: skeletal muscle biopsie after clamp;sex = male; Age = 25

source_name: Muscle 1 Control canada before HIEG clamp

tag: skeletal muscle biopsie before clamp; sex = male; Age = 25; Phenotype = lean


title: P0_Cre_Dicer_MT1

tag: gender


title: Control 3

city: San Francisco

first: Xin

last: Chen

state: CA

institute: UCSF

description: Gene expression data from wildtype mice

hyb_protocol: Standard Affy Array protocol by Gladstone Array Core

data_processing: RMA  normalization

source_name: Wild type mouse colon 3

growth_protocol: P9 to p12 control or mutant mice were harvested and colon tissues were dissected out, put immediately into Trizol.

extract_protocol: Total RNA was isolated according to Trizol protocol.

value: colon

tag: genotype/variation

value: wild type


title: islet of non-pregnant mice 3

description: Gene expression data from islet of non-pregnant mice.

source_name: islet of non-pregnant mice

value: non-pregnant

value: 0 dpc


title: Control 2

description: Gene expression data from wildtype mice

scan_protocol: Standard Affy Array protocol by Gladstone Array Core

source_name: Wild type mouse colon 2


title: Soybean_Nanahomare_Bean5mm2

source_name: soybean seed when the bean's length is 5mm

value: Bean 5mm


title: islet of 12.5 dpc pregnant mice 1


title: islet of non-pregnant mice 2


title: HepG2 high glucose rep5

description: replicate 5

value: high glucose


title: HepG2 high glucose rep4

description: replicate 4


title: islet of 12.5 dpc pregnant mice 2


title: Mutant 3

description: Gene expression data from Ihh mutant mice

source_name: Ihh mutant mouse colon 3

label_protocol: Standard Affy Array protocol by Gladstone Array Core

value: Ihh mutant


title: Soybean_Nanahomare_Fullygrown1


title: Soybean_Nanahomare_Bean5mm1